Convergent evolution of the genomes of marine mammals

Abstract

Marine mammals from different mammalian orders share several phenotypic traits adapted to the aquatic environment and are therefore a classic example of convergent evolution. To investigate convergent evolution at the genomic level, we sequenced and de novo assembled the genomes of three species of marine mammals (the killer whale, walrus and manatee) from three mammalian orders that share independently evolved phenotypic adaptations to a marine existence. Our comparative genomic analyses found that convergent amino acid substitutions were widespread throughout the genome, and that a subset were in genes evolving under positive selection and putatively associated with a marine phenotype. However, we found higher levels of convergent amino acid substitutions in a control set of terrestrial sister taxa to the marine mammals. Our results suggest that while convergent molecular evolution is relatively common, adaptive molecular convergence linked to phenotypic convergence is comparatively rare.

Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore

“…Both studies found instances of homoplasy in genes with plausible links to their convergent phenotypes 26,27 . However, similar amounts of homoplasy were also detected between non-convergent species 26 . Further analyses showed that homoplasious substitutions between marine mammals were largely consistent with relaxed purifying selection 28 .…”

“…Under this assumption, molecular convergence in orthologous loci is suggested be an important driver of phenotypic convergence 25 . Recent genome-wide studies have attempted to identify homoplasious amino acids in protein-coding genes, notably among several marine mammal lineages and among echolocating mammals 26,27 . Both studies found instances of homoplasy in genes with plausible links to their convergent phenotypes 26,27 .…”

“…Recent genome-wide studies have attempted to identify homoplasious amino acids in protein-coding genes, notably among several marine mammal lineages and among echolocating mammals 26,27 . Both studies found instances of homoplasy in genes with plausible links to their convergent phenotypes 26,27 . However, similar amounts of homoplasy were also detected between non-convergent species 26 .…”

Bat Biology, Genomes, and the Bat1K Project: To Generate Chromosome-Level Genomes for All Living Bat Species

“…With high-quality reference genomes, this can be studied at levels ranging from the nucleotide up to the chromosome. At the nucleotide level, one series of questions of growing interest relates to constrained sequence evolution, for example, whether specific nucleotides or amino acids are under convergent evolution in phylogenetically disparate taxa, as has been showcased with regard to the evolution of echolocation in bats and marine mammals (e.g., 65,161). At the larger scale, there is considerable focus today on evolutionary trajectories of autosomal and sex chromosomes (162), and in particular whether major evolutionary transitions accompany significant chromosome-scale rearrangements.…”

Rates and patterns of molecular evolution in freshwater versus terrestrial insects

“…Furthermore, the most extreme difference in terms of counts of changes observed (between I and V) was between amino acids in the same physico-chemical category and at a site with low amino acid diversity across the lineages, and thus likely reflects exchangeability rather than adaptation. Using genomic data, more biological information on the genetic basis of habitat shifts could firstly be obtained through consideration of convergence and similarities in gene types under differential selection pressures between habitats (e.g., Foote et al 2015).…”