Phylogenetics

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In biology, phylogenetics /ˌfaɪloʊdʒəˈnɛtɪks, -lə-/ (Greek: φυλή, φῦλον – phylé, phylon = tribe, clan, race + γενετικός – genetikós = origin, source, birth) is a part of systematics that addresses the inference of the evolutionary history and relationships among or within groups of organisms (e.g. species, or more inclusive taxa). Phylogenetics_sentence_0

These relationships are hypothesized by phylogenetic inference methods that evaluate observed heritable traits, such as DNA sequences or morphology, often under a specified model of evolution of these traits. Phylogenetics_sentence_1

The result of such an analysis is a phylogeny (also known as a phylogenetic tree)—a diagrammatic hypothesis of relationships that reflects the evolutionary history of a group of organisms. Phylogenetics_sentence_2

The tips of a phylogenetic tree can be living taxa or fossils, and represent the 'end', or the present, in an evolutionary lineage. Phylogenetics_sentence_3

A phylogenetic diagram can be rooted or unrooted. Phylogenetics_sentence_4

A rooted tree diagram indicates the hypothetical common ancestor, or ancestral lineage, of the tree. Phylogenetics_sentence_5

An unrooted tree diagram (a network) makes no assumption about the ancestral line, and does not show the origin or "root" of the taxa in question or the direction of inferred evolutionary transformations. Phylogenetics_sentence_6

In addition to their proper use for inferring phylogenetic patterns among taxa, phylogenetic analyses are often employed to represent relationships among gene copies or individual organisms. Phylogenetics_sentence_7

Such uses have become central to understanding biodiversity, evolution, ecology, and genomes. Phylogenetics_sentence_8

Taxonomy is the identification, naming and classification of organisms. Phylogenetics_sentence_9

Classifications are now usually based on phylogenetic data, and many systematists contend that only monophyletic taxa should be recognized as named groups. Phylogenetics_sentence_10

The degree to which classification depends on inferred evolutionary history differs depending on the school of taxonomy: phenetics ignores phylogenetic speculation altogether, trying to represent the similarity between organisms instead; cladistics (phylogenetic systematics) tries to reflect phylogeny in its classifications by only recognizing groups based on shared, derived characters (synapomorphies); evolutionary taxonomy tries to take into account both the branching pattern and "degree of difference" to find a compromise between them. Phylogenetics_sentence_11

Inference of a phylogenetic tree Phylogenetics_section_0

Main article: Computational phylogenetics Phylogenetics_sentence_12

Usual methods of phylogenetic inference involve computational approaches implementing the optimality criteria and methods of parsimony, maximum likelihood (ML), and MCMC-based Bayesian inference. Phylogenetics_sentence_13

All these depend upon an implicit or explicit mathematical model describing the evolution of characters observed. Phylogenetics_sentence_14

Phenetics, popular in the mid-20th century but now largely obsolete, used distance matrix-based methods to construct trees based on overall similarity in morphology or similar observable traits (i.e. in the phenotype or the overall similarity of DNA, not the DNA sequence), which was often assumed to approximate phylogenetic relationships. Phylogenetics_sentence_15

Prior to 1950, phylogenetic inferences were generally presented as narrative scenarios. Phylogenetics_sentence_16

Such methods are often ambiguous and lack explicit criteria for evaluating alternative hypotheses. Phylogenetics_sentence_17

History Phylogenetics_section_1

The term "phylogeny" derives from the German Phylogenie, introduced by Haeckel in 1866, and the Darwinian approach to classification became known as the "phyletic" approach. Phylogenetics_sentence_18

Ernst Haeckel's recapitulation theory Phylogenetics_section_2

During the late 19th century, Ernst Haeckel's recapitulation theory, or "biogenetic fundamental law", was widely accepted. Phylogenetics_sentence_19

It was often expressed as "ontogeny recapitulates phylogeny", i.e. the development of a single organism during its lifetime, from germ to adult, successively mirrors the adult stages of successive ancestors of the species to which it belongs. Phylogenetics_sentence_20

But this theory has long been rejected. Phylogenetics_sentence_21

Instead, 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. Phylogenetics_sentence_22

