Mapping and SNP calling
Cutadapt v1.4 (Martin, 2011) was used to remove adapter sequences and trim bases with a Phred score of less than 20 at the 3’ end, retaining only reads with a minimum length of 35 bp. These were then demultiplexed and assigned to individuals using iPyrad v0.7.13 (Eaton, 2014)⁠. To increase mapping success, we used the published M. glareolusreference genome, which we improved with the pipeline Cross-Species Scaffolding (Grau et al., 2018) using the prairie vole (Microtus ochrogaster ) reference genome (GCA_000317375.1⁠, Table S3), Only biallelic SNPs with a minimum base quality of 20, minor allele frequency greater than 0.05, minimum p-value threshold for calling a SNP of 10-6, minimum read depth of 5, and maximum read depth of 100 per sample were considered. In addition, a site had to be present in at least 12 individuals in each of the 12 populations to be considered.