Phylogenetics
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Ben Tillman
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{{redirect|Phylogenesis|the science fiction novel|Phylogenesis (novel)}}
{{evolution3}}
In [[biology]], '''phylogenetics''' ([[Greek language|Greek]]: ''phyle'' = tribe, race and ''genetikos'' = relative to birth, from ''[[genesis]]'' = birth) is the study of [[evolution]]ary relatedness among various groups of [[organism]]s (e.g., [[species]], populations). Also known as '''[[phylogenetic systematics]]''' or '''[[cladistics]]''', phylogenetics treats each species as a group of lineage-connected individuals<ref>{{cite web
| last = Speer
| first = Vrian
| title = UCMP Glossary: Phylogenetics
| publisher = UC Berkeley
| date = 1998
| url = http://www.ucmp.berkeley.edu/glossary/glossary_1.html
| accessdate = 2008-03-22}}</ref>. [[Taxonomy]], the classification of organisms according to similarity, has been richly informed by phylogenetics but remains methodologically and logically distinct.<ref>{{cite book
|author=[[A.W.F. Edwards]] & [[L.L. Cavalli-Sforza]]
|year=1964
|title=Reconstruction of evolutionary trees
|editor=Systematics Assoc. Publ. No. 6: Phenetic and Phylogenetic Classification
|pages=67-76
}}</ref>
Evolution is regarded as a branching process, whereby populations are altered over time and may [[speciate]] into separate branches, [[Hybrid (biology)|hybrid]]ize together, or terminate by [[extinction]]. This may be [[scientific visualization|visualize]]d as a [[multidimensional scaling|multidimensional]] character-space that a population moves through over time. The problem posed by phylogenetics is that [[genetics|genetic]] data are only available for the present, and [[fossil]] records ([[osteometric]] data) are sporadic and less reliable. Our knowledge of how evolution operates is used to reconstruct the full tree.<ref>{{cite journal
|author=[[L.L. Cavalli-Sforza]] and [[A.W.F. Edwards]]
|month=Sep.,
|year=1967
|title=Phylogenetic analysis: Models and estimation procedures
|journal=Evol.
|volume=21
|issue=3
|pages=550–570
|url=http://links.jstor.org/sici?sici=0014-3820%28196709%2921%3A3%3C550%3APAMAEP%3E2.0.CO%3B2-I
|doi=10.2307/2406616
}}</ref>
[[Cladistics]] provides a simplified method of understanding phylogenetic trees. There are some terms that describe the nature of a grouping. For instance, all birds and reptiles are believed to have descended from a single common ancestor, so this taxonomic grouping (yellow in the diagram) is called [[Monophyly|monophyletic]]. "Modern reptile" ([[cyan]] in the diagram) is a grouping that contains a common ancestor, but does not contain all descendents of that ancestor (birds are excluded). This is an example of a [[Paraphyly|paraphyletic]] group. A grouping such as [[warm-blooded]] animals would include only mammals and birds (red/orange in the diagram) and is called [[Polyphyly|polyphyletic]] because the members of this grouping do not include the most recent common ancestor.
The [[Computational phylogenetics|most commonly used methods]] to infer phylogenies include [[parsimony]], [[maximum likelihood]], and [[Markov chain Monte Carlo|MCMC]]-based [[Bayesian inference]]. [[Phenetics|Distance-based methods]] construct trees based on overall similarity which is often assumed to approximate phylogenetic relationships. All methods depend upon an implicit or explicit [[mathematical model]] describing the evolution of characters observed in the species included, and are usually used for [[molecular phylogeny]] where the characters are aligned [[nucleotide]] or [[amino acid]] sequences.
== Ernst Haeckel's recapitulation theory ==
[[Image:Phylogenetic-Groups.svg|thumb|300px|Phylogenetic groups, or [[Taxon|''taxa'']], can be [[Monophyly|monophyletic]], [[Paraphyly|paraphyletic]], or [[Polyphyly|polyphyletic]].]]
During the late 19th century, [[Ernst Haeckel]]'s [[recapitulation theory]], or biogenetic law, was widely accepted. This theory was often expressed as "[[ontogeny]] recapitulates phylogeny", i.e. the development of an organism exactly mirrors the evolutionary development of the species. Haeckel's early version of this hypothesis (that the embryo mirrors ''adult'' evolutionary ancestors) has since been rejected, and the hypothesis amended as the embryo's development mirroring ''embryos'' of its evolutionary ancestors. Most modern biologists recognize numerous connections between ontogeny and phylogeny, explain them using [[Evolutionary developmental biology|evolutionary theory]], or view them as supporting evidence for that theory. [[Donald Williamson]] suggested that larvae and embryos represented adults in other taxa that have been transferred by hybridization (the larval transfer theory)<ref>Williamson, D. I. (2003) ''The Origins of Larvae''. Kluwer. Dordrecht. xviii + 261 pp.</ref>
<ref>Williamson, D. I. (2006) Hybridization in the evolution of animal form and life-cycle. ''Zoological Journal of the Linnean Society'' 148: 585-602.</ref>
== Gene transfer ==
Organisms can generally inherit genes in two ways: from parent to offspring (vertical gene transfer), or by horizontal or [[Horizontal gene transfer|lateral gene transfer]], in which genes jump between unrelated organisms, a common phenomenon in [[prokaryote]]s.
