Genomic approaches to identify hybrids and estimate admixture times in European wildcat populations

Abstract The survival of indigenous European wildcat (Felis silvestris silvestris) populations can be locally threatened by introgressive hybridization with free-ranging domestic cats. Identifying pure wildcats and investigating the ancestry of admixed individuals becomes thus a conservation priorit...

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Autores principales:	Federica Mattucci, Marco Galaverni, Leslie A. Lyons, Paulo C. Alves, Ettore Randi, Edoardo Velli, Luca Pagani, Romolo Caniglia
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2019
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/d6e8531a52ee47cc9a4cd5daf61f54ec
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spelling	oai:doaj.org-article:d6e8531a52ee47cc9a4cd5daf61f54ec2021-12-02T16:08:16ZGenomic approaches to identify hybrids and estimate admixture times in European wildcat populations10.1038/s41598-019-48002-w2045-2322https://doaj.org/article/d6e8531a52ee47cc9a4cd5daf61f54ec2019-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-019-48002-whttps://doaj.org/toc/2045-2322Abstract The survival of indigenous European wildcat (Felis silvestris silvestris) populations can be locally threatened by introgressive hybridization with free-ranging domestic cats. Identifying pure wildcats and investigating the ancestry of admixed individuals becomes thus a conservation priority. We analyzed 63k cat Single Nucleotide Polymorphisms (SNPs) with multivariate, Bayesian and gene-search tools to better evaluate admixture levels between domestic and wild cats collected in Europe, timing and ancestry proportions of their hybrids and backcrosses, and track the origin (wild or domestic) of the genomic blocks carried by admixed cats, also looking for possible deviations from neutrality in their inheritance patterns. Small domestic ancestry blocks were detected in the genomes of most admixed cats, which likely originated from hybridization events occurring from 6 to 22 generations in the past. We identified about 1,900 outlier coding genes with excess of wild or domestic ancestry compared to random expectations in the admixed individuals. More than 600 outlier genes were significantly enriched for Gene Ontology (GO) categories mainly related to social behavior, functional and metabolic adaptive processes (wild-like genes), involved in cognition and neural crest development (domestic-like genes), or associated with immune system functions and lipid metabolism (parental-like genes). These kinds of genomic ancestry analyses could be reliably applied to unravel the admixture dynamics in European wildcats, as well as in other hybridizing populations, in order to design more efficient conservation plans.Federica MattucciMarco GalaverniLeslie A. LyonsPaulo C. AlvesEttore RandiEdoardo VelliLuca PaganiRomolo CanigliaNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 9, Iss 1, Pp 1-15 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Federica Mattucci Marco Galaverni Leslie A. Lyons Paulo C. Alves Ettore Randi Edoardo Velli Luca Pagani Romolo Caniglia Genomic approaches to identify hybrids and estimate admixture times in European wildcat populations
description	Abstract The survival of indigenous European wildcat (Felis silvestris silvestris) populations can be locally threatened by introgressive hybridization with free-ranging domestic cats. Identifying pure wildcats and investigating the ancestry of admixed individuals becomes thus a conservation priority. We analyzed 63k cat Single Nucleotide Polymorphisms (SNPs) with multivariate, Bayesian and gene-search tools to better evaluate admixture levels between domestic and wild cats collected in Europe, timing and ancestry proportions of their hybrids and backcrosses, and track the origin (wild or domestic) of the genomic blocks carried by admixed cats, also looking for possible deviations from neutrality in their inheritance patterns. Small domestic ancestry blocks were detected in the genomes of most admixed cats, which likely originated from hybridization events occurring from 6 to 22 generations in the past. We identified about 1,900 outlier coding genes with excess of wild or domestic ancestry compared to random expectations in the admixed individuals. More than 600 outlier genes were significantly enriched for Gene Ontology (GO) categories mainly related to social behavior, functional and metabolic adaptive processes (wild-like genes), involved in cognition and neural crest development (domestic-like genes), or associated with immune system functions and lipid metabolism (parental-like genes). These kinds of genomic ancestry analyses could be reliably applied to unravel the admixture dynamics in European wildcats, as well as in other hybridizing populations, in order to design more efficient conservation plans.
format	article
author	Federica Mattucci Marco Galaverni Leslie A. Lyons Paulo C. Alves Ettore Randi Edoardo Velli Luca Pagani Romolo Caniglia
author_facet	Federica Mattucci Marco Galaverni Leslie A. Lyons Paulo C. Alves Ettore Randi Edoardo Velli Luca Pagani Romolo Caniglia
author_sort	Federica Mattucci
title	Genomic approaches to identify hybrids and estimate admixture times in European wildcat populations
title_short	Genomic approaches to identify hybrids and estimate admixture times in European wildcat populations
title_full	Genomic approaches to identify hybrids and estimate admixture times in European wildcat populations
title_fullStr	Genomic approaches to identify hybrids and estimate admixture times in European wildcat populations
title_full_unstemmed	Genomic approaches to identify hybrids and estimate admixture times in European wildcat populations
title_sort	genomic approaches to identify hybrids and estimate admixture times in european wildcat populations
publisher	Nature Portfolio
publishDate	2019
url	https://doaj.org/article/d6e8531a52ee47cc9a4cd5daf61f54ec
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Genomic approaches to identify hybrids and estimate admixture times in European wildcat populations

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