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Team Tackles Convergent Evolution Questions Using Marine Mammal Genomes

NEW YORK (GenomeWeb) – A new Nature Genetics study suggests that while convergent molecular evolution may be quite common amongst marine mammals, such genomic adaptations are not necessarily linked to convergent evolution of the same physical features.

"[A]lthough convergent phenotypic evolution can result from convergent molecular evolution, these cases are rare, and evolution more frequently makes use of different molecular pathways to reach the same phenotypic outcome," senior author Richard Gibbs, director of the Baylor College of Medicine's Human Genome Sequencing Center, and colleagues wrote.

Gibbs led an international team that sequenced the genomes of the killer whale, walrus, and manatee — and improved the bottlenose dolphin's draft genome assembly — in an effort to understand convergent evolutionary processes at molecular and phenotypic levels. The genomes spanned three marine mammal orders that tend to share physical features and marine adaptations despite their phylogenetic differences.

By comparing the four genomes to one another and to non-marine mammals, the researchers saw fairly frequent overlap in amino acid changes and sites of positive selection across the genomes. Nevertheless, they reported, this molecular convergence only infrequently led to convergent adaptations of the same physical features. 

Multiple marine mammal orders have achieved similar physical features through convergent evolution, the researchers explained. But there is still debate about whether this convergence more often reflects parallel molecular adaptations or whether it typically occurs via distinct genetic pathways.

The team used a combination of Sanger, Illumina, and Roche 454 technologies to tackle the killer whale, Pacific walrus, and West Indian manatee genomes, using DNA from a female killer whale from the Netherlands, male and female walruses from Alaska and Wrangel Island, and a captive female manatee from Florida that belonged to a West Indian manatee sub-species.

In addition to de novo assemblies produced for those three species, the researchers generated new Roche 454 and Illumina HiSeq sequence data to improve the existing draft genome of the bottlenose dolphin with DNA from dolphin necroscopy samples collected as part of the US Navy's Marine Mammal Program.

Using predicted protein-coding sequences in these genomes and other available genome data, the team winnowed down to a set of almost 17,000 orthologous genes in the genomes of the four marine mammals as well as those of the human, cow, dog, alpaca, elephant, and opossum.

Next, the researchers looked for clues regarding convergent changes in the genome — from instances of amino acid substitutions in orthologous genes that seemed to crop up in parallel in different lineages or regions of the genome showing signs of positive selection stemming from convergent evolution rather than shared ancestry alone.

In the three marine mammalian orders considered, for example, they uncovered signs of convergent positive selection acting on glutathione metabolism pathway genes, along with almost four-dozen substitutions that appear to alter the resulting amino acid sequence of the same genes in each of the marine mammal lineages.

While some of the genes showing convergent molecular changes fall in pathways that could conceivably mediate physical features prone to convergent adaptation in the marine mammals, though, other convergent substitutions were shared with land mammals that don't have the same sorts of specializations for sea life.

The study's authors speculated that this seemingly discordant result might reflect the "pleiotropic and often deleterious nature of most mutations," which causes non-synonymous substitutions to persist at a shared set of sites in certain genes.