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.