The evolution of similar traits in different species, a process known as convergent evolution, is widespread not only at the physical level, but also at the genetic level, and scientists who investigated the genomic basis for echolocation, one of the most well-known examples of convergent evolution, sought to examine the frequency of the process at a genomic level. 

Echolocation is a complex physical trait that involves the production, reception and auditory processing of ultrasonic pulses for detecting unseen obstacles or tracking down prey, and has evolved separately in different groups of bats and cetaceans (including dolphins).

The scientists carried out one of the largest genome-wide surveys of its type to discover the extent to which convergent evolution of a physical feature involves the same genes.

They compared genomic sequences of 22 mammals, including the genomes of bats and dolphins, which independently evolved echolocation, and found genetic signatures consistent with convergence in nearly 200 different genomic regions concentrated in several 'hearing genes'.

a, For each locus, the goodness-of-fit of three separate phylogenetic hypotheses was considered: (left) H₀, the accepted species phylogeny based on recent findings (for example, refs 14, 23, 24, 25); (top-right panel) H₁, or ‘bat–bat convergence’, in which echolocating bat lineages (shown in brown) are forced to form a monophyletic group to the exclusion of non-echolocating Old World fruit bats (shown in orange); and (bottom-right panel) H₂, or ‘bat–dolphin convergence’, in which the echolocating bat lineages and the dolphin (blue) form a monophyletic group to the exclusion of all non-echolocating mammals. See Methods for details of model fitting and topologies. b, The distribution of convergence signal across 2,326 loci in 14–22 representative mammalian taxa, as measured by locus-wise mean site-specific likelihood support for the species topology (H₀) over (left) the ‘bat–bat’ hypothesis uniting echolocating bats (that is, ΔSSLS (H₁)) and (right) bat–dolphin hypothesis (that is, ΔSSLS (H₂)). Representative hearing and vision loci are shown in green and blue, respectively; for each locus significance levels based on simulation denote whether it had significant counts of convergent sites after correcting for expected counts in random (control) phylogenies (*), and additionally whether strength of positive selection (dN/dS) and convergence (ΔSSLS) at sites under selection in echolocators were correlated (**); see Supplementary Table 4 and Methods. Credit and link: 
doi:10.1038/nature12511

To perform the analysis, the team had to sift through millions of letters of genetic code using a computer program developed to calculate the probability of convergent changes occurring by chance, so they could reliably identify 'odd-man-out' genes. 

Consistent with an involvement in echolocation, signs of convergence among bats and the bottlenose dolphin were seen in many genes previously implicated in hearing or deafness.

"We had expected to find identical changes in maybe a dozen or so genes but to see nearly 200 is incredible," explains Dr. Joe Parker, first author on the paper. "We know natural selection is a potent driver of gene sequence evolution, but identifying so many examples where it produces nearly identical results in the genetic sequences of totally unrelated animals is astonishing."

Dr. Georgia Tsagkogeorga, who undertook the assembly of the new genome data for this study, added, "We found that molecular signals of convergence were widespread, and were seen in many genes across the genome. It greatly adds to our understanding of genome evolution."

Group leader, Dr. Stephen Rossiter, said, "These results could be the tip of the iceberg. As the genomes of more species are sequenced and studied, we may well see other striking cases of convergent adaptations being driven by identical genetic changes." 

Citation: Joe Parker, Georgia Tsagkogeorga, James A. Cotton, Yuan Liu, Paolo Provero, Elia Stupka& Stephen J. Rossiter, 'Genome-wide signatures of convergent evolution in echolocating mammals', Nature 4 September 2013 doi:10.1038/nature12511