Genomic reconstruction of the successful establishment of a feralized bovine population on the subantarctic island of Amsterdam
International audience The feral cattle of the subantarctic island of Amsterdam provide an outstanding case study of a large mammalian population that was established by a handful of founders and thrived within a few generations in a seemingly inhospitable environment. Here, we investigated the gene...
Main Authors: | , , , , , , , , , , |
---|---|
Other Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
HAL CCSD
2024
|
Subjects: | |
Online Access: | https://hal.inrae.fr/hal-04622010 https://hal.inrae.fr/hal-04622010/document https://hal.inrae.fr/hal-04622010/file/msae121.pdf https://doi.org/10.1093/molbev/msae121/7695851 |
id |
ftagroparistech:oai:HAL:hal-04622010v1 |
---|---|
record_format |
openpolar |
institution |
Open Polar |
collection |
AgroParisTech: HAL (Institut des sciences et industries du vivant et de l'environnement) |
op_collection_id |
ftagroparistech |
language |
English |
topic |
cattle Amsterdam island demographic inference genetic load feralization adaptation [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry Molecular Biology/Genomics [q-bio.GN] [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health [SDV.SA.SPA]Life Sciences [q-bio]/Agricultural sciences/Animal production studies |
spellingShingle |
cattle Amsterdam island demographic inference genetic load feralization adaptation [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry Molecular Biology/Genomics [q-bio.GN] [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health [SDV.SA.SPA]Life Sciences [q-bio]/Agricultural sciences/Animal production studies Gautier, Mathieu Micol, Thierry Camus, Louise Moazami-Goudarzi, Katayoun Naves, Michel Guéret, Elise Engelen, Stéfan Lemainque, Arnaud Colas, François Flori, Laurence Druet, Tom Genomic reconstruction of the successful establishment of a feralized bovine population on the subantarctic island of Amsterdam |
topic_facet |
cattle Amsterdam island demographic inference genetic load feralization adaptation [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry Molecular Biology/Genomics [q-bio.GN] [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health [SDV.SA.SPA]Life Sciences [q-bio]/Agricultural sciences/Animal production studies |
description |
International audience The feral cattle of the subantarctic island of Amsterdam provide an outstanding case study of a large mammalian population that was established by a handful of founders and thrived within a few generations in a seemingly inhospitable environment. Here, we investigated the genetic history and composition of this population using genotyping and sequencing data. Our inference showed an intense but brief founding bottleneck around the late 19th century and revealed contributions from European taurine and Indian Ocean zebu in the founder ancestry. Comparative analysis of whole genome sequences further revealed a moderate reduction in genetic diversity despite high levels of inbreeding. The brief and intense bottleneck was associated with high levels of drift, a flattening of the site frequency spectrum and a slight relaxation of purifying selection on mildly deleterious variants. Unlike some populations that have experienced prolonged reductions in effective population size, we did not observe any significant purging of highly deleterious variants.Interestingly, the population's success in the harsh environment can be attributed to pre-adaptation from their European taurine ancestry, suggesting no strong bioclimatic challenge, and also contradicting evidence for insular dwarfism. Genome scan for footprints of selection uncovered a majority of candidate genes related to nervous system function, likely reflecting rapid feralization driven by behavioral changes and complex social restructuring. The Amsterdam Island cattle offers valuable insights into rapid population establishment, feralization, and genetic adaptation in challenging environments. It also sheds light on the unique genetic legacies of feral populations, raising ethical questions according to conservation efforts. |
author2 |
Centre de Biologie pour la Gestion des Populations (UMR CBGP) Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD France-Sud )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM) Ligue pour la Protection des Oiseaux (LPO) Génétique Animale et Biologie Intégrative (GABI) AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) Agroécologie, génétique et systèmes d’élevage tropicaux (ASSET) Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) Institut de Génomique Fonctionnelle - Montpellier GenomiX (IGF MGX) Institut de Génomique Fonctionnelle (IGF) Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-BioCampus (BCM) Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS) Laboratoire de Bioinformatique pour la Génomique et la Biodiversité (LBGB) Génomique métabolique (UMR 8030) Genoscope - Centre national de séquençage Evry (GENOSCOPE) Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)) Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)) Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Genoscope - Centre national de séquençage Evry (GENOSCOPE) Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS) Institut de Biologie François