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

Nery MF, González DJ, Opazo JC - PLoS ONE (2013)

Bottom Line: 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 used the cow as the sister group and compared estimates of selection in the cetacean genome to this using the same methods.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.

View Article: PubMed Central - PubMed

Affiliation: Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile ; Programa de Doctorado en Ciencias mención Ecología y Evolución, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.

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.

No MeSH data available.


GO distribution in the three gene ontology domains (biological processes, molecular function and cellular component) among positively selected genes.Only the first 15 categories from each domain are shown. PSG, positively selected genes.
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pone-0065491-g003: GO distribution in the three gene ontology domains (biological processes, molecular function and cellular component) among positively selected genes.Only the first 15 categories from each domain are shown. PSG, positively selected genes.

Mentions: To understand the biological significance of the PSGs we used the program CateGOrizer to classify them according to the scheme established by the Gene Ontology project (Fig. 3). This analysis revealed the most GO hits in ‘biological process’ (Fig. 3) with significantly fewer hits in ‘molecular function’ and ‘cellular component’ (Fig. 3). Within the ‘biological process’ category, most gene classes were distributed similarly between dolphin and cow, with the exception of development and metabolism, in which the dolphin lineage had considerable more GO hits in comparison to the cow (Fig. 3).


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

Nery MF, González DJ, Opazo JC - PLoS ONE (2013)

GO distribution in the three gene ontology domains (biological processes, molecular function and cellular component) among positively selected genes.Only the first 15 categories from each domain are shown. PSG, positively selected genes.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3686761&req=5

pone-0065491-g003: GO distribution in the three gene ontology domains (biological processes, molecular function and cellular component) among positively selected genes.Only the first 15 categories from each domain are shown. PSG, positively selected genes.
Mentions: To understand the biological significance of the PSGs we used the program CateGOrizer to classify them according to the scheme established by the Gene Ontology project (Fig. 3). This analysis revealed the most GO hits in ‘biological process’ (Fig. 3) with significantly fewer hits in ‘molecular function’ and ‘cellular component’ (Fig. 3). Within the ‘biological process’ category, most gene classes were distributed similarly between dolphin and cow, with the exception of development and metabolism, in which the dolphin lineage had considerable more GO hits in comparison to the cow (Fig. 3).

Bottom Line: 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 used the cow as the sister group and compared estimates of selection in the cetacean genome to this using the same methods.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.

View Article: PubMed Central - PubMed

Affiliation: Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile ; Programa de Doctorado en Ciencias mención Ecología y Evolución, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.

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.

No MeSH data available.