Testing Convergent Evolution in Auditory Processing Genes between Echolocating Mammals and the Aye-Aye, a Percussive-Foraging Primate

Abstract

Several taxonomically distinct mammalian groups-certain microbats and cetaceans (e.g., dolphins)-share both morphological adaptations related to echolocation behavior and strong signatures of convergent evolution at the amino acid level across seven genes related to auditory processing. Aye-ayes (Daubentonia madagascariensis) are nocturnal lemurs with a specialized auditory processing system. Aye-ayes tap rapidly along the surfaces of trees, listening to reverberations to identify the mines of wood-boring insect larvae; this behavior has been hypothesized to functionally mimic echolocation. Here we investigated whether there are signals of convergence in auditory processing genes between aye-ayes and known mammalian echolocators. We developed a computational pipeline (Basic Exon Assembly Tool) that produces consensus sequences for regions of interest from shotgun genomic sequencing data for nonmodel organisms without requiring de novo genome assembly. We reconstructed complete coding region sequences for the seven convergent echolocating bat-dolphin genes for aye-ayes and another lemur. We compared sequences from these two lemurs in a phylogenetic framework with those of bat and dolphin echolocators and appropriate nonecholocating outgroups. Our analysis reaffirms the existence of amino acid convergence at these loci among echolocating bats and dolphins; some methods also detected signals of convergence between echolocating bats and both mice and elephants. However, we observed no significant signal of amino acid convergence between aye-ayes and echolocating bats and dolphins, suggesting that aye-aye tap-foraging auditory adaptations represent distinct evolutionary innovations. These results are also consistent with a developing consensus that convergent behavioral ecology does not reliably predict convergent molecular evolution.

Keywords: comparative genomics; convergent evolution; evolutionary ecology.

Fig. 1.—

The basic workflow used by BEAT when assembling a single query sequence from a short read data set. BEAT maps all short-reads provided to a reference genome in parallel, removes low-quality and duplicate reads, then merges the mapped files to produce a map of all reads in the data set. Mapped reads are then scanned nucleotide-by-nucleotide against the reference, and a call for each position is generated by taking the quality-weighted median call of all mapping reads at positions with a depth of coverage >2. To avoid genotyping error when generating consensus sequences for loci of interest from a distantly related reference, BEAT should be run twice, with the second iteration using the consensus generated by the first as its reference.

Fig. 2.—

Illustration of the pairwise convergent evolution analysis used in this study. The example shown is for a section of the CDH23 gene, here comparing two lemurs, Daubentonia and Propithecus diadema, with the echolocating dolphin Tursiops truncatus. For each lemur, we computed the number of positions out of the total aligned positions (2,345 for this gene) for which that species shared an amino acid with T. truncatus, but for which that amino acid was different than that of the other lemur species and the multi-species consensus sequence determined from the multiple-species alignment. A section of CDH23 is shown that contains two Daubentonia—T. truncatus convergent amino acids. For the whole gene, the ratio of convergent amino acids for Daubentonia and T. truncatus (5) and P. diadema and T. truncatus (2) = 2.5, providing a magnitude and directionality of relative convergence between aye-aye and dolphin, with a phylogenic correction based on the sister lemur species. These ratio values are depicted in figure 3 for all tested comparisons, summed across the seven genes analyzed in this study. The difference in the number of convergent amino acids is evaluated with a Fisher’s exact test computed based on the 2×2 contingency table, not the convergence ratio; for the illustrated CDH23 comparison, P = 0.4528, prior to Bonferroni multiple test correction.

Fig. 3.—

Observed seven gene convergence ratios for three pairs of known echolocator: Nonecholocator sister taxa and for Daubentonia: Propithecus, each compared with other echolocating and nonecholocating mammalian taxa. Ratio of the number of convergent/total amino acids with outgroup species in the phylogeny for indicated species 1: Species 2 pairs, summed across seven auditory processing genes. Colored symbols represent the ratio between the number of convergent amino acids shared between the first species in the indicated pair and the species on the corresponding row of the phylogeny (the “test species”) relative to that for the second species in the indicated pair, after results were summed over the seven auditory genes considered in this analysis. All statistical tests were performed on a comparison of the sum of convergent/total amino acids for each species pair, not the ratio between the proportions thus formed. The dashed line indicates a ratio of 1, or no difference in the observed level of convergence with the outgroup test species between the two sister species. For the bat–bat comparisons, pairs were chosen at random from the set of four possible comparisons (Rhinolophus: Eidolon, Rhinolophus: Pteropus, Megaderma: Eidolon, Megaderma: Pteropus); similar results were obtained from the other possible pairs (see supplementary table S1, Supplementary Material online, for all comparisons). The indicated significance values have been corrected for multiple tests using the Bonferroni method, within each set of pairwise comparisons across the phylogeny.