The effects of social structure, geographical structure, and population size on the evolution of mitochondrial DNA:...

A program simulating the distribution of variation in mitochondrial DNA in macaques is described. Empirical studies of the rates of nucleotide substitution and geographical patterning of mtDNA variation in these and other monkey species have demonstrated striking differences from equivalent measures of nuclear DNA and called into question the assumptions informing the use of mtDNA to elucidate phylogenetic relationships in organisms with relatively complex social organization. The model presented here incorporates social-structural variables as well as geographical structure and population size in order to clarify the determinants of the pattern of mtDNA evolution in macaques. The program, SHINES (Simulation of Hereditary Innovations in Neutral Evolution of Simians), employs an economical procedure for representing the haplotypes of the animals in the simulated population.