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,...
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ftunivporto:oai:repositorio-aberto.up.pt:10216/109254 2023-06-18T03:40:08+02:00 Evaluating purifying selection in the mitochondrial DNA of various mammalian species Soares, P Abrantes, D Rito, T Thomson, N Radivojac, P Li, B Macaulay, V Samuels, DC Pereira, L Instituto de Investigação e Inovação em Saúde 2013 application/pdf application/msword application/vnd.ms-excel http://hdl.handle.net/10216/109254 https://doi.org/10.1371/journal.pone.0058993 eng eng Public Library of Science info:eu-repo/grantAgreement/FCT/5876-PPCDTI/113832/PT PLoS One, vol. 8(3):e58993 http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058993 1932-6203 http://hdl.handle.net/10216/109254 doi:10.1371/journal.pone.0058993 info:eu-repo/semantics/openAccess Animals Cattle DNA Mitochondrial/genetics Dogs Mammals Mice Phylogeny Sus scrofa Whale Killer info:eu-repo/semantics/article 2013 ftunivporto https://doi.org/10.1371/journal.pone.0058993 2023-06-06T21:58:32Z 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. Article in Journal/Newspaper Canis lupus Orca Orcinus orca Repositório Aberto da Universidade do Porto PLoS ONE 8 3 e58993 |
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Open Polar |
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Repositório Aberto da Universidade do Porto |
op_collection_id |
ftunivporto |
language |
English |
topic |
Animals Cattle DNA Mitochondrial/genetics Dogs Mammals Mice Phylogeny Sus scrofa Whale Killer |
spellingShingle |
Animals Cattle DNA Mitochondrial/genetics Dogs Mammals Mice Phylogeny Sus scrofa Whale Killer Soares, P Abrantes, D Rito, T Thomson, N Radivojac, P Li, B Macaulay, V Samuels, DC Pereira, L Evaluating purifying selection in the mitochondrial DNA of various mammalian species |
topic_facet |
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. |
author2 |
Instituto de Investigação e Inovação em Saúde |
format |
Article in Journal/Newspaper |
author |
Soares, P Abrantes, D Rito, T Thomson, N Radivojac, P Li, B Macaulay, V Samuels, DC Pereira, L |
author_facet |
Soares, P Abrantes, D Rito, T Thomson, N Radivojac, P Li, B Macaulay, V Samuels, DC Pereira, L |
author_sort |
Soares, P |
title |
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_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 |
publisher |
Public Library of Science |
publishDate |
2013 |
url |
http://hdl.handle.net/10216/109254 https://doi.org/10.1371/journal.pone.0058993 |
genre |
Canis lupus Orca Orcinus orca |
genre_facet |
Canis lupus Orca Orcinus orca |
op_relation |
info:eu-repo/grantAgreement/FCT/5876-PPCDTI/113832/PT PLoS One, vol. 8(3):e58993 http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058993 1932-6203 http://hdl.handle.net/10216/109254 doi:10.1371/journal.pone.0058993 |
op_rights |
info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.1371/journal.pone.0058993 |
container_title |
PLoS ONE |
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8 |
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3 |
container_start_page |
e58993 |
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1769004940490964992 |