Using evolutionary algorithms to estimate transition rates of discrete characteristics in phylogenetic trees

Phylogenetics is the study of evolutionary relationships between and among species or individuals, and involves the construction and analysis of evolutionary trees. In particular, certain questions frequently arise which can be examined by analysing a tree in terms of maximum likelihood with respect to a particular characteristic or set of characteristics. An important concept in these respects is the 'transition rate' between two states of a character over evolutionary time. Various analyses based on given phylogenetic trees involve a search for a set of transition rates which maximise the likelihood of the given tree. We investigate the preliminary use of an evolutionary algorithm for this search problem, and find that it seems significantly superior to the existing method (a conjugate-gradient search) used in the evolutionary biology community for this purpose. Our test case is drawn from the field of evolutionary linguistics, emphasising the broad applicability of this search problem.