We used our gene loss detection approach to investigate which of the genes that are lost in the cetacean stem lineage are also convergently lost in other aquatic (manatee) or semi-aquatic (pinnipeds) mammalian lineages. Because pinnipeds were only represented by the Weddell seal (family Phocidae) and the walrus, we downloaded the genome of the Antarctic fur seal (family Otariidae) (https://datadryad.org/resource/doi:10.5061/dryad.8kn8c.2), aligned it to the hg38 assembly as described above, and applied our gene loss detection pipeline. All genes convergently lost between cetaceans and manatees and/or pinnipeds are indicated in table S2.

We further screened for genes that are convergently lost between any aquatic or semi-aquatic mammalian lineages and compared the prevalence of these convergent gene losses to convergent losses between their terrestrial sister species. To this end, we first extracted from our dataset those genes that are classified as lost in one representative of the three (semi-) aquatic lineages but that are classified as intact in their respective terrestrial sister species, focusing on genes not belonging to keratin-associated and olfactory receptor gene families. Specifically, we extracted genes lost in the killer whale but not in the cow, genes lost in the Pacific walrus but not in the polar bear, and genes lost in the manatee but not in the elephant. Then, we asked how many of these genes are convergently lost in at least two (semi-) aquatic mammals (table S5). We compared this number to the number of convergent losses detected when swapping the three (semi-) aquatic and three terrestrial mammals. These data are visualized as Venn diagrams in fig. S27.

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