Timeline of key points Phylogenetics_section_3

Phylogenetics_unordered_list_0

  • 14th century, lex parsimoniae (parsimony principle), William of Ockam, English philosopher, theologian, and Franciscan friar, but the idea actually goes back to Aristotle, precursor conceptPhylogenetics_item_0_0
  • 1763, Bayesian probability, Rev. Thomas Bayes, precursor conceptPhylogenetics_item_0_1
  • 18th century, Pierre Simon (Marquis de Laplace), perhaps first to use ML (maximum likelihood), precursor conceptPhylogenetics_item_0_2
  • 1809, evolutionary theory, Philosophie Zoologique, Jean-Baptiste de Lamarck, precursor concept, foreshadowed in the 17th century and 18th century by Voltaire, Descartes, and Leibniz, with Leibniz even proposing evolutionary changes to account for observed gaps suggesting that many species had become extinct, others transformed, and different species that share common traits may have at one time been a single race, also foreshadowed by some early Greek philosophers such as Anaximander in the 6th century BC and the atomists of the 5th century BC, who proposed rudimentary theories of evolutionPhylogenetics_item_0_3
  • 1837, Darwin's notebooks show an evolutionary treePhylogenetics_item_0_4
  • 1843, distinction between homology and analogy (the latter now referred to as homoplasy), Richard Owen, precursor conceptPhylogenetics_item_0_5
  • 1858, Paleontologist Heinrich Georg Bronn (1800–1862) published a hypothetical tree to illustrating the paleontological "arrival" of new, similar species following the extinction of an older species. Bronn did not propose a mechanism responsible for such phenomena, precursor concept.Phylogenetics_item_0_6
  • 1858, elaboration of evolutionary theory, Darwin and Wallace, also in Origin of Species by Darwin the following year, precursor conceptPhylogenetics_item_0_7
  • 1866, Ernst Haeckel, first publishes his phylogeny-based evolutionary tree, precursor conceptPhylogenetics_item_0_8
  • 1893, Dollo's Law of Character State Irreversibility, precursor conceptPhylogenetics_item_0_9
  • 1912, ML recommended, analyzed, and popularized by Ronald Fisher, precursor conceptPhylogenetics_item_0_10
  • 1921, Tillyard uses term "phylogenetic" and distinguishes between archaic and specialized characters in his classification systemPhylogenetics_item_0_11
  • 1940, term "clade" coined by Lucien CuénotPhylogenetics_item_0_12
  • 1949, Jackknife resampling, Maurice Quenouille (foreshadowed in '46 by Mahalanobis and extended in '58 by Tukey), precursor conceptPhylogenetics_item_0_13
  • 1950, Willi Hennig's classic formalizationPhylogenetics_item_0_14
  • 1952, William Wagner's groundplan divergence methodPhylogenetics_item_0_15
  • 1953, "cladogenesis" coinedPhylogenetics_item_0_16
  • 1960, "cladistic" coined by Cain and HarrisonPhylogenetics_item_0_17
  • 1963, first attempt to use ML (maximum likelihood) for phylogenetics, Edwards and Cavalli-SforzaPhylogenetics_item_0_18
  • 1965Phylogenetics_item_0_19
    • Camin-Sokal parsimony, first parsimony (optimization) criterion and first computer program/algorithm for cladistic analysis both by Camin and SokalPhylogenetics_item_0_20
    • character compatibility method, also called clique analysis, introduced independently by Camin and Sokal (loc. cit.) and E. O. WilsonPhylogenetics_item_0_21
  • 1966Phylogenetics_item_0_22
    • English translation of HennigPhylogenetics_item_0_23
    • "cladistics" and "cladogram" coined (Webster's, loc. cit.)Phylogenetics_item_0_24
  • 1969Phylogenetics_item_0_25
    • dynamic and successive weighting, James FarrisPhylogenetics_item_0_26
    • Wagner parsimony, Kluge and FarrisPhylogenetics_item_0_27
    • CI (consistency index), Kluge and FarrisPhylogenetics_item_0_28
    • introduction of pairwise compatibility for clique analysis, Le QuesnePhylogenetics_item_0_29
  • 1970, Wagner parsimony generalized by FarrisPhylogenetics_item_0_30
