Evaluating purifying selection in the mitochondrial DNA of various mammalian species

Detalhes bibliográficos
Autor(a) principal: Soares, P
Data de Publicação: 2013
Outros Autores: Abrantes, D, Rito, T, Thomson, N, Radivojac, P, Li, B, Macaulay, V, Samuels, DC, Pereira, L
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10216/109254
Resumo: Mitochondrial DNA (mtDNA), the circular DNA molecule inside the mitochondria of all eukaryotic cells, has been shown to be under the effect of purifying selection in several species. Traditional testing of purifying selection has been based simply on ratios of nonsynonymous to synonymous mutations, without considering the relative age of each mutation, which can be determined by phylogenetic analysis of this non-recombining molecule. The incorporation of a mutation time-ordering from phylogeny and of predicted pathogenicity scores for nonsynonymous mutations allow a quantitative evaluation of the effects of purifying selection in human mtDNA. Here, by using this additional information, we show that purifying selection undoubtedly acts upon the mtDNA of other mammalian species/genera, namely Bos sp., Canis lupus, Mus musculus, Orcinus orca, Pan sp. and Sus scrofa. The effects of purifying selection were comparable in all species, leading to a significant major proportion of nonsynonymous variants with higher pathogenicity scores in the younger branches of the tree. We also derive recalibrated mutation rates for age estimates of ancestors of these various species and proposed a correction curve in order to take into account the effects of selection. Understanding this selection is fundamental to evolutionary studies and to the identification of deleterious mutations.
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spelling Evaluating purifying selection in the mitochondrial DNA of various mammalian speciesAnimalsCattleDNA Mitochondrial/geneticsDogsMammalsMicePhylogenySus scrofaWhale KillerMitochondrial DNA (mtDNA), the circular DNA molecule inside the mitochondria of all eukaryotic cells, has been shown to be under the effect of purifying selection in several species. Traditional testing of purifying selection has been based simply on ratios of nonsynonymous to synonymous mutations, without considering the relative age of each mutation, which can be determined by phylogenetic analysis of this non-recombining molecule. The incorporation of a mutation time-ordering from phylogeny and of predicted pathogenicity scores for nonsynonymous mutations allow a quantitative evaluation of the effects of purifying selection in human mtDNA. Here, by using this additional information, we show that purifying selection undoubtedly acts upon the mtDNA of other mammalian species/genera, namely Bos sp., Canis lupus, Mus musculus, Orcinus orca, Pan sp. and Sus scrofa. The effects of purifying selection were comparable in all species, leading to a significant major proportion of nonsynonymous variants with higher pathogenicity scores in the younger branches of the tree. We also derive recalibrated mutation rates for age estimates of ancestors of these various species and proposed a correction curve in order to take into account the effects of selection. Understanding this selection is fundamental to evolutionary studies and to the identification of deleterious mutations.Public Library of Science20132013-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfapplication/mswordapplication/mswordapplication/vnd.ms-excelapplication/mswordapplication/mswordapplication/mswordapplication/mswordapplication/mswordhttp://hdl.handle.net/10216/109254eng1932-620310.1371/journal.pone.0058993Soares, PAbrantes, DRito, TThomson, NRadivojac, PLi, BMacaulay, VSamuels, DCPereira, Linfo:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-11-29T15:01:49Zoai:repositorio-aberto.up.pt:10216/109254Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T00:14:03.185705Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv Evaluating purifying selection in the mitochondrial DNA of various mammalian species
title Evaluating purifying selection in the mitochondrial DNA of various mammalian species
spellingShingle Evaluating purifying selection in the mitochondrial DNA of various mammalian species
Soares, P
Animals
Cattle
DNA Mitochondrial/genetics
Dogs
Mammals
Mice
Phylogeny
Sus scrofa
Whale Killer
title_short Evaluating purifying selection in the mitochondrial DNA of various mammalian species
title_full Evaluating purifying selection in the mitochondrial DNA of various mammalian species
title_fullStr Evaluating purifying selection in the mitochondrial DNA of various mammalian species
title_full_unstemmed Evaluating purifying selection in the mitochondrial DNA of various mammalian species
title_sort Evaluating purifying selection in the mitochondrial DNA of various mammalian species
author Soares, P
author_facet Soares, P
Abrantes, D
Rito, T
Thomson, N
Radivojac, P
Li, B
Macaulay, V
Samuels, DC
Pereira, L
author_role author
author2 Abrantes, D
Rito, T
Thomson, N
Radivojac, P
Li, B
Macaulay, V
Samuels, DC
Pereira, L
author2_role author
author
author
author
author
author
author
author
dc.contributor.author.fl_str_mv Soares, P
Abrantes, D
Rito, T
Thomson, N
Radivojac, P
Li, B
Macaulay, V
Samuels, DC
Pereira, L
dc.subject.por.fl_str_mv Animals
Cattle
DNA Mitochondrial/genetics
Dogs
Mammals
Mice
Phylogeny
Sus scrofa
Whale Killer
topic Animals
Cattle
DNA Mitochondrial/genetics
Dogs
Mammals
Mice
Phylogeny
Sus scrofa
Whale Killer
description Mitochondrial DNA (mtDNA), the circular DNA molecule inside the mitochondria of all eukaryotic cells, has been shown to be under the effect of purifying selection in several species. Traditional testing of purifying selection has been based simply on ratios of nonsynonymous to synonymous mutations, without considering the relative age of each mutation, which can be determined by phylogenetic analysis of this non-recombining molecule. The incorporation of a mutation time-ordering from phylogeny and of predicted pathogenicity scores for nonsynonymous mutations allow a quantitative evaluation of the effects of purifying selection in human mtDNA. Here, by using this additional information, we show that purifying selection undoubtedly acts upon the mtDNA of other mammalian species/genera, namely Bos sp., Canis lupus, Mus musculus, Orcinus orca, Pan sp. and Sus scrofa. The effects of purifying selection were comparable in all species, leading to a significant major proportion of nonsynonymous variants with higher pathogenicity scores in the younger branches of the tree. We also derive recalibrated mutation rates for age estimates of ancestors of these various species and proposed a correction curve in order to take into account the effects of selection. Understanding this selection is fundamental to evolutionary studies and to the identification of deleterious mutations.
publishDate 2013
dc.date.none.fl_str_mv 2013
2013-01-01T00:00:00Z
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dc.identifier.uri.fl_str_mv http://hdl.handle.net/10216/109254
url http://hdl.handle.net/10216/109254
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dc.relation.none.fl_str_mv 1932-6203
10.1371/journal.pone.0058993
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application/msword
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application/msword
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dc.publisher.none.fl_str_mv Public Library of Science
publisher.none.fl_str_mv Public Library of Science
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
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