Parallel signatures of sequence evolution among hearing genes in echolocating mammals: an emerging model of genetic convergence

Abstract

Recent findings of sequence convergence in the Prestin gene among some bats and cetaceans suggest that parallel adaptations for high-frequency hearing have taken place during the evolution of echolocation. To determine if this gene is an exception, or instead similar processes have occurred in other hearing genes, we have examined Tmc1 and Pjvk, both of which are associated with non-syndromic hearing loss in mammals. These genes were amplified and sequenced from a number of mammalian species, including echolocating and non-echolocating bats and whales, and were analysed together with published sequences. Sections of both genes showed phylogenetic signals that conflicted with accepted species relationships, with coding regions uniting laryngeal echolocating bats in a monophyletic clade. Bayesian estimates of posterior probabilities of convergent and divergent substitutions provided more direct evidence of sequence convergence between the two groups of laryngeal echolocating bats as well as between echolocating bats and dolphins. We found strong evidence of positive selection acting on some echolocating bat species and echolocating cetaceans, contrasting with purifying selection on non-echolocating bats. Signatures of sequence convergence and molecular adaptation in two additional hearing genes suggest that the acquisition of high-frequency hearing has involved multiple loci.

Figure 1

Tree topologies recovered by Bayesian and maximum likelihood (ML) analyses for (a) 2139 bp of Tmc1 and (b) 1059 bp of Pjvk. Nodal support values are Bayesian posterior probabilities and bootstrap values based on 1000 replicates (- indicates topology differed in ML, ^*/ indicates BPP >0.95 and /^* indicates BS >95%). Branch colours are as follows: non-bat species (black); Old World fruit bats (red); laryngeal echolocating Yinpterochiroptera (green); and Yangochiroptera (blue).

Figure 2

(a) Simplified species tree including taxa involved in the focal bat–dolphin branch comparisons. Branch-pair plots of total posterior probability divergence vs total posterior probability convergence for (b) Tmc1 and (c) Pjvk. T. truncatus–bat comparisons are indicated by diamonds and R. ferrumequinum–Yangochiroptera comparisons by circles. Points are coloured according to the second branch in the comparison and follow the species tree (a). The remaining points (grey circles) correspond to comparisons between the remaining non-echolocating mammal species.

Figure 3

Distribution of sites along (a) TMC1 and (b) PJVK with posterior probability (PP) of convergent substitutions, >0.1, for T. truncatus–bat comparisons (diamonds) and R. ferrumequinum–Yangochiroptera comparisons (circles). Colours are according to Figure 2a. Functional peptide domains of each protein were identified from published sources; in (a) the TMC1 transmembrane domains are numbered (i–vi) and shown as pale grey blocks, and the highly conserved TMC domain (TMC) is shown as a dark grey block. In (b) dark grey blocks indicate the (i) highly conserved Gasdermin domain, (ii) the putative nuclear localisation signal and (iii) the zinc-binding motif.

Figure 4

Positive selection and convergent substitutions in (a) Tmc1 and (b) Pjvk. Sites with probability of convergent substitutions, in parentheses, are shown in black text; arrows indicate branches that share the convergence. Significant branch-site models are indicated by coloured text, site-wise probability of being under positive selection shown in parentheses. Sites are listed if identified as undergoing convergent substitutions and positive selection. For each gene the upper tree displays convergence between echolocating Yinpterochiroptera and Yangochiroptera, and the lower between the dolphin and echolocating bats. NS, not significant; ^*P<0.05.