Phylogenetics
In
biology,
phylogenetics (
Greek:
phylon = tribe, race and
genetikos = relative to birth, from
genesis = birth) is the study of evolutionary relatedness among various groups of
organisms (e.g.,
species, populations). Also known as
phylogenetic systematics, phylogenetics treats a species as a group of lineage-connected individuals over time. Phylogenetic
taxonomy, which is an offshoot of, but not a logical consequence of, phylogenetic systematics, constitutes a means of classifying groups of organisms according to degree of evolutionary relatedness.
Phylogeny (or phylogenesis) is the origin and
evolution of a set of organisms, usually a set of species. A major task of
systematics is to determine the ancestral relationships among known species (both living and
extinct). The most commonly used methods to infer phylogenies include
parsimony,
maximum likelihood, and
MCMC-based
Bayesian inference.
Distance-based methods construct trees based on overall similarity which is often assumed to approximate phylogenetic relationships. All methods depend upon an implicit or explicit
mathematical model describing the evolution of characters observed in the species included, and are usually used for
molecular phylogeny where the characters are aligned
nucleotide or
amino acid sequences.
During the late
19th century,
Ernst Haeckel's
recapitulation theory, or biogenetic law, was widely accepted. This theory was often expressed as "
ontogeny recapitulates phylogeny", i.e. the development of an organism exactly mirrors the evolutionary development of the species. The early version of this hypothesis has since been rejected as being oversimplified. However, most modern biologists recognize numerous connections between ontogeny and phylogeny, explain them using evolutionary theory, or view them as supporting evidence for that theory.
Organisms can generally inherit genes in two ways: by speciation (vertical gene transfer), from parent to offspring, or by horizontal or
lateral gene transfer, in which genes jump between unrelated organisms, a common phenomenon in
prokaryotes.
Lateral gene transfer has complicated the determination of phylogenies of organisms since inconsistences have been reported depending on the gene chosen.
Carl Woese came up with the three domain theory of life (Eubacteria, Archaea and Eukaryotes) based on his discovery that the genes encoding ribosomal RNA are ancient and distributed over all lineages of life with little or no lateral gene transfer. Therefore rRNA are commonly recommended as molecular clocks for reconstructing phylogenies.
This has been particularly useful for the phylogeny of microorganisms, to which the species concept does not apply and which are too morphologically simple to be classified based on phenotypic traits.
Due 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 estimate
phylogenies. For example, it is not rare to find studies with character matrices based on whole mitochondrial genomes. However, it has been proposed 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, the more robust is the resulting phylogeny. This is partly due to the breaking up of
long branches. It has been argued that this is an important reason to incorporate data from fossils into phylogenies where possible.
Using simulations, Zwickl and Hillis (2002) found that increasing taxon sampling in phylogenetic inference has a positive effect on the accuracy of phylogenetic analyses.
*. 2002. Increased taxon sampling greatly reduces phylogenetic error. Systematic Biology 51:588-598.
*
The Tree of Life*
PhyloCode*
UCMP Exhibit Halls: Phylogeny Wing 
