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Study Sees Convergent Evolution at Hundreds of Echolocation Loci

NEW YORK (GenomeWeb News) – A study appearing online today in Nature suggests that convergent evolution at hundreds of sites across the genome has helped animals in at least three mammalian lineages acquire the ability to navigate with the help of sound.

Researchers from the UK, Denmark, and Italy started by doing whole-genome sequencing on four new bat species, including three representatives that are capable of echolocation and one that is not.

Their analysis of the new bat genomes, together with existing sequence data for another 18 echolocating and non-echolocating mammals, suggest that convergent changes at almost 200 sites across the genome have contributed to the evolution of echolocation in two bat lineages and in a cetacean lineage that includes dolphins and whales.

"We know natural selection is a potent driver of gene sequence evolution," co-first author Joe Parker, a biology and chemical sciences researcher with Queen Mary University of London, said in a statement, "but identifying so many examples where it produces nearly identical results in the genetic sequences of totally unrelated animals is astonishing."

Echolocation was already known to have evolved independently in bats and cetaceans such as whales and dolphins, Parker and his co-authors noted. Recent studies have suggested that echolocation has appeared on at least two separate occasions in the bat lineage, but the degree of genetic overlap behind this and other forms of convergent evolution are not well understood.

To explore the extent of genomic convergence associated with echolocation, researchers started by using Illumina's HiSeq 2000 instrument to generate draft genome sequences for four bat species: the echolocating greater horseshoe (Rhinolophus ferrumequinum), greater false vampire (Megaderma lyra), and Parnell's mustached (Pteronotus parnellii) bats, as well as the non-echolocating straw-colored fruit bat (Eidolon helvum).

The team tracked down more than 20,000 predicted protein-coding genes in each of the newly assembled bat genomes. Then they added sequence data from 18 more published mammalian genomes, identifying 2,326 orthologous coding gene sequences that subsequently served as the basis for their phylogenetics-based look at echolocation-related sequence convergence.

Taking cues from more than 800,000 amino acid sequences encoded within the orthologous sequence set, they verified a role for convergence in the genomes of the echolocating bats and bottlenose dolphin included in the analysis.

Together with protein-protein interaction profiles, that data helped the group tally up a set of around 200 loci that are most strongly linked to such convergent evolution.

Perhaps not surprisingly, the overlapping adaptive alterations associated with echolocation included a swath of genes implicated in hearing or deafness. But the researchers also unearthed convergent adaptations affecting genes linked to vision and other sensory processes.

"Our findings strongly suggest that, despite many recent papers reporting sequencing convergence in particular candidate genes, the importance of this mode of molecular evolutionary change is relatively underappreciated and is under-exploited in seeking to understand the genetic basis of complex traits such as echolocation," Parker and his co-authors concluded.

"These results could be the tip of the iceberg," senior author Stephen Rossiter, with Queen Mary University of London, said in a statement. "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."

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