The genomic impact of historical hybridization with massive mitochondrial DNA introgression
International audience Background: The extent to which selection determines interspecific patterns of genetic exchange enlightens the role of adaptation in evolution and speciation. Often reported extensive interspecific introgression could be selection-driven, but also result from demographic proce...
Published in: | Genome Biology |
---|---|
Main Authors: | , , |
Other Authors: | , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
HAL CCSD
2018
|
Subjects: | |
Online Access: | https://hal.umontpellier.fr/hal-02346728 https://hal.umontpellier.fr/hal-02346728/document https://hal.umontpellier.fr/hal-02346728/file/s13059-018-1471-8.pdf https://doi.org/10.1186/s13059-018-1471-8 |
id |
ftccsdartic:oai:HAL:hal-02346728v1 |
---|---|
record_format |
openpolar |
institution |
Open Polar |
collection |
Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe) |
op_collection_id |
ftccsdartic |
language |
English |
topic |
Introgressive hybridization Iberian hares Whole genome sequencing Range invasion Adaptation [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE] [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] |
spellingShingle |
Introgressive hybridization Iberian hares Whole genome sequencing Range invasion Adaptation [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE] [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] Seixas, Fernando Boursot, Pierre Melo-Ferreira, José The genomic impact of historical hybridization with massive mitochondrial DNA introgression |
topic_facet |
Introgressive hybridization Iberian hares Whole genome sequencing Range invasion Adaptation [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE] [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] |
description |
International audience Background: The extent to which selection determines interspecific patterns of genetic exchange enlightens the role of adaptation in evolution and speciation. Often reported extensive interspecific introgression could be selection-driven, but also result from demographic processes, especially in cases of invasive species replacements, which can promote introgression at their invasion front. Because invasion and selective sweeps similarly mold variation, population genetics evidence for selection can only be gathered in an explicit demographic framework. The Iberian hare, Lepus granatensis, displays in its northern range extensive mitochondrial DNA introgression from L. timidus, an arctic/boreal species that it replaced locally after the last glacial maximum. We use whole-genome sequencing to infer geographic and genomic patterns of nuclear introgression and fit a neutral model of species replacement with hybridization, allowing us to evaluate how selection influenced introgression genome-wide, including for mtDNA. Results: Although the average nuclear and mtDNA introgression patterns contrast strongly, they fit a single demographic model of post-glacial invasive replacement of timidus by granatensis. Outliers of elevated introgression include several genes related to immunity, spermatogenesis, and mitochondrial metabolism. Introgression is reduced on the X chromosome and in low recombining regions. Conclusions: General nuclear and mtDNA patterns of introgression can be explained by purely demographic processes. Hybrid incompatibilities and interplay between selection and recombination locally modulate levels of nuclear introgression. Selection promoted introgression of some genes involved in conflicts, either interspecific (parasites) or possibly cytonuclear. In the latter case, nuclear introgression could mitigate the potential negative effects of alien mtDNA on mitochondrial metabolism and male-specific traits. |
author2 |
Institut des Sciences de l'Evolution de Montpellier (UMR ISEM) Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE) Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement IRD : UR226-Centre National de la Recherche Scientifique (CNRS) Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-UP) Universidade do Porto-CESPU ANR-12-ISV7-0002,HybridAdapt,Hybridation, adaptation et histoire des peuplements: une approche génomique.(2012) |
format |
Article in Journal/Newspaper |
author |
Seixas, Fernando Boursot, Pierre Melo-Ferreira, José |
author_facet |
Seixas, Fernando Boursot, Pierre Melo-Ferreira, José |
author_sort |
Seixas, Fernando |
title |
The genomic impact of historical hybridization with massive mitochondrial DNA introgression |
title_short |
The genomic impact of historical hybridization with massive mitochondrial DNA introgression |
title_full |
The genomic impact of historical hybridization with massive mitochondrial DNA introgression |
title_fullStr |
The genomic impact of historical hybridization with massive mitochondrial DNA introgression |
title_full_unstemmed |
The genomic impact of historical hybridization with massive mitochondrial DNA introgression |
