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In biology, phylogenetics (/faɪldʒɪˈnɛtɪks/) is the study of evolutionary relation among groups of organisms (e.g. species, populations), which is discovered through molecular sequencing data and morphological data matrices. The term phylogenetics derives from the Greek terms phyle (φυλή), denoting "tribe" and "race"; and the term genetikos (γενετικός), denoting "relative to birth", from genesis (γένεσις) "origin" and "birth". The result of phylogenetic studies is a hypothesis about the evolutionary history of taxonomic groups: their phylogeny.

Evolution is regarded as a branching process, whereby populations are altered over time and may split into separate branches, hybridize together, or terminate by extinction. This may be visualized in a phylogenetic tree, a hypothesis of the order in which evolutionary events are assumed to have occurred.

Phylogenetic analyses have become essential in researching the evolutionary tree of life. The overall goal of National Science Foundation's Assembling the Tree of Life activity (AToL) is to resolve evolutionary relationships for large groups of organisms throughout the history of life, with the research often involving large teams working across institutions and disciplines. Investigators are typically supported for projects in data acquisition, analysis, algorithm development and dissemination in computational phylogenetics and phyloinformatics. For example, RedToL aims at reconstructing the Red Algal Tree of Life.

Taxonomy, the classification, identification, and naming of organisms, is usually richly informed by phylogenetics, but remains methodologically and logically distinct. The degree to which taxonomy depends on phylogenies differs between schools of taxonomy: numerical taxonomy ignored phylogeny altogether, trying to represent the similarity between organisms instead; phylogenetic systematics tries to reproduce phylogeny in its classification without loss of information; evolutionary taxonomy tries to find a compromise between them in order to represent stages of evolution.

Construction of a phylogenetic tree

The scientific methods of phylogenetics are often grouped under the term cladistics. The most common ones are parsimony, maximum likelihood, and MCMC-based Bayesian inference. All methods depend upon an implicit or explicit mathematical model describing the evolution of characters observed in the species included; all can be, and are, used for molecular data, wherein the characters are aligned nucleotide or amino acid sequences, and all but maximum likelihood (see below) can be, and are, used for morphological data.

Phenetics, popular in the mid-20th century but now largely obsolete, uses distance matrix-based methods to construct trees based on overall similarity, which is often assumed to approximate phylogenetic relationships.

Limitations and workarounds

Ultimately, there is no way to measure whether a particular phylogenetic hypothesis is accurate or not, unless the true relationships among the taxa being examined are already known (which may happen with bacteria or viruses under laboratory conditions). The best result an empirical phylogeneticist can hope to attain is a tree with branches that are well supported by the available evidence. Several potential pitfalls have been identified:

Homoplasy

Certain characters are more likely to evolve convergently than others; logically, such characters should be given less weight in the reconstruction of a tree. Weights in the form of a model of evolution can be inferred from sets of molecular data, so that maximum likelihood or Bayesian methods can be used to analyze them. For molecular sequences, this problem is exacerbated when the taxa under study have diverged substantially. As time since the divergence of two taxa increase, so does the probability of multiple substitutions on the same site, or back mutations, all of which result in homoplasies. For morphological data, unfortunately, the only objective way to determine convergence is by the construction of a tree – a somewhat circular method. Even so, weighting homoplasious characters does indeed lead to better-supported trees. Further refinement can be brought by weighting changes in one direction higher than changes in another; for instance, the presence of thoracic wings almost guarantees placement among the pterygote insects, although because wings are often lost secondarily, there is no evidence that they have been gained more than once.

Horizontal gene transfer

In general, organisms can inherit genes in two ways: vertical gene transfer and horizontal gene transfer. Vertical gene transfer is the passage of genes from parent to offspring, and horizontal (also called lateral) gene transfer occurs when genes jump between unrelated organisms, a common phenomenon especially in prokaryotes; a good example of this is the acquired antibiotic resistance as a result of gene exchange between various bacteria leading to multi-drug-resistant bacterial species.

Horizontal gene transfer has complicated the determination of phylogenies of organisms, and inconsistencies in phylogeny have been reported among specific groups of organisms depending on the genes used to construct evolutionary trees. The only way to determine which genes have been acquired vertically and which horizontally is to parsimoniously assume that the largest set of genes that have been inherited together have been inherited vertically; this requires analyzing a large number of genes.

