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Norman/Germanic - Viking heritage - Language and Culture in Sicily.

My cousin through marriage David Neilson assumed my surname was biological ‘Raciti’. I am biological in fact a Caggegi. He told me that I needed to wait in line before I could consider my Norman/Germanic - Viking heritage.

He believes he is of Danish heritage (through his surname - Neilson). He has brown hair and brown eyes. I personally don't see it at all. My daughter Racheal has blonde hair and blue eyes - and is most likely to be of that area.

I have found the original form of my biological name to be of a 'North Sea Germanic language' of Norse Origin: 'Keggeg', specifically from the Ingaevones, Jastorf and Langobardic cultures that migrated into North Italy in the 6th and 7th centuries.

History tells us that there were significant Lombard (with their Gallo-Italic idiom) settlements in Randazzo, Sicily.

The Langobardi tribe could have been biologically very similar to The Cimbri (Danes) and The Frisii tribes.

The one thing I do know is that The Lombards through The Jastorf culture - were in locations in Sweden - were I find other 'Keggeg's.

http://en.wikipedia.org/Image:Pre_Migration_Age_Germanic.png

Upgrade, cont

Since we all seem to be in the mood for some changes, I will cont from above. I suggest that we include something about genetic studies, so the average reader can understand them more, their limitations and assumptions. This will hence put the rest of the article in a better context, in that nothing is definite. A discussion on European sub-structure, without the ad nauseaum discussion of R1b prevelance in western Europe. Then Progress chronologically about European mirgations, as theorized by genetic data, incl. the so-called 'classic' stuff incoporated into it.

Here is what I have done so far ...

===Genetic studies===

One of the first scholars to perform genetic studies was Luigi Luca Cavalli-Sforza. He used ‘classical genetic markers’, which are an indirect way of analysing DNA. This method studies differences in the frequencies of particular allelic traits, namely polymorphisms from proteins found within human blood (such as the ABO blood groups, Rhesus blood antigens, HLA loci, immunoglobulins, G-6-P-D isoenzymes, amongst others). Subsequently his team calculated genetic distances between populations, based on the principle that two populations that share similar frequencies of a trait are more closely related than populations that have more divergent frequencies of the trait. From this, he constructed phylogenetic trees which showed genetic distances diagrammatically. In addition, they performed principal component analyses on the data, from which they generated ‘synthetic maps’. These maps revealed several clinal patterns. Genetic clines can be generated in several ways: including adaptation to environment (natural selection), continuous gene flow between two initially different populations, or a demographic expansion into a scarcely populated environment with little initial admixture with pre-existing populations (Archaeological Genetics; The peopling of Europe, page 390). Cavalli-Sforza connected these gradients with postulated pre-historic population movements based on known archaeological and linguistic theories. Given that the time depths of such patterns are not known, “associating them with particular demographic events is usually speculative” (Rosser 2000).

Studies using direct DNA evidence are now abundant, and may be utilize mitochondiral DNA, Y-chromosomal DNA or autosomal DNA. The first two are particularly popular. MtDNA and the non-recombining portion of the Y-chromosome (henceforth NRY) share some similar features which have made them useful in genetic anthropology. These properties include the direct, unaltered inheritence of mtDNA and NRY DNA from mother to offspring, and father to son, respectively, without the ‘scrambling’ effects of genetic recombination. We also presume that these genetic loci are not affected by natural selection, and that the major process responsible for changes in base pairs has been mutation (which can calculated) (European Prehistory. Sarunas Milisauskas, page 58). The smaller effective population size of the NRY and mtDNA enhances the consequences of drift and founder effect relative to the autosomes, making NRY and mtDNA variation a potentially sensitive index of population composition (Semino 2000; Rosser 2000, Richards 1998). However, these biologically plausible assumptions are nevertheless not concrete. For example, Rosser suggests that climactic conditions may affect the fertility of certain lineages (Rosser 2000). Even more problematic, however, is the underlying mutation rate used by the geneticists. They often use different mutation rates, and can therefore arrive at vastly different conclusions (as we will see later) (Rosser 2001). Moroever, NRY and mtDNA may be so susceptible to drift that some ancient patterns may have become obscured over time. Another implicit assumption is that population genealogies are approximated by allele genealogies. Barbujani points out that this only holds if population groups develop from a genetically monomorphic set of founders. However, that the populations who colonized Europe throughout pre-history were polymorphic has been deemed likely by Barbujani (Genetics and the population history of Europe Guido Barbujani* and Giorgio BertorellePNAS January 2, 2001 vol. 98 no. 1 22-25. ). Moreover, scholars assume that, for example, modern Basques and Near Eastern peoples are proxy representatives for Mesolithic Europeans and Neolithic agriculturalists, respectively. This assumption has, however, been questioned by Levy-Coffman (Levy-Coffman 2005).

Although sharing similarities, there are some observed differences between mitochondrial and NRY DNA. The Y chromosome, which is much larger, is particularly useful because it has many slowly mutating biallelic markers (SNPs) to help resolve genealogical clades as well as rapidly mutating microsatellite markers (STRs) to aid in the dating of very recent events (Y Chromosome Evidence for Anglo-Saxon Mass Migration. Michael E. Weale. . In addition, the NRY and mtDNA haplogroup (Hg henceforth) patterns appear to be different. As it is apparent below, Y haplgroups show a high degree of geographic structuring, whereas mtDNA haplgroups are more uniformly and ubiquitously distributed. This may be due to socio-cultural factors, namely the phenomena of polygyny and patrilocality (Rosser 2000).

Whereas Y-DNA and mtDNA Hgs represent but a small component of a person’s DNA pool, autosomal DNA has the advantage of containing hundreds and thousands of examinable genetic loci, thus giving a more complete picture of genetic composition (eg see Seldin). However, descent relationships can only to be determined on a statistical basis because autosomal DNA undergoes recombination and is liable to the process of natural selection.

Genetic studies operate on numerous assumptions and suffer from usual methodological limitations such as selection bias and confounding. Furthermore, no matter how accurate the methodology, conclusions derived from such studies are complied on the basis of how the authors envisages the data fits with established archaeological or linguistic theories. The relationship between language, archaeology and genetics is a precarious one.

===European population structure===

====Relation to other populations====

From Cavalli-Sforza’s original works, the genetic data found that all non-African populations are more closely related to each other than to Africans; this supports the hypothesis that all non-Africans descend from a single population originating in Africa. The genetic distance from Africa to Europe (16.6) is shorter than the genetic distance from Africa to East Asia (20.6), and much shorter than that from Africa to Australia (24.7). The simplest explanation for this short genetic distance is that substantial gene exchange has taken place between the nearby continents. Cavalli-Sforza suggests that this admixture took place 30,000 years ago.

A later study by Bauchet, which utilised ~ 10 thousand autosomal DNA SNPs arrived at similar results. Principal component analysis clearly identified four widely dispersed groupings corresponding to Europe, South Asia, Central Asia, and Africa. PC1 separated Africans from the other populations, PC2 divided Asians from Europeans and Africans, whilst PC3 split Central Asians apart from South Asians (Bauchet).

====Internal diversity====

Geneticists agree that Europe is the most homogeneous continent in the world (Cavalli-Sforza; Bauchet, Lao). However, some patterns are discernable. Cavalli-Sforza’s principal component analyses revealed five major clinal patterns through out Europe. He also constructed a phylogenetic tree based on genetic distances. He identified major ‘outliers’ such as Basques, Lapps, Finns and Icelanders; a result of genetic drift due to their relative isolation. Greeks and Yugoslavs represented a second group of less extreme outliers. He explained that yugoslavs did not cluster with any of the below groups due to high levels of internal diversity, whilst he did not elaborate upon Greece’s position. The remaining samples clustered into five major groups. The ‘Celts’ (Irish and Scots) grouped together, as did south-western Europeans (Italians, Spanish, Portuguese). Norweigians and Swedes formed a ‘Scandinavian’ cluster. A ‘Germanic group’ was itself composed of two sub-clusters – a northern Germanic (Dutch, Danish, English) and central Germanic (German, Belgian, Austrian) group. Eastern Europeans clustered together (Russians, Poles, Hungarians), with the Czechs laying intermediate between the eastern European cluster and the central Gemanic one. The French clustered with the ‘Germanic’ group, but he clarified that there was appreciable heterogeneity between southern and northern France.

Semino and Rosser independently performed PCA analyses based on NRY data from several European popluations. As noted above, Y haplogroups show high degrees of geographic structuring. Semino’s data showed three distinct clusters. Western Europeans, dominated by the presence of Hg R1b, clustered together (Basques, French, Spanish, northern Italians, German, Dutch); as did eastern Europeans, who are dominated by the presence of R1a and I2 (Polish, Hungarians, Macedonians, Croats, Czechs, Ukrainians). A middle eastern group was characterised by J lineages (Syrians, Lebanese, Turks). Greeks occupied an intermediate position between European and Middle Eastern populations (Rosser 2000). However, later studies looking at genetic diversity on a more micro –regional scale have revealed significant internal heterogeneity existing internally within some countries, cautioning us from assuming that frequencies quoted in pan-continental studies are representative of entire national communities or ethnic groups. This complexity prompts caution in equating similarity in the frequencies of one or more Y chromosomal haplogroups among populations and common descent (Di Giacomo 2003).

Data from mtDNA haplogroups is more homogeneous and lacks clear geographical patterning. Apart from the outlying Saami, all Europeans are characterized by the predominance of haplogroups H, U and T.

Studies using autosomal DNA have showed various patterns. Chikhi’s 1998 study, using only 7 loci, reproduced the southeastern – northwestern cline represented by Cavalli-Sforza’s first principlal component. A later study by Seldin (2006) used over five thousand autosomal SNPs and showed that the only significant population structuring followed a north – south distribution. Hungarians, Poles, Germans, Irish and Ukrainians clustered into the ‘northern group’, whilst Italians, Greeks, Portuguese and Spaniards clustered into the ‘southern group’ (Seldin 2006 * However, this study had a large number of participants who were in fact Americans claiming a particular European origin, as per grandparent’s place of birth). Another study by Bauchet (2006) found a major separation to lie within a northern-southeastern axis (in agreement with abovementioned studies), as well a second west to east axis. Basques and Finns were again found to lie relatively separate from other Europeans.

The latest autosomal DNA study, using the largest number of participants and genetic loci to date (300, 000 SNPs), found that, with the exception of usual isolates such as Basques, Finns and Sardinians, the European population lacked sharp discontinuities (clustering), although there was a discernable south to north gradient. Overall, they found only a low level of genetic differentiation between subpopulations, and differences which did exist were characterized by a strong continent-wide correlation between geographic and genetic distance. In addition, they found that diversity was greatest in southern Europe due a larger effective population size and/or population expansion from southern to northern Europe, as expected (Lao 2008)

Lao’s study corroborated Rosser’s earlier study which found that geography, more than language, is the major determinant of genetic diversity (Rosser 2000). For example, Hungarians speak an Uralic language, but cluster eastern Europeans rather than other Uralic speakers in Asia, corroborating Renfrew’s theory about the role of ‘’Elite Dominance” in language replacement.

Sub-Saharan DNA admixture

The article Sub-Saharan DNA admixture in Europe was recently deleted. This article was patrolled primarily by Small Victory. Recently Causteau, SOPHIAN and The Ogre were the primary editors to the article. The deletion of the article Sub-Saharan DNA admixture in Europe means that the community rejected the content of the article. The community has rejected the approach that editors to the article were using. Therefore, users should not transfer the same content onto this article. This time, we have administrative recourse, it is no longer a content dispute. If the same content is transferred into this article we can request administrative intervention based on the findings of Misplaced Pages:Articles for deletion/Sub-Saharan DNA admixture in Europe (2nd nomination). Likewise, I will delete the content that has been transferred from the deleted article. Wapondaponda (talk) 13:17, 19 July 2009 (UTC)

I agree that any use of this material needs to be very carefully agreed to by editors. I really think nothing in that article can be salvaged in a neutral form.

But I also want to point out once more that this article is currently broken up in one specific way, which is not the only possible way. All material added to this article should be inserted in a way which sticks to the current structure or otherwise we'll have big redundancy problems.--Andrew Lancaster (talk) 13:26, 19 July 2009 (UTC)

It's funny that the person who, just the other day, accused me (falsely) of trying to suppress evidence of Sub-Saharan admixture in Europe is now himself suppressing said evidence as I'm trying to incorporate it into the article (as was originally proposed). Of course, these genetic lineages are present in Europe and must be mentioned in this article that's called "Genetic history of Europe", just like their Central/East Asian counterparts in that same section. You're not seriously going to disagree with that, are you? ---- Small Victory (talk) 13:37, 19 July 2009 (UTC)

Small Victory, this is clearly a controversial bundle of material you inserted here, and so slowing down seems to be the least we can do. Please first consider two things:

1. Please make sure we only put in material which is uncontroversial and neutral and well sourced, AND which is relevant to this article.

2. Look at the structure of THIS article and consider where this subject might fit, and indeed whether it is not ALREADY covered. For example this article covers a lot of the haplotypes being considered already. BUT this article is NOT broken into geographical source areas.--Andrew Lancaster (talk) 13:43, 19 July 2009 (UTC)

The previous approach to the article has been rejected as discussed in the deletion process. Independent editors viewed the previous material as POV fork. So we need a new approach, I suggest not including any material in this article until we reach a consensus. It is even possible that the a separate article can be created, but it has to be neutral. So I agree with Andrew that we need to slow down. At this stage a draft is probably the best way to go. I suggest someone neutral, other than myself or Small Victory, should lay a foundation to the article. Wapondaponda (talk) 14:52, 19 July 2009 (UTC)

Well, here is the "draft" as it currently appears in the article:

Sub-Saharan African mtDNA (haplogroups L1, L2 and L3) and Y-DNA (haplogroups A, B and E (excluding E1b1b), particularly the ubiquitous Bantu marker E1b1a) are present at generally low levels throughout Europe.

Maternal (mtDNA) lineages are the more common and likely represent gene flow from historical events, such as slavery. They've been found in Portugal (6.9%), Spain (2.1%), Slovakia (1%), Italy (0.87%), Finland (0.83%), Bulgaria (0.71%), Bosnia (0.69%), Basques (0.64%), England (0.6%), Greece (0.44%), Switzerland (0.44%), Czech Republic (0.4%), Russia (0.3%), France (0.3%), Poland (0.18%), Germany (0.17%) and Scotland (0.1%).

Paternal (Y-DNA) lineages occur much less frequently. They've been found in Portugal (3%), Albanians from Italy (2.9%), France (2.5%), Germany (2%), Sardinia, Italy (1.6%), Calabria, Italy (1.3%), Austria (0.78%), Italy (0.45%), Spain (0.42%) and Greece (0.27%).

Genome-wide autosomal DNA analyses using the STRUCTURE clustering program, which is designed to accurately detect and quantify admixture, show equally negligible levels of sub-Saharan African admixture in all Europeans, including Iberians.

Please discuss.--Andrew Lancaster (talk) 15:23, 19 July 2009 (UTC)

I think that putting aside the various statistics pasted in there are only a few short sentences. Basically these sentences are stating a theory. The theory has the following points...

• Certain Y and mt haplogroups are "sub Saharan", and clear well-defined lists of these can be made
• The haplogroups in these lists are not common at all in Europe, and where they appear this is because of slavery
• Mitochondrial types in this sub Saharan classification are more common than Y lineages in this classification in Europe
• (The link, as I understand it is that in some versions of the story being proposed earlier by the same editors on the deleted article it was being argued that slaves who have children are more likely to be women than men.)

Not one of these proposals can be read in any of the sources cited, or in any other source, unless we draw conclusions based on synthesizing the data ourselves. The sourcing, if I understand correctly, is supposed to work like this (based on extensive discussion over on the now deleted article where all this stuff was cut and paste from)...

• In order to get the near lists of which haplogroups are sub Saharan, comments from genetics papers calling a lineage sub Saharan are cherry picked. This raises the question of whether calling a lineage sub Saharan in one context, means it is always sub Saharan; and the even more controversial point in practice of whether this mean other lineages are known NOT to be sub Saharan. Geneticists simply do not write this way, and it is a gross misunderstanding of the literature. NOTE: There is no source which gives clear well defined lists, and no source which explains in a clear way how you would even define "sub Saharan" in a way which is going to be consistent for every type of discussion. So this is clearly original research.
• Concerning the slavery claim, again there are some sources cherry picked who mention slavery as a POSSIBLE explanation for unexpected looking results here and there in isolated studies. There is absolutely no source stating that slavery is responsible for the lineages designated (in Misplaced Pages) as sub Saharan all over Europe. This is original research.
• There is not even any attempt to source any statement that mitochondrial sub-Saharan lineages are more common in Europe than sub Saharan male lines. This is original research.

So I see nothing in this proposed section which should be kept. This is the same original research which was recently deleted from another part of Misplaced Pages. It is compressed only.--Andrew Lancaster (talk) 06:23, 20 July 2009 (UTC)

I concur with Andrew. Essentially this is the same POV material that was in the article and the article was deleted because it was a POV fork. Small Victory and Co, rejected my contributions. They also rejected the compromises that Andrew offered. So the deletion process was a referendum on the approach used by Small Victory et al. Andrew has highlighted how the data in the article was used to present a POV that is actually quite unpleasant. Since this approach was rejected by the community, a new approach is warranted. It is only fair, that others who were not given a chance to contribute have their chance to present the material and subject it to the scrutiny of the community. Wapondaponda (talk) 13:06, 20 July 2009 (UTC)

If anyone cares

Regarding the draft, this is what I have picked up. But my experience so far, is nobody cares about verifying content, so some editors are adding content that may be inconsistent with the sources that they add. I will waste some of my energy to illustrate this, because I have some energy left to waste.

Sources not about Europe

The first four references are.

• Martinez et al Admixture estimates for Caracas, Venezuela, based on autosomal, Y-chromosome, and mtDNA markers.
  • This has nothing to do with Europe but Venezuela.
• Abu-Amero, 2007, Eurasian and African mitochondrial DNA influences in the Saudi Arabian population, once again, not about Europe but Saudi Arabia
• Richards et al, Extensive Female-Mediated Gene Flow from Sub-Saharan Africa into Near Eastern Arab Populations , Near Eastern, not Europe.
• Goncalvez et al, Y-chromosome lineages in Cabo Verde Islands witness the diverse geographic origin of its first male settlers Cape Verde is off the coast of West Africa, not Europe.

It seems that the editor is trying to find definitions of admixture from sources not related to Europe. This potentially could be original research. Much better to deal with sources that deal directly with Europe and not other places.

Exclusion of E3b from African admixture

The sources cited by footnotes Richards et al, and Goncalvez et al do not exclude E3b from Sub-Saharan Africa. Goncalvez et al state:

E3b, characterized by mutation M35, probably has an east African origin. The group occurs among Ethiopians (Semino et al. 2002) and Sudanese (Underhill et al. 2000) and appears at frequencies 12%–23% in various Jewish populations (Nebel et al. 2001).

and

The total frequency of haplogroups A and E covering 100% of the 276 Guinean Y-chromosomes is 48% in CVN and 46% in CVS. These values represent the maximum proportion of the west African lineages in the islands. However, since E3b has a significantly higher frequency in north Africans and Middle Eastern populations (12%–22% in Jews; Nebel et al. 2001) than in west Africans (6%), it seems likely that the E3b lineages arrived in Cabo Verde largely from a different source.

So the authors acknowledge the African origin of E3b, but assess two possible routes to Cape Verde. Either via West Africa, but most likely via Jewish immigrants from Iberia. In short, we cannot exclude e3b from Sub-Saharan admixture in such a simplistic manner.

I propose including a quote from Shriver et al, 2008, where they state:

We observed patterns of apportionment similar to those described previously using sex and autosomal markers, such as European admixture for African Americans (14.3%) and Mexicans (43.2%), European (65.5%) and East Asian affiliation (27%) for South Asians, and low levels of African admixture (2.8-10.8%) mirroring the distribution of Y E3b haplogroups among various Eurasian populations.

and

In Mediterranean and Middle Eastern populations, African admixture increases proportionately farther south into North Africa and Southeast into Asia. This distribution appeared to mirror that for the ‘‘African’’ Y chromosome E3b haplogroup (Underhill et al., 2001; Jobling et al., 2003; Cruciani et al., 2004)

. Wapondaponda (talk) 05:21, 20 July 2009 (UTC)

Slavery

The is an overly simplistic statement

"Maternal (mtDNA) lineages are the more common and likely represent gene flow from historical events, such as slavery.

This is sourced to Pereira et al 2000 and is somewhat accurately sourced as they argue that the widespread presence of L lineages in Iberia is due to the slave trade. Firstly the authors state

The geographical distributions of both haplogroups were quite different, with U6 being restricted to North Portugal whereas L was widespread all over the country.

So I don't think it is accurate to describe Sub-Saharan admixture as Negligeable. But back to slavery. Pereira et al 2000 state:

The introduction of L sequences in Portugal was tentatively imputed mainly to the modern slave trade that occurred between the 15th and 19th centuries. Both the great number of slaves that entered Portugal and their very diverse African geographic origin are consistent with the data set now reported. However, we cannot exclude some North-African contribution to present-day Portuguese L lineages.

In general many scholars have started to reassess the overly simplistic almost stereotypical assumption that the presence of L lineages anywhere outside of Africa represents the slave trade. A more recent study by Gonzalez et al 2003, actually contradicts Pereira et al's theory of predominantly slavery era admixture. They state.

However, with respect to the sub-Saharan Africa lineages, the recent history of the Black slave trade carried out by the Portuguese (mainly in the 15th and 16th centuries), with a well-documented import in southern Portugal, also be a plausible alternative to explain the presence of these African haplotypes in this region (Pereira et al., 2000). To test this possibility, we compared the proportion of sub-Saharan Africa haplotype matches between the Iberian Peninsula and northwest Africa (0.75%) with those of the Iberian Peninsula and a sample of sub-Saharan Africans from the Gulf of Guinea. The sample includes 45 Bubis from Bioko and 49 individuals from Saˆo Tome´, 32 Yoruba 1, and 72 Equatorial Guineans. The percentage obtained (0.35%) is roughly half of the former, and in addition, the majority of them (97%) are also shared with northwest Africa, although matches between sub-Saharan and North African samples are only 0.95%. These results suggest that, although both prehistoric and historical influences likely contributed to the sub-Saharan African haplotype pool present in the Iberian Peninsula, the former seems to be more important. Our results are in agreement with the gene flow (19.5%) from northwest Africa to the Iberian Peninsula estimated in a recent study of variation in the autosomic CD4 locus (Flores et al., 2000b), and with the evidence of northwest African male input in Iberia calculated at around 20%, using the relative frequency of northwest African Y-chromosome- specific markers in Iberian samples. Furthermore, our results clearly reinforce, extend, and clarify the preliminary clues of an important mtDNA contribution from northwest Africa into the Iberian Peninsula. On the basis of the L1b frequencies detected in Spanish and Portuguese samples (2–3%) and those found in western Africa (10–30%), a significant influence (at least 10%) of North Africans in the Iberian gene pool has also been admitted

Summary, they argue that L in Iberia is actually of prehistoric origin and not from the recent slave trade. This is not reflected in the current draft, or was not reflected in the deleted article. Wapondaponda (talk) 05:21, 20 July 2009 (UTC)

I agree that the Pereira article is not a valid source for the much stronger claims being put into this article. It does not even claim to be about all of Europe, or all mitochondrial haplogroups. It is about a specific haplogroup, and only in Portugal. But even then it only it is likely that a part of these lineages were due to slave trade. I also agree that looking at the literature more broadly, even this one citation starts to look over-blown and inappropriate.--Andrew Lancaster (talk) 06:00, 20 July 2009 (UTC)

Percentages

Maternal (mtDNA) lineages are the more common and likely represent gene flow from historical events, such as slavery. They've been found in Portugal (6.9%), Spain (2.1%)or (0.36%) , Slovakia (1%), Italy (0.87%), Finland (0.83%), Bulgaria (0.71%), Bosnia (0.69%), Basques (0.64%), England (0.6%), Greece (0.44%), Switzerland (0.44%), Czech Republic (0.4%), Russia (0.3%), France (0.3%), Poland (0.18%), Germany (0.17%) and Scotland (0.1%). Paternal (Y-DNA) lineages occur much less frequently. They've been found in Portugal (3%), Albanians from Italy (2.9%), France (2.5%), Germany (2%), Sardinia, Italy (1.6%), Calabria, Italy (1.3%), Austria (0.78%), Italy (0.45%), Spain (0.42%) and Greece (0.27%).

Andrew refers to such as "Accurate sounding" figures. Wapondaponda (talk) 05:21, 20 July 2009 (UTC)

There is also no source being given for saying that maternal lineages are more common than paternal ones. Apparently Wikipedians are coming to this conclusion themselves based on looking at particular datasets. This is OR.--Andrew Lancaster (talk) 06:01, 20 July 2009 (UTC)

Structure, Negligeable African admixture

Genome-wide autosomal DNA analyses using the STRUCTURE clustering program, which is designed to accurately detect and quantify admixture, show equally negligible levels of sub-Saharan African admixture in all Europeans, including Iberians

The sources cited include

• Pritchard et al. I could not find in this article, anywhere that states that Sub-Saharan African admixture is negligeable.
• Genetic_history_of_Europe#cite_note-95 states that Auton et al, say the following

Auton et al. 2009 note higher haplotype diversity in Southwestern Europe, and in particular a higher number of haplotypes shared with the Yoruba, for which they propose four possible explanations: 1) West African admixture, 2) North African admixture, 3) the recolonization of Europe from Iberia after the Ice Age, and 4) a combination of two or all three of these, stating that further research needs to be done. However, in Figure S3 A of the supplementary material, which shows the results of a STRUCTURE-based admixture analysis, neither the Spanish nor the Portuguese have any significant membership in the Yoruba (YRI) cluster.

