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Increased rate of hair keratin gene loss in the cetacean lineage.

Nery MF, Arroyo JI, Opazo JC - BMC Genomics (2014)

Bottom Line: To determine whether different repertoire of keratin genes among mammals can potentially explain the phenotypic hair features of different lineages, we characterized the type I and II clusters of alpha keratins from eight mammalian species, including the hairless dolphin and minke whale representing the order Cetacea.We combined the available genomic information with phylogenetic analysis to conduct a comprehensive analysis of the evolutionary patterns of keratin gene clusters.Our study provides support for the idea that pseudogenes are not simply 'genomic fossils' but instead have adaptive roles during the evolutionary process.

View Article: PubMed Central - PubMed

Affiliation: Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile. mariananery@gmail.com.

ABSTRACT

Background: Hair represents an evolutionary innovation that appeared early on mammalian evolutionary history, and presumably contributed significantly to the rapid radiation of the group. An interesting event in hair evolution has been its secondary loss in some mammalian groups, such as cetaceans, whose hairless phenotype appears to be an adaptive response to better meet the environmental conditions. To determine whether different repertoire of keratin genes among mammals can potentially explain the phenotypic hair features of different lineages, we characterized the type I and II clusters of alpha keratins from eight mammalian species, including the hairless dolphin and minke whale representing the order Cetacea.

Results: We combined the available genomic information with phylogenetic analysis to conduct a comprehensive analysis of the evolutionary patterns of keratin gene clusters. We found that both type I and II gene clusters are fairly conserved among the terrestrial mammals included in this study, with lineage specific gene duplication and gene loss. Nevertheless, there is also evidence for an increased rate of pseudogenization in the cetacean lineage when compared to their terrestrial relatives, especially among the hair type keratins.

Conclusions: Here we present a comprehensive characterization of alpha-keratin genes among mammals and elucidate the mechanisms involved in the evolution of this gene family. We identified lineage-specific gene duplications and gene loss among the Laurasiatherian and Euarchontoglires species included in the study. Interestingly, cetaceans present an increased loss of hair-type keratin genes when compared to other terrestrial mammals. As suggested by the 'less-is-more' hypothesis, we do not rule out the possibility that the gene loss of hair-type keratin genes in these species might be associated to the hairless phenotype and could have been adaptive in response to new selective pressures imposed by the colonization of a new habitat. Our study provides support for the idea that pseudogenes are not simply 'genomic fossils' but instead have adaptive roles during the evolutionary process.

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Phylogenetic tree of type II keratins. Maximum likelihood phylogram describing phylogenetic relationships among the type II keratin genes. Numbers above the nodes correspond to maximum likelihood bootstrap support values, and numbers below the nodes correspond to Bayesian posterior probabilities. Branches in blue indicated hair-type keratins.
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Fig3: Phylogenetic tree of type II keratins. Maximum likelihood phylogram describing phylogenetic relationships among the type II keratin genes. Numbers above the nodes correspond to maximum likelihood bootstrap support values, and numbers below the nodes correspond to Bayesian posterior probabilities. Branches in blue indicated hair-type keratins.

Mentions: Maximum likelihood and Bayesian phylogenies arranged type I and type II genes into well-supported clades (FiguresĀ 2 and 3), being possible to define the orthologous relationships. Given the small length of some pseudogenes (i.e. few exons identified), and their high evolutionary rate that may obscure their phylogenetic history, the identity of some pseudogenes were determined according to their location in the genome rather by their position in the phylogenetic tree.Figure 2


Increased rate of hair keratin gene loss in the cetacean lineage.

Nery MF, Arroyo JI, Opazo JC - BMC Genomics (2014)

Phylogenetic tree of type II keratins. Maximum likelihood phylogram describing phylogenetic relationships among the type II keratin genes. Numbers above the nodes correspond to maximum likelihood bootstrap support values, and numbers below the nodes correspond to Bayesian posterior probabilities. Branches in blue indicated hair-type keratins.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4195889&req=5

Fig3: Phylogenetic tree of type II keratins. Maximum likelihood phylogram describing phylogenetic relationships among the type II keratin genes. Numbers above the nodes correspond to maximum likelihood bootstrap support values, and numbers below the nodes correspond to Bayesian posterior probabilities. Branches in blue indicated hair-type keratins.
Mentions: Maximum likelihood and Bayesian phylogenies arranged type I and type II genes into well-supported clades (FiguresĀ 2 and 3), being possible to define the orthologous relationships. Given the small length of some pseudogenes (i.e. few exons identified), and their high evolutionary rate that may obscure their phylogenetic history, the identity of some pseudogenes were determined according to their location in the genome rather by their position in the phylogenetic tree.Figure 2

Bottom Line: To determine whether different repertoire of keratin genes among mammals can potentially explain the phenotypic hair features of different lineages, we characterized the type I and II clusters of alpha keratins from eight mammalian species, including the hairless dolphin and minke whale representing the order Cetacea.We combined the available genomic information with phylogenetic analysis to conduct a comprehensive analysis of the evolutionary patterns of keratin gene clusters.Our study provides support for the idea that pseudogenes are not simply 'genomic fossils' but instead have adaptive roles during the evolutionary process.

View Article: PubMed Central - PubMed

Affiliation: Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile. mariananery@gmail.com.

ABSTRACT

Background: Hair represents an evolutionary innovation that appeared early on mammalian evolutionary history, and presumably contributed significantly to the rapid radiation of the group. An interesting event in hair evolution has been its secondary loss in some mammalian groups, such as cetaceans, whose hairless phenotype appears to be an adaptive response to better meet the environmental conditions. To determine whether different repertoire of keratin genes among mammals can potentially explain the phenotypic hair features of different lineages, we characterized the type I and II clusters of alpha keratins from eight mammalian species, including the hairless dolphin and minke whale representing the order Cetacea.

Results: We combined the available genomic information with phylogenetic analysis to conduct a comprehensive analysis of the evolutionary patterns of keratin gene clusters. We found that both type I and II gene clusters are fairly conserved among the terrestrial mammals included in this study, with lineage specific gene duplication and gene loss. Nevertheless, there is also evidence for an increased rate of pseudogenization in the cetacean lineage when compared to their terrestrial relatives, especially among the hair type keratins.

Conclusions: Here we present a comprehensive characterization of alpha-keratin genes among mammals and elucidate the mechanisms involved in the evolution of this gene family. We identified lineage-specific gene duplications and gene loss among the Laurasiatherian and Euarchontoglires species included in the study. Interestingly, cetaceans present an increased loss of hair-type keratin genes when compared to other terrestrial mammals. As suggested by the 'less-is-more' hypothesis, we do not rule out the possibility that the gene loss of hair-type keratin genes in these species might be associated to the hairless phenotype and could have been adaptive in response to new selective pressures imposed by the colonization of a new habitat. Our study provides support for the idea that pseudogenes are not simply 'genomic fossils' but instead have adaptive roles during the evolutionary process.

Show MeSH
Related in: MedlinePlus