DOI: 10.5061/dryad.qnk98sfrp
title: Genetic evidence of a hybrid swarm between Alpine ibex (Capra ibex) and domestic goat (C. hircus)

description: 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 between the two species and good survival and reproductive
 success of the hybrids. Hybridization was locally intense, alike a hybrid
 swarm, but not spread across the rest of the species distribution. Most of
 the hybrids were discovered in two locations in the North-West of Italy,
 while random sampling of individuals from different areas did not provide
 evidence of recent hybridization. Our method, based on Amplicon sequencing
 of 63 diagnostic SNPs specifically developed for this purpose, allowed us
 to identify hybrids and back crosses up to the 4th-5thgeneration and was
 suitable for genetic samples of different quality, although with varying
 levels of certainty regarding the exact number of generations passed since
 hybridization. Based on the paired analysis of genotype and phenotype, we
 provide guidelines for a first identification of hybrids in the field and
 suggest a procedure for the reliable identification of hybrids.
description: 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.  Vcftools (Danecek et
 al., 2011) was used to convert to vcf format, set the minimal genotype
 quality to 50 and the minimal read depth to 20.
description: # 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 between Alpine ibex (Capra ibex) and domestic goat (C. hircus)" for detailed description on how the raw data analysis was performed.