Abstract
BackgroundGenome-wide signatures of convergent evolution are widely expected but rarely revealed in animals. Subterranean rodent genome and transcriptome data produced by next-generation sequencing facilitate the use of phylogenetic methods to infer non-synonymous and synonymous substitution rates within coding regions, which can reveal changes at the molecular level that are correlated with the dramatic shift from a terrestrial to subterranean habitat.ResultsOur study used previously sequenced genome or transcriptome data of two subterranean rodents, the blind mole rat and naked mole rat, and their terrestrial relatives, the mouse and guinea pig, to investigate the genetic basis of rodent subterranean adaptation. An analysis of 4996 orthologous genes revealed that the substitution pace of coding sequences was significantly slower in the blind mole rat than in the mouse, and slower in the naked mole rat than in the guinea pig. The dN/dS ratio was significantly higher in the blind mole rat than in the mouse and in the naked mole rat than in the guinea pig. These patterns are most likely related to the longer generation time and lower effective population size of subterranean rodents caused by subterranean ecological constraints. We also identified some genes and gene ontology (GO) categories that might be candidates for adaptation to subterranean life.ConclusionsOur study reveals a case of subterranean convergent evolution in rodents that is correlated with change in the pace and mode of molecular evolution observed at the genome scale. We believe that this genomic signature could have also evolved in other cases of subterranean convergence. Additionally, the genes that displayed the most radical changes in their patterns of evolution and their associated GO categories provide a strong basis for further comparative and functional studies, and potentially reveal molecular signatures of adaptation to subterranean life.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0564-1) contains supplementary material, which is available to authorized users.
Highlights
Genome-wide signatures of convergent evolution are widely expected but rarely revealed in animals
Slow substitution rate and high dN/dS ratios associated with subterranean rodent lineages To investigate non-synonymous and synonymous substitution rates related to subterranean convergence in genomic coding regions, we identified 4996 1:1:1:1:1:1 orthologues in genomes of the blind mole rat (BMR), naked mole rat (NMR), mouse, guinea pig, kangaroo rat and rabbit (Fig. 1a)
Unlike the rates of non-synonymous substitutions (rN) and rS, the average dN/dS ratio was significantly higher in the BMR than that in the mouse (p < 0.0001, Wilcoxon signed-rank test) and significantly higher in the NMR than that in the guinea pig (p < 2.2e−16, Wilcoxon signed-rank test) (Fig. 1d; Table 1; Additional file 1: Table S1), which reveals that non-synonymous substitutions are more prevalent in subterranean rat lineages
Summary
Genome-wide signatures of convergent evolution are widely expected but rarely revealed in animals. Parker et al analysed genome data of echolocating mammals and suggested that sequence convergence is widespread in Burrowing subterranean rodents spend their lives underground in conditions, such as darkness, low ventilation, Du et al BMC Evolutionary Biology (2015) 15:287 hypoxia and high moisture, that are unsuitable for the survival of many animals [8]. By comparison with their surface counterparts, subterranean rodents have evolved many different genetically coded morphological and physiological traits, such as digging forearms or teeth, and modified vestibular organs, eyes and visual processing [9,10,11]. They provide a good model to study the genetic signature of subterranean convergence
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