Positive selection over the mitochondrial genome and its role in the diversification of gentoo penguins in response to adaptation in isolation
International audience Although mitochondrial DNA has been widely used in phylogeography, evidence has emerged that factors such as climate, food availability, and environmental pressures that produce high levels of stress can exert a strong influence on mitochondrial genomes, to the point of promot...
Main Authors: | , , , , , , , , , , , , |
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Other Authors: | , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
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HAL CCSD
2022
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Online Access: | https://hal.archives-ouvertes.fr/hal-03618085 https://hal.archives-ouvertes.fr/hal-03618085/document https://hal.archives-ouvertes.fr/hal-03618085/file/s41598-022-07562-0.pdf |
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ftunivlyon1:oai:HAL:hal-03618085v1 |
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HAL Lyon 1 (University Claude Bernard Lyon 1) |
op_collection_id |
ftunivlyon1 |
language |
English |
topic |
[SDV]Life Sciences [q-bio] |
spellingShingle |
[SDV]Life Sciences [q-bio] Noll, D. Leon, F. Brandt, D. Pistorius, P. Le Bohec, Céline Bonadonna, F. Trathan P., N. Barbosa, A. Rey A., R. Dantas G. P., M. Bowie R. C., K. Poulin, E. Vianna J., A. Positive selection over the mitochondrial genome and its role in the diversification of gentoo penguins in response to adaptation in isolation |
topic_facet |
[SDV]Life Sciences [q-bio] |
description |
International audience Although mitochondrial DNA has been widely used in phylogeography, evidence has emerged that factors such as climate, food availability, and environmental pressures that produce high levels of stress can exert a strong influence on mitochondrial genomes, to the point of promoting the persistence of certain genotypes in order to compensate for the metabolic requirements of the local environment. As recently discovered, the gentoo penguins (Pygoscelis papua) comprise four highly divergent lineages across their distribution spanning the Antarctic and sub-Antarctic regions. Gentoo penguins therefore represent a suitable animal model to study adaptive processes across divergent environments. Based on 62 mitogenomes that we obtained from nine locations spanning all four gentoo penguin lineages, we demonstrated lineage-specific nucleotide substitutions for various genes, but only lineage-specific amino acid replacements for the ND1 and ND5 protein-coding genes. Purifying selection (dN/dS < 1) is the main driving force in the protein-coding genes that shape the diversity of mitogenomes in gentoo penguins. Positive selection (dN/dS > 1) was mostly present in codons of the Complex I (NADH genes), supported by two different codon-based methods at the ND1 and ND4 in the most divergent lineages, the eastern gentoo penguin from Crozet and Marion Islands and the southern gentoo penguin from Antarctica respectively. Additionally, ND5 and ATP6 were under selection in the branches of the phylogeny involving all gentoo penguins except the eastern lineage. Our study suggests that local adaptation of gentoo penguins has emerged as a response to environmental variability promoting the fixation of mitochondrial haplotypes in a non-random manner. Mitogenome adaptation is thus likely to have been associated with gentoo penguin diversification across the Southern Ocean and to have promoted their survival in extreme |
author2 |
University of South Carolina Columbia DST/NRF Centre of Excellence at the Percy FitzPatrick Institute for African Ornithology South Africa Nelson Mandela Metropolitan University Port Elizabeth, South Africa Département Ecologie, Physiologie et Ethologie (DEPE-IPHC) Institut Pluridisciplinaire Hubert Curien (IPHC) Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS) Ecologie comportementale (EC) École normale supérieure - Paris (ENS-PSL) Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université Paris-Sud - Paris 11 (UP11)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Rennes 1 (UR1) Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université Claude Bernard Lyon 1 (UCBL) Université de Lyon-Université de Lyon-Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS) Universidad de Chile = University of Chile Santiago (UCHILE) |
format |
Article in Journal/Newspaper |
author |
Noll, D. Leon, F. Brandt, D. Pistorius, P. Le Bohec, Céline Bonadonna, F. Trathan P., N. Barbosa, A. Rey A., R. Dantas G. P., M. Bowie R. C., K. Poulin, E. Vianna J., A. |
author_facet |
Noll, D. Leon, F. Brandt, D. Pistorius, P. Le Bohec, Céline Bonadonna, F. Trathan P., N. Barbosa, A. Rey A., R. Dantas G. P., M. Bowie R. C., K. Poulin, E. Vianna J., A. |
author_sort |
Noll, D. |
title |
Positive selection over the mitochondrial genome and its role in the diversification of gentoo penguins in response to adaptation in isolation |
title_short |
Positive selection over the mitochondrial genome and its role in the diversification of gentoo penguins in response to adaptation in isolation |
title_full |
Positive selection over the mitochondrial genome and its role in the diversification of gentoo penguins in response to adaptation in isolation |
title_fullStr |
Positive selection over the mitochondrial genome and its role in the diversification of gentoo penguins in response to adaptation in isolation |
