Read mapping and genotyping
Reads obtained from sequencing were trimmed to remove adapter sequences and bases with Phred quality less than 20 using Cutadapt v. 1.14 (Martin, 2011). Trimmed reads were then mapped to the publicly available monarch reference genome assembly ,
using BWA-MEM v. 0.7.12 (Li & Durbin, 2009). The resulting alignment files were then sorted using SAMtools v. 1.2 (Li et al. , 2009). Indel realignment, base recalibration and variant recalibration were performed using GATK v. 3.8.0 (McKenna et al. , 2010). Variants were called for each sample using the Haplotypecaller module in GATK v. 3.8.0 and were then genotyped using the GenotypeGVCFs module in GATK v. 3.8.0 (McKenna et al. , 2010). High confidence variants with variant quality score greater than 80 were selected to recalibrate variant quality scores using VQSR filtering in GATK v. 3.8.0 (McKenna et al. , 2010). Indels and variants within the repeat regions of the reference genome were then removed using Vcftools v. 0.1.15 (Danecek et al. , 2011). One sample (PL3) with the lowest mapping success and genome-wide depth was removed prior to downstream analysis. Our bioinformatic pipeline is visualized in Fig. S1.