JACOB (JACOB) Direction de Recherche Fondamentale (CEA) (DRF (CEA)) Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA) Terres Australes et Antarctiques Françaises (T.A.A.F.) Terres Australes et Antarctiques Françaises Retraité Systèmes d'Elevage Méditerranéens et Tropicaux - Laboratoire de Recherche sur le Développement de l'Elevage (SELMET-LRDE) GIGA Université Liège Université de Liège Unit of Animal Genomics GIGA-R B34 The genotyping of individuals from the Amsterdam island cattle breed and from the Moka cattle breed was supported by the National Institute of Agronomic Research (INRA, Animal Genetics Division, France; “SNPDOM” and “PERSAFRICA” projects). The sequencing was supported by EU (FORWARD RITA DEFI-ANIMAL project, 2015-2020) and France Génomique (CEA, Evry-Courcouronnes, France; High impact project funded “CAHWA”). MGX acknowledges financial support from France G´enomique National infrastructure, funded as part of “Investissement d’Avenir” program managed by Agence Nationale pour la Recherche (contract ANR-10-INBS-0009). The sequencing of individuals from the Amsterdam island cattle was supported by the Fonds de la Recherche Scientifique – FNRS (F.R.S-FNRS) under Grant J.0134.16. Tom Druet is Research Director from the F.R.S.-FNRS. Computational resources have been provided by the genotoul bioinformatics platform Toulouse Occitanie (Bioinfo Genotoul, https://doi.org/10.15454/1.5572369328961167E12); and by the Consortium des Equipements de Calcul Intensif (CECI), funded by the Fonds de la Recherche Scientifique de Belgique (F.R.S.-FNRS) under Grant No. 2.5020.11 and by the Walloon Region. ANR-10-INBS-0009,France Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010) |
format |
Article in Journal/Newspaper |
author |
Gautier, Mathieu Micol, Thierry Camus, Louise Moazami-Goudarzi, Katayoun Naves, Michel Guéret, Elise Engelen, Stéfan Lemainque, Arnaud Colas, François Flori, Laurence Druet, Tom |
author_facet |
Gautier, Mathieu Micol, Thierry Camus, Louise Moazami-Goudarzi, Katayoun Naves, Michel Guéret, Elise Engelen, Stéfan Lemainque, Arnaud Colas, François Flori, Laurence Druet, Tom |
author_sort |
Gautier, Mathieu |
title |
Genomic reconstruction of the successful establishment of a feralized bovine population on the subantarctic island of Amsterdam |
title_short |
Genomic reconstruction of the successful establishment of a feralized bovine population on the subantarctic island of Amsterdam |
title_full |
Genomic reconstruction of the successful establishment of a feralized bovine population on the subantarctic island of Amsterdam |
title_fullStr |
Genomic reconstruction of the successful establishment of a feralized bovine population on the subantarctic island of Amsterdam |
title_full_unstemmed |
Genomic reconstruction of the successful establishment of a feralized bovine population on the subantarctic island of Amsterdam |
title_sort |
genomic reconstruction of the successful establishment of a feralized bovine population on the subantarctic island of amsterdam |
publisher |
HAL CCSD |
publishDate |
2024 |
url |
https://hal.inrae.fr/hal-04622010 https://hal.inrae.fr/hal-04622010/document https://hal.inrae.fr/hal-04622010/file/msae121.pdf https://doi.org/10.1093/molbev/msae121/7695851 |
geographic |
Indian |
geographic_facet |
Indian |
genre |
Amsterdam Island |
genre_facet |
Amsterdam Island |
op_source |
ISSN: 0737-4038 EISSN: 1537-1719 Molecular Biology and Evolution https://hal.inrae.fr/hal-04622010 Molecular Biology and Evolution, In press, pp.msae121. ⟨10.1093/molbev/msae121/7695851⟩ https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msae121/7695851 |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1093/molbev/msae121/7695851 info:eu-repo/semantics/altIdentifier/pmid/38889245 hal-04622010 https://hal.inrae.fr/hal-04622010 https://hal.inrae.fr/hal-04622010/document https://hal.inrae.fr/hal-04622010/file/msae121.pdf doi:10.1093/molbev/msae121/7695851 PUBMED: 38889245 |
op_rights |
http://creativecommons.org/licenses/by-nc/ info:eu-repo/semantics/OpenAccess |
op_doi |
https://doi.org/10.1093/molbev/msae121/7695851 |
_version_ |
1809934150415679488 |
spelling |
ftagroparistech:oai:HAL:hal-04622010v1 2024-09-09T18:59:31+00:00 Genomic reconstruction of the successful establishment of a feralized bovine population on the subantarctic island of Amsterdam Gautier, Mathieu Micol, Thierry Camus, Louise Moazami-Goudarzi, Katayoun Naves, Michel Guéret, Elise Engelen, Stéfan Lemainque, Arnaud Colas, François Flori, Laurence Druet, Tom Centre de Biologie pour la Gestion des Populations (UMR CBGP) Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD France-Sud )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM) Ligue pour la Protection des Oiseaux (LPO) Génétique Animale et Biologie Intégrative (GABI) AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) Agroécologie, génétique et systèmes d’élevage tropicaux (ASSET) Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) Institut de Génomique Fonctionnelle - Montpellier GenomiX (IGF MGX) Institut de Génomique Fonctionnelle (IGF) Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-BioCampus (BCM) Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS) Laboratoire de Bioinformatique pour la Génomique et la Biodiversité (LBGB) Génomique métabolique (UMR 8030) Genoscope - Centre national