Evaluating purifying selection in the mitochondrial DNA of various mammalian species.
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,...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2013-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3606437?pdf=render |
| _version_ | 1818034402822717440 |
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| author | Pedro Soares Diogo Abrantes Teresa Rito Noel Thomson Predrag Radivojac Biao Li Vincent Macaulay David C Samuels Luísa Pereira |
| author_facet | Pedro Soares Diogo Abrantes Teresa Rito Noel Thomson Predrag Radivojac Biao Li Vincent Macaulay David C Samuels Luísa Pereira |
| author_sort | Pedro Soares |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-10T06:38:36Z |
| format | Article |
| id | doaj.art-3270374122c04dd5868c208e1050d8f3 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-10T06:38:36Z |
| publishDate | 2013-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-3270374122c04dd5868c208e1050d8f32022-12-22T01:58:51ZengPublic Library of Science (PLoS)PLoS ONE1932-62032013-01-0183e5899310.1371/journal.pone.0058993Evaluating purifying selection in the mitochondrial DNA of various mammalian species.Pedro SoaresDiogo AbrantesTeresa RitoNoel ThomsonPredrag RadivojacBiao LiVincent MacaulayDavid C SamuelsLuísa PereiraMitochondrial 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.http://europepmc.org/articles/PMC3606437?pdf=render |
| spellingShingle | Pedro Soares Diogo Abrantes Teresa Rito Noel Thomson Predrag Radivojac Biao Li Vincent Macaulay David C Samuels Luísa Pereira Evaluating purifying selection in the mitochondrial DNA of various mammalian species. PLoS ONE |
| title | 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_short | Evaluating purifying selection in the mitochondrial DNA of various mammalian species. |
| title_sort | evaluating purifying selection in the mitochondrial dna of various mammalian species |
| url | http://europepmc.org/articles/PMC3606437?pdf=render |
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