title_sort |
genomic impact of historical hybridization with massive mitochondrial dna introgression |
publisher |
HAL CCSD |
publishDate |
2018 |
url |
https://hal.umontpellier.fr/hal-02346728 https://hal.umontpellier.fr/hal-02346728/document https://hal.umontpellier.fr/hal-02346728/file/s13059-018-1471-8.pdf https://doi.org/10.1186/s13059-018-1471-8 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
ISSN: 1465-6906 EISSN: 1474-760X Genome Biology https://hal.umontpellier.fr/hal-02346728 Genome Biology, BioMed Central, 2018, 19 (1), ⟨10.1186/s13059-018-1471-8⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1186/s13059-018-1471-8 hal-02346728 https://hal.umontpellier.fr/hal-02346728 https://hal.umontpellier.fr/hal-02346728/document https://hal.umontpellier.fr/hal-02346728/file/s13059-018-1471-8.pdf doi:10.1186/s13059-018-1471-8 |
op_rights |
http://creativecommons.org/licenses/by/ info:eu-repo/semantics/OpenAccess |
op_doi |
https://doi.org/10.1186/s13059-018-1471-8 |
container_title |
Genome Biology |
container_volume |
19 |
container_issue |
1 |
_version_ |
1766343930172932096 |
spelling |
ftccsdartic:oai:HAL:hal-02346728v1 2023-05-15T15:13:22+02:00 The genomic impact of historical hybridization with massive mitochondrial DNA introgression Seixas, Fernando Boursot, Pierre Melo-Ferreira, José Institut des Sciences de l'Evolution de Montpellier (UMR ISEM) Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE) Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement IRD : UR226-Centre National de la Recherche Scientifique (CNRS) Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-UP) Universidade do Porto-CESPU ANR-12-ISV7-0002,HybridAdapt,Hybridation, adaptation et histoire des peuplements: une approche génomique.(2012) 2018-12 https://hal.umontpellier.fr/hal-02346728 https://hal.umontpellier.fr/hal-02346728/document https://hal.umontpellier.fr/hal-02346728/file/s13059-018-1471-8.pdf https://doi.org/10.1186/s13059-018-1471-8 en eng HAL CCSD BioMed Central info:eu-repo/semantics/altIdentifier/doi/10.1186/s13059-018-1471-8 hal-02346728 https://hal.umontpellier.fr/hal-02346728 https://hal.umontpellier.fr/hal-02346728/document https://hal.umontpellier.fr/hal-02346728/file/s13059-018-1471-8.pdf doi:10.1186/s13059-018-1471-8 http://creativecommons.org/licenses/by/ info:eu-repo/semantics/OpenAccess ISSN: 1465-6906 EISSN: 1474-760X Genome Biology https://hal.umontpellier.fr/hal-02346728 Genome Biology, BioMed Central, 2018, 19 (1), ⟨10.1186/s13059-018-1471-8⟩ Introgressive hybridization Iberian hares Whole genome sequencing Range invasion Adaptation [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE] [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] info:eu-repo/semantics/article Journal articles 2018 ftccsdartic https://doi.org/10.1186/s13059-018-1471-8 2021-11-21T00:31:45Z International audience Background: The extent to which selection determines interspecific patterns of genetic exchange enlightens the role of adaptation in evolution and speciation. Often reported extensive interspecific introgression could be selection-driven, but also result from demographic processes, especially in cases of invasive species replacements, which can promote introgression at their invasion front. Because invasion and selective sweeps similarly mold variation, population genetics evidence for selection can only be gathered in an explicit demographic framework. The Iberian hare, Lepus granatensis, displays in its northern range extensive mitochondrial DNA introgression from L. timidus, an arctic/boreal species that it replaced locally after the last glacial maximum. We use whole-genome sequencing to infer geographic and genomic patterns of nuclear introgression and fit a neutral model of species replacement with hybridization, allowing us to evaluate how selection influenced introgression genome-wide, including for mtDNA. Results: Although the average nuclear and mtDNA introgression patterns contrast strongly, they fit a single demographic model of post-glacial invasive replacement of timidus by granatensis. Outliers of elevated introgression include several genes related to immunity, spermatogenesis, and mitochondrial metabolism. Introgression is reduced on the X chromosome and in low recombining regions. Conclusions: General nuclear and mtDNA patterns of introgression can be explained by purely demographic processes. Hybrid incompatibilities and interplay between selection and recombination locally modulate levels of nuclear introgression. Selection promoted introgression of some genes involved in conflicts, either interspecific (parasites) or possibly cytonuclear. In the latter case, nuclear introgression could mitigate the potential negative effects of alien mtDNA on mitochondrial metabolism and male-specific traits. Article in Journal/Newspaper Arctic Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe) Arctic Genome Biology 19 1 |