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In biology, phylogenetics (pron.: //) is the study of evolutionary relationships among groups of organisms (e.g. species, populations), which are discovered through molecular sequencing data and morphological data matrices. The term phylogenetics derives from the Greek terms phylé (φυλή) and phylon (φῦλον), denoting "tribe", "clan", "race" and the adjectival form, genetikós (γενετικός), of the word genesis (γένεσις) "origin", "source", "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:
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[how?] 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 because, although 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. There have also been well-documented cases of horizontal gene transfer between eukaryotes.
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.
Continuous characters 
Morphological characters that sample a continuum may contain phylogenetic signal, but are hard to code as discrete characters. Several methods have been used, one of which is gap coding, and there are variations on gap coding. In the original form of gap coding:
group means for a character are first ordered by size. The pooled within-group standard deviation is calculated … and differences between adjacent means … are compared relative to this standard deviation. Any pair of adjacent means is considered different and given different integer scores … if the means are separated by a "gap" greater than the within-group standard deviation … times some arbitrary constant.
If more taxa are added to the analysis, the gaps between taxa may become so small that all information is lost. Generalized gap coding works around that problem by comparing individual pairs of taxa rather than considering one set that contains all of the taxa.
Missing data 
In general, the more data that are available when constructing a tree, the more accurate and reliable the resulting tree will be. Missing data are no more detrimental than simply having fewer data, although the impact is greatest when most of the missing data are in a small number of taxa. Concentrating the missing data across a small number of characters 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 requires expansion. (September 2012)|
The term "phylogeny" derives from the German Phylogenie, introduced by Haeckel in 1866.
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 to which it belongs. 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 
- Coalescent theory
- Computational phylogenetics
- EDGE of Existence programme
- Evolutionary taxonomy
- Joe Felsenstein
- Language family
- Maximum parsimony
- Microbial phylogenetics
- Molecular phylogeny
- Ontogeny (psychoanalysis)
- Phylogenetic comparative methods
- Phylogenetic network
- Phylogenetic nomenclature
- Phylogenetic tree
- Phylogenetic tree viewers
- Phylogenetics software
- Phylogeny (psychoanalysis)
- Liddell, Henry George; Scott, Robert; Jones, Henry Stuart (1968). A Greek-English lexicon (9 ed.). Oxford: Clarendon Press. p. 1961.
- Liddell, Henry George; Scott, Robert; Jones, Henry Stuart (1968). A Greek-English lexicon (9 ed.). Oxford: Clarendon Press. p. 343.
- "phylogeny". Biology online. Retrieved 2013-02-15.
- Edwards AWF; Cavalli-Sforza LL (1964). "Reconstruction of evolutionary trees". In Heywood, Vernon Hilton; McNeill, J. 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."
- 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.
- 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.
- 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.
- 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.
- 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.
- Archie, J.W. (1985). "Methods for coding variable morphological features for numerical taxonomic analysis". Systematic Zoology 34 (3): 326–345. doi:10.2307/2413151.
- 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.
- 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.
- Huelsenbeck, John P. (1994). "Comparing the Stratigraphic Record to Estimates of Phylogeny". Paleobiology 20 (4): 470–83. JSTOR 2401230.
- Harper, Douglas (2010). "Phylogeny". Online Etymology Dictionary. Retrieved March 18, 2013.
Further reading 
- Schuh, Randall T.; Brower, Andrew V.Z. (2009). Biological Systematics: principles and applications (2nd ed.). Ithaca: Comstock Pub. Associates/Cornell University Press. ISBN 978-0-8014-4799-0. OCLC 312728177.
|Look up phylogenetics in Wiktionary, the free dictionary.|
- The Tree of Life
- Interactive Tree of Life
- 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
- 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.
- 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.