  • 1971Phylogenetics_item_0_31
    • first successful application of ML to phylogenetics (for protein sequences), NeymanPhylogenetics_item_0_32
    • Fitch parsimony, FitchPhylogenetics_item_0_33
    • NNI (nearest neighbour interchange), first branch-swapping search strategy, developed independently by Robinson and Moore et al.Phylogenetics_item_0_34
    • ME (minimum evolution), Kidd and Sgaramella-Zonta (it is unclear if this is the pairwise distance method or related to ML as Edwards and Cavalli-Sforza call ML "minimum evolution")Phylogenetics_item_0_35
  • 1972, Adams consensus, AdamsPhylogenetics_item_0_36
  • 1976, prefix system for ranks, FarrisPhylogenetics_item_0_37
  • 1977, Dollo parsimony, FarrisPhylogenetics_item_0_38
  • 1979Phylogenetics_item_0_39
    • Nelson consensus, NelsonPhylogenetics_item_0_40
    • MAST (maximum agreement subtree)((GAS)greatest agreement subtree), a consensus method, GordonPhylogenetics_item_0_41
    • bootstrap, Bradley Efron, precursor conceptPhylogenetics_item_0_42
  • 1980, PHYLIP, first software package for phylogenetic analysis, FelsensteinPhylogenetics_item_0_43
  • 1981Phylogenetics_item_0_44
    • majority consensus, Margush and MacMorrisPhylogenetics_item_0_45
    • strict consensus, Sokal and RohlfPhylogenetics_item_0_46
    • first computationally efficient ML algorithm, FelsensteinPhylogenetics_item_0_47
  • 1982Phylogenetics_item_0_48
    • PHYSIS, Mikevich and FarrisPhylogenetics_item_0_49
    • branch and bound, Hendy and PennyPhylogenetics_item_0_50
  • 1985Phylogenetics_item_0_51
    • first cladistic analysis of eukaryotes based on combined phenotypic and genotypic evidence Diana LipscombPhylogenetics_item_0_52
    • first issue of CladisticsPhylogenetics_item_0_53
    • first phylogenetic application of bootstrap, FelsensteinPhylogenetics_item_0_54
    • first phylogenetic application of jackknife, Scott LanyonPhylogenetics_item_0_55
  • 1986, MacClade, Maddison and MaddisonPhylogenetics_item_0_56
  • 1987, neighbor-joining method Saitou and NeiPhylogenetics_item_0_57
  • 1988, Hennig86 (version 1.5), FarrisPhylogenetics_item_0_58
    • Bremer support (decay index), BremerPhylogenetics_item_0_59
  • 1989Phylogenetics_item_0_60
    • RI (retention index), RCI (rescaled consistency index), FarrisPhylogenetics_item_0_61
    • HER (homoplasy excess ratio), ArchiePhylogenetics_item_0_62
  • 1990Phylogenetics_item_0_63
    • combinable components (semi-strict) consensus, BremerPhylogenetics_item_0_64
    • SPR (subtree pruning and regrafting), TBR (tree bisection and reconnection), Swofford and OlsenPhylogenetics_item_0_65
  • 1991Phylogenetics_item_0_66
    • DDI (data decisiveness index), GoloboffPhylogenetics_item_0_67
    • first cladistic analysis of eukaryotes based only on phenotypic evidence, LipscombPhylogenetics_item_0_68
  • 1993, implied weighting GoloboffPhylogenetics_item_0_69
  • 1994, reduced consensus: RCC (reduced cladistic consensus) for rooted trees, WilkinsonPhylogenetics_item_0_70
  • 1995, reduced consensus RPC (reduced partition consensus) for unrooted trees, WilkinsonPhylogenetics_item_0_71
  • 1996, first working methods for BI (Bayesian Inference)independently developed by Li, Mau, and Rannala and Yang and all using MCMC (Markov chain-Monte Carlo)Phylogenetics_item_0_72
  • 1998, TNT (Tree Analysis Using New Technology), Goloboff, Farris, and NixonPhylogenetics_item_0_73
  • 1999, Winclada, NixonPhylogenetics_item_0_74
  • 2003, symmetrical resampling, GoloboffPhylogenetics_item_0_75
  • 2004,2005, symmilarity metric (using an approximation to Kolmogorov complexity) or NCD (normalized compression distance), Li et al., Cilibrasi and Vitanyi.Phylogenetics_item_0_76

See also Phylogenetics_section_4

Credits to the contents of this page go to the authors of the corresponding Wikipedia page: en.wikipedia.org/wiki/Phylogenetics.