Taxon sampling

Owing to the development of advanced sequencing techniques in molecular biology, it has become feasible to gather large amounts of data (DNA or amino acid sequences) to infer phylogenetic hypotheses. For example, it is not rare to find studies with character matrices based on whole mitochondrial genomes (~16,000 nucleotides, in many animals). However, simulations have shown that it is more important to increase the number of taxa in the matrix than to increase the number of characters, because the more taxa there are, the more accurate and more robust is the resulting phylogenetic tree. This may be partly due to the breaking up of long branches.

Phylogenetic signal

Another important factor that affects the accuracy of tree reconstruction is whether the data analyzed actually contain a useful phylogenetic signal, a term that is used generally to denote whether a character evolves slowly enough to have the same state in closely related taxa as opposed to varying randomly. Tests for phylogenetic signal exist.

Missing data

In general, the more data that is available when constructing a tree, the more accurate and reliable the resulting tree will be. Missing data is no less detrimental than simply having less data, although its impact is greatest when most of the missing data is in a small number of taxa. The fewer characters that have missing data, the better; concentrating the missing data across a small number of character states produces a more robust tree.

The role of fossils

Because many characters involve embryological, or soft-tissue or molecular characters that (at best) hardly ever fossilize, and the interpretation of fossils is more ambiguous than living taxa, extinct taxa almost invariably have higher proportions of missing data than living ones. However, despite these limitations, the inclusion of fossils is invaluable, as they can provide information in sparse areas of trees, breaking up long branches and constraining intermediate character states; thus, fossil taxa contribute as much to tree resolution as modern taxa. Fossils can also constrain the age of lineages and thus demonstrate how consistent a tree is with the stratigraphic record; stratocladistics incorporates age information into data matrices for phylogenetic analyses.

History of phylogenetics

This section needs expansion. You can help by adding to it. (September 2012)

Ernst Haeckel's recapitulation theory

During the late 19th century, Ernst Haeckel's recapitulation theory, or "biogenetic fundamental law", was widely accepted. It was often expressed as "ontogeny recapitulates phylogeny", i.e. the development of an organism successively mirrors the adult stages of successive ancestors of the species it belongs to. This theory has long been rejected. In fact, ontogeny evolves – the phylogenetic history of a species cannot be read directly from its ontogeny, as Haeckel thought would be possible, but characters from ontogeny can be (and have been) used as data for phylogenetic analyses; the more closely related two species are, the more apomorphies their embryos share.

See also

• Bauplan
• Bioinformatics
• Biomathematics
• Cladistics
• Evolutionary taxonomy
• Coalescent theory
• Computational phylogenetics
• EDGE of Existence Programme
• Language family
• Maximum parsimony
• Molecular phylogeny
• PhyloCode
• Joe Felsenstein
• Systematics
• Phylogenetic tree
• Phylogenetic network
• Phylogenetic nomenclature
• Phylogenetics software
• Phylogenetic tree viewers
• Phylogenomics
• Phylogeography
• Phylodynamics
• Phylogenetic comparative methods
• Microbial phylogenetics
• Ontogeny (psychoanalysis)
• Ontogeny
• Phylogeny (psychoanalysis)