de séquençage Evry (GENOSCOPE) Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)) Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)) Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Genoscope - Centre national de séquençage Evry (GENOSCOPE) Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS) Institut de Biologie François JACOB (JACOB) Direction de Recherche Fondamentale (CEA) (DRF (CEA)) Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA) Terres Australes et Antarctiques Françaises (T.A.A.F.) Terres Australes et Antarctiques Françaises Retraité Systèmes d'Elevage Méditerranéens et Tropicaux - Laboratoire de Recherche sur le Développement de l'Elevage (SELMET-LRDE) GIGA Université Liège Université de Liège Unit of Animal Genomics GIGA-R B34 The genotyping of individuals from the Amsterdam island cattle breed and from the Moka cattle breed was supported by the National Institute of Agronomic Research (INRA, Animal Genetics Division, France; “SNPDOM” and “PERSAFRICA” projects). The sequencing was supported by EU (FORWARD RITA DEFI-ANIMAL project, 2015-2020) and France Génomique (CEA, Evry-Courcouronnes, France; High impact project funded “CAHWA”). MGX acknowledges financial support from France G´enomique National infrastructure, funded as part of “Investissement d’Avenir” program managed by Agence Nationale pour la Recherche (contract ANR-10-INBS-0009). The sequencing of individuals from the Amsterdam island cattle was supported by the Fonds de la Recherche Scientifique – FNRS (F.R.S-FNRS) under Grant J.0134.16. Tom Druet is Research Director from the F.R.S.-FNRS. Computational resources have been provided by the genotoul bioinformatics platform Toulouse Occitanie (Bioinfo Genotoul, https://doi.org/10.15454/1.5572369328961167E12); and by the Consortium des Equipements de Calcul Intensif (CECI), funded by the Fonds de la Recherche Scientifique de Belgique (F.R.S.-FNRS) under Grant No. 2.5020.11 and by the Walloon Region. ANR-10-INBS-0009,France Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010) 2024 https://hal.inrae.fr/hal-04622010 https://hal.inrae.fr/hal-04622010/document https://hal.inrae.fr/hal-04622010/file/msae121.pdf https://doi.org/10.1093/molbev/msae121/7695851 en eng HAL CCSD Oxford University Press (OUP) info:eu-repo/semantics/altIdentifier/doi/10.1093/molbev/msae121/7695851 info:eu-repo/semantics/altIdentifier/pmid/38889245 hal-04622010 https://hal.inrae.fr/hal-04622010 https://hal.inrae.fr/hal-04622010/document https://hal.inrae.fr/hal-04622010/file/msae121.pdf doi:10.1093/molbev/msae121/7695851 PUBMED: 38889245 http://creativecommons.org/licenses/by-nc/ info:eu-repo/semantics/OpenAccess ISSN: 0737-4038 EISSN: 1537-1719 Molecular Biology and Evolution https://hal.inrae.fr/hal-04622010 Molecular Biology and Evolution, In press, pp.msae121. ⟨10.1093/molbev/msae121/7695851⟩ https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msae121/7695851 cattle Amsterdam island demographic inference genetic load feralization adaptation [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry Molecular Biology/Genomics [q-bio.GN] [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health [SDV.SA.SPA]Life Sciences [q-bio]/Agricultural sciences/Animal production studies info:eu-repo/semantics/article Journal articles 2024 ftagroparistech https://doi.org/10.1093/molbev/msae121/7695851 2024-07-02T23:34:22Z International audience The feral cattle of the subantarctic island of Amsterdam provide an outstanding case study of a large mammalian population that was established by a handful of founders and thrived within a few generations in a seemingly inhospitable environment. Here, we investigated the genetic history and composition of this population using genotyping and sequencing data. Our inference showed an intense but brief founding bottleneck around the late 19th century and revealed contributions from European taurine and Indian Ocean zebu in the founder ancestry. Comparative analysis of whole genome sequences further revealed a moderate reduction in genetic diversity despite high levels of inbreeding. The brief and intense bottleneck was associated with high levels of drift, a flattening of the site frequency spectrum and a slight relaxation of purifying selection on mildly deleterious variants. Unlike some populations that have experienced prolonged reductions in effective population size, we did not observe any significant purging of highly deleterious variants.Interestingly, the population's success in the harsh environment can be attributed to pre-adaptation from their European taurine ancestry, suggesting no strong bioclimatic challenge, and also contradicting evidence for insular dwarfism. Genome scan for footprints of selection uncovered a majority of candidate genes related to nervous system function, likely reflecting rapid feralization driven by behavioral changes and complex social restructuring. The Amsterdam Island cattle offers valuable insights into rapid population establishment, feralization, and genetic adaptation in challenging environments. It also sheds light on the unique genetic legacies of feral populations, raising ethical questions according to conservation efforts. Article in Journal/Newspaper Amsterdam Island AgroParisTech: HAL (Institut des sciences et industries du vivant et de l'environnement) Indian |