Data from: The relation between the neutrality index for mitochondrial genes and the distribution of mutational effects on fitness

We explore factors affecting patterns of polymorphism and divergence (as
captured by the neutrality index) at mammalian mitochondrial loci. To do
this, we develop a population genetic model that incorporates a fraction
of neutral amino acid sites, mutational bias, and a probability
distribution of selection coefficients against new nonsynonymous
mutations. We confirm, by reanalyzing publicly available data sets, that
the mitochondrial cyt-b gene shows a broad range of neutrality indices
across mammalian taxa, and explore the biological factors that can explain
this observation. We find that observed patterns of differences in the
neutrality index, polymorphism and divergence are not caused by
differences in mutational bias. They can, however, be explained by a
combination of a small fraction of neutral amino acid sites, weak
selection acting on most amino acid mutations, and differences in
effective population size among taxa.