Linking population genetics to phylogenetics
Population geneticists study the variability of gene sequences within a species, whereas phylogeneticists compare gene sequences between species and usually have only one representative sequence per species. Stochastic models in population genetics are used to determine probability distributions for gene frequencies and to predict the probability that a new mutation will become fixed in a population. Stochastic models in phylogenetics describe the substitution process in the single sequence that represents a species. These latter models are of great practical use in inferring evolutionary trees, but they ignore population genetics. Here, we consider the way that the two fields are linked. In a finite population with a low mutation rate, most sites in a gene are monomorphic; therefore it is a reasonable approximation to represent a species by a single sequence and to ignore within population variability. We show that population genetics theory can be used to predict the substitution rates that will be seen in phylogenetic models. However, a substitution in the phylogenetic sense is really the fixation of a new mutation in the population genetics sense. Substitution rates are dependent on mutation, selection and random drift, not just on mutation. An appreciation of the relationship with population genetics is important when designing new empirical models for phylogenetics, for example, paired-site models for RNA sequences with secondary structure and codon-based models for protein-coding regions of DNA.