Reference datasets for consistency tests of GENAPOPOP 1.0 software: a user-friendly software to analyse genetic diversity and structure in partially clonal and selfed polyploid organisms.
Datasets companion of the manuscript entitled GenAPoPop 1.0: a user-friendly software to analyse genetic diversity and structure in partially clonal and selfed polyploid organisms, used to achieve consistency test with Spagedi 1.5 software, and used as reference datasets to demonstrate the new possi...
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ftzenodo:oai:zenodo.org:8164531 2023-08-15T12:40:25+02:00 Reference datasets for consistency tests of GENAPOPOP 1.0 software: a user-friendly software to analyse genetic diversity and structure in partially clonal and selfed polyploid organisms. Dominique Barloy Ekaterina Bocharova Maryline Harang Luis Portillo Solenn Stoeckel 2022-11-07 https://zenodo.org/record/8164531 https://doi.org/10.5281/zenodo.8164531 eng eng doi:10.5281/zenodo.7299913 https://zenodo.org/record/8164531 https://doi.org/10.5281/zenodo.8164531 oai:zenodo.org:8164531 info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/legalcode Population genetic Autopolyploidy Reproductive mode selfing Partial clonality info:eu-repo/semantics/other dataset 2022 ftzenodo https://doi.org/10.5281/zenodo.816453110.5281/zenodo.7299913 2023-07-25T22:59:09Z Datasets companion of the manuscript entitled GenAPoPop 1.0: a user-friendly software to analyse genetic diversity and structure in partially clonal and selfed polyploid organisms, used to achieve consistency test with Spagedi 1.5 software, and used as reference datasets to demonstrate the new possibilities allowed by GenAPoPop software. Raw datasets used for testing GenAPoPop 1.0, A user-friendly software for easily compute genetic analyses of autopolyploid populations packaged for Linux, MacOS and Windows; Results obtained from Spagedi 1.5 (Hardy & Vekemans 2001) and GenAPoPop1.0. Four pseudo-observed genotyping autotetrapolyploid SNP datasets, corresponding respectively to panmictic (A), highly clonal (B), highly selfed (C) and half-clonal-half-selfed (D) reproductive mode scenario. In all these four scenarios, we simulated two populations of 100 individuals each, connected with a migration rate of 0.01 and mutating at a rate of 0.01, genotyped at 10 SNPs. Datasets were recorded 1000 generations after an initial randomly drawing population with equal allele frequencies. One SNP tetraploid genotyping dataset from two French Ludwigia grandiflora subsp. hexapetala populations (aquatic plant from the Angiosperm clade): two populations in which we collected 75 individuals, each genotyped with 36 SNPs using the Hiplex method allowing confident allele dosage (Delord et al. 2018). One microsatellite tetraploid genotyping dataset on two Aulactinia stella populations (sea-anemone from the Cnidaria phylum), sampled on the coast of the arctic ocean. One population of 21 individuals and one population of 15 individuals, both genotyped with 10 microsatellites. We also report here the consistency tests with GenAlex and Spagedi, results of analyses (GPP tab) on 6300 independant simulations and inferences of the quantitative reproductive modes using the bayesian method on CEMP tab made on 6300 another independant simulations. Dataset Arctic Arctic Ocean Zenodo Arctic Arctic Ocean Stella ENVELOPE(-64.254,-64.254,-65.249,-65.249) |
institution |
Open Polar |
collection |
Zenodo |
op_collection_id |
ftzenodo |
language |
English |
topic |
Population genetic Autopolyploidy Reproductive mode selfing Partial clonality |
spellingShingle |
Population genetic Autopolyploidy Reproductive mode selfing Partial clonality Dominique Barloy Ekaterina Bocharova Maryline Harang Luis Portillo Solenn Stoeckel Reference datasets for consistency tests of GENAPOPOP 1.0 software: a user-friendly software to analyse genetic diversity and structure in partially clonal and selfed polyploid organisms. |
topic_facet |
Population genetic Autopolyploidy Reproductive mode selfing Partial clonality |
