Molecular data generation and processing
DNA extraction, mitochondrial COI gene amplification, ddRAD
(Peterson et al. 2012) and two-enzyme GBS (Poland et al.2012) library preparation and sequencing, and initial mitochondrial and
SNP data processing follows Campbell et al. (2017, 2019) and so
are not described in detail here. SNPs were genotyped de novousing the Stacks v. 2.3 pipeline (Catchen et al. 2011; Rochetteet al. 2019) with default parameter settings except for the
following: the n parameter, which controls the number of
mismatches tolerated per locus during catalog construction incstacks , was set to 2 instead of 1; we only retained loci that
were found in 80% of any single population (the “r80” principle of
Paris et al. 2017); and a single, random SNP from each locus was
output during final processing in the populations program of
Stacks to reduce genomic linkage. We conducted additional SNP filtering
in vcftools 0.1.14 (Danecek et al. 2011) to retain only loci with
a minimum minor allele frequency of 3% and to further reduce the global
missing data per locus to a maximum of 20%.