Contrasting patterns of nonneutral evolution in proteins encoded in nuclear and mitochondrial genomes

We report that patterns of nonneutral DNA sequence evolution among publishe d nuclear and mitochondrially encoded protein-coding loci differ significan tly in animals. Whereas an apparent excess of amino acid polymorphism is se en in most (25/31) mitochondrial genes, this pattern is seen in fewer than half (15/36) of the nuclear data sets. This differentiation is even greater among data sets with significant departures from neutrality (14/15 vs. 1/6 ). Using forward simulations, we examined patterns of nonneutral evolution using parameters chosen to mimic the differences between mitochondrial and nuclear genetics (we varied recombination rate, population size, mutation r ate, selective dominance, and intensity of germ line bottleneck). Patterns of evolution were correlated only with effective population size and streng th of selection, and no single genetic factor explains the empirical contra st in patterns. We further report that in Arabidopsis thaliana, a highly se lf-fertilizing plant with effectively low recombination, five of six publis hed nuclear data sets also exhibit an excess of amino acid polymorphism. We suggest that the contrast between nuclear and mitochondrial nonneutrality in animals stems from differences in rates of recombination in conjunction with a distribution of selective effects. If the majority of mutations segr egating in populations are deleterious, high linkage may hinder the spread of the occasional beneficial mutation.