Phylogenetics

In biology, phylogenetics (/ˌfaɪloʊdʒəˈnɛtɪks, -lə-/)^[1][2][3] is the study of the evolutionary history and relationships among or within groups of organisms. These relationships are determined by phylogenetic inference methods that focus on observed heritable traits, such as DNA sequences, protein amino acid sequences, or morphology. The result of such an analysis is a phylogenetic tree—a diagram containing a hypothesis of relationships that reflects the evolutionary history of a group of organisms.^[4]

The tips of a phylogenetic tree can be living taxa or fossils, and represent the "end" or the present time in an evolutionary lineage. A phylogenetic diagram can be rooted or unrooted. A rooted tree diagram indicates the hypothetical common ancestor of the tree. 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.^[5]

In addition to their use for inferring phylogenetic patterns among taxa, phylogenetic analyses are often employed to represent relationships among genes or individual organisms. Such uses have become central to understanding biodiversity, evolution, ecology, and genomes.

Phylogenetics is part of systematics.

Taxonomy is the identification, naming and classification of organisms. Classifications are now usually based on phylogenetic data, and many systematists contend that only monophyletic taxa should be recognized as named groups. 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.

Even in the field of cancer, phylogenetics makes it possible to study the clonal evolution of tumors and molecular chronology, showing how cell populations vary throughout the progression of the disease, even during treatment, using whole genome sequencing techniques. ^[6]

Inference of a phylogenetic tree

Main article: Computational phylogenetics

Usual methods of phylogenetic inference involve computational approaches implementing the optimality criteria and methods of parsimony, maximum likelihood (ML), and MCMC-based Bayesian inference. All these depend upon an implicit or explicit mathematical model describing the evolution of characters observed.

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.

Prior to 1950, phylogenetic inferences were generally presented as narrative scenarios. Such methods are often ambiguous and lack explicit criteria for evaluating alternative hypotheses.^[7][8][9]

History

The term "phylogeny" derives from the German Phylogenie, introduced by Haeckel in 1866,^[10] and the Darwinian approach to classification became known as the "phyletic" approach.^[11]

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 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. But this theory has long been rejected.^[12][13] 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.

Timeline of key points

 

Branching tree diagram from Heinrich Georg Bronn's work (1858)

 

Phylogenetic tree suggested by Haeckel (1866)