This is a very dangerous case of original research, because this is not what the authors say. They specifically state, and this is a direct quote, so their is no chance of misinterpreting them.

Our analyses also have direct relevance to current debates in human population genetics regarding the extent of historical gene flow among Africa, Europe, and the Middle East Our observation of a north–south gradient in diversity with the highest estimates of diversity in the southern part of the continent is consistent with the initial founding of Europe from the Middle East, the influence of Neolithic farmers within the last 10,000 yr, or migrations south followed by a recolonization of Europe after the last glacial maximum. The unusually high number of haplotypes in South Western Europe is indicative of recurrent gene flow into these regions. Furthermore, when we considered the extent of haplotype sharing with the HapMap YRI population in Europe, we found that the South and South-Western subpopulations showed the highest proportion of shared haplotypes. If gene flow had occurred solely through the Middle East, we would expect the South-Eastern subpopulations to have the highest haplotype diversity and sharing of YRI haplotypes. These two results therefore suggest that while the initial migrations into Europe came via the Middle East, at least some degree of subsequent gene flow has occurred directly from Africa. A potential concern is that the HapMap YRI are not representative of diversity in North Africa, and the levels of haplotype sharing must be interpreted with this in mind. It is currently unclear how patterns of genetic diversity in the Yoruba are representative of the wider region, although genetic similarity appears to decline with distance. Nonetheless, the haplotype sharing between Europe and the YRI are suggestive of gene flow from Africa, albeit from West Africa and not necessarily North Africa. Future studies will hopefully be able to better resolve this question by comparing haplotypes from further populations around the Mediterranean.

My proposal is to include excerpts from this quote, per Misplaced Pages:PROVEIT#cite_note-1, to avoid confusion or even misrepresenting sources. Wapondaponda (talk) 05:21, 20 July 2009 (UTC)

You think that because the 'Sub-Saharan African' article's talk page is gone you can pretend that you weren't proven wrong on these issues? Not a chance.

Re: Sources not about Europe

Those sources don't have to be about Europe because they're not being cited in reference to admixture in Europeans. They're being cited in reference to the haplogroups that they use (and don't use) as evidence Sub-Saharan African admixture. But of course, you already knew that. You just needed an excuse to dismiss them all because you don't like the consensus they arrive at. Too bad the excuse you came up with is beyond lame.

Hi Small Victory, I had understood that you were using these articles as a source for building up a case. These sources show which haplogroups are to be called "Sub Saharan". Right? And from these definitions, you put together a case using other information from other articles.--Andrew Lancaster (talk) 14:30, 20 July 2009 (UTC)

Re: Shriver et al. 2008

That study is co-authored by one of the founders of DNAPrint Genomics, and it applies that organization's methodology (AIMs), which has been harshly criticized for "involv loci that have undergone strong selection, which makes it unclear whether these markers indicate shared ancestry or parallel selective pressures." That alone bars the study from inclusion in the article.

Hi Small Victory, that article making the criticism is making a much bigger argument which basically means a lot of what you are citing and arguing should not be cited and included. You should be careful not to cherry a criticism and only apply it to some data you want to delete.--Andrew Lancaster (talk) 14:36, 20 July 2009 (UTC)

On a side note, the authors' E3b explanation for their (already unreliable) findings makes no sense. They found more West African admixture in Iberians than in Greeks, yet Greeks have much more E3b than Iberians. And they totally ignore E3a and L mtDNA, which are actually West African in most cases and much higher in Iberia than in Greece. So maybe, just maybe, they're barking up the wrong tree with their E3b reference, which would be characteristic of the low level of their DNAPrint-style "research".

Yes, indeed these published authors might have made mistakes. This is something we can argue about any source, which would then lead to Misplaced Pages needing to be a research institution, or else unable to function, and so Misplaced Pages came up with some policies about things like that.--Andrew Lancaster (talk) 14:36, 20 July 2009 (UTC)

Re: Auton et al. 2009

The note I added (as a compromise to you, btw) perfectly summarizes what that study says about the haplotypes shared between Southwestern Europeans and West Africans:

The high number of samples spanning Europe allowed us to investigate geographic patterns of haplotype diversity at a more localized level. We see a North-South gradient in the number of haplotypes present for both H10 and H25 (Figure 3A) with the highest levels of diversity being found in the Southern regions. In particular, South Western Europe has a higher mean number of haplotypes than South Eastern Europe and Western and Central Europe. This is unexpected, as many current models of historical human migration predict numerous migrations into Europe from Africa via the Middle East, and one would therefore expect the highest diversity in the South East, with decreasing diversity moving North and West . The excess haplotype diversity in South Western Europe has at least two possible explanations. First, it may reflect direct migration from North Africa across the Mediterranean. Alternatively, it may represent a recolonization of Europe after a period of glaciation during which the Southern areas of Europe became a refugium for the prehistorical human population .

To address this issue, we investigated the level of haplotype sharing between African and European populations. In the absence of 500K data from North African populations (the HGDP having been genotyped on a different platform), we investigated patterns of haplotype sharing with the HapMap Yoruba (YRI) population. Using the 25 SNP haplotype windows outlined above, we found that South West Europe had the highest proportion of haplotypes that are shared with YRI (Supplementary Table S5). Furthermore, there were significantly more shared haplotypes between South West Europe and YRI relative to South East Europe and YRI (p-value 0.0072; Mann-Whitney U test), which suggests that the unusually high haplotype diversity in South Western Europe is indicative of gene flow from Africa. However, it is perhaps worth noting that this does not preclude the refugium hypothesis from also contributing to the pattern.

A potential concern is that the HapMap YRI are not representative of diversity in North Africa, and the levels of haplotype sharing must be interpreted with this in mind. It is currently unclear how patterns of genetic diversity in the Yoruba are representative of the wider region, although genetic similarity appears to decline with distance . Nonetheless, the haplotype sharing between Europe and the YRI are suggestive of gene flow from Africa, albeit from West Africa and not necessarily North Africa. Future studies will hopefully be able to better resolve this question by comparing haplotypes from further populations around the Mediterranean.

So no, the authors are not at all clear about how to interpret their finding. Whenever they mention gene flow from Africa, they say "suggestive of". Then they propose the alternative explanations of North African admixture and the Iberian postglacial refugium, pointing out that further research needs to be done.

And they don't indicate a direct YRI contribution either. They indicate haplotypes that are shared between YRI and Europeans, which is not the same thing. Open your eyes and look at Figure S3 A in the supplementary material. It shows virtually none of the YRI component in any of the European samples. ---- Small Victory (talk) 13:06, 20 July 2009 (UTC)

But you admit that the authors do not say as you propose, that gene flow from Africa is negligible, as they suggest gene flow from Africa. You are focusing on their alternate hypothesis, not their main hypothesis. Their main point is that pattern of haplotype diversity is consistent with gene flow from Africa. Their alternate hypothesis is that it is due to the LGM refugium. I have no problem with including their alternate hypothesis. But if you genuinely look at the data, African admixture in Iberia, is consistent with the several independent studies, Pereira et al, Gonzalez et al etc. So the alternate hypothesis is a less likely explanation for the presence of haplogroup L lineages in Iberia. The YRI haplotype sharing is clearly shown in the YRI table in supplementary materials which is about 5%, so they may not even be referring to YRI in this specific case but to haplotype diversity in general.

Secondly, you highlight their argument that YRI diversity may not be representative of North African admixture and the wider region. This is precisely what I had been discussing. YRI admixture is not necessarily representative of Sub-Saharan admixture. But YRI is always Sub-Saharan. In short YRI admixture will always represent a minimum of Sub-Saharan admixture. The absence of YRI doesn't imply the absence of Sub-Saharan admixture. But the presence of YRI implies the presence of Sub-Saharan admixture. If say, the study were to incorporate admixture from say indigenous East African populations, Central Africans and Nilotic populations. We would expect the proportion of Sub-Saharan admixture to even be greater than YRI. Recall that African populations are genetically very diverse, and YRI is only one population in Africa.

So I suggest not sidt-tracking from their main argument, and highlighting their alternate hypothesis as their main hypothesis. Rather their main hypothesis should be given prominence Wapondaponda (talk) 13:47, 20 July 2009 (UTC)

Wapondaponda, I think that these studies look only for similarities and what their words mean is "we do not know which migrations happened we just see these similarities and think they must be caused by something interesting". For example the Yoruba and Iberian might both have a lot of North African admixture. It is the same point I was making on the deleted article talkpage about Ethiopians. When "admixture analysis" clusters Ethiopians as a "mix" between Western Eurasians and "Black Africans" this does not mean the geneticists are saying that there were two source populations who were mixed together to give a cocktail. It means that they pretended something like this in their mathematical analysis, in order to get a perspective. Many different types of migrations can explain a single result like these. Obviously my point applies to Small Victory as well because what I am saying is that any attempt to take one admixture analysis and make big claims about directions of migrations is something we have to be very careful of.--Andrew Lancaster (talk) 14:44, 20 July 2009 (UTC)

I agree in that, the precise details of prehistoric migrations are not known. The purpose of the Hapmap, was simply to take samples from a "representative population" in each continent, and make their DNA profiles available to the public for study. The hapmap project specifically state:

These samples were collected in a particular community in Ibadan, Nigeria, from individuals who identified themselves as having four Yoruba grandparents. It is important to include a reference to "Ibadan, Nigeria" when describing the source of these samples out of respect for the community's wishes. Including the name of the city and country where these particular Yoruba samples were collected also reinforces the point that the sample set does not necessarily represent all Yoruba people, whose population history is complex. These samples should not be described merely as "African," "Sub-Saharan African," "West African," or "Nigerian," since each of those designators encompasses many populations with many different ancestral geographies. Note that the adjective form is "Yoruba," as in "the Yoruba samples," not "Yoruban." The accent is on the first syllable (YOR-u-ba).

So in this case YRI is a stand-in for Sub-Saharan Africa, albeit an imperfect one. We can say, with some degree of confidence, that it wasn't Yoruba people who migrated into the Iberian peninsula in pre-Neolithic times, since the expansion of people from West Africa is a fairly recent event, coincident with the Bantu Expansion around 5,000 years ago. However, as I have previously posted, pre-Neolithic North African populations, were probably related to the ancestors of Yorubas and other Sub-Saharan Africans. Over time these North Africans seem to have admixed with incoming peoples from the Near East as hypothesized by Rando et al 1998, and Arredi et al 2004 creating the current genetic structure of Modern day North Africans. The Berbers have a genetic structure of >70% E-M81, which is East African and up to 48% haplogroup L and M1 lineages. Traditionally these L lineages have been ascribed to the slave trade. But this view is changing now, because many of these L lineages are unique to North Africa, per Gonzalez et al 2003. We can therefore state, that the emerging consensus is that the prehistoric North African immigrants to Europe, especially through Iberia, were not contemporary West African peoples, but they were related to them. The Shriver study, basically found the exact same pattern as Auton et al by also using YRI/West African samples. Science is based on replicability. If numerous independent studies converge on the same finding, then we approach a mainstream consensus. Wapondaponda (talk) 15:59, 20 July 2009 (UTC)

As usual, you have no idea what you're talking about. E-M81 and M1 subclades are indigenous North African markers that arose in populations who had migrated from West Asia. They're no more "East African" than any other haplogroup on earth. And no, Shriver and Auton didn't produce the exact same pattern. Auton's admixture analysis found virtually no Sub-Saharan African admixture anywhere in Europe. Shriver's found elevated levels of admixture that are undoubtedly a product of the faulty methodology used. ---- Small Victory (talk) 13:18, 21 July 2009 (UTC)

Auton et al.'s main hypothesis was given precedence in my note. Out of the four possible interpretations, I listed it first. What more do you want? Should we just ignore the other hypotheses and the results of the admixture analysis? I'll bet you'd like that, but it's not going to happen.

Also, you're still misunderstanding what Auton actually found. Haplotypes shared between the Yoruba and SW Europeans means exactly that, and nothing more. It does not necessarily mean that one population is admixed with the other. They could both be admixed with a third group (such as North Africans, who weren't tested in the study) or it could simply be the result of genetic drift linked to human migrations that ultimately trace back to Africa (hence the Iberian refugium hypothesis).

It isn't up to us to decide which hypothesis will turn out to be correct. All we can do is report what's in the study, which is what I did. ---- Small Victory (talk) 13:01, 21 July 2009 (UTC)

Yes you did mention it, but the text mentioned a lot more of the other hypothesis than the main one.

If two populations share a similar haplotype, then three scenarios apply

• Convergent evolution
• Common ancestry
• Admixture

It is standard for scientists to consider all three scenarios when comparing two populations.

• Convergent evolution does occur but due to the randomness of mutations, it is usually the least likely scenario.
• Common ancestry is also possible because humans are apparently something like 99.97% alike. But for two populations to randomly converge on similar frequencies of rare traits is unlikely. Most likely if two populations converge to have similar frequencies of a haplotype, then they face similar selection pressures.
• Admixture-If there is evidence of contact or gene flow.

Typically the scientists will chose one of these as their main hypothesis by weighing the evidence at hand. So you are right in that haplotype sharing between Yoruba and SW Europe, may indeed be a coincidence. But in this study, they hypothesize in the discussion when the say

Nonetheless, the haplotype sharing between Europe and the YRI are suggestive of gene flow from Africa, albeit from West Africa and not necessarily North Africa.

The acknowledge that they would like to investigate North African populations as well. But my sentiment, is that won't change much. Genetic Diversity is clinal, so most likely there will be a cline from West Africa across North Africa to Iberia of YRI haplotypes. This has already been demonstrated by studies of Berbers which show they occupy an intermediate position between Sub-Saharan Africa and Eurasia. Wapondaponda (talk) 13:40, 21 July 2009 (UTC)

Please Make it easy

Please tell (on this talk page) me how many people where studied to get the 2.1% figure for Spain if you are going to revert my edit The Count of Monte Cristo (talk) 02:21, 20 July 2009 (UTC)

Most of the mtDNA data comes from Achilli et al., which is a comprehensive survey of Europeans. It includes a large sample of Spaniards from all over the country. Here's the breakdown:

Spain-North-West ... 8/216 ... 3.7%

Spain-North-East ... 3/179 ... 1.68%
Spain-Center ....... 1/148 ... 0.68%
Andalusia .......... 2/114 ... 1.75%
---

TOTAL ............. 14/657 ... 2.1%

--- Small Victory (talk) 13:15, 20 July 2009 (UTC)

I'll make a general point about this kind of problem, because I have come across it before. If this was a key point for the article, for example if the article was about Iberian DNA, then it might be a good idea to put in more data, but given that this article is about the whole of Europe I think if anything we need less detail. In practice, these are small percentages for these haplogroups and you are talking about the difference between finding 1, 2, or 3 people. If you think the % will mislead people why not write "3 out of 179"?--Andrew Lancaster (talk) 14:26, 20 July 2009 (UTC)

The 95% Confidence intervals for rows are:

8/216 - 3.7%.. 1.9% to 7.3%

3/179 - 1.68%. 0.61% to 4.9%

1/148 - 0.68%. 0.016% to 3.8%

2/114 - 1.75%. 0.054% to 6.3%

14/657 - 2.1%. 1.27% to 3.6%

PB666  22:50, 21 July 2009 (UTC)

Not fair unless you include Basques and data from rhouda et al. The Count of Monte Cristo (talk) 15:55, 20 July 2009 (UTC)

I have moved the posts so they can be read properly. SOPHIAN, please take more care where you insert words on talkpages. This is not the first time you inserted right in the middle of someone else's posting. People have to be able to read this. Doesn't Basque country come under North East normally? Surely we don't need a statistic for every region in Europe.--Andrew Lancaster (talk) 17:04, 20 July 2009 (UTC)

Rhouda et al. Studied 844 Spanish people and 3 had L (0.355%) Achilli et al. Studied in addition to what you say 156 Basques and 1 had L Leaving 18 cases of L in 1657 Spanish people or 1.09% The Count of Monte Cristo (talk) 21:48, 21 July 2009 (UTC)

Draft

I have started a draft here Talk:Genetic history of Europe/ Sub-Saharan African admixture in Europe. I am just throwing some ideas out and nothing is concrete. But if anyone has some good ideas we can incorporate them into the draft. Wapondaponda (talk) 06:10, 20 July 2009 (UTC)

I fail to see why the old article had to be deleted only to start over with a new article on the topic. If the content of the old article was flawed, the standard appoach would have been just to fix it. I also fail to see the relevance of the topic as a standalone article. As in many of our genetics articles, we are mostly looking at random detail cobbled together from academic papers directly (as opposed to via a secondary or tertiary, encyclopedic source). This makes for a "better than nothing" collection of factoids, but nothing that can be used to draw any sort of conclusion. Of course there is genetic flow everywhere, even across the Sahara. It is just a matter of "more" vs. "less" admixture. Prehistoric Sub-Saharan admixture in Europe will be practically impossible to measure without (extremely difficult) recourse to ancient DNA because it is so weak that it can hardly be distinguished from Early Modern admixture.

The result of the AfD is to eliminate the article as it was principally opinion and junk science, and retain a very small bit of the article in the merge to this article, the delete and merge was part of the consensus opinion. I have no great problems with what was written with this regard and I was for the articles deletion.PB666  22:23, 21 July 2009 (UTC)

In a nutshell, I do not see the point of such an article. --dab (𒁳) 13:20, 21 July 2009 (UTC)

A more fruitful approach imho would be an attempt to compile a discussion of the major barriers to human gene flow. The Sahara will feature very near the top in that, probably just second to the major Oceans. This would be a topic very relevant indeed to prehistoric human migration and one that I think could be made into a coherent, meaningful article. --dab (𒁳) 13:24, 21 July 2009 (UTC)

I think recent prehistoric admixture can be measured because it is still present in the European gene pool. Overtime, as the genome gets sliced and diced and people migrate back and forth, it would become impossible to discern. But presently, patterns of prehistoric African admixture are apparent. Wapondaponda (talk) 14:35, 21 July 2009 (UTC)

Editors showing their true colors

Now that we're "sharing space" with another type of admixture in Europeans, we can bear witness to the agenda-driven double standard that's applied by certain editors here (namely Wapondaponda and Andrew Lancaster). Notice that neither one of them has any problem whatsoever with the Central/East Asian admixture section, even though it's constructed identically to the Sub-Saharan African admixture section. They haven't laid so much as a finger on it, and it barely even registers on their radar. There have been no "citation needed" links added to it, no concern expressed about neutrality, no questioning the definition of "East/Central Asian admixture", no attempts to include R1a or R1b (whose ancestors, R and P, originated in Central/East Asia, just like the ancestors of E-M78, E-V13 and E-M81 originated in East Africa), no insistence on qualifiers regarding "older connections" or populations not necessarily being "separate entities", no nitpicky rewrites and deletions of material without cause, and no petitions to have the entire section removed altogether. Only the Sub-Saharan African admixture section is subjected to that kind of scrutiny and that kind of thinly-veiled OR and POV-pushing. I wonder why that is. It couldn't possibly have anything to do with Afrocentrism, could it? Perish the thought. ---- Small Victory (talk) 13:51, 21 July 2009 (UTC)

I don't think one would consider Andrew an Afrocentrist. Wapondaponda (talk) 13:57, 21 July 2009 (UTC)

But one would sure consider you an Afrocentrist (which you don't even attempt to deny). And Andrew is turning into your clone. ---- Small Victory (talk) 12:06, 22 July 2009 (UTC)

There are talk page guidelines. Please do not insult people in this manner. Talk pages are for the improvement of the main page, not for insulting people. Secondarily Andrew seems to have a pretty good handle on the literature, ergo if he sees contribution from Africa, it probably indicates he has information that supports his belief.PB666  15:21, 23 July 2009 (UTC)

I didn't insult anyone. I simply criticized other editors' approaches, just as Wapondaponda did to me below. Funny how you have no problem with that. ---- Small Victory (talk) 12:49, 24 July 2009 (UTC)

I have no idea what the above means, it is argumentative, a rant and should be refactored. Talk pages are for the improvement of the article, they are not a forum, a soapbox, your psychiatrist, etc.PB666  13:59, 21 July 2009 (UTC)

If you have no idea what it means, then don't make assumptions about what it is. I assure you that it's related to the quality of the article, and its implications are perfectly clear, which is why the response has been so underwhelming. ---- Small Victory (talk) 12:06, 22 July 2009 (UTC)

Insults have nothing to do with improving the quality of the Article. I am going to say this same thing here that I said on the E1b1b page. The argumentative and non-cooperative attitude of the editors on the main page have seriously diminished the readability of the page. By creating a combative environment what you have done is created a contorted almost legalistic text which is not of benefit to the general public. The idea that 'my opinion is right and everyone else is wrong, I don't care what author X, Y and Z say' only results in diatribe here and a reflection of diatribe on the main. This is an encyclopedia, it is designed for people with an eight grade reading skill and up, it is not a place where we hammer out which set of authors have their head screwed on strait.PB666  15:27, 23 July 2009 (UTC)

I agree with Pdeitiker. From now I will avoid entering into discussions with Small Victory, because they always seem to deteriorate into personal attacks. Similar complaints are seen here User_talk:Small_Victory#Tone_of_discussion Wapondaponda (talk) 17:59, 23 July 2009 (UTC)

Small Victory, I have edited in most sections in this article over time and also given a lot of further comments on this talkpage. When a new section arrives, people watching the article do tend to give that new section a bit more attention. The sub saharan had fundamental technical problems when it was in the deleted article, and I think it is obvious that we should not be keeping anything of that nature. This does not mean that I am a "clone" of all the other editors who agree with me on this basic point. There is certainly no pattern of agreement between me and Wapondaponda concerning anything much. I think your posting above is unjustified and silly. I believe you should explain your thinking in neutral terms, and focus purely on the article and wat should be in it. If I have done something wrong concerning this article, explain it. This constant obsession with perceived Afrocentrism that some editors have is really a terrible distraction to normal work on the quality of Misplaced Pages. There is no point being obsessed with people's POV. Everyone has a POV, and this is not a problem as long as they follow the normal standards.--Andrew Lancaster (talk) 01:52, 24 July 2009 (UTC)

Well, Andrew, if you weren't so singularly and obsessively focused on the Sub-Saharan African admixture section, you might have noticed (or cared) that the Central/East Asian admixture section is also new. I gave it a major overhaul at the same time that I added the refashioned SSA material. In fact, the two sections are virtually identical in construction and in the kinds of markers they use, which is appropriate since they're reporting on similar phenomena. Yet in your mind, one has "fundamental technical problems" while the other doesn't. Care to explain that? Oh wait, you can't without admitting bias. ---- Small Victory (talk) 12:43, 24 July 2009 (UTC)

go it alone editing

Small Victory, concernint this edit, just to remind you again, the deleted article was entirely your baby. You rejected contributions from myself and compromises from Andrew. The community rejected your approach with ]. That was essentially a referendum on your approach. So this time, we have to use another approach. SOPHIAN was blocked yesterday for recreating the article Sub-Saharan DNA admixture in Europe, what you are doing comes awfully close to what SOPHIAN is trying to do. I suggest you accept that you must work with others to achieve a consensus. Wapondaponda (talk) 14:11, 21 July 2009 (UTC)

You're quite delusional. That article was deleted because it was a WP:CFORK. And your POV-pushing, original research, 3RR violations and sock puppets had more to do with it than anything I ever did. In fact, the article was problem-free until you (and Andrew Lancaster) came along and started tampering with it. Let's remember that you're the one who's been blocked for repeated rule violations. My record is clean. So if anything, the deletion was a referendum on your approach. Take the hint. ---- Small Victory (talk) 12:18, 22 July 2009 (UTC)

Technically you have no blocks, but that doesn't make your record clean. Your account is basically a single purpose account, which is almost devoted entirely to enforcing POV material on SSA DNA admixture in Europe article. SPA editing is not a healthy type of editing. In fact, your editing record is somewhat disappointing. In three years since you opened an account, you have only edited 17 unique articles. Since the deletion of SSADAE, more than half your edits have been deleted, so you only have about 91 live edits. I think this explains why you are quite uncivil towards other editors and why you have difficulty collaborating with others.

This is a summary of comments from the AFD

• CFORK
• Essay
• Socking has nothing to do with
• One quote doesn't make sense
• what material in this article is worth saving?
• POV fork
• POV fork

Nothing to do with me here.

Wapondaponda (talk) 13:32, 22 July 2009 (UTC)

Nothing to do with me either. But more to do with you than you think. I'd been involved with that article almost since its creation three years ago, and there was never any problem with "my approach" (which is based on up-to-date, peer-reviewed research and usually backed up by consensus). Then you and Andrew came along with your POV-pushing, OR and edit warring, and a few months later the article was gone. Coincidence? I don't think so.

