Genes and Ecology: Accelerated Rates of Replacement Substitutions in the Cytochrome b Gene of Subterranean Rodents

South American tuco-tucos (genus Ctenomys) and related coruros (genus Spalacopus), North American pocket gophers (family Geomyidae), and African mole rats (family Bathyergidae) are lineages of rodents that colonized the subterranean niche independently. An energetically demanding lifestyle, coupled with the hypoxic atmosphere characteristic of the subterranean environment may change the selective regime of genes that encode proteins involved in cellular respiration. Here, we examined the molecular evolution of the cytochome b gene, a mitochondrially-encoded gene participating in oxidative phosphorylation, in these lineages and their above-ground relatives. Using maximum-likelihood and Bayesian approaches, we estimated rates of synonymous (dS) and nonsynonymous (dN) substitutions. We found a significantly higher ratio (dN/dS) in each of the subterranean groups with respect to their non-subterranean counterparts. Using an alternative procedure that tests for positive selection on quantitative physicochemical amino acid properties, we found that i) subterranean mole rats and tucu-tucus showed more sites whose amino acid properties may be under positive selection in the cytochome b gene than their non-subterranean relatives, and ii) some of the sites identified to be under selection exclusively in subterranean taxa were shared among all subterranean taxa. The results given by these two approaches are consistent with each other and suggest a link between directional selection at the molecular level and niche shift.