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). 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. 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. The tips of a phylogenetic tree can be living taxa or fossils, and represent the 'end', or the present, in an evolutionary lineage. A phylogenetic diagram can be rooted or unrooted. A rooted tree diagram indicates the hypothetical common ancestor, or ancestral lineage, 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. 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. Such uses have become central to understanding biodiversity, evolution, ecology, and genomes.
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.
Prior to 1950, phylogenetic inferences were generally presented as narrative scenarios. Such methods are often ambiguous and lack explicit criteria for evaluating alternative hypotheses.
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.
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. 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, 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, 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
1837, Darwin's notebooks show an evolutionary tree
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.
1858, elaboration of evolutionary theory, Darwin and Wallace, 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, 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
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