And btw, that's not my editing record, it's my editing history. Apparently, you're not familiar with the expression "clean record". Look it up with "criminal record" and find out what it means. I've never been blocked for rule violations, therefore my record is clean. You have, several times, therefore yours is not. Period. The length of my editing history is of no relevance whatsoever. And as far as having a "single purpose account", let's take a look at your editing history. It can be summed up in one word: AFROCENTRISM. ---- Small Victory (talk) 12:00, 23 July 2009 (UTC)

Small Victory, the version which everyone agreed to delete was largely the version with all the stuff you objected to removed. Wapondaponda is right to say that the problems with the article went far beyond what you think of as Afrocentrism. Look at the comments of the editors who came to comment on the deletion page, and they are very much directed at the same materials which I posted tags on and removed when it appeared again in this article, for example the theory that sub Saharan lineages in Africa are mainly due to slavery, which is pure OR. Wapondaponda had been kept from editing (his own fault) during that period.--Andrew Lancaster (talk) 00:56, 25 July 2009 (UTC)

They didn't agree to delete a specific version of the article. They agreed to delete the article at a specific point in time. Namely the time that an edit war broke out because you and Wapondaponda were inserting OR and POV. The main reason given was WP:CFORK, which was caused by the two of you (and Wapondaponda still hasn't quit). The second reason was that the subject wasn't notable enough to have its own article and should instead be dealt with more briefly here, which is exactly what I did. And none of the materials I included in the new version received negative comments on the deletion page. That's a huge lie. I just included the basics to match the 'Central/East Asia' section.

Btw, in case you didn't notice, I added a new source for the claim that L mtDNA in Europe is associated mostly with "historical events, such as slavery". It covers the whole of Europe (actually the whole of Eurasia), not just Portugal, and it makes reference to both the Atlantic and Arab slave trades, as well as the Arab/Berber conquest of Iberia and Sicily as a possible source for the transmission of L markers. ---- Small Victory (talk) 13:35, 25 July 2009 (UTC)

OK, into details and deflecting from reality as usual, yes of course there were several versions while discussion went on. All were dominated by you and SOPHIAN's editing, not Wapondaponda's. The discussion on the deletion proposal page also made it very clear what types of stuff was being seen as OR.--Andrew Lancaster (talk) 22:23, 27 July 2009 (UTC)

Still haven't learned how to read, huh? The only accusations of OR on the deletion proposal page are leveled against you and Wapondaponda by SOPHIAN. My name isn't even mentioned once. ---- Small Victory (talk) 10:02, 28 July 2009 (UTC)

Please don't keep looking for details to deflect from the real point, and please cease writing in such an aggressive tone, which is also a distraction. Not all descriptions of OR use these 2 letters as an abbreviation. Remember, I proposed the deletion and gave the most detailed reasoning about why. Several people simply agreed with my description, including Wikiscribe and Causteau. Telling me I don't understand myself seems particularly silly. Let's just get back to the subject. Here are the types of comments which were tagged and later deleted when they reappeared in THIS article. These are the ones you think are being treated unfairly:-

• Maternal (mtDNA) lineages of sub Saharan origin are the more common than Y lineages in Europe.
• The maternal lineages "likely represent gene flow from historical events, such as slavery".

Other theories you've defended putting in Misplaced Pages in this area include ideas about how male lineage arrive in Europe, and that lineages are only named after a region of origin if they are still present in that region. You need to defend such things case by case, not by attacking the people who question them.--Andrew Lancaster (talk) 23:46, 3 August 2009 (UTC)

Luigi Luca Cavalli-Sforza

Once again I have been invited to come over and see what my fellow wikipedians are up to. Folks, y'all need to put the coffee cups down (or what ever source the caffiene is injected from) and slow down your discussion and remember the talk page guidelines.

Regarding this author - he was a prominent author back in the 60s - 80s. The basic problem is that most of the work came before the age of precise genetic methods. He used serological techniques and a whole slew of methods that are clearly out-of-fashion now. A.C. Wilson and company really introduced the age and genre of information we are now in, and much of ACs conclusions have effectively replaced Cavalli-Sforza's early conclusion, including the OoA and timing of the OoA issues. This article focuses way to much on C-Ss work, it sort of reminds me of the types of discussions that came from books in sci.anthropology.paleo in the mid 1990s. He is still somewhat active with Y chromosome interpretations but alot of the things I have seen him suggest lately are pretty much off by a factor of 50% anyway. I really do not like articles with alot of 'this famous guy' name dropping. Name dropping IMHO is a form of propoganda and excessive use violates WP NPOV guidelines.PB666  14:20, 21 July 2009 (UTC)

I agree that CS's work is relatively dated, but it was one of the first comprehensive analyses of human genetic diversity. Yes apparently, he only used a few markers to synthesize his principal components. Since the sequencing of the whole genome, it is now possible for more detailed scientific investigations. My impression is that CS's studies have not been completely invalidated by recent studies, rather recent studies have refined much of CS's work. What is great about CS's work, is that it is fairly easy for lay people to understand, which makes it ideal for wikipedia, because wikipedia tends to have a general audience. Of course other's may argue that if it's for lay people, then it is an oversimplification, but we have to live with this dichotomy. Wapondaponda (talk) 14:29, 21 July 2009 (UTC)

The difference is much like the difference between the Bohr atom and the Heisenberg/Quantum mechanical Atom. Unfortunately one is wrong, the other is not.

Despite the simplicity of his conclusions, the approach is rather wrong. And if NPOV is to be employed why is Wilson's work not covered. Here is the basic problem, and I apologize if I seem to insult anyone here, this is not my intent. There was a first person who left Africa as such or a group, there is archaeological evidence that this might have occurred 125 kya (both from the levant, but supported by Liujiang). There are archaeological sites in India that date to about 80kya that also support this. These migrations are occurring ealier than the earliest fixation dates for the Y-chromosome, and given the 2N rule we can estimate that a TMRCA for Y chromosome is occurring and constrictive evolution that fixes it for at least 30ky after the TMRCA it places Y-chromosome in a constrictive context in Africa to 90kya which is rougly about the time people are reaching East Asia. While the mtDNA does not suggest migrations this early its confidence interval allows such early migrations. So the discussions about Y-chromosome and timings of migrations as seen in Journey of Man are basically idealizations, not reality. Either there are some mistaken assumptions with molecular clocking of the Y chromosome, or Y-chromosome underwent a post exodus selective sweep, and therefore it is an unreliable marker for early migrations anywhere. Frankly, I think exit dates which include the previous interglacial period (up to 131 kya). In addition, the dates archaeology generally agrees upon is that humans had reached Eastern Europe by 40kya, and that by 34 kya there was occupation within central Europe, by 30 kya they had reached Iberian and were affecting the tool industries of the region (therefore the dates in the article are not correct). There is molecular evidence that there was early geneflow from Africa, and although there is little archeaological support, at least by the epipaleolithic most of the archaeological evidence comes from coastal regions of iberia, suggesting a shift from open range hunting, which could indicate the dominance of one culture during the glacial period which favored eastern migrants but a shift to coastal foraging which favor migrants from the south. There appears to be a meshing of African and Eastern DNA in Iberia.

Here is my basic problem, migrations and the alleles or haplotypes that these migrations introduce are not general or diffuse, particularly when one talks about crossing bodies of waters. Molecular studies now clearly indicate that many founding or settlement events are quite discrete, both in size and within a temporal context. HLA studies of Iberians and Europeans indicate quite clearly that discrete contributions from Africa have occurred in the past. The problem is not that these discrete events occurred, the problem is how do we create a context which is correct (this was my problem with the Subsaharan page). A recent study of Eastern Islanders for example showed not native American mtDNA or Y chromosomes, but 2 individuals had HLA that came from South America, reproting the fallibility of both analysis. When did this admixture occur, before Europeans or after Easter Island became part of Chile. The result is not unexpected because HLA is under heterozygous selection and mtDNA and Y are haploids with tendencies to undergo fixation. Effectively HLA preserves about 3 times the added diversity of mtDNA and Y combined in real time.

There is a problem when using mtDNA and Y is that the fix rapidly often leaving the impression that an event occurred once and from a single source(and yet mtDNA will give a date of say 60 kya and Y for the same date 20kya, and the HLA studies will indicate that both dates and other dates might be correct). Scientist compound the problem with what is statistically known as B-error (type-II error), that means not to collect enough data to show a significant separation when a significant separation exists (a major problem I have with C-Ss work). Consequently, the mtDNA people claim there was a single event for exodus, when in-fact, there were multiple events. This is pertinent to European claims because certain mtDNA that appear to have arrived into Iberia are either contemporary to this migration (60 to 130 kya) or different. The archaeology makes no claim that AMHs were in Iberia before 35 kya which leaves 'silent' period of 25 to 70 kya. It is imperative to look at the potential flaws of every claim. So that many discrete events may occur, we often don't have enough data, the proper tools to 'parse' that data objectively, or we don't have a means of properly calibrating the molecular clocks to time the events (For example, these new Mitogenomic clocks have a huge problem with selection at coding sites that corrupts the clock, removal of these sites makes a less precise clock that is more accurate).

• Every claim should be critiqued, the weakest claims, no matter how historic, popular should be pruned from the article. I can give an example of this, the Topper archaeo-philes are presenting now that humans came from Europe to the New World (preclovis) and this is gaining popularity. THere have been claims of sites in S America that Africans came across the atlantic and settled 50 to 60 kya. Even some claims that Homo erectus or Neandertals made it first to the new world. There is no apparent molecular evidence from mtDNA, HLA, or Y supporting these beliefs. In addition these claims are based on tools that are not obviously of human origin.
• Speculative genetic claims, and I know most of them, really cannot be founded in archaeology and the molecular clocking makes some rather large assumptions. It is very difficult to assign migration to a specific paleoanthropological context, and even if one can, the variance on these clockings are -50/+75% about a relative range.
• Equity in speculative claims, if two claims are equally speculative, don't add more speculative claims, instead cite the reasons for why a speculative claim should be removed here, bring in the most recent literature in support of its speculation and remove it.
• Molecular anthropology is what it is. It cannot be dressed up to be made more than it is, the tools we have are frequently abused to create speculation. Many papers from the 80s, 90s and even some recent papers make conclusions that cannot be supported by their data or statistics, many of these have proven to be incorrect. What happened to MREH? What became of Ayala's "Myth about Eve"? The mhc16 study? The recent AfD highlighted the questionable conclusion of an individual who works on HLA, and the situation between Africa and the Greeks. For the mtDNA folks here, be aware the from 2000 to 2004 there were a number of papers published with a fantastice number of sequencing errors, particularly papers dealing with Europeans . From every perspective there are errors in the data set.

mtDNA has a number of supervariable sites such as 16129 and 16183-16192 that are not useful. 16183-16192 and some other sites have been noted to change from different samples of the same individual. The mtDNA genomic clocking on rarely mutated sites...I simply do not trust, these sites may be variably selective and disappear as soon as people migrate or a culture shift occurs. As stated above there is a rather large history of sequencing errors. Historic comparisons are based on assumptions between HVR mtDNAs and genomic mtDNAs may introduce inaccuracies.

Y chromosome. It is good to see a refinement of Y chromosomal SNP typing, the STRs had been used in the past and these often betray ancestry. Some older schemes of ancestral typing may not be comparable to the most recent schemes. Beware studies that rely on molecular clocking of Y chromosome, there are assumption errors in the clocking that cannot yet be explained. Y-chromosome may be heavily influenced by cultural selection and fixation could be much more rapid in certain instances that is currently believed. The 2N rules are based on variable selection, if selection is positive for any length of time the 2n rule cannot be applied.

HLA. HLA suffers from similar historic problems. Early studies typed A9 for instance that then became A23 and A24 and then evolved to A*23 and A*24 which then resolved into A*2301, A*2302, A*2303, ...,A*2402, A*2403, ..... and one has to be very careful when conclusions are made based on old typing technology or typing kits. Cross references need to carefully resolved, for instance why A24 can be called A*2402. There is another problem with HLA, and that is haplotype frequencies are frequently reported as 1 or 2 occurances. The relative frequencies that can give rise that can give rise to 1 to 5 observations have a wide relative variance. This fact also needs to be applied to frequencies based on Y and mtDNA. Let say A paper finds the haplotype A*3108-B*5112 and this is deemed to be of native american origin, how can we be sure unless all A31-B51 that exists in Asia has had the same degree of typing.

• Be critical of research that might be speculative or synthesis based on limited or partial evidence, with comparisons have the proper background work on all possible contributing populations been carefully done. How will the results reflect reality if new mutations in a sequence are found, or if another population it typed with more individuals and thus showing more haplotypes that give it better statistical power.

PB666  17:54, 21 July 2009 (UTC)

North Africa

This section needs some clarification. North African admixture in this case, should strictly speaking consist of E-M81 and U6. These are the only clades that are specific only to contemporary North African populations. E-M78 has a presence in Sub-Saharan Africa. In addition, and we know that the expansion of E-M35 started in Sub-Saharan Africa, proceeded to North Africa, the levant and then Europe. Currently the initial expansion from Sub-Saharan Africa has been ommitted, and an arbitrary region, North Africa has been selected as the source population. So even E-M81, does also represent the expansion from SSA as well, but its may or may not have involved contemporary North Africans. Wapondaponda (talk) 16:41, 21 July 2009 (UTC)

Pictures of children

A user added a series of photos of children. I don't see what relevance they have in a genetics article, so I have deleted them. Wapondaponda (talk) 18:35, 21 July 2009 (UTC)

Genetics section

I am going to go through the genetics section presenting paragraphs 1 by 1 point out problems with each paragraph.

One of the first scholars to perform genetic studies was Luigi Luca Cavalli-Sforza. He used classical genetic markers to analyse DNA by proxy. This method studies differences in the frequencies of particular allelic traits, namely polymorphisms from proteins found within human blood (such as the ABO blood groups, Rhesus blood antigens, HLA loci, immunoglobulins, G-6-P-D isoenzymes, amongst others). Subsequently his team calculated genetic distance Subsequyently the genetic distance between populations was calculated, based on the principle that two populations that share similar frequencies of a trait are more closely related than populations that have more divergent frequencies of the trait. and phylogenetic trees were constructed that showed genetic distances diagrammatically. His team also performed principal component analyses, which is good at analysing multivariate data with minimal loss of information. The information that is lost can be partly restored by generating a second principal component, and so on. In turn, the information from each individual principal component (PC) can be presented graphically in synthetic maps. These maps show peaks and troughs, which represent populations whose gene frequencies take extreme values compared to others in the studied area. Peaks and troughs usually, but not necessarily, connected by smooth gradients, called clines. Genetic clines can be generated in several ways: including adaptation to environment (natural selection), continuous gene flow between two initially different populations, or a demographic expansion into a scarcely populated environment with little initial admixture with pre-existing populations. Cavalli-Sforza connected these gradients with postulated pre-historic population movements based on known archaeological and linguistic theories. However, given that the time depths of such patterns are not known, “associating them with particular demographic events is usually speculative”.

Rewrite.

Luigi Luca Cavalli-Sforza performed studies on classical genetic markers to assess the geographic relationships between peoples in order to analyse DNA by proxy. Subsequently, the genetic distances between populations were calculated and phylogenetic trees were constructed that illustrated the genetic distances. These studies indicated relationships between geographically populations with modes and anti-modes connected generally by smooth gradients called clines.

This is all that is encyclopedic with regard to this page, the remainder of information belongs on a techniques page as it pertains to typing and phylogenetic techniques in general. For passages the need special emphasis please use footnotes.PB666  19:09, 21 July 2009 (UTC)

Studies using direct DNA analysis are now abundant use utilize mitochondrial DNA (mtDNA), the non-recombining portion of the Y chromosome (NRY) or autosomal DNA. MtDNA and NRY DNA share some similar features which have made them particularly useful in molecular anthropology. These properties include the direct, unaltered inheritance of mtDNA and NRY DNA from mother to offspring, and father to son, respectively, without the 'scrambling' effects of genetic recombination . We also presume that these genetic loci are not affected by natural selection , and that the major process responsible for changes in base pairs has been mutation (which can calculated). The smaller effective population size of the NRY and mtDNA enhances the consequences of drift and founder effect relative to the autosomes, making NRY and mtDNA variation a potentially sensitive index of population composition. However, these biologically plausible assumptions are nevertheless not concrete. For example, Rosser suggests that climactic conditions may affect the fertility of certain lineages. Even more problematic, however, is the underlying mutation rate used by the geneticists. They often use different mutation rates, and therefore studies are frequently arriving at vastly different conclusions. Moroever, NRY and mtDNA may be so susceptible to drift that some ancient patterns may have become obscured over time. Another implicit assumption is that population genealogies are approximated by allele genealogies. Barbujani points out that this only holds if population groups develop from a genetically monomorphic set of founders. However, Barbujani argues that there is no reason to believe that Europe was colonized by monomorphic populations. This would result in an overestimation of haplogroup age, thus falsely extending the demographic history of Europe into the Late Paleolithic rather than the Neolithic era. (See also Genetic drift, Founder effect, Population bottleneck.)

Here the question is do people who understand the complexity of human molecular anthropology produce alot of speculation or are they simply sitting back and waiting for better data to come that produces a non-speculative result. And if we are offering up speculation here what is its future value, here.PB666  19:46, 21 July 2009 (UTC)

Whereas Y-DNA and mtDNA haplogroups represent but a small component of a person’s DNA pool, autosomal DNA has the advantage of containing hundreds and thousands of examinable genetic loci, thus giving a more complete picture of genetic composition (eg see Seldin). However, descent relationships can only to be determined on a statistical basis because autosomal DNA undergoes recombination and is liable to the process of natural selection.

Genetic studies operate on numerous assumptions and suffer from usual methodological limitations such as selection bias and confounding. Furthermore, no matter how accurate the methodology, conclusions derived from such studies are ultimately compiled on the basis of how the author envisages their data fits with established archaeological or linguistic theories.

How does all of this pertain to the main? Is it a red flag on a bull's tail.PB666  19:42, 21 July 2009 (UTC)

Backward emphasis

Its interesting reading this article that the emphasis on genetics is almost the opposite of the genetic reliability of the markers used. S-Cs work is generally the least reliable, as it uses structure that are not discrete measures of molecular genetics, the Y chromosome which has all sorts of problem is treated as secondary importance, and the mtDNA which probably best represents the process gets a paragraph. Tishkoff's CD4 intron study is not mentioned at all, this was the first study showing some more recent african contribution at the molecular genetic level. HLA studies are not mentioned at all. There is way too much emphasis on old studies proxy methods that can have multiple interpretations, some of the conclusions fly against some of the more recent conclusions based on mtDNA and can be confirmed by HLA.PB666  19:55, 21 July 2009 (UTC)

References for trans-Mediterranean African genetic contribution

General

• Genes peoples languages CS for genetic distances
• Bowcock; et al. (1991). "Drift, admixture, and selection in human evolution: A study with DNA polymorphisms". {{cite journal}}: Cite journal requires |journal= (help); Explicit use of et al. in: |last= (help)
• Halder; et al. (2008). "A panel of ancestry informative markers for estimating individual biogeographical ancestry and admixture from four continents: utility and applications". {{cite journal}}: Cite journal requires |journal= (help); Explicit use of et al. in: |last= (help)
• Auton; et al. (2009). "Global distribution of genomic diversity underscores rich complex history of continental human populations". {{cite journal}}: Cite has empty unknown parameter: |1= (help); Cite journal requires |journal= (help); Explicit use of et al. in: |last= (help)
• Reich (2008). "Principal component analysis of genetic data". {{cite journal}}: Cite journal requires |journal= (help)
• Shimada MK, Panchapakesan K, Tishkoff SA, Nato AQ, Hey J (2007). "Divergent haplotypes and human history as revealed in a worldwide survey of X-linked DNA sequence variation". Mol. Biol. Evol. 24 (3): 687–98. doi:10.1093/molbev/msl196. PMID 17175528. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Tishkoff SA, Dietzsch E, Speed W; et al. (1996). "Global patterns of linkage disequilibrium at the CD4 locus and modern human origins". Science. 271 (5254): 1380–7. PMID 8596909. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Frudakis, Tony (2007). "Apportionment of Autosomal Diversity with Continental Markers". Molecular photofitting. p. 326. ISBN 0120884925. {{cite book}}: External link in |chapterurl= (help); Unknown parameter |chapterurl= ignored (|chapter-url= suggested) (help)

HLA

• Middleton D, Menchaca L, Rood H, Komerofsky R (2003). "New allele frequency database: http://www.allelefrequencies.net". Tissue Antigens. 61 (5): 403–7. PMID 12753660. {{cite journal}}: External link in |title= (help)CS1 maint: multiple names: authors list (link)

Iberia

• Spínola H, Middleton D, Brehm A (2005). "HLA genes in Portugal inferred from sequence-based typing: in the crossroad between Europe and Africa". Tissue Antigens. 66 (1): 26–36. doi:10.1111/j.1399-0039.2005.00430.x. PMID 15982254. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Pacho A, Mancebo E, del Rey MJ; et al. (2004). "HLA haplotypes associated with hemochromatosis mutations in the Spanish population". BMC Med. Genet. 5: 25. doi:10.1186/1471-2350-5-25. PMC 529258. PMID 15498100. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link) CS1 maint: unflagged free DOI (link)
• Pérez-Miranda AM, Alfonso-Sánchez MA, Peña JA, Calderón R (2003). "HLA-DQA1 polymorphism in autochthonous Basques from Navarre (Spain): genetic position within European and Mediterranean scopes". Tissue Antigens. 61 (6): 465–74. PMID 12823770. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Sanchez-Velasco P, Gomez-Casado E, Martinez-Laso J; et al. (2003). "HLA alleles in isolated populations from North Spain: origin of the Basques and the ancient Iberians". Tissue Antigens. 61 (5): 384–92. PMID 12753657. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Muro M, Marín L, Torío A; et al. (2001). "HLA polymorphism in the Murcia population (Spain): in the cradle of the archaeologic Iberians". Hum. Immunol. 62 (9): 910–21. PMID 11543893. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Synek V, Reuben JR, Du Boulay GH (1976). "Comparing Evans' index and computerized axial tomography in assessing relationship of ventricular size to brain size". Neurology. 26 (3): 231–3. PMID 1082559. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Grimaldi MC, Crouau-Roy B, Amoros JP; et al. (2001). "West Mediterranean islands (Corsica, Balearic islands, Sardinia) and the Basque population: contribution of HLA class I molecular markers to their evolutionary history". Tissue Antigens. 58 (5): 281–92. PMID 11844138. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)

Central Mediterranean

• Grimaldi MC, Crouau-Roy B, Contu L, Amoros JP (2002). "Molecular variation of HLA class I genes in the Corsican population: approach to its origin". Eur. J. Immunogenet. 29 (2): 101–7. PMID 11918634. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Lampis R, Morelli L, De Virgiliis S, Congia M, Cucca F (2000). "The distribution of HLA class II haplotypes reveals that the Sardinian population is genetically differentiated from the other Caucasian populations". Tissue Antigens. 56 (6): 515–21. PMID 11169241. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Contu L, Arras M, Carcassi C, La Nasa G, Mulargia M (1992). "HLA structure of the Sardinian population: a haplotype study of 551 families". Tissue Antigens. 40 (4): 165–74. PMID 1471143. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)

Eastern Mediterranean

• Arnaiz-Villena A, Dimitroski K, Pacho A; et al. (2001). "HLA genes in Macedonians and the sub-Saharan origin of the Greeks". Tissue Antigens. 57 (2): 118–27. PMID 11260506. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Petlichkovski A, Efinska-Mladenovska O, Trajkov D, Arsov T, Strezova A, Spiroski M (2004). "High-resolution typing of HLA-DRB1 locus in the Macedonian population". Tissue Antigens. 64 (4): 486–91. doi:10.1111/j.1399-0039.2004.00273.x. PMID 15361127. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• For Romanian HLA as with many recent studies the work of Constantinescu I is presented directly to www.allelefrequencies.net however Reed E, Ho E, Lupu F; et al. (1992). "Polymorphism of HLA in the Romanian population". Tissue Antigens. 39 (1): 8–13. PMID 1542880. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link) but the techniques of 1992 were picked up many SSA alleles as nulls.
• Ivanova M, Rozemuller E, Tyufekchiev N, Michailova A, Tilanus M, Naumova E (2002). "HLA polymorphism in Bulgarians defined by high-resolution typing methods in comparison with other populations". Tissue Antigens. 60 (6): 496–504. PMID 12542743. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Arnaiz-Villena A, Iliakis P, González-Hevilla M; et al. (1999). "The origin of Cretan populations as determined by characterization of HLA alleles". Tissue Antigens. 53 (3): 213–26. PMID 10203014. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Uyar FA, Dorak MT, Saruhan-Direskeneli G (2004). "Human leukocyte antigen-A, -B and -C alleles and human leukocyte antigen haplotypes in Turkey: relationship to other populations". Tissue Antigens. 64 (2): 180–7. doi:10.1111/j.1399-0039.2004.00258.x. PMID 15245373. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Arnaiz-Villena A, Karin M, Bendikuze N; et al. (2001). "HLA alleles and haplotypes in the Turkish population: relatedness to Kurds, Armenians and other Mediterraneans". Tissue Antigens. 57 (4): 308–17. PMID 11380939. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)

