Methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversity

Recently, populations of various species with very low genetic diversity have been discovered. Some of these persist in the long term, but others could face extinction due to accelerated loss of fitness. In this work, we characterize 45 individuals of one of these populations, belonging to the Iberi...

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Autores: Escoda, Lídia, Hawlitschek, Oliver, González-Esteban, Jorge, Castresana, José
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2022
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/295531
Acceso en línea:http://hdl.handle.net/10261/295531
Access Level:acceso abierto
Palabra clave:Conservation genomics
Genetic variation
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spelling Methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversityEscoda, LídiaHawlitschek, OliverGonzález-Esteban, JorgeCastresana, JoséConservation genomicsGenetic variationRecently, populations of various species with very low genetic diversity have been discovered. Some of these persist in the long term, but others could face extinction due to accelerated loss of fitness. In this work, we characterize 45 individuals of one of these populations, belonging to the Iberian desman (Galemys pyrenaicus). For this, we used the ddRADseq technique, which generated 1421 SNPs. The heterozygosity values of the analyzed individuals were among the lowest recorded for mammals, ranging from 26 to 91 SNPs/Mb. Furthermore, the individuals from one of the localities, highly isolated due to strong barriers, presented extremely high inbreeding coefficients, with values above 0.7. Under this scenario of low genetic diversity and elevated inbreeding levels, some individuals appeared to be almost genetically identical. We used different methods and simulations to determine if genetic identification and parentage analysis were possible in this population. Only one of the methods, which does not assume population homogeneity, was able to identify all individuals correctly. Therefore, genetically impoverished populations pose a great methodological challenge for their genetic study. However, these populations are of primary scientific and conservation interest, so it is essential to characterize them genetically and improve genomic methodologies for their research.This work was financially supported by research projects PID2020-113586GB-I00 and CGL2017-84799-P of MCIN/AEI/100.13039/501100011033, the latter also co-funded by "ERDF A way of making Europe", to J.C. O.H. was funded by DFG postdoctoral grant HA7255/1-1.Springer NatureMinisterio de Ciencia e Innovación (España)Agencia Estatal de Investigación (España)European CommissionGerman Research FoundationConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]2023202320222023info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionapplication/pdfhttp://hdl.handle.net/10261/295531reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2020-113586GB-I00info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/CGL2017-84799-PCastresana, José; 2022; Methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversity [Dataset]; Dryad; https://doi.org/10.5061/dryad.brv15dvckhttps://doi.org/10.1038/s41598-022-25619-ySíinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/2955312026-05-22T06:33:51Z
dc.title.none.fl_str_mv Methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversity
title Methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversity
spellingShingle Methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversity
Escoda, Lídia
Conservation genomics
Genetic variation
title_short Methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversity
title_full Methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversity
title_fullStr Methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversity
title_full_unstemmed Methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversity
title_sort Methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversity
dc.creator.none.fl_str_mv Escoda, Lídia
Hawlitschek, Oliver
González-Esteban, Jorge
Castresana, José
author Escoda, Lídia
author_facet Escoda, Lídia
Hawlitschek, Oliver
González-Esteban, Jorge
Castresana, José
author_role author
author2 Hawlitschek, Oliver
González-Esteban, Jorge
Castresana, José
author2_role author
author
author
dc.contributor.none.fl_str_mv Ministerio de Ciencia e Innovación (España)
Agencia Estatal de Investigación (España)
European Commission
German Research Foundation
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Conservation genomics
Genetic variation
topic Conservation genomics
Genetic variation
description Recently, populations of various species with very low genetic diversity have been discovered. Some of these persist in the long term, but others could face extinction due to accelerated loss of fitness. In this work, we characterize 45 individuals of one of these populations, belonging to the Iberian desman (Galemys pyrenaicus). For this, we used the ddRADseq technique, which generated 1421 SNPs. The heterozygosity values of the analyzed individuals were among the lowest recorded for mammals, ranging from 26 to 91 SNPs/Mb. Furthermore, the individuals from one of the localities, highly isolated due to strong barriers, presented extremely high inbreeding coefficients, with values above 0.7. Under this scenario of low genetic diversity and elevated inbreeding levels, some individuals appeared to be almost genetically identical. We used different methods and simulations to determine if genetic identification and parentage analysis were possible in this population. Only one of the methods, which does not assume population homogeneity, was able to identify all individuals correctly. Therefore, genetically impoverished populations pose a great methodological challenge for their genetic study. However, these populations are of primary scientific and conservation interest, so it is essential to characterize them genetically and improve genomic methodologies for their research.
publishDate 2022
dc.date.none.fl_str_mv 2022
2023
2023
2023
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/295531
url http://hdl.handle.net/10261/295531
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
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info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2020-113586GB-I00
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/CGL2017-84799-P
Castresana, José; 2022; Methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversity [Dataset]; Dryad; https://doi.org/10.5061/dryad.brv15dvck
https://doi.org/10.1038/s41598-022-25619-y
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Springer Nature
publisher.none.fl_str_mv Springer Nature
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
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