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

Federica Mattucci, Marco Galaverni, Leslie A Lyons, Paulo C. Alves, Ettore Randi, Edoardo Velli, Luca Pagani, Romolo Caniglia

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Article number11612
JournalScientific reports
Volume9
Issue number1
DOIs
StatePublished - Dec 1 2019

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genomics
ancestry
cats
genes
Felis
neural crest
social behavior
cognition
lipid metabolism
introgression
single nucleotide polymorphism
immune system
inheritance (genetics)
hybridization
genome

ASJC Scopus subject areas

  • General

Cite this

Genomic approaches to identify hybrids and estimate admixture times in European wildcat populations. / Mattucci, Federica; Galaverni, Marco; Lyons, Leslie A; Alves, Paulo C.; Randi, Ettore; Velli, Edoardo; Pagani, Luca; Caniglia, Romolo.

In: Scientific reports, Vol. 9, No. 1, 11612, 01.12.2019.

Research output: Contribution to journalArticle

Mattucci, F, Galaverni, M, Lyons, LA, Alves, PC, Randi, E, Velli, E, Pagani, L & Caniglia, R 2019, 'Genomic approaches to identify hybrids and estimate admixture times in European wildcat populations', Scientific reports, vol. 9, no. 1, 11612. https://doi.org/10.1038/s41598-019-48002-w
Mattucci, Federica ; Galaverni, Marco ; Lyons, Leslie A ; Alves, Paulo C. ; Randi, Ettore ; Velli, Edoardo ; Pagani, Luca ; Caniglia, Romolo. / Genomic approaches to identify hybrids and estimate admixture times in European wildcat populations. In: Scientific reports. 2019 ; Vol. 9, No. 1.
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