Phylogenetics is the study of evolutionary relationships among organisms or genes. The purpose of phylogenetic studies are: (1) to reconstruct evolutionary ties between organisms; (2) to estimate the time of divergence between organisms since they last shared a common ancestor.

Phylogenetic trees can be constructed to illustrate the evolutionary relationships among a group of organisms or genes. There are several types of data that can be used to build phylogenetic trees. Traditionally, phylogenetic trees were built from morphological features (beak shapes, presence of feathers, number of legs). Today, we use mostly molecular data such as DNA and protein sequences.

Species trees are different from gene trees.  For example, the divergence of a gene may predate the divergence of species, due to genetic  polymorphism in the population. Thus, using this gene to infer the species tree can  lead to an overestimate of branch lengths as well as incorrect topology. Furthermore,  another complication is that during evolution, gene duplications are common, and  these duplicated genes continue to evolve separately. Genes that diverged because of  speciation (e.g., matching genes in different organisms) are called orthologues. Genes  that diverged by duplication are called paralogues. Usually, a protein is more similar to its orthologue in another genome (after all, it is the “same” or corresponding gene)  than it is to any paralogues in its own genome. Finally, things such as horizontal  gene transfer (i.e., the transfer of genetic material from one genome to another)  may complicate matters. Typically, to infer a species tree, you should use many orthologous genes.