Data from: Applicability of RAD-tag genotyping for inter-familial comparisons: empirical data from two cetaceans
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...
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ftzenodo:oai:zenodo.org:5009938 2023-06-06T11:58:34+02:00 Data from: Applicability of RAD-tag genotyping for inter-familial comparisons: empirical data from two cetaceans Viricel, Amélia Pante, Eric Dabin, Willy Simon-Bouhet, Benoît 2013-11-21 https://zenodo.org/record/5009938 https://doi.org/10.5061/dryad.mk364 unknown doi:10.1111/1755-0998.12206 https://zenodo.org/communities/dryad https://zenodo.org/record/5009938 https://doi.org/10.5061/dryad.mk364 oai:zenodo.org:5009938 info:eu-repo/semantics/openAccess https://creativecommons.org/publicdomain/zero/1.0/legalcode Genomics/Proteomics Delphinus delphis Phocoena phocoena info:eu-repo/semantics/other dataset 2013 ftzenodo https://doi.org/10.5061/dryad.mk36410.1111/1755-0998.12206 2023-04-13T20:44:00Z 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. Description of files deposited to DryadDescription of files deposited to DryadDryad_File_descriptions.txtR script: 1_SlacksThis script allows testing multiple values for two stacks parameters used in the denovo_map command: M and n. It runs both denovo_map and populations commands.1_Slacks.RR script: 2_RAD_Parse_tagsThis script was used to ... Dataset Phocoena phocoena Zenodo |
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ftzenodo |
language |
unknown |
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Genomics/Proteomics Delphinus delphis Phocoena phocoena |
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Genomics/Proteomics Delphinus delphis Phocoena phocoena Viricel, Amélia Pante, Eric Dabin, Willy Simon-Bouhet, Benoît Data from: Applicability of RAD-tag genotyping for inter-familial comparisons: empirical data from two cetaceans |
topic_facet |
Genomics/Proteomics Delphinus delphis Phocoena phocoena |
description |
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. Description of files deposited to DryadDescription of files deposited to DryadDryad_File_descriptions.txtR script: 1_SlacksThis script allows testing multiple values for two stacks parameters used in the denovo_map command: M and n. It runs both denovo_map and populations commands.1_Slacks.RR script: 2_RAD_Parse_tagsThis script was used to ... |
format |
Dataset |
author |
Viricel, Amélia Pante, Eric Dabin, Willy Simon-Bouhet, Benoît |
author_facet |
Viricel, Amélia Pante, Eric Dabin, Willy Simon-Bouhet, Benoît |
author_sort |
Viricel, Amélia |
title |
Data from: Applicability of RAD-tag genotyping for inter-familial comparisons: empirical data from two cetaceans |
title_short |
Data from: Applicability of RAD-tag genotyping for inter-familial comparisons: empirical data from two cetaceans |
title_full |
Data from: Applicability of RAD-tag genotyping for inter-familial comparisons: empirical data from two cetaceans |
title_fullStr |
Data from: Applicability of RAD-tag genotyping for inter-familial comparisons: empirical data from two cetaceans |
title_full_unstemmed |
Data from: Applicability of RAD-tag genotyping for inter-familial comparisons: empirical data from two cetaceans |
title_sort |
data from: applicability of rad-tag genotyping for inter-familial comparisons: empirical data from two cetaceans |
publishDate |
2013 |
url |
https://zenodo.org/record/5009938 https://doi.org/10.5061/dryad.mk364 |
genre |
Phocoena phocoena |
genre_facet |
Phocoena phocoena |
op_relation |
doi:10.1111/1755-0998.12206 https://zenodo.org/communities/dryad https://zenodo.org/record/5009938 https://doi.org/10.5061/dryad.mk364 oai:zenodo.org:5009938 |
op_rights |
info:eu-repo/semantics/openAccess https://creativecommons.org/publicdomain/zero/1.0/legalcode |
op_doi |
https://doi.org/10.5061/dryad.mk36410.1111/1755-0998.12206 |
_version_ |
1767947272725725184 |