Genome-Wide Scans for Candidate Genes Involved in the Aquatic Adaptation of Dolphins

Since their divergence from the terrestrial artiodactyls, cetaceans have fully adapted to an aquatic lifestyle, which represents one of the most dramatic transformations in mammalian evolutionary history. Numerous morphological and physiological characters of cetaceans have been acquired in response...

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Main Authors:	Sun, Yan-Bo, Zhou, Wei-Ping, Liu, He-Qun, Irwin, David M., Shen, Yong-Yi, Zhang, Ya-Ping
Format:	Online
Language:	English
Published:	Oxford University Press 2013
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3595024/

id	pubmed-3595024
recordtype	oai_dc
spelling	pubmed-35950242013-03-12 Genome-Wide Scans for Candidate Genes Involved in the Aquatic Adaptation of Dolphins Sun, Yan-Bo Zhou, Wei-Ping Liu, He-Qun Irwin, David M. Shen, Yong-Yi Zhang, Ya-Ping Research Article Since their divergence from the terrestrial artiodactyls, cetaceans have fully adapted to an aquatic lifestyle, which represents one of the most dramatic transformations in mammalian evolutionary history. Numerous morphological and physiological characters of cetaceans have been acquired in response to this drastic habitat transition, such as thickened blubber, echolocation, and ability to hold their breath for a long period of time. However, knowledge about the molecular basis underlying these adaptations is still limited. The sequence of the genome of Tursiops truncates provides an opportunity for a comparative genomic analyses to examine the molecular adaptation of this species. Here, we constructed 11,838 high-quality orthologous gene alignments culled from the dolphin and four other terrestrial mammalian genomes and screened for positive selection occurring in the dolphin lineage. In total, 368 (3.1%) of the genes were identified as having undergone positive selection by the branch-site model. Functional characterization of these genes showed that they are significantly enriched in the categories of lipid transport and localization, ATPase activity, sense perception of sound, and muscle contraction, areas that are potentially related to cetacean adaptations. In contrast, we did not find a similar pattern in the cow, a closely related species. We resequenced some of the positively selected sites (PSSs), within the positively selected genes, and showed that most of our identified PSSs (50/52) could be replicated. The results from this study should have important implications for our understanding of cetacean evolution and their adaptations to the aquatic environment. Oxford University Press 2013 2012-12-16 /pmc/articles/PMC3595024/ /pubmed/23246795 http://dx.doi.org/10.1093/gbe/evs123 Text en © The Author(s) 2012. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by-nc/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Sun, Yan-Bo Zhou, Wei-Ping Liu, He-Qun Irwin, David M. Shen, Yong-Yi Zhang, Ya-Ping
spellingShingle	Sun, Yan-Bo Zhou, Wei-Ping Liu, He-Qun Irwin, David M. Shen, Yong-Yi Zhang, Ya-Ping Genome-Wide Scans for Candidate Genes Involved in the Aquatic Adaptation of Dolphins
author_facet	Sun, Yan-Bo Zhou, Wei-Ping Liu, He-Qun Irwin, David M. Shen, Yong-Yi Zhang, Ya-Ping
author_sort	Sun, Yan-Bo
title	Genome-Wide Scans for Candidate Genes Involved in the Aquatic Adaptation of Dolphins
title_short	Genome-Wide Scans for Candidate Genes Involved in the Aquatic Adaptation of Dolphins
title_full	Genome-Wide Scans for Candidate Genes Involved in the Aquatic Adaptation of Dolphins
title_fullStr	Genome-Wide Scans for Candidate Genes Involved in the Aquatic Adaptation of Dolphins
title_full_unstemmed	Genome-Wide Scans for Candidate Genes Involved in the Aquatic Adaptation of Dolphins
title_sort	genome-wide scans for candidate genes involved in the aquatic adaptation of dolphins
description	Since their divergence from the terrestrial artiodactyls, cetaceans have fully adapted to an aquatic lifestyle, which represents one of the most dramatic transformations in mammalian evolutionary history. Numerous morphological and physiological characters of cetaceans have been acquired in response to this drastic habitat transition, such as thickened blubber, echolocation, and ability to hold their breath for a long period of time. However, knowledge about the molecular basis underlying these adaptations is still limited. The sequence of the genome of Tursiops truncates provides an opportunity for a comparative genomic analyses to examine the molecular adaptation of this species. Here, we constructed 11,838 high-quality orthologous gene alignments culled from the dolphin and four other terrestrial mammalian genomes and screened for positive selection occurring in the dolphin lineage. In total, 368 (3.1%) of the genes were identified as having undergone positive selection by the branch-site model. Functional characterization of these genes showed that they are significantly enriched in the categories of lipid transport and localization, ATPase activity, sense perception of sound, and muscle contraction, areas that are potentially related to cetacean adaptations. In contrast, we did not find a similar pattern in the cow, a closely related species. We resequenced some of the positively selected sites (PSSs), within the positively selected genes, and showed that most of our identified PSSs (50/52) could be replicated. The results from this study should have important implications for our understanding of cetacean evolution and their adaptations to the aquatic environment.
publisher	Oxford University Press
publishDate	2013
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3595024/
_version_	1611961449823862784

Genome-Wide Scans for Candidate Genes Involved in the Aquatic Adaptation of Dolphins

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