How to Make a Dolphin: Molecular Signature of Positive Selection in Cetacean Genome

Abstract

Cetaceans are unique in being the only mammals completely adapted to an aquatic environment. This adaptation has required complex changes and sometimes a complete restructuring of physiology, behavior and morphology. Identifying genes that have been subjected to selection pressure during cetacean evolution would greatly enhance our knowledge of the ways in which genetic variation in this mammalian order has been shaped by natural selection. Here, we performed a genome-wide scan for positive selection in the dolphin lineage. We employed models of codon substitution that account for variation of selective pressure over branches on the tree and across sites in a sequence. We analyzed 7,859 nuclear-coding ortholog genes and using a series of likelihood ratio tests (LRTs), we identified 376 genes (4.8%) with molecular signatures of positive selection in the dolphin lineage. We used the cow as the sister group and compared estimates of selection in the cetacean genome to this using the same methods. This allowed us to define which genes have been exclusively under positive selection in the dolphin lineage. The enrichment analysis found that the identified positively selected genes are significantly over-represented for three exclusive functional categories only in the dolphin lineage: segment specification, mesoderm development and system development. Of particular interest for cetacean adaptation to an aquatic life are the following GeneOntology targets under positive selection: genes related to kidney, heart, lung, eye, ear and nervous system development.

Comparative transcriptomics of Entelegyne spiders (Araneae, Entelegynae), with emphasis on molecular evolution of orphan genes

“…In comparison with several recent genome-wide scans for positive selection (e.g., [103–105]), our results suggest that a much smaller proportion of entelegyne spider genes have evolved under positive selection. The only other comparable study of spider genomics for a large number of loci found evidence of positive selection in a similarly low proportion of sequences ([34], but also see [35,36]).…”

“…Finally, another important factor likely driving down the incidence of observed adaptive evolution may have been our choice to examine only single-copy ortholog groups. Although other similar studies have found higher rates of positive selection among single-copy orthologs ([103–105]), it may be the case that these gene families are subject to lower rates of positive selection than multi-copy gene families. As more large-scale scans for positive selection are performed on spider genomic data, it will be important to see whether or not the pattern of low rates of positive selection in spider lineages seen here and in previous work is maintained.…”

Two isoforms of aquaporin 2 responsive to hypertonic stress in bottlenose dolphin

“…Several studies have recently reported that AQP2 was positively selected for during the secondary adaptation in cetacean species, suggesting that the evolution of the gene was an important event in the development of enhanced capacity for water reabsorption in the renal tubules (Nery et al, 2013;Xu et al, 2013;Yim et al, 2014). Extensive information can be obtained from genome-scale analyses, providing insight into the nature and extent of selective pressures that contributed to the evolution of a particular group.…”

“…For these characteristics of AQP2 and in view of reports that AQP2 was positively selected during the secondary adaptation of cetacean species to the marine environment (Nery et al, 2013;Xu et al, 2013;Yim et al, 2014), for this study it was hypothesized that AQP2 could play some roles in cellular osmoregulation in cetaceans, who are living in a hypertonic environment in comparison to their body fluids. It was previously reported that AQP2 is distributed in the principal cells of the kidneys of the bottlenose dolphin and Baird's beaked whale, similar to terrestrial mammals (Suzuki et al, 2008).…”

High‐quality whole‐genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena)

“…Among the nonmodel organisms, cetaceans are a valuable group of animals to invest in high‐quality genomic resources (Cammen et al., ): Cetaceans display a suite of interesting adaptations associated with their fully aquatic lifestyle (Geisler, McGowen, Yang, & Gatesy, ; Kishida, Thewissen, Hayakawa, Imai, & Agata, ; Nery, Gonzalez, & Opazo, ). Across their aquatic habitats, specific adaptations to variable temperature, salinity and food availability are also well documented (e.g., Bolaños‐Jiménez et al., ; Fontaine et al., ; Gatesy et al., ; Geisler et al., ; Zhou et al., ).…”