Our Nature paper! Genome-wide molecular convergence in echolocating mammals

Exciting news from the lab this week… we’ve published in one of the leading journals, Nature!!!

Much of my work in the Rossiter BatLab for the last couple of years has centred around the search for genomic signatures of molecular convergence. This means looking for similar genetic changes in otherwise unrelated organisms. We’d normally expect unrelated organisms to differ considerably in their genetic sequences, because over time random mutations occur in their genomes; the more time has passed since two species diverged, the more changes we expect. However, we know that similar structures may evolve in unrelated species due to shared selection pressures (think of the streamlined body shapes of sharks, icthyosaurs and dolphins, for example). Can these pressures produce identical changes right down at the level of genetic sequences? We hoped to detect identical genetic changes in unrelated species (in this case, the echolocation – ‘sonar hearing’ – in some species of bats and whales) caused by similar selection pressures operating on the evolution of the genes required for those traits.

It’s been a long slog – we’ve had to write a complicated computer program to look at millions of letters of DNA – but this week it all bears fruit. We found that a <em>staggering</em> number of genes in the genomes of echolocating bats and whales (a bottlenose dolphin, if you must) showed evidence of these similar genetic changes, known technically as ‘genetic convergence’.

Obviously we started jumping up and down when we found this, and because we imagined other scientists would too, we wrote up our findings and sent them to the journal <em>Nature</em>, one of the top journals in the world of science… and crossed our fingers.

Well, today we can finally reveal that we were able to get through the peer-review process (where anonymous experts scrutinise your working – a bit like an MOT for your experiments), and the paper is out today!

But what do we actually say? Well:
<blockquote>Evolution is typically thought to proceed through divergence of genes, proteins and ultimately phenotypes. However, similar traits might also evolve convergently in unrelated taxa owing to similar selection pressures. Adaptive phenotypic convergence is widespread in nature, and recent results from several genes have suggested that this phenomenon is powerful enough to also drive recurrent evolution at the sequence level. Where homoplasious substitutions do occur these have long been considered the result of neutral processes. However, recent studies have demonstrated that adaptive convergent sequence evolution can be detected in vertebrates using statistical methods that model parallel evolution, although the extent to which sequence convergence between genera occurs across genomes is unknown. Here we analyse genomic sequence data in mammals that have independently evolved echolocation and show that convergence is not a rare process restricted to several loci but is instead widespread, continuously distributed and commonly driven by natural selection acting on a small number of sites per locus. Systematic analyses of convergent sequence evolution in 805,053 amino acids within 2,326 orthologous coding gene sequences compared across 22 mammals (including four newly sequenced bat genomes) revealed signatures consistent with convergence in nearly 200 loci. Strong and significant support for convergence among bats and the bottlenose dolphin was seen in numerous genes linked to hearing or deafness, consistent with an involvement in echolocation. Unexpectedly, we also found convergence in many genes linked to vision: the convergent signal of many sensory genes was robustly correlated with the strength of natural selection. This first attempt to detect genome-wide convergent sequence evolution across divergent taxa reveals the phenomenon to be much more pervasive than previously recognized.</blockquote>
Congrats to Steve, Georgia and Joe! After a few deserved beers we’ll have our work cut out to pick through all these genes and work out exactly what all of them do (guessing the genes’ biological functions, especially in non-model (read:not us or things we eat) organisms like bats and dolphins is notoriously tricky. So we’ll probably stick our heads out of the lab again in <em>another</em> two years…

The full citation is: Parker, J., Tsagkogeorga, G., Cotton, J.A.C., Liu, R., Stupka, E., Provero, P. &amp; Rossiter, S.J. (2013) Genome-wide signatures of convergent evolution in echolocating mammals. <em>Nature</em> (epub ahead of print), 4th September 2013. doi:10.1038/nature12511. This work was funded by Biotechnology and Biological Sciences Research Council (UK) grant BB/H017178/1.