title_full_unstemmed |
Positive selection over the mitochondrial genome and its role in the diversification of gentoo penguins in response to adaptation in isolation |
title_sort |
positive selection over the mitochondrial genome and its role in the diversification of gentoo penguins in response to adaptation in isolation |
publisher |
HAL CCSD |
publishDate |
2022 |
url |
https://hal.archives-ouvertes.fr/hal-03618085 https://hal.archives-ouvertes.fr/hal-03618085/document https://hal.archives-ouvertes.fr/hal-03618085/file/s41598-022-07562-0.pdf |
geographic |
Antarctic Southern Ocean The Antarctic |
geographic_facet |
Antarctic Southern Ocean The Antarctic |
genre |
Antarc* Antarctic Antarctica Gentoo penguin Pygoscelis papua Southern Ocean |
genre_facet |
Antarc* Antarctic Antarctica Gentoo penguin Pygoscelis papua Southern Ocean |
op_source |
ISSN: 2045-2322 EISSN: 2045-2322 Scientific Reports https://hal.archives-ouvertes.fr/hal-03618085 Scientific Reports, Nature Publishing Group, 2022, 12, pp.3767 |
op_relation |
hal-03618085 https://hal.archives-ouvertes.fr/hal-03618085 https://hal.archives-ouvertes.fr/hal-03618085/document https://hal.archives-ouvertes.fr/hal-03618085/file/s41598-022-07562-0.pdf |
op_rights |
http://creativecommons.org/licenses/by/ info:eu-repo/semantics/OpenAccess |
_version_ |
1766253532215771136 |
spelling |
ftunivlyon1:oai:HAL:hal-03618085v1 2023-05-15T13:50:29+02:00 Positive selection over the mitochondrial genome and its role in the diversification of gentoo penguins in response to adaptation in isolation Noll, D. Leon, F. Brandt, D. Pistorius, P. Le Bohec, Céline Bonadonna, F. Trathan P., N. Barbosa, A. Rey A., R. Dantas G. P., M. Bowie R. C., K. Poulin, E. Vianna J., A. University of South Carolina Columbia DST/NRF Centre of Excellence at the Percy FitzPatrick Institute for African Ornithology South Africa Nelson Mandela Metropolitan University Port Elizabeth, South Africa Département Ecologie, Physiologie et Ethologie (DEPE-IPHC) Institut Pluridisciplinaire Hubert Curien (IPHC) Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS) Ecologie comportementale (EC) École normale supérieure - Paris (ENS-PSL) Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université Paris-Sud - Paris 11 (UP11)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Rennes 1 (UR1) Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université Claude Bernard Lyon 1 (UCBL) Université de Lyon-Université de Lyon-Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS) Universidad de Chile = University of Chile Santiago (UCHILE) 2022 https://hal.archives-ouvertes.fr/hal-03618085 https://hal.archives-ouvertes.fr/hal-03618085/document https://hal.archives-ouvertes.fr/hal-03618085/file/s41598-022-07562-0.pdf en eng HAL CCSD Nature Publishing Group hal-03618085 https://hal.archives-ouvertes.fr/hal-03618085 https://hal.archives-ouvertes.fr/hal-03618085/document https://hal.archives-ouvertes.fr/hal-03618085/file/s41598-022-07562-0.pdf http://creativecommons.org/licenses/by/ info:eu-repo/semantics/OpenAccess ISSN: 2045-2322 EISSN: 2045-2322 Scientific Reports https://hal.archives-ouvertes.fr/hal-03618085 Scientific Reports, Nature Publishing Group, 2022, 12, pp.3767 [SDV]Life Sciences [q-bio] info:eu-repo/semantics/article Journal articles 2022 ftunivlyon1 2022-07-26T22:43:33Z International audience Although mitochondrial DNA has been widely used in phylogeography, evidence has emerged that factors such as climate, food availability, and environmental pressures that produce high levels of stress can exert a strong influence on mitochondrial genomes, to the point of promoting the persistence of certain genotypes in order to compensate for the metabolic requirements of the local environment. As recently discovered, the gentoo penguins (Pygoscelis papua) comprise four highly divergent lineages across their distribution spanning the Antarctic and sub-Antarctic regions. Gentoo penguins therefore represent a suitable animal model to study adaptive processes across divergent environments. Based on 62 mitogenomes that we obtained from nine locations spanning all four gentoo penguin lineages, we demonstrated lineage-specific nucleotide substitutions for various genes, but only lineage-specific amino acid replacements for the ND1 and ND5 protein-coding genes. Purifying selection (dN/dS < 1) is the main driving force in the protein-coding genes that shape the diversity of mitogenomes in gentoo penguins. Positive selection (dN/dS > 1) was mostly present in codons of the Complex I (NADH genes), supported by two different codon-based methods at the ND1 and ND4 in the most divergent lineages, the eastern gentoo penguin from Crozet and Marion Islands and the southern gentoo penguin from Antarctica respectively. Additionally, ND5 and ATP6 were under selection in the branches of the phylogeny involving all gentoo penguins except the eastern lineage. Our study suggests that local adaptation of gentoo penguins has emerged as a response to environmental variability promoting the fixation of mitochondrial haplotypes in a non-random manner. Mitogenome adaptation is thus likely to have been associated with gentoo penguin diversification across the Southern Ocean and to have promoted their survival in extreme Article in Journal/Newspaper Antarc* Antarctic Antarctica Gentoo penguin Pygoscelis papua Southern Ocean HAL Lyon 1 (University Claude Bernard Lyon 1) Antarctic Southern Ocean The Antarctic |