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. 2015 Sep 30;2(9):150156.
doi: 10.1098/rsos.150156. eCollection 2015 Sep.

A Phylogenomic Analysis of the Role and Timing of Molecular Adaptation in the Aquatic Transition of Cetartiodactyl Mammals

Free PMC article

A Phylogenomic Analysis of the Role and Timing of Molecular Adaptation in the Aquatic Transition of Cetartiodactyl Mammals

Georgia Tsagkogeorga et al. R Soc Open Sci. .
Free PMC article


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.

Keywords: Cetartiodactyla; RNA-sequencing; mammals; transcriptome.


Figure 1.
Figure 1.
Evolutionary relationships among laurasiatherian mammals as used in molecular evolution analyses. The four clades tested for divergent selection are shown in colour and numbered in uppercase: (I) Whippomorpha (Hippopotamidae + Cetacea); (II) Cetacea; (III) Mysticeti and (IV) Odontoceti. Branches tested for positive selection are numbered in lowercase: (i) Whippomorpha (Hippopotamidae + Cetacea); (ii) Cetacea; (iii) Mysticeti; (iv) Odontoceti and (v) hippo.
Figure 2.
Figure 2.
Protein–protein interaction networks for 105 protein-coding gene products tested in both cetaceans and the hippo that were found to be under positive selection in cetaceans. Inset: protein–protein interaction networks for 20 protein-coding genes found to be under positive selection in the hippo. Nodes are labelled with the standard protein names, and the thickness of each connection is scaled to represent the strength of support, with thicker lines representing higher support. (a) Highlights proteins involved in the circulatory system (red) and (b) highlights proteins involved in muscle (yellow) the nervous system (blue) or both (yellow with blue).

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    1. Gatesy J, Geisler JH, Chang J, Buell C, Berta A, Meredith RW, Springer MS, McGowen MR. 2013. A phylogenetic blueprint for a modern whale. Mol. Phyl. Evol. 66, 479–506. (doi:10.1016/j.ympev.2012.10.012) - DOI - PubMed
    1. Caulin AF, Maley CC. 2011. Peto's paradox: evolution's prescription for cancer prevention. Trends Ecol. Evol. 26, 175–182. (doi:10.1016/j.tree.2011.01.002) - DOI - PMC - PubMed
    1. Venn-Watson SK, Ridgway SH. 2007. Big brains and blood glucose: common ground for diabetes mellitus in humans and healthy dolphins. Comp. Med. 57, 390–395. - PubMed
    1. McGowen MR, Spaulding M, Gatesy J. 2009. Divergence date estimation and a comprehensive molecular tree of extant cetaceans. Mol. Phyl. Evol. 53, 891–906. (doi:10.1016/J.Ympev.2009.08.018) - DOI - PubMed
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