Applicability of RAD-tag genotyping for inter-familial comparisons: empirical data from two cetaceans
International audience Restriction site-Associated DNA tag (RAD-tag) sequencing has become a popular approach to generate thousands of SNPs used to address diverse questions in population genomics. Comparatively, the suitability of RAD-tag genotyping to address evolutionary questions across divergen...
Published in: | Molecular Ecology Resources |
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ftccsdartic:oai:HAL:hal-00908459v1 2023-05-15T17:59:14+02:00 Applicability of RAD-tag genotyping for inter-familial comparisons: empirical data from two cetaceans Viricel, Amélia Pante, Eric Dabin, Willy Simon-Bouhet, Benoit LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs) Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS) Observatoire PELAGIS UMS 3462 (PELAGIS) Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS) CPER Poitou-Charente 2007-2013, Action Internationales et Rayonnement de l'Université de La Rochelle, UMR 7266 LIENSs CNRS-Université de La Rochelle 2014 https://hal.archives-ouvertes.fr/hal-00908459 https://hal.archives-ouvertes.fr/hal-00908459/document https://hal.archives-ouvertes.fr/hal-00908459/file/mer_viricel_rad_phocoena_25Oct13.pdf https://doi.org/10.1111/1755-0998.12206 en eng HAL CCSD Wiley/Blackwell info:eu-repo/semantics/altIdentifier/doi/10.1111/1755-0998.12206 info:eu-repo/semantics/altIdentifier/pmid/24267050 hal-00908459 https://hal.archives-ouvertes.fr/hal-00908459 https://hal.archives-ouvertes.fr/hal-00908459/document https://hal.archives-ouvertes.fr/hal-00908459/file/mer_viricel_rad_phocoena_25Oct13.pdf doi:10.1111/1755-0998.12206 PUBMED: 24267050 info:eu-repo/semantics/OpenAccess ISSN: 1755-098X EISSN: 1755-0998 Molecular Ecology Resources https://hal.archives-ouvertes.fr/hal-00908459 Molecular Ecology Resources, Wiley/Blackwell, 2014, 14 (3), pp.597-605. ⟨10.1111/1755-0998.12206⟩ RAD sequencing phylogenetics genomics inter-familial divergence Delphinidae Phocoenidae [SDV.BID]Life Sciences [q-bio]/Biodiversity info:eu-repo/semantics/article Journal articles 2014 ftccsdartic https://doi.org/10.1111/1755-0998.12206 2021-10-24T14:21:32Z International audience Restriction site-Associated DNA tag (RAD-tag) sequencing has become a popular approach to generate thousands of SNPs used to address diverse questions in population genomics. Comparatively, the suitability of RAD-tag genotyping to address evolutionary questions across divergent species has been the subject of only a few recent studies. Here, we evaluate the applicability of this approach to conduct genome-wide scans for polymorphisms across two cetacean species belonging to distinct families: the short-beaked common dolphin (Delphinus delphis; n = 5 individuals) and the harbor porpoise (Phocoena phocoena; n = 1 individual). Additionally, we explore the effects of varying two parameters in the Stacks analysis pipeline on the number of loci and level of divergence obtained. We observed a 34% drop in the total number of loci that were present in all individuals when analyzing individuals from the distinct families compared to analyses restricted to intra-specific comparisons (i.e., within D. delphis). Despite relatively stringent quality filters, 3,595 polymorphic loci were retrieved from our inter-familial comparison. Cetaceans have undergone rapid diversification and the estimated divergence time between the two families is relatively recent (14 to 19 My). Thus, our results showed that, for this level of divergence, a large number of orthologous loci can still be genotyped using this approach, which is on par with two recent in silico studies. Our findings constitute one of the first empirical investigations using RAD-tag sequencing at this level of divergence and highlights the great potential of this approach in comparative studies and to address evolutionary questions. Article in Journal/Newspaper Phocoena phocoena Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe) Molecular Ecology Resources 14 3 597 605 |
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 |
RAD sequencing phylogenetics genomics inter-familial divergence Delphinidae Phocoenidae [SDV.BID]Life Sciences [q-bio]/Biodiversity |
spellingShingle |
RAD sequencing phylogenetics genomics inter-familial divergence Delphinidae Phocoenidae [SDV.BID]Life Sciences [q-bio]/Biodiversity Viricel, Amélia Pante, Eric Dabin, Willy Simon-Bouhet, Benoit Applicability of RAD-tag genotyping for inter-familial comparisons: empirical data from two cetaceans |
