Genetic evidence of a hybrid swarm between Alpine ibex (Capra ibex) and domestic goat (C. hircus)

Improving the understanding of the causes and effects of anthropogenic hybridization is fundamental to ensure species conservation, particularly in the case of hybridization between wild species and their domestic relatives. Knowledge is missing for many species also because of a lack of appropriate tools for hybrid identification. Here, coupling genotype and phenotype analysis, we carried out an extensive investigation of ongoing hybridization in Alpine ibex Capra ibex, a mountain ungulate of conservation concern from a genetic perspective. By genotyping at 63 diagnostic and 465 neutral SNPs 20 suspected hybrids and 126 Alpine ibex without suspicious phenotype, representing eight populations across a major part of the species distribution, we found evidence for ongoing hybridization between Alpine ibex and domestic goat. We identified different levels of hybridization including back crosses into both Alpine ibex and domestic goat. Our results suggest a lack of reproductive barriers bet..., Genotyping using a microfluidics-based amplicon sequencing assay (Juno system, Fluidigm) specifically designed for Alpine ibex by Kessler et al. (2022). 
Sequencing on a NextSeq 500 system (Illumina, San Diego Ca, USA) in mid-output mode. 
Demultiplexing with default settings using Bcl2fastq v2.19 (Illumina®, 2019).
Trimming with Trimmomatic v0.36 (Bolger et al., 2014). 
Forward and reverse reads were merged using Flash v1.2.11 (Magoč & Salzberg, 2011) 
Mapping to the domestic goat reference genome ARS1 (Bickhart et al., 2017) using bwa mem 0.7.13 (Li, 2013). 
The mpileup and call functions of Bcftools v1.17 (https://www.htslib.org/) were used for variant calling. 
Bcftools mpileup was run with min-MQ 10, only retaining sites with a minimal mapping quality of 10 and -a DP, AD, ADF, ADR to retain read depth information. 
Bcftools call was run using -mv -Ob -f GQ for outputting only variant sites in default calling mode, outputting to bcf-format and outputting genotype qualities. 
Vcf..., , # Filtered VCF File (amplicon data) for \"genetic evidence of a hybrid swarm between Alpine ibex (Capra ibex) and domestic goat (C. hircus)\"

[https://doi.org/10.5061/dryad.qnk98sfrp](https://doi.org/10.5061/dryad.qnk98sfrp)

We publish here the VCF file (targets.dp20gq50.recode.vcf) used for the analysis of hybridization between Alpine ibex and domestic goat. Analysis were based on 465 neutral genome-wide markers and 63 diagnostic SNP markers.

## Description of the data and file structure

Classical VCF file with individual genotypes including GT:PL:DP:ADF:ADR:AD:GQ information.
VCF files can be accessed with the free software VCFtools (The Variant Call Format and VCFtools, Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A. Albers, Eric Banks, Mark A. DePristo, Robert Handsaker, Gerton Lunter, Gabor Marth, Stephen T. Sherry, Gilean McVean, Richard Durbin and 1000 Genomes Project Analysis Group, Bioinformatics, 2011). See the Methods section of \"genetic evidence of a hybrid swarm b...