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

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

[Usage notes] ddRAD_reads.zip. Quality-filtered reads for each individual in FASTQ format.

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Bibliographic Details
Main Author: Castresana, José
Other Authors: German Research Foundation
Format: dataset biblioteca
Language:English
Published: Dryad 2022-12-19
Subjects:Heterozygosity, Inbreeding, Biological sciences, ddRAD, Galemys pyrenaicus, Iberian desman, Pyrenean desman,
Online Access:http://hdl.handle.net/10261/312334
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spelling dig-ibe-es-10261-3123342023-06-19T14:35:51Z Methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversity [Dataset] Castresana, José German Research Foundation Ministerio de Ciencia e Innovación (España) Agencia Estatal de Investigación (España) European Commission Castresana, José [0000-0002-9391-8050] Heterozygosity Inbreeding Biological sciences ddRAD Galemys pyrenaicus Iberian desman Pyrenean desman [Usage notes] ddRAD_reads.zip. Quality-filtered reads for each individual in FASTQ format. ecently, 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 1,421 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. Deutsche Forschungsgemeinschaft, Award: HA7255/1-1. MCIN/AEI/10.13039/501100011033, Award: PID2020-113586GB-I00, MCIN/AEI/10.13039/501100011033, Award: CGL2017-84799-P, "ERDF A way of making Europe", Award: CGL2017-84799-P. Peer reviewed 2023-06-19T13:14:37Z 2023-06-19T13:14:37Z 2022-12-19 dataset http://purl.org/coar/resource_type/c_ddb1 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 http://hdl.handle.net/10261/312334 10.5061/dryad.brv15dvck en #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-I00/ES/GENOMICA APLICADA A LA CONSERVACION DE ESPECIES EN PELIGRO DE EXTINCION/ info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/CGL2017-84799-P/ES/SECUENCIACION DEL GENOMA DEL DESMAN IBERICO PARA SU APLICACION EN ESTUDIOS DE EVOLUCION POBLACIONAL Y CONSERVACION/ Escoda, Lídia; Hawlitschek, Oliver; González-Esteban, Jorge; Castresana, José. Methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversity. https://doi.org/10.1038/s41598-022-25619-y . http://hdl.handle.net/10261/295531 https://doi.org/10.5061/dryad.brv15dvck Sí open Dryad
institution IBE ES
collection DSpace
country España
countrycode ES
component Bibliográfico
access En linea
databasecode dig-ibe-es
tag biblioteca
region Europa del Sur
libraryname Biblioteca del IBE España
language English
topic Heterozygosity
Inbreeding
Biological sciences
ddRAD
Galemys pyrenaicus
Iberian desman
Pyrenean desman
Heterozygosity
Inbreeding
Biological sciences
ddRAD
Galemys pyrenaicus
Iberian desman
Pyrenean desman
spellingShingle Heterozygosity
Inbreeding
Biological sciences
ddRAD
Galemys pyrenaicus
Iberian desman
Pyrenean desman
Heterozygosity
Inbreeding
Biological sciences
ddRAD
Galemys pyrenaicus
Iberian desman
Pyrenean desman
Castresana, José
Methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversity [Dataset]
description [Usage notes] ddRAD_reads.zip. Quality-filtered reads for each individual in FASTQ format.
author2 German Research Foundation
author_facet German Research Foundation
Castresana, José
format dataset
topic_facet Heterozygosity
Inbreeding
Biological sciences
ddRAD
Galemys pyrenaicus
Iberian desman
Pyrenean desman
author Castresana, José
author_sort Castresana, José
title Methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversity [Dataset]
title_short Methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversity [Dataset]
title_full Methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversity [Dataset]
title_fullStr Methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversity [Dataset]
title_full_unstemmed Methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversity [Dataset]
title_sort methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversity [dataset]
publisher Dryad
publishDate 2022-12-19
url http://hdl.handle.net/10261/312334
work_keys_str_mv AT castresanajose methodologicalchallengesinthegenomicanalysisofanendangeredmammalpopulationwithlowgeneticdiversitydataset
_version_ 1777668845697236992

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