North Africa

• ReviewPiancatelli D, Canossi A, Aureli A; et al. (2004). "Human leukocyte antigen-A, -B, and -Cw polymorphism in a Berber population from North Morocco using sequence-based typing". Tissue Antigens. 63 (2): 158–72. PMID 14705987. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Choukri F, Chakib A, Himmich H, Raissi H, Caillat-Zucman S (2002). "HLA class I polymorphism in a Moroccan population from Casablanca". Eur. J. Immunogenet. 29 (3): 205–11. PMID 12047355. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Arnaiz-Villena A, Benmamar D, Alvarez M; et al. (1995). "HLA allele and haplotype frequencies in Algerians. Relatedness to Spaniards and Basques". Hum. Immunol. 43 (4): 259–68. PMID 7499173. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Hajjej A, Kâabi H, Sellami MH; et al. (2006). "The contribution of HLA class I and II alleles and haplotypes to the investigation of the evolutionary history of Tunisians". Tissue Antigens. 68 (2): 153–62. doi:10.1111/j.1399-0039.2006.00622.x. PMID 16866885. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Ayed K, Ayed-Jendoubi S, Sfar I, Labonne MP, Gebuhrer L (2004). "HLA class-I and HLA class-II phenotypic, gene and haplotypic frequencies in Tunisians by using molecular typing data". Tissue Antigens. 64 (4): 520–32. doi:10.1111/j.1399-0039.2004.00313.x. PMID 15361135. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Hajjej A, Hmida S, Kaabi H; et al. (2006). "HLA genes in Southern Tunisians (Ghannouch area) and their relationship with other Mediterraneans". Eur J Med Genet. 49 (1): 43–56. doi:10.1016/j.ejmg.2005.01.001. PMID 16473309. {{cite journal}}: Explicit use of et al. in: |author= (help)CS1 maint: multiple names: authors list (link)

MtDNA

• Gonzalez; et al. (2003). "Mitochondrial DNA Affinities at the Atlantic Fringe of Europe" (PDF). {{cite journal}}: Cite journal requires |journal= (help); Explicit use of et al. in: |last= (help)
• Malyarchuk; et al. (2008). "Reconstructing the phylogeny of African mitochondrial DNA lineages in Slavs". {{cite journal}}: Cite journal requires |journal= (help); Explicit use of et al. in: |last= (help)
• Malyarchuk; et al. (2005). "African DNA Lineages in the Mitochondrial Gene Pool of Europeans". {{cite journal}}: Cite journal requires |journal= (help); Explicit use of et al. in: |last= (help)
• Pereira L, Prata MJ, Amorim A (2000). "Diversity of mtDNA lineages in Portugal: not a genetic edge of European variation". Ann. Hum. Genet. 64 (Pt 6): 491–506. PMID 11281213. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• McEvoy B, Richards M, Forster P, Bradley DG (2004). "The Longue Durée of genetic ancestry: multiple genetic marker systems and Celtic origins on the Atlantic facade of Europe". Am. J. Hum. Genet. 75 (4): 693–702. doi:10.1086/424697. PMC 1182057. PMID 15309688. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Achilli A, Rengo C, Magri C; et al. (2004). "The molecular dissection of mtDNA haplogroup H confirms that the Franco-Cantabrian glacial refuge was a major source for the European gene pool". Am. J. Hum. Genet. 75 (5): 910–8. doi:10.1086/425590. PMC 1182122. PMID 15382008. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)

Y chromosome

• King (2007). "Africans in Yorkshire? - the deepest-rooting clade of the Y phylogeny within an English genealogy". {{cite journal}}: Cite journal requires |journal= (help)
• Cruciani; et al. (2004). "Phylogeographic Analysis of Haplogroup E3b (E-M215) Y Chromosomes Reveals Multiple Migratory Events Within and Out Of Africa". {{cite journal}}: Cite journal requires |journal= (help); Explicit use of et al. in: |last= (help)
• Underhill; et al. (2001). "The phylogeography of Y chromosome binary haplotypes and the origins of modern human populations" (PDF). {{cite journal}}: Cite journal requires |journal= (help); Explicit use of et al. in: |last= (help)
• Lancaster, Andrew (2009), "Y Haplogroups, Archaeological Cultures and Language Families: a Review of the Multidisciplinary Comparisons using the case of E-M35" (PDF), Journal of Genetic Genealogy, 5 (1)

Wapondaponda (talk) 00:29, 22 July 2009 (UTC)

Backflow

• Cherni L, Fernandes V, Pereira JB; et al. (2009). "Post-last glacial maximum expansion from Iberia to North Africa revealed by fine characterization of mtDNA H haplogroup in Tunisia". Am. J. Phys. Anthropol. 139 (2): 253–60. doi:10.1002/ajpa.20979. PMID 19090581. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Gonzalez; et al. (2007). "Mitochondrial lineage M1 traces an early human backflow to Africa". {{cite journal}}: Cite journal requires |journal= (help); Explicit use of et al. in: |last= (help)
• Ennafaa H, Cabrera VM, Abu-Amero KK; et al. (2009). "Mitochondrial DNA haplogroup H structure in North Africa". BMC Genet. 10: 8. doi:10.1186/1471-2156-10-8. PMC 2657161. PMID 19243582. {{cite journal}}: Explicit use of et al. in: |author= (help)CS1 maint: multiple names: authors list (link) CS1 maint: unflagged free DOI (link)

Comments

I have reorganized your list and added to it.PB666  13:35, 22 July 2009 (UTC) I recommend a further reorganization of the top section.

Great. I have also been thinking about how best to organize the material. We have different 3 measures, Y, mtdna and autosomal and at least two distinct periods of gene flow(recent and prehistoric). We also have two points of entry, Iberia and the Mediterranean. Any suggestions.Wapondaponda (talk) 17:27, 22 July 2009 (UTC)

I will be adding references for HLA. I am working on a private page at the moment that drafts the tables from allelefrequencies.net. these Tables will clarify that of A. A-V that is credible and that which is 'not so credible' as a reference his work is referencable as long as more recent work in the field upholds his findings. The best evidence IMHO is from the HLA, far more work has been done with HLA than Y and mtDNA and consequently it is more sensitive, but there are problems.PB666  18:15, 22 July 2009 (UTC) BTW, the reason I cite two papers dealing the the Franco-Iberian refuge is that this can be thought of as a conveyor belt, if African alleles make it to the region prior to the end of the YD then they can be conveyed into Europe. What that means is that those haplotypes that make it to Iberia are filtered upward by selection and drift, but once they get into the 'feed' area the conveyor belt can feed them Northward. Some of the haplotypes we see in Europe are from ancient migrations from NW Africa; however minor haplotypes that have undergone extensive recombination overtime are difficult to recognize. So that as the feild progresses and we have more expansive and allele and haplotype sensitive studies, it becomes easier to resolve these. This is the essence of the critique of C-S because his studies are more or less like a far-sighted old man look for fleas on a dog. As for suggestions, look at the box on the top of the page.PB666  18:22, 22 July 2009 (UTC)

Malyarchuk et al seem to be in agreement with the Franco-Iberian refuge theory as the conveyor belt of L lineages into Eastern Europe. Wapondaponda (talk) 20:19, 22 July 2009 (UTC)

BTW, why do we want to retain this name for the section SubSaharan Africa. Although there is some trace evidence that some of these haplotypes originated in Subsaharan Africa most of the composite evidence suggests that the Transmediterrean gene flow was mediated by North African components. The only evidence I have for any Subsaharan migration into Eurasia, directly was via the horn into Arabia, and possibly from eastern Sudan, Erithrea or Ethiopia toward the Indus Valley. Having gone over a considerable number of markers it looks as if North Africa (Tunis) was a source of African markers in Portugal, that other sites contributed to the make-up of Sardinia, and there was NW source that contributed to Iberia, A nile source that contributed to the Aegean and Black Sea region. Should this whole line of thought be treated under a North African contribution section?PB666  02:21, 23 July 2009 (UTC)

I agree that all gene flow from SSA to Europe had to pass through North Africa. However there seems to be a notion that North African gene flow is completely distinct from Sub-Saharan gene flow which I believe is an incomplete oversimplification. The very notion of Sub-Saharan Africa itself is not realistic in those prehistoric times when the Sahara desert wasn't a desert but a savanna.During the wet phases, people from SSA would expand northwards and occupy much of savannas of the Sahara. Gonzalez et. al. 2003 suggest a neolithic expansion of Subsaharan L lineages into the Sahara as the possible source population of Iberian L. I was thinking of renaming the article just African admixture so that we don't have to limit ourselves to direct SSA admixture. Wapondaponda (talk) 05:33, 23 July 2009 (UTC)

There is a difference between actually what is in the data and what people say in discussions. The basic problem here for you is that the Egyptian and Sudanese peoples are poorly analyzes. I have only recently seen Sudanese HLA show up in the HLA literature. And the Egyptian resource that I have, still useful, is very old was not used by A A-V in his analysis of the Greeks. According to that study of Egyptians some of the nodal haplotypes may have come from ancient Egypt as with the modal haplotypes within the Sardinians. The www.allelefrequencies.net (see HLA references) database has the most recent allele typing including many new papers from Africa. In addition the format has been reorganized so that one can search haplotypes.

• The obvious connections at the moment are between Tunisia and Portugal (I have an HLA reference for this)
• There is a connection between the Berbers and Iberia. However I have to offer a stong word of caution on this connection, the recent work indicates backflow from Iberia to North Africa, the paleoclimatologist are saying that during the LGM, 24 to 18 kya, conditions in Iberia were severe, and the finding of Neanderthals on Gibraltar, the last N find, is an indication of the severity of the climate. This back flow from Iberia carries European alleles backward, one author claims that A2-B7-DR15 as evidence of gene flow into Iberia, the reverse is probably the case, A2-B7-DR15 probably recombined in Iberia and moved backwards into NW Africa. Other genes moved the other direction, either prior to the LGM or immediately after the LGM as climate improved in Iberia. Another haplotype A24-B8-DR3-DQ2.5 could be the progenitor to A1-B8-DR3-DQ2.5 however A24 did not come from W.Africa. A24 is a gene convertant of A23 which was a minor allele in East Africa and expanded asymmetrically into SE Asia, its presence in Iberia may be the consequence of gene conversion between A24-B35 and A1-B8-DR3-DQ2.5 and the A24-B8 haplotype is found in Tunisia and Morocco. Therefore we have a problem of deducing direction.
• With regard to what A A-V has claimed, I found 2 additional papers (different authors) that support his claim, and a paper that makes no mention on the association but provides even better support. The Subsaharan origin of Attica Greeks falls in the backdrop of extremely poor typing in Muslim North Africa (particularly Egypt and proximal regions) consequently it is drawing a conclusion from a partial vacuum of information. When good studies have been done, such as in Tunisia and Morocco we find the Subsaharan alleles that are found in Europe are often found at levels intermediate between the European levels and the Africa levels. For example A*41 in Tunisia (Cited in the literature). We need to consider this with regard to N.Africa absence of evidence is not evidence of absence and apply this summarily to any N. Africa population that has not been genetically typed.
• With regard to ancient genetic contributions, while there is a tendency for allele associations to decline from south to north in some instances because of the way people expanded after the LGM, it is simply not possible to discriminate this. The evidence at hand is that DR3-DQ2 and DR7-DQ2 which are nodal in West Africa (DR7-DQ2 is also high in the mid east) are very high along the Atlantic coast. A29-Cw16-B44-DR&-DQ2 is but one component of putative west African origin, there are other DR7-DQ2 that could have easily come from the middle East were DR7-DQ2 is high. Because of the nature of diffusion/migration and because of the cyclical occupation of Europe it is very difficult to define when exact alleles arrived, and with back migration the picture becomes muddled even more. I would argue that the same logical constraint also applies to mtDNA and Y chromosome studies.
• Let us take an example of genetic contributions. According to archaeology Sardinia was initially occupied ~9000 years ago, I would contend it probably occurred earlier. By HLA we have one haplotype in strong linkage disequilibrium indicating a founder affect, this haplotype A30-cw5-B18-DR3-DQ2 (I credit this haplotype as of Africa origin and the consequence of a founder affect, probably N or NE Africa) occurs in 15% of Sardinians and is the highest frequency 4 locus haplotype in Europe. A second haplotype A2-Cw7-B58-DR16 is believed to also be of African origin. So that in this instance we have the blazing set of markers in Sardinia, but what about Europe. 13,000 Germans (26,000 chromosomes serotyped) typed A30-B18-DR3 = 0.16% IOW a 100 fold decline in haplotype frequency over a distance ~1000 kilometers (800 miles from Sardinia to Berlin -other frequencies- Basque 8.1, Spanish = 2.6%, French = <0.6%, Italian = 0.4%). This contrasts with A3-B7-DR15, a classic example of W.Eurasian marker is found over 1000s of miles east west. A2-B58-DR16 is not found in the German (chromosomes typed = 26000). So that we have evidence here just how quickly this recent African contribution drops into Europe. I want to emphasize the point, the evidence we have of genetic contributions is not (wide - as in a hand waving motion), it is rather local, punctuated, or from a point to a point. This nature of the evidence needs to be conveyed in the description. And to reiterate the point, from what place did a people contribute these Subsaharan influences to the Greeks? Consider if the haplotype is in the Basque and the proto-Basque were the Proto-Atlantic Europeans why isn't this hap more frequent now in other Europeans? (Answer) because the Basque are an admixture of more recent migrations and their previous genetic makeup. A few areas of Europe have been receptive to recent African contribution in the Mesolithic/Neolithic periods, but most areas of Europe have not. In contrast France has been heavily influenced by migrations from Italy, Greece, Anatolia, and Middle East and these areas. When we see markers of recent Africa input, it is difficult in instances were there is a trace, whether this influence is local (Basco-Sardinian), via the Eastern Mediterranean or direct. Occam's razor suggests often the simplest answer is the best answer, in which case these alleles appear to be carried with measurable gene flow from Ionian, Aegean, Northeastern Mediterranean regions. .

Something to be considered as you read the conclusions of these HLA papers.PB666  13:54, 23 July 2009 (UTC)

Refining the analysis of Y-chromosomal diversity in Alentejo (Portugal), This particular article failed to detect Y lineages of "Sub-Saharan African descent", yet they report significant frequencies of (HBB*S) and glucose-6-phosphatedehydrogenase (G6PD) deficiency, which are known to be of Sub-Saharan descent. The alternatives could be that these alleles entered through females, or very simply that "North African lineages" of e3b, that were detected, are basically "Sub-Saharan". Wapondaponda (talk) 19:19, 25 July 2009 (UTC)

STRUCTURE

SOPHIAN has been blocked for a week for several recent infractions, including edit warring on this article.

Small Victory writes in the article, and I quote

Genome-wide autosomal DNA analyses using the STRUCTURE clustering program, which is designed to accurately detect and quantify admixture, show equally negligible levels of sub-Saharan African admixture in all Europeans, including Iberians;

I challenge him to provide a direct quote from the reference cited, to verify this claim. This is an official wikipedia policy per WP:PROVEIT which states

The burden of evidence lies with the editor who adds or restores material. All quotations and any material challenged or likely to be challenged must be attributed to a reliable, published source using an inline citation. The source cited must unambiguously support the information as it is presented in the article. The source should be cited clearly and precisely to enable readers to find the text that supports the article content in question

and more specifically Misplaced Pages:PROVEIT#cite_note-1, which states:

When there is dispute about whether the article text is fully supported by the given source, direct quotes from the source and any other details requested should be provided as a courtesy to substantiate the reference.

I am officially disputing Small Victory's claim and requesting direct quotes. If Small Victory has integrity, then he will either provide such a quote, if it exists, or withdraw his claim if it doesn't. I also ask that independent editors verify Small Victory's assertion. In the meantime, I will proceed to remove the quote, because I cannot verify it. Should a direct quote that supports this claim be found and independently verified, then I will not object to its inclusion in the article. Wapondaponda (talk) 17:56, 25 July 2009 (UTC)

This is not the way to go about solving the disputes. If you guys cannot manage to bring forth a neutral point of view I recommend this page be deleted or restarted from scratch. It does not matter if you cannot find evidence at one locus in one people. The nature of drift and founder bias means that sometimes the evidence is going to be glaringly obvious, for example A30-B18 in Sardinia. On other occasions the evidence is going to be hard to detect. Imagine all the possible scenarios in Europe. You have African females as founders (Iberia), eurasian females as founders, male Africans and recent immigrants, male Europeans as recent immigrants, there are potential population events (like LGM and YD) and there are repetitous migrations. Sometimes you get lucky, for example the Pas lie exactly on a node of E1b1b1b in N Iberia. What is interesting in the Pas is that outside of the valley all A29-Cw16-B44 are basically in strong linkage disequilibrium, particularly at the high resolution typing level. The Pas are the only exception, they show numerous other haplotypes of Cw16 indicating that they are closer to the site of entry into Iberia. In addition the HFE locus is the result of gene conversion between A29-Cw16 and A*0301-Cw*0702, the highest level of both of these is within this area of Iberia. As I was telling you previous, much of the evidence for gene flow from Africa into Europe is very punctate, it is not diffuse. I will have the A30-B18 page up soon and you can see what I mean. From an observational perspective scientist are supposed to explain the observation and come up with more accurate interpretations, that means combining evidence against a hypothesis with evidence for a hypothesis.

The critical feature that you keep forgetting is that recent migrations did not contribute greatly to European genetic makeup. However all humans are originally from subsaharan africa, and non-recent contributions, particularly those before the LGM but after the first wave of humans from Africa are not easy to detect because there is a huge confidence range associated with any molecular genetic data. If I take a very strict statistical interpretation on many loci favored by scientist, the null hypothesis is only disproved with great refinement of technique and large samplings in Europe and Africa. Many areas of africa are very poorly typed, and there has been subsequent scattering of peoples prior to and after the post-glacial climate optimum. PB666  01:58, 26 July 2009 (UTC)

I agree that recent migrations did not contribute greatly to the European genetic make up. But what is unclear is the role of Ancient migrations. Certainly the migration of haplogroup E seems to have had a significant impact, since it reaches frequencies as high as 50% in the Balkans. Whether it was only one man who introduced his genes into Europe or many men, remains to be elucidated. How much autosomal DNA remains in Europe from the migration of Haplogroup E is also not yet known. Of course population differentiation and no gene flow is the null hypothesis. But we consistently see hints of gene flow, that tend to differentiate Europeans from other non-African populations, in that Europeans seem to have slightly more common ancestry with Africans, than say East Asians or Native Americans. Maybe much of this DNA is no longer in LD, so it is harder to detect, and because Europe is the most mixed continent, DNA is scattered around the continent, causing the someone disjunct distribution of certain African haplotypes. Wapondaponda (talk) 03:33, 26 July 2009 (UTC)

I don't know how true this is or not. I see putative evidence of Ancient contributions from both direct and Indirect sources. MtDNA groups X appears to move into Europe from the East, there is the potent migration of A1-B8-DR3 from Iberia. We can't even say at the moment whether these haplotypes and groups underwent extreme assymetric expansion. What I have examined is the rectangular occupation that was bordered by the Alps, Mediterranean, Atlantic and Retreating glaciers. Within that context there are a handful of haplotypes 2 of which are potentially of more ancient NW African origin. The problem is both are in acute linkage disequilibrium 12,000 years after the fact, how badly were they in linkage disequilibrium 12 kya. Ergo we have alot of room for random drift and binomial probability puts a pretty wide distribution of frequencies that can produce 1/4 or 2/4. In terms of Gene flow from the East, from tribes of peoples of middle eastern ancestry that accumulated African genes as a consequence of climate driven migrations or transcontinental nomadic behaviors in peoples. I cannot reiterate the point, there are clines in Europe, this is true, but they are not radial clines from mode to antimode, they are highly assymetric. AH8.1 declines along a slope from Ireland to Yugoslavia, there is a rapid drop in SE England and NE France and a rise going into Scandinavia a drop in Poland and a rise into the Hungary and a drop going into Romanian and another rise going into Serbia. The dips and rises are the consequence often of specific migration events. The drop in Paris is due to migration from Italy and Greece, the cline across N. Europe may be due to Negative selection since the Neolithic, which both suppressed but may have also promoted migrations from the South. The was a specific migration from Anatolia to SE France that appears to have touched Tuscan region and Switzerland, but all but moved through France without leaving a trace. You have to get out of you head C-S, that is old school. This specific injections of Y chromosome, they are not as these clines painted on the map, there is a blotch here, a big blotch over their, and places with very sharp frequency drop offs. The only reason that AH8.1, AH7.3, AH7.2, AH2.44 have produced the appearance of clines because they seeded an immense area of northern Europe with a founder affect. Consequently as the produce migrations in different direction this gives the appearance that there is a cline, but if you take a look at the end of the Haplotype, the DP loci, you will find that these haplotypes did not expand from a single point. One of the biggest problems right now with genome-wide surveys is the following: One large scale study will pick up an association in one region and another study will pick up another association in a different regions, we have had two large scale genome studies of Celiac disease and both studies managed to find loci with stupendous linkage, neither study found the same linkage (Except DQ2.5). How does one go about reconciling these inconsistencies. Easy human genetics does not serve scientist or clinicians, it serves the dogma survive and reproduce. There are all kinds of underlying regional factors that promote the ability to migrate into and the desire to migrate out of regions we don't understand, but what we can gather is that these regional selections are involved in regional survival, so that we have a basketwoven Eurasia particularly in interior and well traveled regions. I have read in history books this group invaded and wiped out this other group. And yet we find no evidence in the HLA that group X was wiped out or the the genes in place are overrepresented by group Y. We look at Arabia and how history tells about all the population events, but then look at certain HLA allele frequencies and haplotypes, and we find patterns suggestive of strong isolation, and then go 500 miles over to a parcel of land virtually ignored by history and it looks like an LA Freeway at 5:30PM. Apriori assumptions have got it so wrong so many times, it best to wait for thorough studies using the best available data and tools.

The problem is that Wapondaponda doesn't understand how the STRUCTURE program works (or he's pretending not to, as he seems to have no problem with it in the 'Central/East Asian admixture' section). Here's a very clear, easy-to-follow explanation from its creators, which shows that it's perfectly acceptable -- indeed ideal -- for quantifying Sub-Saharan African admixture in Europeans:

We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci.

http://pritch.bsd.uchicago.edu/publications/structure.pdf

Results are displayed in a color-coded chart like this one that shows population affinities and admixture proportions for each of the populations tested. A look at Figure S3A of the supplementary material from Auton et al.'s study will reveal an identical chart showing virtually no Sub-Saharan African admixture in any European groups. ---- Small Victory (talk) 09:00, 26 July 2009 (UTC)

No text supporting your claim, as I expected. The above quote is not from Auton et al but is a general statement about STRUCTURE program. This is WP:SYNTH. Find specific unambiguous text supporting your claim, and I will agree to include your statement. WP:No original research states,

This includes unpublished facts, arguments, speculation, and ideas; and any unpublished analysis or synthesis of published material that serves to advance a position. This means that Misplaced Pages is not the place to publish your own opinions, experiences, arguments, or conclusions.

In other words, Misplaced Pages editors shouldn't analyze data to advance a position, especially if the authors of the study have not done so. Your statements are an unpublished analysis. Wapondaponda (talk) 12:15, 26 July 2009 (UTC)

Since STRUCTURE results are most often presented visually, the chart is in effect a "direct quote from the reference cited". Therefore, your request is nonsensical and betrays either a poor understanding of the method, or a ruse to have material you don't like removed from the article (or both). And btw, the reason there's no text reference to African admixture is that none of the populations tested had any to speak of. ---- Small Victory (talk) 13:46, 26 July 2009 (UTC)

The outputs from the STRUCTURE simulation depend on the input parameters that are used. So while admixture can be inferred from it, we require the authors of the study to interpret the results for us. We should not read their charts and come up with conclusions. For example, one structure input is the number of clusters, in this study they used k=2 to 5 clusters. With each value of K we get a different chart. As a result we get a complex pattern which is best left to the authors to interpret. So the first chart has only two clusters, East Asian and European. There is no YRI at all which is unrealistic. YRI is instead represented by a mixture of East Asian and European. Native american only appears when K=5. Native americans show no crossover, with East Asia which is somewhat absurd given that they share recent ancestry. The authors state

While the global STRUCTURE analysis reveals broad patterns of population �differentiation (Supplementary Figure S3), the method is limited to using a small fraction of the available SNPs due to high computational cost. Furthermore, as the number of specifi�ed clusters is increased, the patterns of population structure become increasingly difficult to interpret.

