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). Phylogenetics, also known as phylogenetic systematics, 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 cladistics, phenetics, maximum likelihood, and MCMC-based Bayesian inference. These last two depend upon a 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.

Ernst Hacekel's recapitulation theory
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.dun dun drive theory

Horizontal gene transfer
New developments in the understanding of horizontal gene transfer have complicated the matter a bit.


 * Sequence comparisons suggest recent horizontal transfer of many genes among diverse species including across the boundaries of phylogenetic "domains". Thus determining the phylogenetic history of a species can not be done conclusively by determining evolutionary trees for single genes.