topic_facet |
RAD sequencing phylogenetics genomics inter-familial divergence Delphinidae Phocoenidae [SDV.BID]Life Sciences [q-bio]/Biodiversity |
description |
International audience Restriction site-Associated DNA tag (RAD-tag) sequencing has become a popular approach to generate thousands of SNPs used to address diverse questions in population genomics. Comparatively, the suitability of RAD-tag genotyping to address evolutionary questions across divergent species has been the subject of only a few recent studies. Here, we evaluate the applicability of this approach to conduct genome-wide scans for polymorphisms across two cetacean species belonging to distinct families: the short-beaked common dolphin (Delphinus delphis; n = 5 individuals) and the harbor porpoise (Phocoena phocoena; n = 1 individual). Additionally, we explore the effects of varying two parameters in the Stacks analysis pipeline on the number of loci and level of divergence obtained. We observed a 34% drop in the total number of loci that were present in all individuals when analyzing individuals from the distinct families compared to analyses restricted to intra-specific comparisons (i.e., within D. delphis). Despite relatively stringent quality filters, 3,595 polymorphic loci were retrieved from our inter-familial comparison. Cetaceans have undergone rapid diversification and the estimated divergence time between the two families is relatively recent (14 to 19 My). Thus, our results showed that, for this level of divergence, a large number of orthologous loci can still be genotyped using this approach, which is on par with two recent in silico studies. Our findings constitute one of the first empirical investigations using RAD-tag sequencing at this level of divergence and highlights the great potential of this approach in comparative studies and to address evolutionary questions. |
author2 |
LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs) Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS) Observatoire PELAGIS UMS 3462 (PELAGIS) Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS) CPER Poitou-Charente 2007-2013, Action Internationales et Rayonnement de l'Université de La Rochelle, UMR 7266 LIENSs CNRS-Université de La Rochelle |
format |
Article in Journal/Newspaper |
author |
Viricel, Amélia Pante, Eric Dabin, Willy Simon-Bouhet, Benoit |
author_facet |
Viricel, Amélia Pante, Eric Dabin, Willy Simon-Bouhet, Benoit |
author_sort |
Viricel, Amélia |
title |
Applicability of RAD-tag genotyping for inter-familial comparisons: empirical data from two cetaceans |
title_short |
Applicability of RAD-tag genotyping for inter-familial comparisons: empirical data from two cetaceans |
title_full |
Applicability of RAD-tag genotyping for inter-familial comparisons: empirical data from two cetaceans |
title_fullStr |
Applicability of RAD-tag genotyping for inter-familial comparisons: empirical data from two cetaceans |
title_full_unstemmed |
Applicability of RAD-tag genotyping for inter-familial comparisons: empirical data from two cetaceans |
title_sort |
applicability of rad-tag genotyping for inter-familial comparisons: empirical data from two cetaceans |
publisher |
HAL CCSD |
publishDate |
2014 |
url |
https://hal.archives-ouvertes.fr/hal-00908459 https://hal.archives-ouvertes.fr/hal-00908459/document https://hal.archives-ouvertes.fr/hal-00908459/file/mer_viricel_rad_phocoena_25Oct13.pdf https://doi.org/10.1111/1755-0998.12206 |
genre |
Phocoena phocoena |
genre_facet |
Phocoena phocoena |
op_source |
ISSN: 1755-098X EISSN: 1755-0998 Molecular Ecology Resources https://hal.archives-ouvertes.fr/hal-00908459 Molecular Ecology Resources, Wiley/Blackwell, 2014, 14 (3), pp.597-605. ⟨10.1111/1755-0998.12206⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1111/1755-0998.12206 info:eu-repo/semantics/altIdentifier/pmid/24267050 hal-00908459 https://hal.archives-ouvertes.fr/hal-00908459 https://hal.archives-ouvertes.fr/hal-00908459/document https://hal.archives-ouvertes.fr/hal-00908459/file/mer_viricel_rad_phocoena_25Oct13.pdf doi:10.1111/1755-0998.12206 PUBMED: 24267050 |
op_rights |
info:eu-repo/semantics/OpenAccess |
op_doi |
https://doi.org/10.1111/1755-0998.12206 |
container_title |
Molecular Ecology Resources |
container_volume |
14 |
container_issue |
3 |
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597 |
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