Modern biology has affirmed Darwin’s hypothesis that all the organisms we know of, present and past, have descended from one ancient common ancestor. Current understanding of the history by which diverse groups have originated reveals fascinating events, such as the symbiotic origin of eukaryotic cells and the multiple origins of multicellular organisms from single-celled ancestors.
A phylogeny is the history of the events by which species or other taxa have successively originated from common ancestors. It may be depicted by a phylogenetic tree, in which each branch point (node) represents the division of an ancestral lineage into two or more lineages. Closely related species have more recent common ancestors than distantly related species. The group of species descended from a particular common ancestor is a monophyletic group, or clade; a phylogenetic tree portrays nested sets of monophyletic groups.
The phylogeny of a focal group of species can be readily estimated by using characters that change so rarely that those species that share a derived (“advanced”) character state can safely be assumed to have inherited it from their common ancestor. A character state that occurs within the group of species can be judged to be derived rather than ancestral if it does not occur among other lineages (outgroups) that are related to the focal group.
In some cases, a phylogeny is not strictly dichotomous (branching), but may include reticulation (joining of separate lineages into one). This can occur if some species have originated by hybridization between different ancestral species or if genes have moved “horizontally” between organisms.
Phylogenetic methods can be used to describe the history not only of species, but also of DNA sequences, gene families, tumors and other cell lineages, and cultural traits such as languages.
Phylogenetic analyses have many uses. An important one is inferring the history of evolution of interesting characters by “mapping” changes in a character onto a phylogeny that has been derived from other data. Such systematic studies have yielded information on common patterns and principles of character evolution.
The rate of evolution of DNA sequences can be shown in some cases to be fairly constant (providing an approximate molecular clock), such that sequences in different lineages diverge at a roughly constant rate. The absolute rate of sequence evolution can sometimes be calibrated if the ages of fossils of some lineages are known. The rate of sequence evolution can then be used to estimate the absolute age of some evolutionary events, such as the origin of other taxa.
New features almost always evolve from pre-existing characters. Homologous characters in different organisms are those that have been inherited from their common ancestors, with or without evolutionary change.
Different characters commonly evolve at different rates (mosaic evolution).
Homoplasy, including convergent evolution and reversal, is often a result of similar adaptations in different lineages.
In an adaptive radiation, numerous related lineages arise in a relatively short time and evolve in many different directions as they adapt to different habitats or ways of life. Radiation, rather than directional trends, is perhaps the most common pattern of long-term evolution.