References

1. Liddell, Henry George (1901). A Greek-English lexicon. Oxford: Clarendon Press. p. 1698. {{cite book}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
2. Liddell, Henry George (1901). A Greek-English lexicon. Oxford: Clarendon Press. p. 305. {{cite book}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
3. "phylogeny". Biology online. Retrieved 2012, August. {{cite web}}: Check date values in: |accessdate= (help)
4. Edwards AWF; Cavalli-Sforza LL (1964). "Reconstruction of evolutionary trees". In Heywood, Vernon Hilton; McNeill, J. (eds.). Phenetic and Phylogenetic Classification. pp. 67–76. OCLC 733025912. Phylogenetics is that branch of life science, which deals with the study of evolutionary relation among various groups of organisms, through molecular sequencing data.
5. ^ Goloboff, Pablo A.; Carpenter, James M.; Arias, J. Salvador; Esquivel, Daniel Rafael Miranda (2008). "Weighting against homoplasy improves phylogenetic analysis of morphological data sets". Cladistics. 24 (5): 758. doi:10.1111/j.1096-0031.2008.00209.x.
6. Goloboff, Pablo A. (1997). "Self-Weighted Optimization: Tree Searches and Character State Reconstructions under Implied Transformation Costs". Cladistics. 13 (3): 225. doi:10.1111/j.1096-0031.1997.tb00317.x.
7. Zwickl, Derrick J.; Hillis, David M. (2002). "Increased Taxon Sampling Greatly Reduces Phylogenetic Error". Systematic Biology. 51 (4): 588–98. doi:10.1080/10635150290102339. PMID 12228001.
8. Wiens, John J. (2006). "Missing data and the design of phylogenetic analyses". Journal of Biomedical Informatics. 39 (1): 34–42. doi:10.1016/j.jbi.2005.04.001. PMID 15922672.
9. Blomberg, Simon P.; Garland, Theodore; Ives, Anthony R. (2003). "Testing for phylogenetic signal in comparative data: Behavioral traits are more labile". Evolution. 57 (4): 717–45. doi:10.1111/j.0014-3820.2003.tb00285.x. PMID 12778543.
10. Prevosti, Francisco J.; Chemisquy, María A. (2009). "The impact of missing data on real morphological phylogenies: Influence of the number and distribution of missing entries". Cladistics. 26 (3): 326. doi:10.1111/j.1096-0031.2009.00289.x.
11. Cobbett, Andrea; Wilkinson, Mark; Wills, Matthew (2007). "Fossils Impact as Hard as Living Taxa in Parsimony Analyses of Morphology". Systematic Biology. 56 (5): 753–66. doi:10.1080/10635150701627296. PMID 17886145.
12. Huelsenbeck, John P. (1994). "Comparing the Stratigraphic Record to Estimates of Phylogeny". Paleobiology. 20 (4): 470–83. JSTOR 2401230.

Further reading

• Schuh, R. T. and A. V. Z. Brower. 2009. Biological Systematics: principles and applications (2nd edn.) ISBN 978-0-8014-4799-0

External links

• The Tree of Life
• Interactive Tree of Life
• PhyloCode
• ExploreTree
• UCMP Exhibit Halls: Phylogeny Wing
• Willi Hennig Society
• Filogenetica.org in Spanish
• PhyloPat, Phylogenetic Patterns
• SplitsTree, program for computing phylogenetic trees and unrooted phylogenetic networks
• Dendroscope, program for drawing phylogenetic trees and rooted phylogenetic networks
• Phylogenetic inferring on the T-REX server
• Mesquite
• NCBI – Systematics and Molecular Phylogenetics
• What Genomes Can Tell Us About the Past – lecture on phylogenetics by Sydney Brenner
• Mikko's Phylogeny Archive
• Who is Who in Phylogenetic Networks research papers related to the phylogenetic network
• Phylogenetic Reconstruction from Gene-Order Data
• ETE: A Python Environment for Tree Exploration This is a programming library to analyze, manipulate and visualize phylogenetic trees. See: Huerta-Cepas, Jaime; Dopazo, Joaquín; Gabaldón, Toni (2010). "ETE: A python Environment for Tree Exploration". BMC Bioinformatics. 11: 24. doi:10.1186/1471-2105-11-24. PMC 2820433. PMID 20070885.{{cite journal}}: CS1 maint: unflagged free DOI (link)
• PhylomeDB: A public database hosting thousands of gene phylogenies ranging many different species. See: Huerta-Cepas, J.; Capella-Gutierrez, S.; Pryszcz, L. P.; Denisov, I.; Kormes, D.; Marcet-Houben, M.; Gabaldon, T. (2010). "PhylomeDB v3.0: An expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions". Nucleic Acids Research. 39 (Database issue): D556–60. doi:10.1093/nar/gkq1109. PMC 3013701. PMID 21075798.
• Lents, N. H.; Cifuentes, O. E.; Carpi, A. (2010). "Teaching the Process of Molecular Phylogeny and Systematics: A Multi-Part Inquiry-Based Exercise". Cell Biology Education. 9 (4): 513. doi:10.1187/cbe.09-10-0076.

• Use dmy dates from July 2012
• Ill-formatted IPAc-en transclusions
• Phylogenetics