So if the authors of the study say they are having difficulty interpreting the data, I don't see how a wikipedian could ace it. Wapondaponda (talk) 21:58, 26 July 2009 (UTC)

OK guys, knock it off. This is really not the place to go about this, these types of discussions belong on your talk pages, not here. Muntuwandi you act like you're seeking attention, this is not the place. Small Victory, are you professionally familiar with how the program works that generates these admixture diagrams, those I have seen reported for the global population used k = 14 clusters to achieve the best results and those levels were particularly important for establishing subdivisions within Africa? I want to remind you guys that although the human genome has been sequenced, there are still alot of variation, undetected variation in the human population and there is still considerable amount of sequencing errors and artifacts. Resolution between different populations and establishing admixture ratios work best when 2 populations have been separated for a period of time, and admixture occurs only once. Constant geneflow between groups over time does not give the best resolution. Populations that exist in genetic clines frequently have undetected alleles that when treated as one create false assumptions about population. The methodology they are using maybe sound but the data they are feeding into the program may not be perfect (or to state otherwise, not good enough to resolve contributions between to groups that were historically more closely related). I have a piece of advice, before placing this material on the Main, why don't you, Small Victory, have some respect for the people here and bring the material here first, both the conclusions you want to add and the tables or figures they are based on, so that we can see how reliable these maybe. Molecular anthropology is full of examples, perfectly sound logic, from the literature in which the data set or population sample was so incomplete that the conclusions drawn were diametrically opposed to reality. Therefore even drawing a conclusion based on what authors say in the conclusion (speculation) section of published literature is risky.PB666  00:36, 27 July 2009 (UTC)

Auton et al. use the results depicted in Figure S3 to quantify admixture in different populations. Of course, they only discuss it in the text when admixture is actually present, which makes Wapondaponda's request for a quote ridiculous. Here they are discussing European admixture in Mexicans based on the above chart (note that they don't mention African admixture for the obvious reason that the Mexican sample they tested doesn't have any):

The results are shown in Supplementary Figure S3D. At K = 2, the Mexican individuals appear admixed between a predominately European cluster and a predominately East Asian cluster, with slightly greater membership in the former cluster. However, at K = 3, the Mexicans form their own cluster and no longer share East Asian admixture, but retain a 'European' admixture component. The average proportion of European admixture in Mexican individuals with K = 3 is 32.5% with a standard deviation of 17.4%.

--- Small Victory (talk) 10:22, 27 July 2009 (UTC)

Pdeitiker, you are right, I am seeking attention, because I recognize that this specific problem can only be resolved by the community.Wapondaponda

The community will fix this page when the COIs back away from the page. Who do you think is going to repair this page in this environment? The hostilities are creating an excess amount parenting peers and almost no time working on the page.PB666 

Small Victory and I alone will not be able to resolve this. This is a very specific and simple issue. Should Wikipedians, in this case Small Victory, be reading, analyzing or interpreting charts, especially in ways not specified in the articles from which they are sourced.Wapondaponda

That is your issue, that is not the specific problem to wikipedia. While NOR is a pillar the basic problem here is how you three cannot see things from the other persons perspective, it is about neutral point of view. Let me make a brief synopsis, you added a collection of content, he considered it bunk, tossed all of it out, inserted his own content, and this has been going on different pages for quite a while. These content oscillation is not encyclopedic. The two contents needs to be merged together, with your content he is allowed to respond with information from the literature (such as Tishkoff et al, 1996) which find no evidence of excessive gene from SSA outside NE Africa or Eurasian as occurred during the first migration.

Academic consensus-The statement that all or most scientists or scholars hold a certain view requires reliable sourcing. Without a reliable source that claims a consensus exists, individual opinions should be identified as those of particular, named sources. Editors should avoid original research especially with regard to making blanket statements based on novel syntheses of disparate material. The reliable source needs to claim there is a consensus, rather than the Misplaced Pages editor. For example, even if every scholarly reliable source located states that the sky is blue, it would be improper synthesis to write that there is a scientific consensus that the sky is blue.

— WP:RS

Since there is no consensus on how much genetic input came from North Africa or from sub-saharan Africa we have a situation in which multiple reliably-sourced opinions can be provided.PB666  04:38, 28 July 2009 (UTC)

From what I can tell, the HAPMAP data is only piggybacking here into the analysis of structure, and it does not constitute the main analysis. Specifically the only subcontinental analysis presented is for East Asia, South Asia, Mexico and Europe(Nelson 2008). There is no subcontinental analysis for Africa(YRI)(page 2 supplementary material). I am still trying to understand what actually the STRUCTURE analysis constitutes. I agree with Pdeitiker, in that the results of structure depend on the inputs. The Tishkoff paper identified 14 clusters worldwide. Each value of K yields different levels of admixture, so admixture results from structure are not absolute values.Wapondaponda

It is in the developemental stage, as they presented in the paper the statistic provided the most reliable interpretation at k = 14. Interestingly the program divided the younger exoafrican groups before dividing older sub-Saharan groups, indicating distance of separation of is a factor in the capacity to recognize admixture. Admixture is most easily recognized in haplotypes if each common mutation or shared source of variation is border on both side by private mutations. Constant geneflow does not allow this. As the number of relevant SNPs increases the ability for these programs to parse out ancestral clusters will also increase. If you are testing the Guarachi against Western Irish, there is a relatively good spatial separation that prevents admixture except through greatly indirect transmigratory genetic exchange. However if the Sengalese have gene flow from the Berbers and Iberians have gene flow from the Berbers it is less easy to find a markers that clearly distinquishes Iberians from Senegalese.PB666 

In any case Small Victory is contending that Sub-Saharan admixture is negligible based on his own reading of the chart. However this directly contradicts what is in the text, when they specifically discuss YRI haplotype sharing and West African gene flow into Southern Europe. That Small Victory is willing to ignore the main conclusions of the study and instead subjectively interpret a chart is at the core of this dispute. Wapondaponda (talk) 12:46, 27 July 2009 (UTC)

Yeah, Tishkoff tested Africans from all over the continent, including the Horn, yet the Europeans they were compared to still didn't have any admixture to speak of.

And you're the one ignoring Auton's conclusions, pretending that West African gene flow is the only interpretation for the shared haplotypes. My version is more neutral because it mentions all possible interpretations, plus the results of the admixture analysis. ---- Small Victory (talk) 13:58, 27 July 2009 (UTC)

I am not going to get in an argument between you two. You are wrecking the Main, neither of you are doing anything to improve the quality, or more important the encyclopedic nature of that page. If you are not here to provide encyclopedic content in line with WP:MOS then don't screw with the Main page. I have asked you, Andy has brought this to the attention of the Admins, and Admin told you guys a couple of days ago to work together. You must learn to work together. Small Victory you have a snide attitude and you blow off these indications of gene flow and others like myself who have papers suggesting gene flow know what is significant and what is not. If you live in Sardinia, then the contribution of African sources of DNA other than the migrations from East Africa is highly significant. If you live in Portugal or Spain the contribution is highly significant. Muntuwandi you cannot invent results that are not there, even if you suspect they are there, you have to go by the science that is out there, and _if anything_ you need to restrict presenting all interpretations because some of the results are not studied in a thorough manner. I have yet to see any result that suggest unequivocable evidence of gene flow from sub-saharan africa into Europe (I have repeatedly told you this), the critical issue is the nature of poor genetic studies done in NE Africa to date. I have 100s of paper on HLA sitting right next to my leg here, many that corroborate what Arniaz-Villena stated in the 2001 publication, but I am not convinced this comes from sub-Saharan Africa. The HLA studies offer the best evidence. But (at some point I will have a page that deals with this issue) when one dives into the issue, one begins repeatedly hitting N. African populations (e.g. the Berbers). How do you discriminate gene flow from Berbers into West Africans (like Senegal) from gene flow of equitorial Africans into Berbers. This is the problem with the YRI HapMap, they did not test a bunch of African groups, they are holding up a single group as a surrogate for whats going on in Africa. By just about every credible molecular anthropologist out there is critical of sampling issues within Africa, sample within Africa should equal or exceed sampling out of Africa. Here is the trouble with Arniaz-Villenas conclusion, There is about 2000 miles betweeen where these genes he called SSA were found, and the first Nile dwelling people to be sampled. Vast empty space of NE Africa that has not been studied according to modern methods of HLA genotyping. Egypt, untyped, Libya, untyped, Sudan, no formal papers presented, some typing, Algeria, typing only of the berbers.

This is all very simple, what is spoken of within the literature, that which best methods show to be reliable and there isn't that much, and every thing else needs to be kept off the Main. IMHO the Sub-saharan african issue should get a couple of sentences in North Africa. I think Arniaz-Villena needs to be introduced along with subsequent papers that support the position and then we can discuss the problems in NE Africa (I have the publications from Egypt and Sudan) to provide NPOV and that is all we need to introduce. Simply because L1, L2, L3 are found in SSA does not mean that they could not have spread slowly northward into N.Africans indigeonous peoples, the same is true with the Y chromosome. As long as you three continue to lock horns on the main page, the main page is not going to attract expert editors to fixe the page, and folks are not going to be able to read the page, so that whatever pearls of wisdom you add are basically thrown in a pigpen.PB666  04:38, 28 July 2009 (UTC)

No original research noticeboard

I have created a thread here. Wapondaponda (talk) 12:51, 26 July 2009 (UTC)

Molecular photofitting

This book by one of the founders of DNAPrint Genomics has more detail on their analysis of continental admixture. Specifically the explain the nomenclature used to describe Haplogroup E and its subclades. Frudakis states:

Underhill et al showed that the frequency of the YAP+ haplogroup commonly referred to as haplogroup E or (III) is relatively high (about 25%) in the Middle East and Mediterranean. This haplogroup E is the major haplogroup in Sub-Saharan Africa(75% of all Y chromosomes). Specifically, Europeans contain the E3b subhaplogroup, which was derived from haplogroup E in sub-Saharan Africa and currently is distributed along the North and East of Africa. Thus we refer to the affiliation as African, West African, or North/East African depending on the time frame we wish to refer to and/or our semantic preference.

To add to the existing sources, here is another one that refers to Haplogroup E as Sub-Saharan and even e3b as well. Wapondaponda (talk) 22:54, 26 July 2009 (UTC)

• Frudakis, Tony (2007). "Apportionment of Autosomal Diversity with Continental Markers". Molecular photofitting. pp. page 326. ISBN 0120884925. {{cite book}}: |pages= has extra text (help); External link in |chapterurl= (help); Unknown parameter |chapterurl= ignored (|chapter-url= suggested) (help)

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While there is no monetary or biographic interest here, it is obvious that at least 2 individuals here are acting against the interest of the encyclopedia in provide WP:POV.

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Neutral point of view is a fundamental Wikimedia principle and a cornerstone of Misplaced Pages. All Misplaced Pages articles and other encyclopedic content must be written from a neutral point of view, representing fairly, and as far as possible without bias, all significant views that have been published by reliable sources.

In addition to the above situations, many aspects of this article appear to be in violation of Occam's razor, that is instead of providing the best information from reliable sources, editors have gone about a process of creating contorted arguments to support weak hypothesis that are not openly supported by reliable sources. In addition the article is over-reliant of Y chromosomal evidence which is not a good marker to investigate levels of admixture.

What the above have done to this article have made it a sense-less bowl of spaghetti. The recent addition of Sub-Saharan African admixture: we have one version that is anti SS Admixture and one version that is Pro SS admixture. Both versions violate WP:NPOV. Editors are supposed to work together, consequently I am going to remove the current section and the reverted section and place them here until these two versions can be messed together. Muntuwandi, where is the clear evidence for uncontrovertal evidence for Subsaharan contributions to Europe. PB666 

Sub-Saharan African admixture

Question of an expert - Is this section head really appropriate?

— PB666  15:55, 27 July 2009 (UTC)

Sub-Saharan African mtDNA (haplogroups L1, L2 and L3) and Y-DNA (haplogroups A, B and E (excluding E1b1b), particularly the ubiquitous Bantu marker E1b1a) are present at generally low levels throughout Europe.

Maternal (mtDNA) lineages are the more common and likely represent gene flow from historical events, such as slavery. They've been found in Portugal (6.9%), Spain (2.1%), Slovakia (1%), Italy (0.87%), Finland (0.83%), Bulgaria (0.71%), Bosnia (0.69%), Basques (0.64%), England (0.6%), Greece (0.44%), Switzerland (0.44%), Czech Republic (0.4%), Russia (0.3%), France (0.3%), Poland (0.18%), Germany (0.17%) and Scotland (0.1%).

Paternal (Y-DNA) lineages occur less frequently. They've been found in Portugal (3%), Albanians from Italy (2.9%), France (2.5%), Germany (2%), Sardinia, Italy (1.6%), Calabria, Italy (1.3%), Austria (0.78%), Italy (0.45%), Spain (0.42%) and Greece (0.27%).

The information above should be submitted in the form of a Table

— PB666  15:53, 27 July 2009 (UTC)

Version Muntuwandi

Apart from the above clear cases, there are also older connections between Europe and Africa, including sub-Saharan Africa. The study of these is part of the study of the genetic diversity of all humanity, which is a complex and developing field wherein European and sub-Saharan African genes do not necessarily represent constant and clearly defined separate entities.

Evidence of prehistoric Gene flow from Sub-Saharan Africa includes:

• The presence of Haplogroup E in Europe. Haplogroup E is one of the main Y-Chromosome haplogroups of Sub-Saharan Africa. In Europe haplogroup E is represented by its main clade E-V13, in addition to several minor clades. The exact nature and timing of the migration of haplogroup E from Sub-Saharan Africa to Europe is the subject of on going study and debate. A number of scholars associate this migration with demographic and cultural changes that took place during the Neolithic transition.. *A 2007 study conducted at Penn State University found low levels of African admixture(2.8-10%) that were distributed along a North South cline. The authors suggest that the distribution of this African admixture mirrors the distribution of haplogroup E3b-M35(E1b1b).

The evidence from Y chromosome should not be treated separately, but collectively. This section should be merged with the section on Y chromosome above. Better yet provide links to the E1b1b page. In addition haplotype E comes to Europe largely via the middle east, so that much of this should go into the middle eastern contribution, only those haplotypes that are not found widely in the middle east but are found widely in Mediterranean should be presented. In addition I would argue that The horn of Africa to Eastern Sahara, and West Africa should be treated separate issues from the rest of subsaharan Africa, as these regions share many similarity with proximal Eurasians. Evidence from recent studies of other loci, using modern techniques should be added See Tishkoff et al. 1996

— PB666 

E in Europe does arrive from the middle east, but as Frudakis mentions, where E comes from simply depends on the time of reference. Further back in time, Haplogroup E has its origins are in SSA. I agree that SSA is an ambiguous classification, however the Eurasian affiliation of North Africans, Horn Africans is all the result of recent events. Most Eurasian gene flow into Africa is post Neolithic, whereas gene flow out of Africa is pre-Neolithic. Technically, pre-Neolithic Africa is largely equivalent to contemporary SSA in terms of the profile the composition of mdDNA and Y-chromosome haplotypes. Furthermore, Shriver, Frudakis detect autosomal African admixture in Europe wherever E3b is found. Wapondaponda (talk) 13:56, 28 July 2009 (UTC)

Tishkoff et all 1996 Treats NE africa differently from the rest of Africa. If the Horn of Africa is the source of Eurasian Diversity, then how can it be considered more different in the past? I think the handling of Red Sea populations/NE african popultion should be handled without two many assumptions.

1. You have movements of Nubians down the nile (to the North).
2. There are Red Sea cultures putatively of regional African descent.
3. There was a development of African Taurids and at least some of these cattle made their way to Iberia before the Iron Age.

So this big influence of Arabs has to be taken against contributions and increases from the Sahul previously. All of this stuff occurs after the LGM, relatively recent in human history.

• Measures of genetic distance between Europe and Sub-Saharan are generally smaller than Genetic distances between Africa and other continental populations. Cavalli-Sforza states that the relatively short genetic distance is likely due to prehistoric admixture.

These conclusions are based on relatively dated studies and techniques that are no longer widely used

— PB666  16:04, 27 July 2009 (UTC)

I agree that this is an older study, but CS and Bowcock are still widely referenced. What I find interesting, is that their findings are consistent with what others have said. CS hypothesizes that an admixture event, would have occurred due to gene flow from the middle East which is in line with other studies. Wapondaponda (talk) 09:06, 28 July 2009 (UTC)

Who is using the techniques, anymore. Anne is currently working on Genome wide associations with skin disorders, she it using the same current techniques (Genome Wide survey) that everyone else is using. If these techniques of C-S are so great why aren't people refining them and using them?PB666  22:57, 28 July 2009 (UTC)

• A 2009 study by Auton et al found a North-South Cline of Hapmap Yoruba haplotypes (YRI) in Europe. The study determined that South and Southwest subpopulations had the highest proportion of YRI This distribution is indicative of recurrent gene flow into Europe from both the Southwest and the Middle East. The authors suggest that the haplotype sharing between Europe and the YRI are suggestive of gene flow from Africa, albeit from West Africa and not necessarily North Africa.

YRI is one of 4 major haplotype groups it is not a globally representative study, see Hawks J, Wang ET, Cochran GM, Harpending HC, Moyzis RK (2007). "Recent acceleration of human adaptive evolution". Proc. Natl. Acad. Sci. U.S.A. 104 (52): 20753–8. doi:10.1073/pnas.0707650104. PMC 2410101. PMID 18087044. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link). Either there has been an increased rate of evolution at these sites or the recombination (rate of equilibration) has come under selection (as appears with AH8.1) therefore this approach is tainted by a large level of uncertainty

— PB666 

I agree that YRI isn't necessarily representative of SSA, and this is specifically mentioned on the hapmap page. However, in continental analysis, they use it as a proxy, in lieu of having to analyze the whole continent. Wapondaponda (talk) 09:06, 28 July 2009 (UTC)

• A principal component analysis of data from Human Genome Diversity Project by Reich et al detected a West-to-East gradient of Bantu related ancestry across Eurasia. The authors suggest that after the Out of Africa migration, there was most likely a later Bantu-related gene flow into Europe.

Bantu related- Bantu is a language family that spread with certain sedentary technologies around Africa about 3000 years ago. The migrations that have reached Europe are at least this old, if not much older. Recent timeframe extends to about 12,000 years ago and what does this have to do with people who speak and extant African language - This does not sound like it fits the criteria of a reliable source

— PB666  16:14, 27 July 2009 (UTC)

I agree, poor choice of words by the authors of the study. However, their study did use samples from contemporary Bantus. In addition they use the term "Bantu-related", which doesn't mean actual Bantu's since the language family didn't exist in the pleistocene, but affiliated to modern day Bantus. Wapondaponda (talk) 09:06, 28 July 2009 (UTC)

So where precisely did 'Modern day bantus' Come from?PB666  22:57, 28 July 2009 (UTC)

Version Small Victory

Genome-wide autosomal DNA analyses using the STRUCTURE clustering program, which is designed to accurately detect and quantify admixture, show equally negligible levels of sub-Saharan African admixture in all Europeans.

Wasn't it concluded that this conclusion was original research? This material should not be returned to main if it under administrative scrutiny

— PB666  16:44, 27 July 2009 (UTC)

Whatever, the case, the sub-saharan admixture section is given too much 'space' for such minimal impact. I agree with PB666 that it would be more simple to give a reference range or table rathern than to ad nauseaum catalogue all the countries with 0.5% sub-Saharan admixture. Someone is obsessed and compelled to include this bit of information that, as far as the whole picture is concerned, is rather minor. Hxseek (talk) 01:59, 28 July 2009 (UTC)

PB666, it seems you've found a lot wrong with "Version Muntuwandi" but very little wrong with "Version Small Victory". And the one thing you did say about mine is false. There's no policy I'm aware of stating that charts, graphs, diagrams and other forms of visual data cannot be cited as evidence for claims.

Your findings should tell you which version belongs in the article and which one doesn't, as well as show you that the labels "anti SS admixture" and "pro SS admixture" are gross mischaracterizations. Better would be "neutrality and factuality" vs. "OR and POV". ---- Small Victory (talk) 09:58, 28 July 2009 (UTC)

A find very little wrong because your version is a magnitude smaller. How does the say 'what belongs to Ceaser . . .' Most of this 'evidence belongs in North African contributions'. What is left, discussions about papers that explicitly mention SSA contributions we need to present the evidence but at the same time point out the faults in these studies.PB666  23:07, 28 July 2009 (UTC)

Eastern Asian admixture

A concern has been raised that the study used to quote the frequencies of 'Asian" mtDNA. The study groups Bulgarians with Turks. They are two entirely different ethnic groups- culturally, religiously and geographically, and would undoubtedly skew the result. I do not conceive that such a methodology meets WP:RS standards. Hxseek (talk) 01:59, 28 July 2009 (UTC)

Proposal

I don't mean to take this article hostage, after all it is about Europe and we are spending a lot of time discussing SSA influences. I see no reason why evidence of SSA gene flow should be censored. I agree that the amount of text should be proportionate to level of importance. I also believe that evidence for SSA gene flow doesn't have to be uncontroversial, but rather evidence for gene flow should be from notable sources as per WP:RS and WP:NOTE. There are a couple of consistent themes that are seen across several publications

• Prehistoric and recent gene flow from SSA
• South to North cline, through Iberia and the Middle East
• Related to Haplogroup E including E1b1b, and mtDNA Ls

I think this can be summarized in one or two paragraphs, and percentages if necessary can be moved to a table as suggested by Pdeitiker. Wapondaponda (talk) 09:37, 28 July 2009 (UTC)

Name changes

The term "genetic history" strikes me as somewhat unusual. What about "Population genetics of Europe".

New articles

At some stage, it would be more appropriate to move the section on SSA influences to a separate article. This will prevent us spending too much time on one topic in the GHOE article, when the article has several other issues. The previous article was deleted because of POV fork issues. So if we are to create a new article, a reasonable consensus would be required. We have a partially complete draft and the reference list above. Pdeitiker can also present a summary of the current research on HLA, since there is some evidence of gene flow from Africa. This article can go live, if a a resonable consensus is achieved, but I don't know what others think. I would rather have an article about African influences, that includes both North African and Sub-Saharan influences because it is practically impossible to separate the two. Genes do not come with a stamp of North African or Sub-Saharan African. Possible names

• African admixture in Europe.
• Gene flow from Africa to Europe
• Any other suggestions.

Finally at some stage it might become necessary to create an article

• Population genetics of Africa or Genetic history of Africa, Asia, Americas, Oceania too.

Wapondaponda (talk) 09:37, 28 July 2009 (UTC)

The AfD is over, the article was deleted. The genetic history of Africa is 10 million years.PB666  03:39, 29 July 2009 (UTC)

I agree. A core problem of that deleted article is that science is not up to it. There is no clear definition of African and sub Saharan in DNA, and there might never be, because Africa is centre of gravity for human genetic diversity. But not only that: most of the details of exactly how are part of the still uncertain field of human genetic diversity overall. Somewhere during the debates about that deletion I made the point that it makes no sense to have an article about this subject while there are still no articles about some of the logically prior areas, for example the types of data analysis used to come up with speculative theories.--Andrew Lancaster (talk) 21:00, 29 July 2009 (UTC)

Xing et al 2009

Fine-scaled human genetic structure revealed by SNP microarrays, Supplemental material table 2

My question is why is the percentage of unique polymorphic SNPs shared between Europe and Africa at 1.59%, double that between Africa and Asia, at 0.74, and double that between Africa and India at 0.62. Shouldn't Europe be in the same range as Asia and India being that Europeans are descended from the same source population as Asians and Indians. Wapondaponda (talk) 15:45, 28 July 2009 (UTC)

You already know the answer to that question. From Cavalli-Sforza's The History and Geography of Human Genes:

http://img248.imageshack.us/img248/3122/cavallisforzaadmix.png

Figure S4 in the supplementary material of the Xing study shows clearly that Europeans have no African admixture. Stop wasting people's time with nonsense. ---- Small Victory (talk) 10:34, 29 July 2009 (UTC)

Y description in SSA

Y-DNA haplogroups A, B and E are the predominant haplogroups in Sub-Saharan Africa. Only Haplogroup E is found at moderate levels(7.2% in one sample ,Cruciani et al 2004) in Europe whereas all others haplogroups are present at low levels, usually less than 1%. Haplogroup E which originated in Sub-Saharan Africa, is thought to have entered Europe via the Middle East in the late Pleistocene or Early Holocene. The main clade found in Europe is E1b1b. Haplogroup E1b1a dispersed recently in Africa, and therefore its sporadic presence in Europe is usually attributed to recent events, such as the slave trade, the Moorish occupation of Iberia and other historical contacts across the Mediterrenean and Atlantic. Haplogroups A, B and E1* are ancient African lineages that are relatively infrequent in Africa. They have sporadically been detected in Europe but their exact mode of entry into Europe is still not understood. A prehistoric entry of these haplogroups into Europe remains a possibility.

Problems:

• Haplogroup E may have originated in SSA, but the E - haplotype E1b1b that gave rise to these various European E originated in East Africa along the NE margin of the continent, proximal to SW Asia. So that its attachment with SSA is not great. The core centers of diversity in sub-saharan african lie from Ethiopia Eastward to the pygmoid populations of central and west Africa, down to the congo and back down the Khoi-san region (no info on Angola) to the Indian ocean at the northern boarder of S. Africa and back up to Ethiopia. In this the core regions extend from SE Tanzania to !kung to the efe, baka, mbuti, the african rift lakes back to Tanzania. Therefore its evolution along the Red Sea really does not offer anything interesting other than it evolved along the continent margin where humans had migrated from in the past. The discription of the evolution of Eurasian E's belongs in the discussion of North African Contributions, not Sub-Saharan. All Y chromosomes have ancestors in sub-Saharan Africa, in which case there is nothing special about E1b1b1a or b in Europe. Not all Y chromosomes haplotypes are shared between Europe and Africa to the extent of E1b1b1a and E1b1b1b. As I have repeated reminded you its not about handwaving arguments (like the above, with lots of weasel words) its about specific genetic contributions from probable points of emigrations to probable points of immigration. This I why I have told you, the evidence based on LL C-S is just such 'hand waving evidence' it is a proxy for genetic studies which are capable of giving refined information.

