Phylogenetics


In biology, phylogenetics is a part of systematics that addresses the inference of the evolutionary history and relationships among or within groups of organisms. 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 —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 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 tries to reflect phylogeny in its classifications by only recognizing groups based on shared, derived characters ; evolutionary taxonomy tries to take into account both the branching pattern and "degree of difference" to find a compromise between them.

Inference of a phylogenetic tree

Usual methods of phylogenetic inference involve computational approaches implementing the optimality criteria and methods of parsimony, maximum likelihood, 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, 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.

History

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 used as data for phylogenetic analyses; the more closely related two species are, the more apomorphies their embryos share.

Timeline of key points