2.3 Reads mapping and SNP calling
Raw sequence reads were mapped to the M. alternatus reference genome using the Burrows–Wheeler Aligner (BWA) with the command ‘mem -t 4 -k 32 –M’ (Li & Durbin, 2009). To reduce mismatches generated by PCR amplification before sequencing, duplicated reads were removed with SAMtools (Li et al., 2009). After alignment, SNP calling was performed on a population scale using a Bayesian approach as implemented in the package SAMtools, and then genotype likelihoods from reads for each individual at each genomic location and the allele frequencies in the sample were calculated with a Bayesian approach. The ‘mpileup’ command was used to identify SNPs with the parameters as ‘-q 1 -C 50 -t SP -t DP -m 2 -F 0.002’. Specifically, a SNP was retained when it met the following criteria: coverage depth ≥2 and ≤30, minor allele frequency (MAF) ≥0.05, MISS ≤0.1.