• I appreciate you taking the effort to critique the material. I tend to disagree on the not great affiliation between E1b1b and SSA. Firstly E1b1b is most closely related to E1b1a, they are siblings and share the PN2 mutation which is now thought to have originated in East Africa/Northeast Africa. Wapondaponda (talk) 08:32, 29 July 2009 (UTC)

• I did not state E1b1b originated in North Africa, I stated in likely originated in East Africa, part of which is in Subsaharan Africa. That E1b1b is of subsaharan origin is irrelevant since the parent haplotype does not exist outside of Africa, and therefore there should be no reason to discuss E1b1b* at all, the discussion of E1b1b1 is also moot, though I think Andy should have some input. You are simply trying to stall and handwave over the basic issue, you are trying to turn evidence for E1b1b1b and E1b1b1a into a discussion of E1b1b's origin. As such it undermines your credibility in this discussion.PB666  20:22, 29 July 2009 (UTC)

Would you dispute that there was a migration of genes from SSA to Europe in the last 15kya. Wapondaponda (talk) 20:27, 29 July 2009 (UTC)

I dispute you have any proof of a direct migration of genes from SSA into Europe that has not undergone admixture with other genes or chromosomes in North Africa of people without much recent Subsaharan African contribution and ditto with the Middle East. All genes have migrated out of Subsaharan Africa. The fact you continue to focus on fluffy old studies and Y DNA which has a known migration/invasion bias indicates your general lack of concern of the importance of the migrations.

Your analysis also violates WP:SYNTHESIS. PB666  20:41, 29 July 2009 (UTC)

Ethiopians have the highest proportion of PN2 ancestral lineages(Semino 2004). This basically means that the Niger-Congo speakers with E1b1a, also have their origins in the same general area as Afro-Asiatic speakers with E1b1b. So what we have is that E1b1b is fully nested within other Sub-Saharan haplogroups, E1b1, E1b, E1 and E*. Furthermore its cousins include E1b1c, E1b12, E1a and E2. All E1b1b's cousins and siblings are exclusively sub-Saharan. Within E1b1b, one clade, E-M293 formerly E3b*, is largely confined to Sub-Saharan Africa, found as far south as South Africa, though it has been observed at frequencies around 1% in southern Europe. Europeans with E1b1b are more closely related to Africans than to non-E1b1b Europeans via the Y-Chromosome.

• I also disagree with the contention that E1b1b is North African or rather exclusively North African. As I previously mentioned, before the Neolithic, the genetic profile of North African haplogroups would have been more similar to Sub-Saharan Africa, with large amount of E lineages and L lineages. Wapondaponda (talk) 08:32, 29 July 2009 (UTC)

1. The question of N African Neolithic is questionable, key to neolithic is settlements. North Africa is not characterized be a classic neolithic period as many H-Gs had no alternative but to adopt nomadic pastoral lifestyles.
2. The discussion of E1b1a, -c etc. Is not relevant Haplotype D is found all over Asia both E and D are found in Asia Ergo, but that has nothing what-so-ever to do with E1b1b1b and E1b1b1a in Europe. Where is the LCA of D in Africa?
3. E1b1a origin is over 25,000 years ago, and here you are talking about Niger-Congo speakers, as if it has some meaning?

You are simply trying to obfuscate the issue with loose facts that you think others will not be able to follow, you are engaging in sophistry and most importantly you are violating the WP:NPOV. PB666  20:22, 29 July 2009 (UTC)

The arrival of most Eurasian haplogroups occurred after the Neolithic in the middle East as suggested by Arredi et al and Mitochondrial DNA haplogroup H in North Africa. Both these articles suggest a Neolithic/late paleolothic migration from Eurasia to North Africa. Which means prior to this migration mostly Sub-Saharan haplogroups were present in North Africa. Wapondaponda (talk) 08:32, 29 July 2009 (UTC)

• No it does not. North African has HLA haplotypes and alleles within its 'negroid' population which are considered to be diagnostic of N. Africans. You are violating WP:SYNTHESIS. PB666  20:22, 29 July 2009 (UTC)

So when people associate E1b1b with North Africans, there is a misconception that people were similar to contemporary North Africans, who are predominantly of Eurasian ancestry. Rather the Sahara, was largely depopulated and Sub-Saharan Africans occupied much of the Nile up through Egypt. It is these people who spilled over into Eurasia to help kick start the Neolithic, after which Eurasian peoples migrated back into Africa bringing with them Neolithic crops and domesticated animals. Wapondaponda (talk) 08:32, 29 July 2009 (UTC)

• This publication by Kujanova et al 2009 Near Eastern Neolithic Genetic Input in a Small Oasis of the Egyptian Western Desert detected 70% African Y chromosomes, E1b1b at 64%, E1b1a at 6%, and 31.4% Sub-Saharan L lineages. Though a small sample, the African/Eurasia contribution is 50% each. This illustrates an African population that absorbed Eurasian populations and became predominantly Eurasian, while maintaining a genetic trace of their SSA roots. Wapondaponda (talk) 08:06, 29 July 2009 (UTC)

• The Epipaleolithic ends about the same time as the onset of the holocene, mesolithic tool technology is not widely observed in Europe, but the Neolithic transition is sharp, working backward from youngest to oldest, the Irish Neolithic is about 3800 to 4300 years old, the first evidence of the British Neolithic is about 7100 year ago, the LBK culture begins around 7500 to 8000 years ago in the Iron gourges region of Austria. The onset in the sub-channel loess belt the range if from 7500 to 6900 years ago. The Central European neolithic is associated with a well defined package of cattle industry (probably from what is called thracia), LBK pottery, and Triticeae cultivation. The Italian neolithic does not have a clear onset, but earliest dates are between 8500 and 9500 calibrated years before present, the later Impressed Cardial Ware seen in Ionia and Impressed Ware along the western coast of Italy and swept the coastal regions of Iberia thereafter. LBK and Impressed Cardial Ware differ in the package, with western European Neolithic pastoral habits including locally domesticate caprids. The onset of the Italian neolithic (scant evidence) greek neolithic and middle eastern neolithic boundaries are fuzzy but generally occur after the onset of the holocene. IOW before 9000 years ago Iberia would be considered preNeolithic. Around 9000 years ago almost all of Italy is assumed to be in the late Mesolithic, only a few river basins would be considered Neolithic. Cattle were believed to have been domesticated in Thracia about 10,000 years ago, and with the discovery of domesticated cattle bones in the Sahara from about the same age there is now a running debate as to when and where cattle were domesticated first (include middle east).

• E1b1b is not found in Europe at all, only the daughter clad E1b1b1 and I don't think E1b1b1* is found in Europe either. You are really not talking about haplogroup E, but the E1b1b1 subclads that entered the middle East after (Note "Cruciani et al. (2007) also note evidence for "trans-Mediterranean migrations directly from northern Africa to Europe (mainly in the last 13.0 ky)") So that generally places in in either a Holocene or post-mesolithic context. E1b1b1b appears to have come from west Africa after 5600 years ago. You can pretty well guess the mode of entry of E1b1b1b involved at least on Male getting in a water craft in NW Africa and touching soil (and other aspects of Iberian fauna, namely homo sapiens) on some parcel of land in Iberia.
• All Y have ancient African lineages.PB666  04:51, 29 July 2009 (UTC)

The bottom line here is that most of the evidence pertains to either Neolithic conveyors of middle eastern genes along the mediterranean (and associated migration/invasion bias for Y expansion) or more recent gene flow from NW Africa. PB666  04:51, 29 July 2009 (UTC)

The trouble with this interpretation, is an arbitrary selection of the time frame and region. Why should we choose say, the Middle East over North Africa, or North Africa over East Africa. Is there an objective reason to do so. If there is, please let me know. We know that the expansion of E didn't start in North Africa. The expansion started in SSA heading Northwards. By arbitrarily selecting North Africa or the Middle East, we are ignoring the earlier periods of expansion. But what is most important here is that we have reliable sources that specifically make a connection between Sub-Saharan Africa and the spread of E3b. Per wikipedia policy we can use them in the article. We are entitled to our own opinions, but we should report what reliable sources say. Much of this confusion originated from the fact that e3b was once thought to have originated in the Middle East, rather than in SSA. So now we will see a reorientation in the way people describe E3b. Wapondaponda (talk) 16:05, 29 July 2009 (UTC)

As mentioned by Frudakis et al, the affiliation depends on the time frame and what subclades we look at. If we only consider E-V13, then we are looking at Europe and the Middle East. But if we consider the parent clades, then E-M35, PN2 right up to E-M40 are all Sub-Saharan markers. We can assign arbitrary terms to E1b1b, and this will simply depend on the preference of the author. I think there are enough reliable sources to demonstrate this. The Out of Africa migration is thought to have occurred at the least 50kya, possibly before. For about 40k years, Europe was devoid of haplogroup E, while E was evolving in SSA. Since the Out of Africa migration, E has spent more time in SSA than it has in Europe, North Africa or anywhere else. The big question is whether autosomal admixture that was brought with E from SSA was significant. Frudakis et al seem to think so stating, "West African affiliation detected for continental Europeans and Middle Eastern populations appears to be anthropoligically meaningful" . When we look at the haplotype sharing by Xing et al, we see an elevated amount of unique haplotypes shared between Europe and Africa. From my perspective the only explanation can be E1b1b because it has such a wide distribution in Europe. Wapondaponda (talk) 08:06, 29 July 2009 (UTC)

Y description SSA and physical appearance

Europeans don't have the parent clades. They have the subclades, which didn't originate in Sub-Saharan Africa. Implying that the two are equivalent is original research.

Also, you quote Frudakis' vague statement that it "appears to be anthropologically meaningful", but I guess you missed the preceding paragraph where he actually discusses the anthropological implications:

http://img339.imageshack.us/img339/6682/frudakis2007.png

Probably not quite what you had in mind. ---- Small Victory (talk) 10:52, 29 July 2009 (UTC)

No I have read the preceding discussion on the paleoanthropological evidence from East Africa. It is nothing unusual, though I think Frudakis is a bit out of his league in discussing prehistoric crania, and should stick to genetics. We know that during paleolithic times, there was fragmentation and population differentiation. In fact the Hoffmeyr skull from South Africa, is said to be more similar to Cro-Magnon Europeans than contemporary Africans. This is consistent with non-Africans being derived from a single African population. Wapondaponda (talk) 16:05, 29 July 2009 (UTC)

Nice try, but Frudakis cites an anthropologist (Howells) as saying that "prehistoric East Africans...were non-African in nature—that is, not Negroid." And he ties that in with the appearance of YAP and E carriers, and potentially all other OOA migrants. Certainly such non-Negroid prehistoric "admixture" shouldn't be mentioned in the same section as historical admixture from Negroid slaves, as if they were both part of the same demographic process, especially when Europeans only have the non-SSA subclades of those haplogroups. That's original research and deliberately misleading. ---- Small Victory (talk) 08:28, 30 July 2009 (UTC)

That has now been debunked, Wapondaponda (talk) 13:10, 30 July 2009 (UTC)

You're very confused. It's Rightmire (1975) who's been debunked by Howells (1995):

Remembering that the Teita series (Bantu speakers of southeastern Kenya), and the recent East African skulls in table 4 above, do clearly exhibit African affiliations, it is fair to say, CONTRA RIGHTMIRE, that there seems to be no clear continuity here in late prehistory. On the broad scale, looking at an "Out-of-Africa" scenario, one would expect that, in some region between southern and northeastern Africa, some differentiation would have been taking place within a Homo sapiens stock, evolving into something beginning to approximate later Sub-Saharan peoples on the one hand, and evolving in another direction on the other hand. East Africa would be a likely locale for appearance of the latter. So anyone is welcome to argue that this is what Elmenteita et al. are manifesting. The ensuing picture for East Africa, that is to say, would later have beeen changed through replacement by the expansion of Bantu or other "Negroid" tribes.

--- Small Victory (talk) 07:53, 31 July 2009 (UTC)

There is nothing inconsistent here, the three skulls clearly exhibit African affiliations. Rather he contradicts Rightmire on the hypothesis of continuity between Bantus and Early holocene skulls( something like three samples from 3kya). Frudakis is incorrect to describe them as "non-Negroid" because this is not what Howell's stated, he just stated that the discriminant analysis failed to cluster them with modern SSAs. Furthermore the Negroid skeletal classification itself is disputed. What Frudakis should have said was that skulls differ from the modern inhabitants of the region. But it is correct to describe Africans as having a high diversity in skeletal measurements. It is true that the Bantu expansion has erased much of the pre-existing diversity in across SSA. It is generally accepted that East Africa has the highest diversity in skull measurements. . Wapondaponda (talk) 15:59, 31 July 2009 (UTC)

Wrong again. Howells is saying that recent East Africans exhibit African affiliations. The prehistoric ones do not:

The DISPOP results here are not indicative of anything, except a general non-African nature for all these skulls. Display of POPKIN distances (infra) reinforces this and seems to find nearer neighbors among such more generalized populations as Peru, Guam, or Ainu, but also Europeans or even Easter Island.

--- Small Victory (talk) 07:39, 1 August 2009 (UTC)

There is nothing unusual here, all humans descend from an African population that lived 50-70kya. The same number of generations separate Europeans, Asians, Native Americans and Australians from the prehistoric African population as modern Africans. There is no reason to think that modern Africans look the same as prehistoric Africans. Even the skulls of modern Khoisans differ from those of modern Niger-congo speakers. Skull shapes are dynamic and are constantly responding to environmental pressures. So it shouldn't come as a surprise that discriminant analysis found differences between prehistoric and modern Africans. But one shouldn't read too much into it. Elmenteita is still fairly recent at 7kya. Furthermore there are actually very few fossil specimens in Africa to make any firm conclusions.

The fossil record of modern humans in Africa is unfortunately too incomplete to provide a morphological dimension to early African diversification

Evolution of Modern Human diversity pages 282-283

I agree that we don't know what the person who first carried E3b looked like. When we look at the phylogeny of y-chromosomes, we see that haplogroup A is found among khoisans, Nilo-Saharans and Ethiopians. B is found with the pygmies. E*, E1, E2, E1b are found among Niger-Congo and Nilo-Saharans. E1b1 is found among Niger Congo and Afro-Asiatic. So there are all kinds of interesting scenarios that could have taken place in history. I think Frudakis was reading blogs when he wrote that section of his book, LOL. Wapondaponda (talk) 08:53, 1 August 2009 (UTC)

The first E3b-carriers were, like all OOA migrants, generalized modern humans who were nonetheless more similar to modern non-Africans than they were to modern Africans. That makes referencing them in a section mainly about modern Negroid slave admixture all the more absurd. Afrocentrism at its finest. ---- Small Victory (talk) 09:25, 1 August 2009 (UTC)

You are entitled to your opinion, as far as I can tell, nobody knows what the carriers of E3b looked like, let alone the migrants from OOA. There aren't any complete human fossils from the period. Even if they were, the soft tissues like skin and hair would have long disintegrated. What we do know, is E3b is more closely to its siblings which include E3a, the Niger-Congo haplogroup, than to any other haplogroups. We also know that the more ancestral E lineages are all found in West Africa. Whatever the case, what they looked like is irrelevant. What is important, is where they lived and the events that led to their migration to North Africa and then to Eurasia. Wapondaponda (talk) 08:52, 2 August 2009 (UTC)

It's not my opinion. It's an anthropologist's assessment of fossils from the OOA period and before:

There are implications for the origins of modern races, too. Herto (and Jebel Irhoud) are H. sapiens, but with primitive features. They are not, racially speaking, Africans. The later Omo and Klasies remains are more modern, but they too are archaic, and certainly show no traces of the features that characterise any modern races. Only Qafzeh and Skhul seem to lack these primitive features, and rate as "generalised modern humans". Our species seems to have existed as an entity long, long before it began to spread outside Africa or the Middle East, let alone split into geographic races.

And of course, Howells confirms that East Africans as recently as a few thousand years ago still had non-African affinities. ---- Small Victory (talk) 13:30, 2 August 2009 (UTC)

And of course, Howells confirms that East Africans as recently as a few thousand years ago still had non-African affinities. ---- Small Victory (talk) 13:30, 2 August 2009 (UTC)

I don't recall ever having introduced the concept of race into this discussion. I think it is you Small Victory who is racializing the discussion. I have simply pointed out that E3b and its parent clade originated among peoples living in Sub-Saharan Africa and therefore its presence outside of SSA is due to gene flow out of SSA, and this gene flow took place several millenia after the OOA migration. What prehistoric Africans and peoples of the world looked like is a very interesting topic, unfortunately there is only a handful of human fossils from the pleistocene periods so we know little. What we do know is it just takes a few thousand years for populations to change their physical appearance. Indo-European speakers from India and Europeans share recent common ancestry, yet Indian people are brown skinned and Europeans tend towards depigmentation. These differences are fairly recent, on the order of about 5000 years. So the appearances of humans have undoubtedly changed multiple times in human history, and continue to change today. On a side note, East Africans and the Khoisan have high frequencies of Haplogroup A (Y-DNA). So we have no idea whether pleistocene East African fossils were haplogroup E or Haplogroup A, both or neither.Ethiopians and Khoisan Share the Deepest Clades of the Human Y-Chromosome Phylogeny Group I is hap A, group II hap b and group III hap E. Wapondaponda (talk) 17:11, 2 August 2009 (UTC)

Bringing up pigmentation in a discussion about craniometry shows that you have very limited understanding of this subject. Suffice it to say that there are fossils from ~100,000+ years ago from East Africa (Herto, Omo), South Africa (Klasies), North Africa (Jebel Irhoud) and West Asia (Qafzeh, Skhul); fossils from Late Pleistocene South Africa (Hofmeyr); and fossils from Holocene East Africa (Howells' study); all of which have been found to have non-African affinities. That more than spans the time periods and geographical areas of both OOA and the later dispersals of E3b. So we actually have a fair picture of these people's appearance, and it doesn't look good for Afrocentrism. ---- Small Victory (talk) 10:41, 3 August 2009 (UTC)

Answering Muntuwandi's question breifly, (his stubborness has become a waste of time). You can either have two approachs, the birth place of the person who migrated, or if not admixed the point of origin of those ancestors (An example, polynesians migrated across the oceans to Hawaii and eventually Easter Island, not admixed with other peoples, however prior to that they admixed at some location and spread, consequently they originated at the point in which the two groups admixed). Since examining this in the prehistoric past is not possible, the second approach is the point of likely origin emigration of a defining SNP or an allele, for example, the A*3002 allele in Europeans likely came from the negroid population in North/NorthWest Africa, this allele likely originated from the forest dwelling peoples of Central/West Africa pygmoid peoples of the cameroon region, but since that time it has recombined into the the A*3002:Cw*0501:B*1801:DRB1*0301:DQA1*0501:DQB1*0201 haplotype, which is not found in Subsaharans (except the Nikohola Mandenka) and therefore can be considered to have originated in North Africa. IOW, the origin of A*3002 remains enigmatic or unclear unless we look at the multigene haplotype, at which point some portion of its origin in N/NW Africa can be explained by specific migration(s). The same thing is true of E, E1b1b, and E1b1b1, the pathway(s) into Europe remain unclear until we look at the subtypes, at which point the points of exit become clear, NorthWest Africa and Middle East. Since these haplotype clarify paths of migration, they superceded the less definative use of haplogroups that did not migrate into Europe In addition we can add levels of parsimony. Since above I have already defined that notable haplotype in the Basque, Sardinians came from North Africa (Actually several) and since we have evidence of distribution similarities with E1b1b1b then therefore we add specific evidence suggesting that the migrations of certain markers initiated from certain regions of NW Africa. Again, I warned against the use of CS's research specifically for this reason. I hope this helps.

Evil Kneival tried to cross the Grand Canyon by Jumping over it with a flying car. Of course 10,000s of years previous with no technologies the native people went down the canyons walls across the river and up the other side, one method lacks success because it attempts to take a big step, the other method is successful because it breaks things down into small solvable problems. Molecular genetics starts with tiny bits of evedince known as SNPs, we then combine SNPs into haplotypes, and and then look for ways to combine those into bigger types, related types.

Note: this does not rule out a hypothesis that people traveled down the Nile, the way to approach this hypothesis since it was first presented from the HLA is to do massive haplotyping from bulgaria to Italy along the mediterranean coastline, in addition to type by haplotype the peoples who live along the nile and surrounding peoples to look for discontinuity. This has not been done. With NW Africa there is a problem, if humans have existed along the African Coast for >40,000 years and SW Europe has only been occupied for <40,000 years, then direct contribution from SSA into SW Europe is not likely without admixture. Since Arabia has been occupied from the last 80ky and since Europe SE has been occupied for <45,000 years then direct admixed DNA from Asia to Europe is unlikely. The nile is a corridor of travel which points a direction of flow, partially during the floods that allows rapid travel to the mediterranean, having followed molecular anthropology and archaeology from almost 2 decades it would not surprise me if this occurred, and in the mediterranean there is a small probability of a founder affect on some of these Islands (Catastrophic volcanism). That it is a possibility and that it happened are two different things. PB666  20:02, 29 July 2009 (UTC)

Y description in SSA section break

If you say that A*3002 allele in Europe likely originated in SSA, then I see no reason why E in Europe should be treated any differently. The main issue I see here is simply time. Is admixture that took place between 10-15kya still considered admixture. I think it is though, its impact is less than say more recent admixture. Both Europeans and SSAs have undergone some microevolution since E3b left Africa, so an argument that E3b is autochthonous to Europe can be made. At the same time its presence in Europe is fairly recent relative to other European y-chromosomes, enough to describe it as admixture. For the record, I don't intend to describe E3b as exclusively SSA. As these Africans moved northwards, it took several generations and they definitely were mixing along the way. Outside of Africa there is a dramatic reduction in L lineages outside Egypt, so it seems that when these Africans left Egypt they were coupling more frequently with Eurasian women, though L2 has a prehistoric presence in Jordan. Another issue is the presence of L lineages in North Africa. When E3b males migrated into North Africa, they obviously travelled with L females from East Africa. The Berber populations have L frequencies that range from 8-48%. These L lineages are now being considered autochthonous to North Africa. However we still describe them as SSA because they originated in East Africa. Likewise the same should apply to E3b. Wapondaponda (talk) 20:24, 29 July 2009 (UTC)

Simply because alleles undergo drift as they undergo migrations and population contraction and expansions, the recombination of A*3002 indicates multiple possible routes into Europe, however the haplotype analysis confirms the direction of only one, from one specific region of Africa, and this region is not Subsaharan Africa. It is not important so much whether Europeans of SSAs have undergone microevolution, what is most important in the evolution that has occurred as the people who carried the allele or haplotype from where it originated to where it ended up. By saying that the allele migrated from SSA to Europe implies that it was born by one common people with closely related ancestry. In the case of Y we know that Y can quickly expand in peoples who are very distantly related to the source of the chromosome. You are pushing the limits of this discussion.

Using the logic of Muntuwandi that any branch point that occurred prior to the clads evident in Europe, in essence all Y chromosomes migrated from SSA, since all early branchpoints default backwards in time to the Y-chromosomal Adam which is from Africa. Therefore using his logic we have no basis for arguing the mtDNA or Y-chromosomes or Nuclear DNA migrated from other points in the world, because they all default backwards into Africa. Native Americans no problem, they migrated from Subsaharan Africa. Indigeonous australians in SE Australia, despite the presence of LM3 ~55 kya, they migrated directly from Africa, just got in the boat and flew over their in the paleolithic seaways bunga seven-four-seven. No matter where-you-are or who-you-are, your last prehistoric ancestor got thier by migrating from Sub-saharan Africa. Neandertals must have a shared Y ancestry from Africa, they are prehistoric, therefore they (each and everyone) came from sub-Saharan Africa. Plessy-versus-Ferguson watch-out, that bus came from subsaharan Africa also. Why stop there, there is obviously a first Y chromosome, lets just say that all prehistoric people came from the place where the first animal that had a Y chromosome was born, that makes Genetic history of Europe, why not? I don't see the word "human" in the page name.

The more Muntuwandi argues with me, the more I see the need to abolish the Genetic_history_of_Europe#Sub-Saharan_African_admixture and move it as a couple of sentences under Genetic_history_of_Europe#North_African_Influences. Anyone agree?PB666  21:34, 29 July 2009 (UTC)

There is no single definition of admixture, one can even have admixture within a continent. Firstly a barrier to gene flow must emerge that separates two populations. This barrier will lead to the genetic isolation and divergence of the two populations. If the barrier to gene flow is breached, then we get admixture. Barriers to gene flow could include, language or ethnicity, oceans deserts, mountains or simply a long distance separating two populations. How much time for divergence or isolation is purely a subjective matter. For instance we have heard scholars describe the pygmies having Bantu admixture, though there are all SSA populations. Europe is a highly heterogeneous population, the French are described as admixed from several European populations. So as long as we have genetic isolation that is significant, when a breach of the barriers to gene flow occurs we have admixture. I think we all agree on certain, things what we disagree on is semantics. This is what we can agree on

• Humans migrate out of Africa 50-70kya without haplogroup E

The upper boundary for the 96% confidence interval for first exit times exceeds 100,000 years. Signs of human activity have been found at Skhul and Qafhez to 125 kya, in South Eastern india to 76 kya, in LiuJiang China to 67 kya. Note the Skhul 5 did not have an austronegroid crania.