• 14th century, lex parsimoniae (parsimony principle), William of Ockam, English philosopher, theologian, and Franciscan friar, but the idea actually goes back to Aristotle, precursor concept
• 1763, Bayesian probability, Rev. Thomas Bayes,^[14] precursor concept
• 18th century, Pierre Simon (Marquis de Laplace), perhaps first to use ML (maximum likelihood), precursor concept
• 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,^[15] 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 evolution^[16]
• 1837, Darwin's notebooks show an evolutionary tree^[17]
• 1843, distinction between homology and analogy (the latter now referred to as homoplasy), Richard Owen, precursor concept
• 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.^[18]
• 1858, elaboration of evolutionary theory, Darwin and Wallace,^[19] also in Origin of Species by Darwin the following year, precursor concept
• 1866, Ernst Haeckel, first publishes his phylogeny-based evolutionary tree, precursor concept
• 1893, Dollo's Law of Character State Irreversibility,^[20] precursor concept
• 1912, ML recommended, analyzed, and popularized by Ronald Fisher, precursor concept
• 1921, Tillyard uses term "phylogenetic" and distinguishes between archaic and specialized characters in his classification system^[21]
• 1940, term "clade" coined by Lucien Cuénot
• 1949, Jackknife resampling, Maurice Quenouille (foreshadowed in '46 by Mahalanobis and extended in '58 by Tukey), precursor concept
• 1950, Willi Hennig's classic formalization^[22]
• 1952, William Wagner's groundplan divergence method^[23]
• 1953, "cladogenesis" coined^[24]
• 1960, "cladistic" coined by Cain and Harrison^[25]
• 1963, first attempt to use ML (maximum likelihood) for phylogenetics, Edwards and Cavalli-Sforza^[26]
• 1965
  • Camin-Sokal parsimony, first parsimony (optimization) criterion and first computer program/algorithm for cladistic analysis both by Camin and Sokal^[27]
  • character compatibility method, also called clique analysis, introduced independently by Camin and Sokal (loc. cit.) and E. O. Wilson^[28]
• 1966
  • English translation of Hennig^[29]
  • "cladistics" and "cladogram" coined (Webster's, loc. cit.)
• 1969
  • dynamic and successive weighting, James Farris^[30]
  • Wagner parsimony, Kluge and Farris^[31]
  • CI (consistency index), Kluge and Farris^[31]
  • introduction of pairwise compatibility for clique analysis, Le Quesne^[32]
• 1970, Wagner parsimony generalized by Farris^[33]
• 1971
  • first successful application of ML to phylogenetics (for protein sequences), Neyman^[34]
  • Fitch parsimony, Fitch^[35]
  • NNI (nearest neighbour interchange), first branch-swapping search strategy, developed independently by Robinson^[36] and Moore et al.
  • ME (minimum evolution), Kidd and Sgaramella-Zonta^[37] (it is unclear if this is the pairwise distance method or related to ML as Edwards and Cavalli-Sforza call ML "minimum evolution")
• 1972, Adams consensus, Adams^[38]
• 1976, prefix system for ranks, Farris^[39]
• 1977, Dollo parsimony, Farris^[40]
• 1979
  • Nelson consensus, Nelson^[41]
  • MAST (maximum agreement subtree)((GAS)greatest agreement subtree), a consensus method, Gordon^[42]
  • bootstrap, Bradley Efron, precursor concept^[43]
• 1980, PHYLIP, first software package for phylogenetic analysis, Felsenstein
• 1981
  • majority consensus, Margush and MacMorris^[44]
  • strict consensus, Sokal and Rohlf^[45]
  • first computationally efficient ML algorithm, Felsenstein^[46]
• 1982
  • PHYSIS, Mikevich and Farris
  • branch and bound, Hendy and Penny^[47]
• 1985
  • first cladistic analysis of eukaryotes based on combined phenotypic and genotypic evidence Diana Lipscomb^[48]
  • first issue of Cladistics
  • first phylogenetic application of bootstrap, Felsenstein^[49]
  • first phylogenetic application of jackknife, Scott Lanyon^[50]
• 1986, MacClade, Maddison and Maddison
• 1987, neighbor-joining method Saitou and Nei^[51]
• 1988, Hennig86 (version 1.5), Farris
  • Bremer support (decay index), Bremer^[52]
• 1989
  • RI (retention index), RCI (rescaled consistency index), Farris^[53]
  • HER (homoplasy excess ratio), Archie^[54]
• 1990
  • combinable components (semi-strict) consensus, Bremer^[55]
  • SPR (subtree pruning and regrafting), TBR (tree bisection and reconnection), Swofford and Olsen^[56]
• 1991
  • DDI (data decisiveness index), Goloboff^[57][58]
  • first cladistic analysis of eukaryotes based only on phenotypic evidence, Lipscomb
• 1993, implied weighting Goloboff^[59]
• 1994, reduced consensus: RCC (reduced cladistic consensus) for rooted trees, Wilkinson^[60]
• 1995, reduced consensus RPC (reduced partition consensus) for unrooted trees, Wilkinson^[61]
• 1996, first working methods for BI (Bayesian Inference)independently developed by Li,^[62] Mau,^[63] and Rannala and Yang^[64] and all using MCMC (Markov chain-Monte Carlo)
• 1998, TNT (Tree Analysis Using New Technology), Goloboff, Farris, and Nixon
• 1999, Winclada, Nixon
• 2003, symmetrical resampling, Goloboff^[65]
• 2004,2005, symmilarity metric (using an approximation to Kolmogorov complexity) or NCD (normalized compression distance), Li et al.,^[66] Cilibrasi and Vitanyi.^[67]

Outside biology

Phylogenetic tools and representations (trees and networks) can also be applied to studying the evolution of languages, in the field of quantitative comparative linguistics.^[68]

See also

• Angiosperm Phylogeny Group
• Bauplan
• Bioinformatics
• Biomathematics
• Coalescent theory
• EDGE of Existence programme
• Evolutionary taxonomy
• Language family
• Maximum parsimony
• Microbial phylogenetics
• Molecular phylogeny
• Noogenesis
• Ontogeny
• PhyloCode
• Phylodynamics
• Phylogenesis
• Phylogenetic comparative methods
• Phylogenetic network
• Phylogenetic nomenclature
• Phylogenetic tree viewers
• Phylogenetics software
• Phylogenomics
• Phylogeny (psychoanalysis)
• Phylogeography
• Systematics

References

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Bibliography

• 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.
• Forster, Peter; Renfrew, Colin, eds. (2006). Phylogenetic Methods and the Prehistory of Languages. McDonald Institute Press, University of Cambridge. ISBN 978-1-902937-33-5. OCLC 69733654.
• Baum, David A.; Smith, Stacey D. (2013). Tree Thinking: an introduction to phylogenetic biology. Greenwood Village, CO: Roberts and Company. ISBN 978-1-936221-16-5. OCLC 767565978.
• Stuessy, Tod F. (2009). Plant Taxonomy: The Systematic Evaluation of Comparative Data. Columbia University Press. ISBN 978-0-231-14712-5.

External links

•   The dictionary definition of phylogenetics at Wiktionary