description |
Datasets companion of the manuscript entitled GenAPoPop 1.0: a user-friendly software to analyse genetic diversity and structure in partially clonal and selfed polyploid organisms, used to achieve consistency test with Spagedi 1.5 software, and used as reference datasets to demonstrate the new possibilities allowed by GenAPoPop software. Raw datasets used for testing GenAPoPop 1.0, A user-friendly software for easily compute genetic analyses of autopolyploid populations packaged for Linux, MacOS and Windows; Results obtained from Spagedi 1.5 (Hardy & Vekemans 2001) and GenAPoPop1.0. Four pseudo-observed genotyping autotetrapolyploid SNP datasets, corresponding respectively to panmictic (A), highly clonal (B), highly selfed (C) and half-clonal-half-selfed (D) reproductive mode scenario. In all these four scenarios, we simulated two populations of 100 individuals each, connected with a migration rate of 0.01 and mutating at a rate of 0.01, genotyped at 10 SNPs. Datasets were recorded 1000 generations after an initial randomly drawing population with equal allele frequencies. One SNP tetraploid genotyping dataset from two French Ludwigia grandiflora subsp. hexapetala populations (aquatic plant from the Angiosperm clade): two populations in which we collected 75 individuals, each genotyped with 36 SNPs using the Hiplex method allowing confident allele dosage (Delord et al. 2018). One microsatellite tetraploid genotyping dataset on two Aulactinia stella populations (sea-anemone from the Cnidaria phylum), sampled on the coast of the arctic ocean. One population of 21 individuals and one population of 15 individuals, both genotyped with 10 microsatellites. We also report here the consistency tests with GenAlex and Spagedi, results of analyses (GPP tab) on 6300 independant simulations and inferences of the quantitative reproductive modes using the bayesian method on CEMP tab made on 6300 another independant simulations. |
format |
Dataset |
author |
Dominique Barloy Ekaterina Bocharova Maryline Harang Luis Portillo Solenn Stoeckel |
author_facet |
Dominique Barloy Ekaterina Bocharova Maryline Harang Luis Portillo Solenn Stoeckel |
author_sort |
Dominique Barloy |
title |
Reference datasets for consistency tests of GENAPOPOP 1.0 software: a user-friendly software to analyse genetic diversity and structure in partially clonal and selfed polyploid organisms. |
title_short |
Reference datasets for consistency tests of GENAPOPOP 1.0 software: a user-friendly software to analyse genetic diversity and structure in partially clonal and selfed polyploid organisms. |
title_full |
Reference datasets for consistency tests of GENAPOPOP 1.0 software: a user-friendly software to analyse genetic diversity and structure in partially clonal and selfed polyploid organisms. |
title_fullStr |
Reference datasets for consistency tests of GENAPOPOP 1.0 software: a user-friendly software to analyse genetic diversity and structure in partially clonal and selfed polyploid organisms. |
title_full_unstemmed |
Reference datasets for consistency tests of GENAPOPOP 1.0 software: a user-friendly software to analyse genetic diversity and structure in partially clonal and selfed polyploid organisms. |
title_sort |
reference datasets for consistency tests of genapopop 1.0 software: a user-friendly software to analyse genetic diversity and structure in partially clonal and selfed polyploid organisms. |
publishDate |
2022 |
url |
https://zenodo.org/record/8164531 https://doi.org/10.5281/zenodo.8164531 |
long_lat |
ENVELOPE(-64.254,-64.254,-65.249,-65.249) |
geographic |
Arctic Arctic Ocean Stella |
geographic_facet |
Arctic Arctic Ocean Stella |
genre |
Arctic Arctic Ocean |
genre_facet |
Arctic Arctic Ocean |
op_relation |
doi:10.5281/zenodo.7299913 https://zenodo.org/record/8164531 https://doi.org/10.5281/zenodo.8164531 oai:zenodo.org:8164531 |
op_rights |
info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/legalcode |
op_doi |
https://doi.org/10.5281/zenodo.816453110.5281/zenodo.7299913 |
_version_ |
1774293202075910144 |