• 50kya Haplogroup E emerges in SSA and is now the predominant haplogroup in SSA
• Europe is settled from western Asia starting about 45kya.
• 20-30ky the PN2 mutation occurred in SSA, most likely in East Africa
• Both Niger-Congo(e3a) and Afro-Asiatic(e3b) carry the PN2 mutation
• E3b emerges in East Africa 17-22kya on a male with the PN2 mutation.
• E3a emerges somewhere in SSA on another male with the PN2 mutation
• E3b migrates North most probably along the Nile
• Between East Africa and North Africa E3b picks up at least 3 new mutations in three different males, m78, m81 and m123.
• E3b enters Eurasia maybe 9-15kya mostly through M78 via the Levant and is carried by farmers into Europe.
• E3b disperses across North Africa, primarily through M81 and M78 and is now the predominant North African male haplogroup
• E3b-M81 enters Europe via Iberia
• E3a is dispersed across much of SSA from the Sahel during the African Neolithic and Bantu expansion.
• Colonization of the New World and Atlantic slave trade E3a is dispersed into the New World,

Wapondaponda (talk) 23:52, 29 July 2009 (UTC)

I can create a subpage off this talk page so that you can blabber on if you like. It still does not change the fact that you have no evidence for a SSA contribution, either as single individuals or as a group of people who collectively migrated, to Europe. AS this I will continue to block adding of the E1b1b1a and b material as evidence of SSA migrations.PB666  02:02, 30 July 2009 (UTC)

I must say I am somewhat disappointed with your approach. I understand that you are knowledgeable about genetics, but at the same time Misplaced Pages is not a venue to express your own personal opinions if they are unrelated to reliable sources. That is not how Misplaced Pages works. You continue to avoid and reject peer reviewed publications without providing any reliable sources to back up your criticism of them. You have criticized Cavalli-Sforza, but with no evidence to state that CS's studies are now completely obsolete. You suggest an Out of Africa exit more than 100k, while such a date may be possible, it is not the date that is most often cited in publications. So this seems like WP:ADVOCACY. Your decision to change "Sub-Saharan admixture" to "Potential Sub-Saharan admixture" and placing it as a level 3 subheading under "North African admixture" is POV. Why is SSA singled out for being "potential" when all other sources of admixture are not. The sources in the SSA section are of the same quality as all the other sources. It is also unencyclopedic to pre-decide to block anything and avoid discussion. Wapondaponda (talk) 05:10, 30 July 2009 (UTC)

It was moved because the evidence you present is not at the level of credible, and since you are mixing evidence of Slavery with handwaving arguments based on incorrect use of Taxonomy as more important then it should be treated as an alternative to N.African contribution. If you decide to act from a NPOV and stop the gamesmanships over work then it can stay, as long as you are willing to fill the section with alternative opinions to N. African contribution then I will continue to move it to N. African section.PB666  16:11, 30 July 2009 (UTC) I fundamentally disagree with your deletion of all references to haplogroup E in Sub-Saharan Africa. This is absurd because haplogroup E makes upwards of 80-90% of all SSA haplogroups and has the highest diversity of lineages in SSA. To completely delete all reference of haplogroup E and place it in North Africa, where the prevalence and diversity of haplogroup E is even lower is unusual. You have only left a mention of haplogroup A, which has frequencies of about 5% in Sub-Saharan Africa, and Haplogroup B which is restricted mostly to the pygmies and Nilotic populations. I will proceed to add the comprehensive analysis of of Sub-Saharan influences. Wapondaponda (talk) 16:21, 31 July 2009 (UTC)

mtDNA in SSA

This section has been moved here because the references are not valid and are based soley of Pubmed Abstracts. Lets make an effort to create traditional references.PB666  20:29, 30 July 2009 (UTC) As I suspected more crap was buried under the improper referencing, references for studies were provided those without references are in the table to the left. Information without valid references should not be placed on the main page.

Almost any large scale study of mtDNA will detect some level of Sub-saharan haplotypes. It is therefore unnecessary to list every single study that detected these haplogroups. A few references that deal directly with the subject would suffice, instead of those that incidentally stumble upon these haplogroups. I suggest Malyarchuk 2005, 2008 and Gonzalez 2003 as these are comprehensive. If there is insistence on listing, a table with each study as a column heading should be introduced. Because of the small sample sizes, no single study is authoritative, and percentages vary from study to study. Wapondaponda (talk) 20:53, 30 July 2009 (UTC)Wapondaponda (talk) 20:50, 30 July 2009 (UTC)

Honestly, I am getting very tired of your attitude, you're sloppy, you apparently can't provide proper referencing for what you stated. I consider it dishonest to bury the results of 20 studies under one reference, and come to find out most of the data set has no valid reference. Instead of playing your little games that foul this Main page up, why don't you actually back up what you state.PB666  21:10, 30 July 2009 (UTC)

The table with peoples who were referenced is placed on the Main, all the unreferenced (meaning the editor who added these made no effort to provide references) If you don't desire to reference them and you don't think every study is needed then why did you add them?PB666  21:19, 30 July 2009 (UTC)

For those 20 studies apparently, I can find 20 more studies that detect some Sub-Saharan lineages. Would you like to list every single study that detected an L. But I didn't add them. Small Victory is the one who insists on using them. Wapondaponda (talk) 21:22, 30 July 2009 (UTC)

Well then its a small victory isn't it because if it is not a valid reference its coming off the page. I See many more of these on the main pages under more of these junked up sections. You can have a thousand if you want, but if you don't have a reference for each one they come off the page.

All of the mtDNA figures have valid references. Most of them come from Table 2 of the Achilli paper, which is quite comprehensive. For countries that were subdivided by region (e.g. Italy, Spain, Greece, Germany etc.), the data was pooled to keep things simple and consistent.

Also, organizing the figures into a table takes up too much space, and then we'd have to do the same for the Y-DNA figures and for the comparable figures in the 'Central/East Asian admixture' section. It's just a bad idea. ---- Small Victory (talk) 07:43, 31 July 2009 (UTC)

Bunching 4 references together as a single reference and then only providing linkouts is not the way to do it. If organizing the figures into tables takes up to much space, meaning the material is not that important that it needs a table, means don't put it on the page. You guys need to start thinking about the reader and stop trying to sell belief. There are numerous comments about this page being dubious science, a dirty laundry list of miscellaneous information, etc. Actually the 4 references that are given paint an adequate picture. Another way of referencing is to have the material listed a repository, such as www.allelefrequencies.net so that only one reference may be required to access. The key here is WP:VERIFY which means a person who has access to the literature is able, without further searching through the literature be able to find the source of information.

Direct quotes

I have gotten some input from the Nor noticeboard regarding direct quotes. In general they are not original research. That is if individuals are not quoted out of context and quotes are attributed correctly. So in this case, I intend to use direct quotes to substantiate some of the material. Accusations of original research should not apply where direct quotes are used. I also intend to use peer reviewed publications and journals, which meet the threshold for reliable sources as defined atRS and Verify. Personal complaints about unreliability have no basis unless backed by sources that counter the reliable sources I intend to include. Wapondaponda (talk) 16:30, 31 July 2009 (UTC)

If you try to make it look like Europeans just have E or E3b, then it's POV because that's based on selective quoting of outdated information. If you acknowledge that they have subclades of E3b, then it's OR because those subclades didn't originate in Sub-Saharan Africa and no source considers them evidence of Sub-Saharan African admixture. Either way, it's unacceptable.

On that notice board page, you wrote the following about including STRUCTURE data:

However, given that they do not mention anything to do with Sub-Saharan admixture, then it would still be original research and POV if placed in an article or section concerning Sub-Saharan admixture.

Heed your own advice. None of your E/E3b quotes even use the word 'admixture'. At least Auton et al. discuss admixture in reference to the chart I'm citing, thereby establishing what it shows:

As discussed in the main text, we quantified the admixture in Mexicans using a STRUCTURE analysis of Mexicans, Europeans and East Asians. The results are shown in Supplementary Figure S3D.

--- Small Victory (talk) 08:07, 1 August 2009 (UTC)

As I stated on the noticeboard, just because someone gave a name to haplogroup E in Europe, by calling it E-V13 doesn't change its history or its membership in haplogroup E. That is why the first letter in the name of the clade is "E". It is still haplogroup E as long as it contains the mutations M40 and M96 and it is E3b(E1b1b) as long as it contains the mutations M215 and M35. Recall that these mutations aren't present in the Y-Chromosomes of all Europeans who are not members of haplogroup E, but these mutations are present in Sub-Saharan Africans. Wapondaponda (talk) 09:05, 1 August 2009 (UTC)

Unless you have a source stating that E-V13 originated in Sub-Saharan Africa and is present in Europe as a result of Sub-Saharan African admixture, then it's OR. ---- Small Victory (talk) 09:44, 1 August 2009 (UTC)

This is a somewhat illogical argument. The mutation that defines E-V13 didn't occur in Sub-Saharan Africa, it occurred most likely in Asia, and I have never said that the mutation occurred in Sub-Saharan Africa. Every human harbors something like 100 new mutations that neither of his/her parents have. That doesn't change the phylogenetic relationship that the human has with his/her parents. By your argument if a child has a unique mutation that occurred during gametogenesis, then the child is no longer related to his parents. E-V13 is part of Haplogroup E and more closely related to all other E clades, than it is to any non-E clade. Wapondaponda (talk) 16:04, 1 August 2009 (UTC)

• I agree with SV on this. If you go about using E3b as evidence, and use quotes then other editors would be justified in citing the other studies that properly qualify these quotations also with quotations and the main page becomes a battle of quotations, Just like the E1b1b page used to be. I should state that this whole discussion has been made on the E1b1b page, and one major reason that page was a train-wreck and needed to be cleaned up. You know what is intellectually honest and dishonest here. Posting Admixture with E1b1b when it only is found in the horn of Africa, and failing to mention E1b1b1a and b and their origins slants the understanding against what. As I pointed out to you many people consider this page a trainwreck. The primary reason is the dependance on outdated studies and the need to explain those studies. In addition to this, Small Victory, the use of trivial information that is unreferenced and should be placed in tables.PB666  14:26, 1 August 2009 (UTC)

Any discussion of how E3b should be handled should be under the North African contribution section, since the best evidence offered is that E3b derivatives came from N. Africa or the Middle East and not Subsaharan Africa. This topic is already discussed in the section on N. Africa.PB666  14:26, 1 August 2009 (UTC)

As I have previously mentioned, E3b derivatives didn't spontaneously appear in North Africa, they occurred on migrants from Sub-Saharan Africa. Some derivatives that have been found in Europe may in fact be local to Sub-Saharan Africa, such as M34 and E3b*. So the expansion of E3b lineages began in Sub-Saharan Africa and this is my point. I don't dispute, that certain E3b derivatives are local to North Africa or West Asia, and I don't dispute the inclusion of such findings. However the net effect is a migration of peoples/genes from Sub-Saharan Africa to Europe as stated by Underhill et al 2001 and Cruciani et al 2004. If we decide to arbitrarily cut out SSA, then we have an incomplete picture, and we are cherry picking information for reasons that are unscientific. In addition there is also a high diversity of E3b lineages in Sudan, as indicated in Hassan et al 2008. The ancestral E-M78* was also found in two individuals who speak Nilo-Saharan/Niger Congo languages. In fact Hassan et al still suggest an East African origin for M78. Battaglia et al suggest that E3b lineages actually dispersed from Sudan. But this is just a side issue. We have a net movement of haplogroup E from West Africa to East Africa, to North Africa, to the Levant and finally into Europe. Wapondaponda (talk) 15:50, 1 August 2009 (UTC)

There is a net movement of all major exoafrican haplogroups from Africa to those various places. There is nothing relevant or special about your claim, you are beating a dead horse. No one yet has come to your support, when are you going to drop the issue and stop trying to draft the wiki community. They have told you once again, to apply your material carefully, that you must work with other editors.PB666  23:01, 1 August 2009 (UTC)

Not exactly, the net movement of exoafrican haplogroups only happened once, 50-70kya. And you know this very well. E3b came out of Africa much later, around 10-15kya and only entered Europe and Southwest Asia. I am disappointed that a person as knowledgeable as yourself, is willing to opt for a very simplistic explanation. Wapondaponda (talk) 05:56, 2 August 2009 (UTC)

PB666 is absolutely right. Every haplogroup's phylogeny ultimately takes it back to Africa. If we go by Wapondaponda's "logic", then every haplogroup on earth is "Sub-Saharan African". We have to go by where each individual haplogroup originated, not where it's great-great...grandparent originated. That's what geneticists do, hence no source calling E-V13 "Sub-Saharan African" or attributing it to admixture from Sub-Saharan Africa. It's West Asian and represents Neolithic admixture from West Asia. Period.

As far as haplogroup E having dispersed more recently, it's still descended from haplogroup CT (M168), which has been called the "Eurasian Adam" because it gave rise to all non-African haplogroups. Wapondaponda likes to emphasize phylogeny over everything else. Well, haplogroup E is more phylogenetically related to "non-African" haplogroups C, F and D than it is to "African" haplogroups A and B. In fact, one might even say that it represents Eurasian admixture in Africans. It may even have originated in Eurasia and back-migrated to Africa. But either way, its phylogeny is the same. ---- Small Victory (talk) 07:49, 2 August 2009 (UTC)

Yes all haplogroups trace their ancestry to Sub-Saharan Africa. But Haplogroup E was not part of the Out of Africa migration 50-70kya. It remained in Africa and only dispersed later into Europe and Southwest Asia 10-15kya. You are right, that phylogenitically E is more closely related to Eurasian Y-chromosomes than to A and B. But this isn't unusual, all non Africans are descended from a single African population. From an estimated 2000 people who were alive 50kya, only 150 may have left Africa from an East African population. So all non Africans are more closely related to descendants of that East African population, then to other African populations for example southern African Khoisan. It is the same with mtDNA, all non Africans are haplogroup L3(M, N), whereas Africans are L0, L1, L2 and L3. Africans with L3 are more closely related to non-Africans than with L3(M) and L3(N) than they are to Africans with L0-L3. Eurasian Adam is technically a misnomer because it includes one African Branch. Simply because, of the four lineages to descend from Eurasian Adam, only 3 left Africa. Anyway read Underhill and Kivisild for a full explanation. As for the back migration, that was simply an error due to incomplete sampling. Nobody supports it. I posted a link of current publications that unambiguosly support an African origin of E on Kwami's talk page. If you have any peer reviewed sources that suggest otherwise, let me know. Wapondaponda (talk) 08:11, 2 August 2009 (UTC)

Chandrasekar is a peer-reviewed source. And some of your sources are far from unambiguous: "suggested originated in Africa", "believed to have an African origin". But that's beside the point. The issue here is not where E originated, it's that you're being inconsistent. When it comes to E3b, phylogeny matters more to you than the geographical origin of its subclades (like E-V13). But when it comes to E itself, all of a sudden geography is the only thing that matters and phylogeny (linking E with Eurasian haplogroups) goes out the window. Total hypocrisy. ---- Small Victory (talk) 12:58, 2 August 2009 (UTC)

Being peer-reviewed is no guarantee of reliability. A quick inspection of the article reveals that Chandrasekar et al 2007 is a clone of Hammer et al 1997, 1998 with no new information. Even Andrew agrees with this assessment . Wapondaponda (talk) 18:24, 2 August 2009 (UTC)

I can see you're very eager to change the subject away from your POV hypocrisy. But you aren't doing a very good job, as you've been shown a million times that Chandrasekar's conclusions are based on their own findings, and not on Hammer's studies. ---- Small Victory (talk) 10:23, 3 August 2009 (UTC)

Actually No, what he is doing is selectively using the nomenclature to violate NPOV. Without the other clads it would be impossible to know where E or E1b1b originated. So that to make the case for an African origin of E or E1b1b he needs the cladistics, what he is then doing is sweeping all the cladistics under the door-mat and claiming that the subclads are not important only the older clads. I believe the proper wording for what he is doing is called 'intellectual dishonesty'. The folks at the notice board told him that quoting out of context or to support a POV may violated NOR. He disregards this. The support of non-NPOV on this page is what destroys the page.PB666  19:01, 2 August 2009 (UTC)

If you have noticed, I have not altered any of the information concerning E1b1b1a. I don't intend to significantly change any of the information that concerns the sub-clades. My problem is simply that there is a notion that somehow E-V13 is not part of sub-saharan haplogroup E. When in fact, phylogenetically, it is no more or no less haplogroup E than E1b1a. My proposal is to add a section that looks at the macro-picture. Which is a prehistoric movement of haplogroup E from SSA to Europe, and there are a number of reliable sources, with direct quotes, that use this approach. Wapondaponda (talk) 01:08, 3 August 2009 (UTC)

Your logic is arbitrary, why stop at E, just say there are derived African lineages in Europe. You can't go wrong with that approach, all Y are derived from African lineages. There are three logical groups of Y chromosomes in Europe, those that can be ancestors by early exit from Africa, Those that can be explained by entry of slaves or historic flow across the mediterranean, and those that cannot be explained by either of the above. Only E1b1b1a and E1b1b1b can be explained and the LCA of these two clades is E1b1b1. Even that is a stretch of logic, because is there actually any E1b1b1* is Europe (1), and from the looks of things they had two very independent entries, and both appear to be from N. Africa. So that why are we discussing this at all in the Subsaharan section. If you want to discuss E in the context of E1b1a as a consequence of Slave trade and leave discussion of E1b1b out all together, since it is discussed in the preceding section, I am all for that.PB666  04:09, 3 August 2009 (UTC)

SV has a point, the DE clad gives rise to D and E but no D is found in Africa, whereas D and E exist in Asia. Therefore without careful cladistics we would argue that E evolved in Eurasia and backmigrated into Africa. However since we have cladistics and improved fine mutations we can argue against this. The same applies to what you are arguing, only the discussion of E1b1a (historical trade activity) belong in the section on SSA, since by phylogenetics the origins of E1b1b1a and E1b1b1b can be defined as being of N. African origin.PB666 

Yes there is E1b1b1* in Europe, read Henn et al 2008. The reliable sources do use this approach. Semino et al is titled Origin, Diffusion, and Differentiation of Y-Chromosome Haplogroups E and J: Inferences on the Neolithization of Europe and Later Migratory Events in the Mediterranean Area. As you can see they use the macro-definition, "Haplogroup E" in their terminology, though they are fully aware of subclades M35 and M78. Since haplogroup E was not part of the initial OOA migration, it does make a difference in how it is approached. A number of studies have made reference to "Neolithic Admixture" in Europe for which haplogroup E was a part. One issue I have with using the term North African, is that it gives the impression that involved admixture from populations similar to modern North Africans. That is not clear, because we don't know exactly when Eurasians entered North Africa and mixed with Africans. This is because E1b1b1a is also in Sudan, among the Nuer, the Nuba, and the Masalit, Shiluk. According to Hassan et al E1b1b1a was more frequent in Nilo-Saharan than in Afro-Asiatic speakers. Wapondaponda (talk) 10:56, 3 August 2009 (UTC)

Yes, all DNA can potentially be called sub Saharan, and this raises questions for not only Muntuwandi's approach but also Small Victories - because seem to want to use a personal definition of when the term can and can not be used. As was discussed in the deleted article, there is no intrinsic problem saying a clade is "sub Saharan" if you define exactly how this term is being used and if other editors agree that it is not confusing and silly. (There has to be a good reason for contrasting the clade with others as somehow more sub Saharan I suppose.) Problem is that we could not reach a consensus on how to use such terms. E-M35* appears to be present in Europe BTW, possibly mainly in northern Spain, though it has not been much tested for M293.--Andrew Lancaster (talk) 22:59, 8 August 2009 (UTC)

Central and East Asian admixture in Bulgarians and Turks

East Asian mtDNA (haplogroups A, B, C, D, M, N9a and Z) is restricted mainly to Eastern Europe and Scandinavia and is found at generally low frequencies: ...Bulgaria/Turkey (6.9%)... Could somebody provide a source that Central and East Asian admixture in Bulgarians is 6.9%? I think this is a simple average calculation by haplotypes from scientific inadmissible common data about two very distant populations. Jingby (talk) 17:48, 31 July 2009 (UTC)

The study used several combined samples. See Table 3. ---- Small Victory (talk) 08:14, 1 August 2009 (UTC)

This info is not reliable. The Turkish people are Asians. Also their data is not directly connected with the topic. There is a direct study about the Turkish mtDNA with their profile -"... Six distinct major clusters, namely H, J, T, M, U and W, were observed in our population. The frequency of the clusters is given in table 1 ... The cumulative frequency of European specific clusters (H, J, T and W) was 43.9% and Asian specific cluster (M) was 10.6% in our population (table 1)..." Check here: Mitochondrial DNA sequence variation in the Anatolian peninsula (Turkey) Mergen et al. 2004. Pleace provide correct data about the Bulgarian population and replace this estimated calculated data about the Turks. If no, I am going to remove this POV! Jingby (talk) 15:23, 8 August 2009 (UTC)

No reference was provided, but blind revert. Pleace provide correct data about the Bulgarian population and replace this estimated calculated data about the Turks. If no, I am going to remove your unscientific original research anain! Regards. Jingby (talk) 11:43, 9 August 2009 (UTC)

Auton does say that STRUCTURE shows admixture

I was so busy looking at the supplementary material that I failed to notice this in the main study:

In order to quantify patterns of population structure and admixture, we utilized STRUCTURE , a commonly used Bayesian clustering method. Setting the number of clusters (K) to five revealed structure largely corresponding to continental regions (Figure 1A).

So it's in fact established within Auton itself that STRUCTURE quantifies admixture between populations corresponding to continental regions. Note that the Figure 1A they refer to is extracted from Figure S3A in the supplementary material. Note also that the source they cite is the very paper published by the program's creators that I've been saying all along supports the use of STRUCTURE to quantify admixture. ---- Small Victory (talk) 13:05, 1 August 2009 (UTC)

noticeboard

I have created a thread on the administrator's noticeboard regarding Small Victory's continued insistence on analyzing charts. Wapondaponda (talk) 11:32, 3 August 2009 (UTC)

The dispute about that hasn't been resolved yet, and anyway you've been shown that I'm not analyzing charts. Going around forum shopping to try to dupe someone into taking your side is a cheap last-resort tactic and a poor reflection on you. ---- Small Victory (talk) 09:09, 4 August 2009 (UTC)

North African influences

What exactly are the genetics of North Africans. North Africans are basically an admixed population of Sub-Saharan Africans and Europeans. Middle Eastern populations, in addition to the aforementioned contributions, may have some minor South-Asian admixture. But essentially there are little differences between Middle Eastern and Mediterranean Europeans. So when we are speaking of North African admixture, what exactly are we referring to. Eurasians markers mixing with Eurasians markers would hardly constitute admixture. The closest thing to a unique North African marker is Haplogroup U6, though it is a subclade of Eurasian haplogroup U. But since it may have been in Africa for 35,000 years, it has evolved enough in situ, for its presence in Europe to be considered admixture. A similar case can be made for M1, if it is considered Eurasian, though most clades originate in East Africa. So basically what we have is a situation where almost all markers used to identify North African admixture are of late pleistocene/neolithic Sub-Saharan origin. The only markers that distinguish North Africans from Eurasians are of Sub-Saharan origin, that is predominantly E1b1b, and to some extent Haplogroup M1. Middle Easterners all speak Afro-Asiatic languages, which originated in Sub-Saharan Africa, and this in itself is evidence of their recent Sub-Saharan ancestry. Consequently, we need to rethink the North African section. I am definitely leaning towards an "African" contribution, rather than a segregated North African and Sub-Saharan sections, because it is impossible to separate the two. Masalit, the Nuba, and the Nuer. All these populations have high frequencies of E1b1b1a, according to Hassan et al 2008, and these are not archetypal North Africans. On page 3 of Y-chromosome Lineages from Portugal, Madeira and A¸cores Record Elements of Sephardim and Berber Ancestry, there is E1b1b*(e3b*). Wapondaponda (talk) 15:07, 3 August 2009 (UTC)

Muntawandi, do yourself a favor and turn the amplifyer down on interpreting Y-chromosome. The HLA present a different and clearer picture of the relative level of paleoAfrican and neoAfrican influences. If you would read Choukri F, Chakib A, Himmich H, Raissi H, Caillat-Zucman S (2002). "HLA class I polymorphism in a Moroccan population from Casablanca". Eur. J. Immunogenet. 29 (3): 205–11. PMID 12047355. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)Oumhani K, Canossi A, Piancatelli D; et al. (2002). "Sequence-Based analysis of the HLA-DRB1 polymorphism in Metalsa Berber and Chaouya Arabic-speaking groups from Morocco". Hum. Immunol. 63 (2): 129–38. PMID 11821160. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)Gómez-Casado E, del Moral P, Martínez-Laso J; et al. (2000). "HLA genes in Arabic-speaking Moroccans: close relatedness to Berbers and Iberians". Tissue Antigens. 55 (3): 239–49. PMID 10777099. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)Ayed K, Ayed-Jendoubi S, Sfar I, Labonne MP, Gebuhrer L (2004). "HLA class-I and HLA class-II phenotypic, gene and haplotypic frequencies in Tunisians by using molecular typing data". Tissue Antigens. 64 (4): 520–32. doi:10.1111/j.1399-0039.2004.00313.x. PMID 15361135. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)Hajjej A, Kâabi H, Sellami MH; et al. (2006). "The contribution of HLA class I and II alleles and haplotypes to the investigation of the evolutionary history of Tunisians". Tissue Antigens. 68 (2): 153–62. doi:10.1111/j.1399-0039.2006.00622.x. PMID 16866885. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link). The primary issue is not how much influence have the Arabs had on N. Africa, but how much North Africans have enfluenced the Arabs. Populations that show substantive recent admixture included the Jordanians, Saudis, Omani (if we want to go further west) Baloch or Iran and Pakistan. If we want to look from the west we see strong influence of Tunisians (Carthaginian as the putative source) paleoAfrican population in Portugal and Iberia with potential influences as far north as Ireland and England. If we look at the NW african influences in Iberia are very strong, and subside quickly through france. In addition I question the statement North-South cline. The direction of the cline is very clear, from SW to NE across Europe.PB666  14:03, 4 August 2009 (UTC)

I will give you a pointer of just how bad it can be. 30% of the HLA in Sardinia is from North Africa, 3 are present as a consequence of a founder affect, but if you look at Y chromosome you would likely conclude that 0% was from N. Africa except via influence from Arabic peoples to the East. Since sardinia is an island and most of its population arrives as a consequence of maritime trade, there was a constant influence of N. Mediterranean Y chromosome on its port areas, eventually pushing Y inward to the center of the country until it disappeared. This is visible in the African HLA, which a present at their highest frequency in the internal parts of the Island. HLA haplotypes tend to preserve diversity the longest, Y chromosome, on the other hand, tends to loose diversity the fastest. Ergo in one place that has a large but anceint african contribution you have the appearance of no contribution, and in another area one can have relatively little contribution, but as a consequence of the last invasion, and leaves a fairly big footprint. This is the danger of overinterpreting Y chromosome. I personally think to much of the main is devoted to Y-chromosome and not enough of the page is devoted to other loci. The followance of Y chromosome is extremely biasing of average ancestry of hologenomic representation.PB666  14:16, 4 August 2009 (UTC)

I have made some corrections to your edits. You wrote that E1b1b1 originated in North Africa when in fact E1b1b and E1b1b1 are in fact the same clade. Maybe you meant E1b1b1a. In any case there are four clades found in Europe. E-M78, E-M34, E-M81 and E-M35(e3b*). Only E-M78 and E-M81 are definitely North African. Whereas M34, is either Near Eastern or East African. E3b* possibly Sub-Saharan, but it consists of several undefined clades. With regard to the cline Auton et al specifically mention a south-to-North gradient. Whereas Frudakis mentions the highest diversity in South East. Either way both state a south to North and not specifically a SW to NE distribution. Wapondaponda (talk) 14:42, 4 August 2009 (UTC) I have taken the article African admixture in Europe live. It is dramatically different from the deleted version, and we can contiue to build on it. Wapondaponda (talk) 14:44, 4 August 2009 (UTC)

Your "new" article is just a rehash of the deleted one, only with the added OR and POV you've been trying to insert here. I've listed it for deletion. ---- Small Victory (talk) 13:36, 6 August 2009 (UTC)

Pdeitiker, I agree that Y-chromosome admixture will not necessarily correlate with autosomal admixture due to differential selection pressures. It is right not to focus too much on the Y-chromosome. But nonetheless there will be some correlation between uniparental and autosomal markers, albeit an imperfect correlation. This is what some of the articles you listed about North African genetics have suggested.

