title: A phylogenomic analysis of the role and timing of molecular adaptation in the aquatic transition of cetartiodactyl mammals.
abstract: Recent studies have reported multiple cases of molecular adaptation in cetaceans related to their aquatic abilities. However, none of these has included the hippopotamus, precluding an understanding of whether molecular adaptations in cetaceans occurred before or after they split from their semi-aquatic sister taxa. Here, we obtained new transcriptomes from the hippopotamus and humpback whale, and analysed these together with available data from eight other cetaceans. We identified more than 11 000 orthologous genes and compiled a genome-wide dataset of 6845 coding DNA sequences among 23 mammals, to our knowledge the largest phylogenomic dataset to date for cetaceans. We found positive selection in nine genes on the branch leading to the common ancestor of hippopotamus and whales, and 461 genes in cetaceans compared to 64 in hippopotamus. Functional annotation revealed adaptations in diverse processes, including lipid metabolism, hypoxia, muscle and brain function. By combining these findings with data on protein-protein interactions, we found evidence suggesting clustering among gene products relating to nervous and muscular systems in cetaceans. We found little support for shared ancestral adaptations in the two taxa; most molecular adaptations in extant cetaceans occurred after their split with hippopotamids.
authors.affiliation: School of Biological and Chemical Sciences, Queen Mary University of London , Mile End Road, London E1 4NS, UK.
authors.forename: Georgia
authors.initials: G
authors.lastname: Tsagkogeorga
authors.affiliation: School of Biological and Chemical Sciences, Queen Mary University of London , Mile End Road, London E1 4NS, UK.
authors.forename: Michael R
authors.initials: MR
authors.lastname: McGowen
authors.affiliation: School of Biological and Chemical Sciences, Queen Mary University of London , Mile End Road, London E1 4NS, UK.
authors.forename: Kalina T J
authors.initials: KT
authors.lastname: Davies
authors.affiliation: Australian Antarctic Division, Channel Highway , Kingston, Tasmania 7050, Australia.
authors.forename: Simon
authors.initials: S
authors.lastname: Jarman
authors.affiliation: Australian Antarctic Division, Channel Highway , Kingston, Tasmania 7050, Australia.
authors.forename: Andrea
authors.initials: A
authors.lastname: Polanowski
authors.affiliation: Center for Zoo and Wild Animal Health, Copenhagen Zoo , Roskildevej 38, Frederiksberg 2000, Denmark.
authors.forename: Mads F
authors.initials: MF
authors.lastname: Bertelsen
authors.affiliation: School of Biological and Chemical Sciences, Queen Mary University of London , Mile End Road, London E1 4NS, UK.
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Rossiter
keywords: Cetartiodactyla; RNA-sequencing; mammals; transcriptome