Lateral gene transfer has complicated the determination of phylogenies of organisms since inconsistencies have been reported depending on the gene chosen.
Carl Woese came up with the three-domain theory of life (eubacteria, archaea and eukaryotes) based on his discovery that the genes encoding ribosomal RNA are ancient and distributed over all lineages of life with little or no lateral gene transfer. Therefore rRNA are commonly recommended as molecular clocks for reconstructing phylogenies.
This has been particularly useful for the phylogeny of microorganisms, to which the species concept does not apply and which are too morphologically simple to be classified based on phenotypic traits.
== Taxon sampling and phylogenetic signal ==
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 estimate phylogenies. For example, it is not rare to find studies with character matrices based on whole mitochondrial genomes. However, it has been proposed 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, the more robust is the resulting phylogeny. This is partly due to the breaking up of [[long branch attraction|long branches]]. It has been argued that this is an important reason to incorporate data from fossils into phylogenies where possible. Using simulations, [[Derrick Zwickl]] and Hillis<ref name=Zwickl2002>{{cite journal |author=Zwickl DJ, Hillis DM |title=Increased taxon sampling greatly reduces phylogenetic error |journal=Systematic Biology |volume=51 |pages=588–598 |year=2002 | doi = 10.1080/10635150290102339 <!--Retrieved from CrossRef by DOI bot-->}}</ref> found that increasing taxon sampling in phylogenetic inference has a positive effect on the accuracy of phylogenetic analyses.
Another important factor that affects the accuracy of tree reconstruction is whether the data analyzed actually contain useful phylogenetic signal, a term that is used generally to denote whether related organisms tend to resemble each other with respect to their genetic material or phenotypic traits.<ref name=Blomberg2003>{{cite journal |author=Blomberg SP, Garland T Jr, Ives AR |title=Testing for phylogenetic signal in comparative data: behavioral traits are more labile |journal=Evolution |volume=57 |pages=717–745 |year=2003}}</ref>
== See also ==
{| width=100%
| valign=top width=33% |
*[[Bauplan]]
*[[Bioinformatics]]
*[[Biomathematics]]
*[[Biosynthetic phylogeny]]
*[[Cladistics]]
*[[Coalescent theory]]
*[[EDGE of Existence Programme]]
| valign=top width=34% |
*[[List of publications in biology#Phylogenetics|Important publications in phylogenetics]]
*[[Language family]]
*[[Maximum parsimony]]
*[[Molecular phylogeny]]
*[[PhyloCode]]
| valign=top width=33% |
*[[Phylogenetic tree]]
*[[Phylogenetic network]]
*[[List of phylogenetics software|Phylogenetics software]]
*[[Phylogeography]]
*[[Phylogenetic comparative methods]]
*[[Systematics]]
|}
==References==
<references/>
==External links==
* [http://tolweb.org/tree/learn/concepts/whatisphylogeny.html The Tree of Life]
* [http://itol.embl.de Interactive Tree of Life]
* [http://www.ohiou.edu/phylocode/ PhyloCode]
* [http://www.ucmp.berkeley.edu/exhibit/phylogeny.html UCMP Exhibit Halls: Phylogeny Wing]
* [http://www.cladistics.org Willi Hennig Society]
* [http://www.filogenetica.org Filogenetica.org in Spanish]
* [http://www.cmbi.ru.nl/phylopat PhyloPat, Phylogenetic Patterns]
* [http://www.trex.uqam.ca Phylogenetic inferring on the T-REX server]
* [http://mesquiteproject.org/mesquite/mesquite.html Mesquite]
* [http://www.ncbi.nlm.nih.gov/About/primer/phylo.html NCBI - Systematics and Molecular Phylogenetics]
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[[Category:Phylogenetics| ]]
[[cs:Fylogenetika]]
[[de:Phylogenese]]
[[eo:Filogenetiko]]
[[ko:계통학]]
[[he:פילוגנטיקה]]
[[hu:Törzsfejlődés]]
[[nl:Fylogenetica]]
[[ja:系統学]]
[[no:Fylogenetikk]]
[[ru:Филогенетика]]
[[uk:Філогенетика]]
[[ur:قبیلہ سازی]]
[[zh:种系发生学]]