• Piancatelli et al state

In details, some alleles common in Africans (A*30, A*3402, A*6802, A*7401, B*1503, B*3910, B*4102, B*4202, B*7801, B*5802, Cw*04, Cw*1701, and Cw*1703) were present in ME. Of these, some alleles have been found in South/sub-Saharan Africa and other were also present in some Mediterraneans. In addition, in common with Bubi from Equatorial Guinea, there was the frequency of Cw*0701/02 andCw*0706 alleles; the absence of Cw*01 was shared with other African populations (sub-Saharan Bubi, Fulani, Mossi, and Rimaibe`). This results suggest the sharing of some common genetic characteristics between Mediterraneans and sub-Saharan populations and are, in part, in agreement with the conclusions of a previous study on HLA-Cw alleles in the Senegalese Mandenka population, which asserted that the HLA-Cw distribution in that population was close to that of Europeans (24).

• Hajjej et al 2006 state:

Our study shows that several alleles found in Sub-Saharans, such as B*5703, B*4201, DRB1*0302, and DRB1*0804 (19), were also detected in Tunisian population. This indicates a genetic relationship to Sub-Saharan populations. The occurrence of these alleles can be understood because the present Tunisian population is constituted by Berbers, Arabic speaking-groups, and Blacks. The latter are frequent particularly in the South, and their contribution to the Tunisian genetic pool is probable

• Coudray et al state

Our results reveal that Moroccan populations have heterogeneous GM profiles with high frequencies of GM haplotypes in Europeans (from 76% for Doukkala to 88% for Bouhria) and relatively high frequencies of GM haplotypes in sub-Saharans (from 11% for Bouhria to 23% for Amizmiz)

Needless to say North African populations are primarily of Eurasian origin but have significant levels of Sub-Saharan admixture. Therefore, we cannot completely divorce North African admixture from Sub-Saharan admixture. Wapondaponda (talk) 21:49, 9 August 2009 (UTC)

• Sardinia is actually the best example for this, ~30% of HLA haplotype frequencies are best explained by contribution from Africa.

Whereas look at the Y-chromosome. Then you see the problem of the last migrations. If there is a constant flow of Y chromosome, even if the rate of flow is a trickle, over time (1000 - 5000 years) that trickle can completely erase all previous Y. The the core Cw5-B18 component is found in the rainforest dwellers (In these peoples they did not study B18-DR3), the bubi. This indicates that some aspect of N. Africa was not colonized from the traditional east Africa as many have claimed, but colonized from the pygmoid peoples via W. African rainforests. When one considers human populations looking at HLA, the major outgroups are the !kung, Efe, and Baka and within the pygmies the N. pygmies have the lowest levels of linkage disequilibrium. Therefore comparing E. Africa with W/C African rainforest there is no reason to suggest peoples were in Eastern Ethiopia or Somalia before they spread west through the rainforest of W. Africa. But by the fact that I have drawn from cw-b haplotypes and the longer haplotypes are not evident, where the genetic contributions between 'negroid' north-africans are evident between N. Africa and Europe, we are are talking about temporal connections to those rainforest dwellers that are quite old.

You see evidence of recent contributions in Southern Tunisia, there is a salient of genetic contribution from the south, but one has two more steps, to reach the southern coast of the mediterranean, and to cross. Whereas I don't treat that as Subsaharan contribution to Europe, but simply African contribution. You had said that N. Africa was considerably repressed because of modern Eurasian contribution. But this is not true, as you state above there is alot of clearly african contribution in the Berbers, and as one goes westward the level of apparent Arabic contribution declines. Cw5-B18, Cw7-B5801, Cw1601-B4403, Cw7-B8, Cw5-B44 and other specific two locus haplotypes tail a story of the direction of African contribution that is much different than that indicated by mtDNA or Y chromosome.PB666  14:02, 10 August 2009 (UTC)

Brace et al and Ricaut et al

Small Victory writes in the edit summary that "Brace and Ricaut are anthropology studies. This is a genetics article. Plus, they don't say what Muntuwandi is claiming". I wrote

Paleoanthropoligical studies by Brace et al and Ricaut et al.have even suggested that the Natufian culture, from which, the European Neolithic was derived, had Sub-Saharan influences of significant importance.Ricaut et al. associate the dispersal of E1b1b with the Sub-Saharan influences detected in a sample of Natufian remains.

Ricaut et al state:

From the Mesolithic to the early Neolithic period different lines of evidence support an out-of-Africa Mesolithic migration to the Levant by northeastern African groups that had biological affinities with sub-Saharan populations. From a genetic point of view, several recent genetic studies have shown that sub-Saharan genetic lineages (affiliated with the Y-chromosome PN2 clade; Underhillet al. 2001) have spread through Egypt into the Near East, the Mediterranean area, and, for some lineages, as far north as Turkey (E3b-M35 Y lineage; Cinniog¢lu et al. 2004; Luis et al. 2004), probably during several dispersal episodes since the Mesolithic. This finding is in agreement with morphological data that suggest that populations with sub-Saharan morphological elements were present in northeastern Africa, from the Paleolithic to at least the early Holocene, and diffused northward to the Levant and Anatolia beginning in the Mesolithic. Indeed, the rare and incomplete Paleolithic to early Neolithic skeletal specimens found in Egypt—such as the 33,000-year-old Nazlet Khater specimen (Pinhasi and Semal 2000), the Wadi Kubbaniya skeleton from the late Paleolithic site in the upper Nile valley (Wendorf et al. 1986), the Qarunian (Faiyum) early Neolithic crania (Henneberg et al. 1989; Midant-Reynes 2000), and the Nabta specimen from the Neolithic Nabta Playa site in the western desert of Egypt (Henneberg et al. 1980)—show, with regard to the great African biological diversity, similarities with some of the sub-Saharan middle Paleolithic and modern sub-Saharan specimens. This affinity pattern between ancient Egyptians and sub-Saharans has also been noticed by several other investigators (Angel 1972; Berry and Berry 1967, 1972; Keita 1995) and has been recently reinforced by the study of Brace et al. (2005), which clearly shows that the cranial morphology of prehistoric and recent northeast African populations is linked to sub-Saharan populations (Niger-Congo populations). These results support the hypothesis that some of the Paleolithic–early Holocene populations from northeast Africa were probably descendents of sub-Saharan ancestral populations.

and

This northward migration of northeastern African populations carrying sub-Saharan biological elements is concordant with the morphological homogeneity of the Natufian populations (Bocquentin 2003), which present morphological affinity with sub-Saharan populations (Angel 1972; Brace et al. 2005). In addition, the Neolithic revolution was assumed to arise in the late Pleistocene Natufians and subsequently spread into Anatolia and Europe (Bar-Yosef 2002), and the first Anatolian farmers, Neolithic to Bronze Age Mediterraneans and to some degree other Neolithic–Bronze Age Europeans, show morphological affinities with the Natufians (and indirectly with sub-Saharan populations; Angel 1972; Brace et al. 2005), in concordance with a process of demic diffusion accompanying the extension of the Neolithic revolution (Cavalli-Sforza et al. 1994).

Brace et al state:

The assessment of prehistoric and recent human craniofacial dimensions supports the picture documented by genetics that the extension of Neolithic agriculture from the Near East westward to Europe and across North Africa was accomplished by a process of demic diffusion. If the Late Pleistocene Natufian sample from Israel is the source from which that Neolithic spread was derived, then there was clearly a Sub-Saharan Africa element present of almost equal importance as the Late Prehistoric Eurasian element."

I apologize, if I have given too much detail, but it has to be done, since SV has made accusations of misrepresentation. Finally, admixture can sometimes be determined, though less accurately, through non-DNA experiments. Forensic anthropologists, for example, can and do determine ethnic profiles of human remains, including possible admixture amounts. Without aDNA, it is the next best thing. Wapondaponda (talk) 22:13, 9 August 2009 (UTC)

We've already been over this. Brace's conclusion about a Sub-Saharan (via Natufian) element in Neolithic farmers is stated in uncertain terms and contradicted by his own findings:

This placement suggests that there may have been a Sub-Saharan African element in the make-up of the Natufians (the putative ancestors of the subsequent Neolithic), although in this particular test there is no such evident presence in the North African or Egyptian samples. As shown in Fig. 1, the Somalis and the Egyptian Bronze Age sample from Naqada may also have a hint of a Sub-Saharan African component. That was not borne out in the canonical variate plot (Fig. 2), and there was no evidence of such an involvement in the Algerian Neolithic (Gambetta) sample.

The Natufian sample from Israel is also problematic because it is so small, being constituted of three males and one female from the Late Pleistocene Epipalaeolithic (34) of Israel, and there was no usable Neolithic sample for the Near East. The generally high D2 values for the Natufian sample in Table 3 are almost certainly a reflection of the very small sample size.



The three Niger-Congo-speaking groups (the Congo from Gabon, the Dahomey from Benin, and the Haya from Tanzania) cluster together away from most of the other samples. When the samples used in Fig. 1 are compared by the use of canonical variate plots as in Fig. 2, the separateness of the Niger-Congo speakers is again quite clear.

Fig. 2 - Canonical Variate Plot

Fig. 4 - Canonical Variate Plot

As for the Ricaut study, it references Brace's (flawed) conclusion, and likewise, its own results contradict the claim of Sub-Saharan affinities in the skeletal remains from Turkey (Sagalassos):

The closest populations to Sagalassos are from Greece, Cyprus and Turkey, Germany, and Scandinavia, followed by the other European and ancient northeast African (ancient Egyptian and Sudanese) populations and then by the Central and East Eurasians and the sub-Saharan Tanzanian population.

And it doesn't matter how many other ways admixture can be determined. The only way that's relevant to this article is DNA testing because the title of the article is "Genetic history of Europe". ---- Small Victory (talk) 13:43, 10 August 2009 (UTC)

Once again, you are analyzing the study providing your own interpretations. The fact that the sample size of Brace et al is small, does not completely eliminate the relevance of his findings. for almost 100 years, the entire theory of human evolution was constructed on fewer than 200 hominid remains, of which Turkana boy and Lucy (Australopithecus) are probably the closest things to a complete human specimen older than 1 million years. A small amount of evidence is better than no evidence at all. It would be great if there were more samples, but unfortunately this is not the case.

Secondly, you seem to misunderstand admixture. Admixture occurs when one population receives genetic input from a different population. This means that the two populations involved should have different genetic profiles. If genetic profiles of two populations are the same, then they aren't really two populations, but rather they are part of the same population. So if the turkish population is closer genetically, to Scandinavians, then it shouldn't be alarming, because, except for distance, there are no significant barriers to gene flow between Scandinavia and Turkey. Nobody is saying that Europeans are predominantly Sub-Saharan, so they should always cluster with Sub-Saharans. Since the settlement of Europe 45kya, Europe has for the most part remained genetically isolated from East Asia and Africa. However admixture events seem to have occurred on a number of occasions to the extent that this admixture is detectable by genetic or even anthropological studies. In some cases, this admixture may be small, due to the effects of time, but nonetheless still present. Nobody here is arguing for admixture levels in excess of 50%.Wapondaponda (talk) 21:10, 10 August 2009 (UTC)

Information Suppression

Wapondaponda has attempted to defend his edits by claiming that all he's doing is using direct quotes, which is never original research. Even if that's true, WP:NOR is not the only guideline with which edits much comply. There's a policy in the NPOV tutorial against information suppression, which has a direct bearing on his defense. It states:

A common way of introducing bias is by one-sided selection of information. Information can be cited that supports one view while some important information that opposes it is omitted or even deleted. Such an article complies with Misplaced Pages:Verifiability but violates NPOV. A Misplaced Pages article must comply with all three guidelines (i.e. Verifiability, NPOV, and No original research) to be considered compliant.

Here are some instances where Wapondaponda is in violation of this policy:

• When he cites Auton et al.'s claim that shared haplotypes are "suggestive of gene flow from Africa, albeit from West Africa" without including the many other possible explanations put forth by the authors, nor the results of the STRUCTURE analysis. (Note that the reference to the Auton study in my version mentioned everything).

• When he cites outdated sources stating that E3b is Sub-Saharan African or East African while omitting more recent sources that have discovered new subclades (some of them separate haplogroups) with West Asian and North African origins, which are the markers that Europeans actually have.

• When he cites Frudakis and Halder without the caveat that their results are very likely inaccurate because they're using markers called AIMs that have been shown to "involve loci that have undergone strong selection, which makes it unclear whether these markers indicate shared ancestry or parallel selective pressures" (Bolnick et al. 2007).

• When he cites Brace and Ricaut (which aren't even genetic studies, btw) without mentioning all of the uncertainty, contradictions and conditional statements in their studies, where it's unclear not only whether Natufians were the source of the European Neolithic, but even whether they actually had Sub-Saharan affinities.

That covers most of his edits to the 'Sub-Saharan African influences' section, meaning that while they may qualify for inclusion on the basis of WP:Verifiability and maybe even WP:NOR, they fail to comply with WP:NPOV and should therefore be disallowed. ---- Small Victory (talk) 14:10, 12 August 2009 (UTC)

Small Victory, without explaining why in detail one more time, the information you say is being suppressed involves your own synthesis of ideas from different filtered (eg your use of Bolnick) sources, in every case you mention (and in each case your ideas are controversial anyway). Such original material is supposed to be "suppressed". To the extent that you are implying that the article wording implies more certainty in the literature than there really is, then this can of course be discussed, but no examples are immediately clear to me. For example the article wording does not currently make strong statements about the Natufians being the source of the European Neolithic, it only makes the very correct statement that this is a common proposal.--Andrew Lancaster (talk) 15:21, 12 August 2009 (UTC)

The issue of analyzing charts has already been dealt with. A couple of things,

• The primary role of STRUCTURE is to determine Clusters, admixture is a secondary role. This is because you can set STRUCTURE to produce clusters with no admixture(Prichard et al). In addition, you can run STRUCTURE with any value of K. Human populations aren't always structured in "clusters" so applying clusters may not always be realistic, even though Structure will process data for whatever value of K. Structure is basically an abstraction of the data it processes and it requires interpretation, even if the results seem obvious.
• SV had stated "negligible levels of Sub-Saharan ancestry", when reading the STRUCTURE chart. This is a somewhat misrepresentation, given that YRI is from 60 individiduals from one tribe in a single city, Yoruba's from Ibadan (YRI). So technically SV should have written "negligible levels of YRI related haplotypes". Sub-Saharan Africans are quite diverse and include Afro-Asiatics, Nilo-Saharans, Niger-Congos and Khoisan. Yorubas are Niger-Congo speakers, but they are part of the Volta-Niger languages sub family. The other major Niger-Congo subfamily is Bantu. Basically YRI is only a sub-set of Sub-Saharan African genetic diversity.
• The structure analysis, YRI individuals made up the smallest sample, only 60 individuals, while the whole analysis was done on 1245 individuals. So the average continent had 300 individuals, compared to Africa's 60. YRI data was obtained solely from Hapmap, whereas the data from the other continents included hapmap, POPRES, LOLIPOP and possibly HGDP
• The study also used a very high threshold, as they filtered out SNPs with a minor allele frequency> 0.2. They state that qualitatively, this doesn't change much, but quantitatively it does make a difference.
• I don't exactly know whether all these issues would make a difference in the STRUCTURE analysis, but at least they require the authors to interpret their own results, and not a Wikipedian.

With regard to the direct quotes SV has discussed above, in general studies will have a main hypothesis, and then they may suggest alternate explanations and provide caveats. This is pretty much standard practice to "hedge your bets". I have deliberately selected the authors' main hypotheses in all these quotes, but have not used any strong or definitive language as this leaves open the door to other scenarios. What SV did was to prop up the caveats and alternate hypotheses and downplay, almost ignore, the authors' main hypotheses. Studies are not conducted for the sake of caveats, or alternative hypotheses. So propping them up is classic POV and WP:UNDUE.

As for information suppression, if anyone has a reliable source, ie a current, mainstream peer reviewed publication, that states that comprehensively, Europeans have "negligible levels of Sub-Saharan" admixture, and direct quotes are available from such a source, then I won't stand in the way of including such information. By comprehensive I mean mtDNA, Y-chromosome, autosomal including HLA and also the entire European continent. The problem is nobody has tried introduce such a source. Rather it is SV et al. who have tried hard to suppress information from current mainstream peer reviewed publications, from which, direct quotes are available to back up every single statement, indicating both recent and prehistoric gene flow from SSA to Europe. If you have direct quotes from reliable sources, then we are in business, if not, please see WP:SOAPBOX, WP:NOTAFORUM and WP:NOTBLOG. Wapondaponda (talk) 21:00, 12 August 2009 (UTC)

Stop your lies and distortions. And don't try to turn this around and make it about me. It's obvious that you're quoting selectively to emphasize admixture, and deliberately omitting anything that calls that admixture into question or finds it to be absent. That's the very definition of WP:Information suppression.

• Auton et al. don't have a "main hypothesis". They propose several different explanations for their finding and conclude that more research needs to be done. You only include the West African admixture theory. That's information suppression.

• Europeans have E-V13 and E-M81. You can't produce a source attributing these markers to Sub-Saharan African admixture, so you ignore them and quote old studies from before the phylogeny of E3b was mapped out. That's information suppression.

• Frudakis and Halder used adaptive markers, but you cite them anyway because you like their inaccurate results. STRUCTURE evidence uses neutral markers, but you try to have it all banned as OR because it doesn't show what you want. That's information suppression.

All of your edits are in violation of this policy and will not be tolerated. ---- Small Victory (talk) 11:45, 13 August 2009 (UTC)

1. Martinez et al. (2007)
2. Abu-Amero et al. (2007)
3. Richards et al. (2003)
4. Gonçalves et al. (2003)
5. Pereira et al. (2000) Diversity of mtDNA lineages in Portugal: not a genetic edge of European variation. Ann Hum Genet; 64(Pt 6):491-506.
6. Achilli et al. 2007, Malyarchuk et al. 2008, Gonzalez et al. (2003)
7. Cruciani et al. 2004, Flores et al. 2004, Brion et al. 2005, Brion et al. 2004, Rosser et al. 2000, Semino et al. 2004, DiGiacomo et al. 2003
8. Pritchard et al. (2000) Inference of Population Structure Using Multilocus Genotype Data. Genetics Society of America; 164(4):1567-87.
9. Rosenberg et al. 2002, Wilson et al. 2001, Bauchet et al. 2007, Auton et al. 2009
10. Martinez et al. (2007)
11. Abu-Amero et al. (2007)
12. Richards et al. (2003)
13. Gonçalves et al. (2003)
14. Salas et al. (2004) The African Diaspora: Mitochondrial DNA and the Atlantic Slave Trade. Am J Hum Genet; 74(3): 454-465: "African types in Eurasia, unlike those in America, can therefore be attributed to gene flow from both eastern Africa -- perhaps partly via the Arab slave trade -- and western and southeastern Africa, more likely as a result of the Atlantic slave trade. A contribution from the medieval Arab/Berber conquest of Iberia and Sicily is also possible. However, there are also discernible western and southeastern African components to the (relatively few) mtDNAs of recent African ancestry within Europe, which are likely to be mainly attributable to the more recent Atlantic trade. Portuguese western, southwestern, and southeastern Africa were the main sources for the Atlantic slave trade to Europe."
15. Achilli et al. 2007, Malyarchuk et al. 2008, Gonzalez et al. (2003)
16. Cruciani et al. 2004, Flores et al. 2004, Brion et al. 2005, Brion et al. 2004, Rosser et al. 2000, Semino et al. 2004, DiGiacomo et al. 2003
17. Semino et al. (2004) harvcoltxt error: no target: CITEREFSemino_et_al.2004 (help) Cruciani et al. (2004) harvcoltxt error: no target: CITEREFCruciani_et_al.2004 (help)
18. Frudakis, Tony (2007). "Apportionment of Autosomal Diversity with Continental Markers". Molecular photofitting. pp. page 326. ISBN 0120884925. {{cite book}}: |pages= has extra text (help); External link in |chapterurl= (help); Unknown parameter |chapterurl= ignored (|chapter-url= suggested) (help)
19. Halder; et al. (2008). "A panel of ancestry informative markers for estimating individual biogeographical ancestry and admixture from four continents: utility and applications". {{cite journal}}: Cite journal requires |journal= (help); Explicit use of et al. in: |last= (help)
20. Cite error: The named reference harvcoltxt was invoked but never defined (see the help page).
21. Cite error: The named reference ReferenceA was invoked but never defined (see the help page).
22. Cite error: The named reference bowcock was invoked but never defined (see the help page).
23. Auton; et al. (2009). "Global distribution of genomic diversity underscores rich complex history of continental human populations". {{cite journal}}: Cite has empty unknown parameter: |1= (help); Cite journal requires |journal= (help); Explicit use of et al. in: |last= (help)
24. Reich (2008). "Principal component analysis of genetic data". {{cite journal}}: Cite journal requires |journal= (help)
25. Pritchard et al. (2000) Inference of Population Structure Using Multilocus Genotype Data. Genetics Society of America; 164(4):1567-87.
26. Rosenberg et al. 2002, Wilson et al. 2001, Bauchet et al. 2007
27. Frudakis, Tony (2007). "Apportionment of Autosomal Diversity with Continental Markers". Molecular photofitting. pp. page 326. ISBN 0120884925. {{cite book}}: |pages= has extra text (help); External link in |chapterurl= (help); Unknown parameter |chapterurl= ignored (|chapter-url= suggested) (help)
28. King (2007). "Africans in Yorkshire? - the deepest-rooting clade of the Y phylogeny within an English genealogy". {{cite journal}}: Cite journal requires |journal= (help)
29. <cite journal|url=http://www.uma.pt/abrehm/v1.1/docs/downloads/pdfs/Goncalves_Y_Portugal_AnnHumGenet2005.pdf%7Clast=Goncalves%7Ctitle=Y-chromosome Lineages from Portugal, Madeira and A¸cores Record Elements of Sephardim and Berber Ancestry|year=2005}}

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