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,...
Published in: | PLoS ONE |
---|---|
Main Authors: | , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Public Library of Science
2013
|
Subjects: | |
Online Access: | http://eprints.gla.ac.uk/106330/ http://eprints.gla.ac.uk/106330/1/106330.pdf |
id |
ftuglasgow:oai:eprints.gla.ac.uk:106330 |
---|---|
record_format |
openpolar |
spelling |
ftuglasgow:oai:eprints.gla.ac.uk:106330 2023-05-15T15:50:25+02:00 Evaluating purifying selection in the mitochondrial DNA of various mammalian species Soares, Pedro Abrantes, Diogo Rito, Teresa Thomson, Noel Radivojac, Predrag Li, Biao Macaulay, Vincent Samuels, David C. Pereira, Luísa 2013-03 text http://eprints.gla.ac.uk/106330/ http://eprints.gla.ac.uk/106330/1/106330.pdf en eng Public Library of Science http://eprints.gla.ac.uk/106330/1/106330.pdf Soares, P., Abrantes, D., Rito, T., Thomson, N., Radivojac, P., Li, B., Macaulay, V. <http://eprints.gla.ac.uk/view/author/12653.html> , Samuels, D. C. and Pereira, L. (2013) Evaluating purifying selection in the mitochondrial DNA of various mammalian species. PLoS ONE <http://eprints.gla.ac.uk/view/journal_volume/PLoS_ONE.html>, 8(3), e58993. (doi:10.1371/journal.pone.0058993 <http://dx.doi.org/10.1371/journal.pone.0058993>) (PMID:23533597) (PMCID:PMC3606437) cc_by CC-BY Articles PeerReviewed 2013 ftuglasgow https://doi.org/10.1371/journal.pone.0058993 2020-01-10T00:54:29Z 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 University of Glasgow: Enlighten - Publications PLoS ONE 8 3 e58993 |
institution |
Open Polar |
collection |
University of Glasgow: Enlighten - Publications |
op_collection_id |
ftuglasgow |
language |
English |
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. |
format |
Article in Journal/Newspaper |
author |
Soares, Pedro Abrantes, Diogo Rito, Teresa Thomson, Noel Radivojac, Predrag Li, Biao Macaulay, Vincent Samuels, David C. Pereira, Luísa |
spellingShingle |
Soares, Pedro Abrantes, Diogo Rito, Teresa Thomson, Noel Radivojac, Predrag Li, Biao Macaulay, Vincent Samuels, David C. Pereira, Luísa Evaluating purifying selection in the mitochondrial DNA of various mammalian species |
author_facet |
Soares, Pedro Abrantes, Diogo Rito, Teresa Thomson, Noel Radivojac, Predrag Li, Biao Macaulay, Vincent Samuels, David C. Pereira, Luísa |
author_sort |
Soares, Pedro |
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://eprints.gla.ac.uk/106330/ http://eprints.gla.ac.uk/106330/1/106330.pdf |
genre |
Canis lupus Orca Orcinus orca |
genre_facet |
Canis lupus Orca Orcinus orca |
op_relation |
http://eprints.gla.ac.uk/106330/1/106330.pdf Soares, P., Abrantes, D., Rito, T., Thomson, N., Radivojac, P., Li, B., Macaulay, V. <http://eprints.gla.ac.uk/view/author/12653.html> , Samuels, D. C. and Pereira, L. (2013) Evaluating purifying selection in the mitochondrial DNA of various mammalian species. PLoS ONE <http://eprints.gla.ac.uk/view/journal_volume/PLoS_ONE.html>, 8(3), e58993. (doi:10.1371/journal.pone.0058993 <http://dx.doi.org/10.1371/journal.pone.0058993>) (PMID:23533597) (PMCID:PMC3606437) |
op_rights |
cc_by |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1371/journal.pone.0058993 |
container_title |
PLoS ONE |
container_volume |
8 |
container_issue |
3 |
container_start_page |
e58993 |
_version_ |
1766385359717924864 |