Marine mammals from different mammalian orders share several phenotypic traits adapted to the aquatic environment and therefore represent a classic example of convergent evolution. To investigate convergent evolution at the genomic level, we sequenced and performed de novo assembly of 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 of these substitutions 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, whereas convergent molecular evolution is relatively common, adaptive molecular convergence linked to phenotypic convergence is comparatively rare.
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- Supplementary Figure 1: Glutathione pathway (KEGG pathway map 00480). (73 KB)
Solid lines indicate direct relationships between enzymes and metabolites, and dashed lines indicate that more than one step is involved in a process. Genes are shown in rectangles. ANPEP highlighted in green was one of only five genes found evolving under positive selection along the combined marine mammal branch after correcting for multiple testing. GCLC highlighted in red was found to be evolving under positive selection along the combined marine mammal branch and the walrus branch and contained a convergent substitution shared by all three marine mammal lineages. GGT6 highlighted in bold font was found to be evolving under positive selection along the walrus branch. Yim et al.11 previously found evidence for GSR evolving under positive selection in the bottlenose dolphin and experimentally demonstrated the importance of glutathione as an antioxidant in cetacean cells during hypoxic or oxidative stress, e.g., during deep or long dives. This figure is adapted from Figure 3a of Yim et al.11.
- Supplementary Figure 2: Percentage of convergent substitutions for all pairwise comparisons among all 14 species in the phylogeny. (27 KB)
The dashed line indicates the average.
- Supplementary Figure 3: Pie charts of genome fractions as identified by RepeatMasker. (58 KB)
(a) Killer whale. (b) Bottlenose dolphin. (c) Manatee. (d) Walrus.
- Supplementary Text and Figures (1,064 KB)
Supplementary Figures 1–3 and Supplementary Tables 1, 2, 4–6, 8 and 14.
- Supplementary Table 3 (62 KB)
Genes identified as evolving under positive selection along the combined marine mammal branch.
- Supplementary Table 7 (48 KB)
Positively selected genes that contain non-identical or 'common' amino acid substitutions at the same residue in all three marine mammal lineages.
- Supplementary Table 9 (44 KB)
Genes identified as evolving under positive selection along the cetacean branch.
- Supplementary Table 10 (79 KB)
Genes identified as evolving under positive selection along the sirenian (manatee) branch.
- Supplementary Table 11 (86 KB)
Genes identified as evolving under positive selection along the pinniped (walrus) branch.
- Supplementary Table 12 (55 KB)
Functional enrichment analysis of positively selected genes along the combined marine mammal branch.
- Supplementary Table 13 (53 KB)
Significant shifts in gene ontology categories along the combined marine mammal branch.