DNA extraction and genotyping
We conducted DNA extraction and genotyping as previously described for
this population . Briefly, we used single nucleotide polymorphism (SNP)
genotyping data from blood or tissue samples. DNA was extracted using
the DNeasy Blood and Tissue Kit (QIAGEN), following the manufacturer’s
protocol, and DNA extracts were stored at ‑80° C. Genotyping was
conducted as per by Diversity Arrays Technology, Canberra, using their
proprietary DArTseqTM technology.
DArTseqTM utilizes a combination of next-generation
sequencing platforms and DArT complexity-reduction methods , and,
similar to DArT methods based on array hybridizations, the protocol is
optimized for a specific organism and application by selecting the most
appropriate complexity reduction method. This is assessed based on
minimizing skewed size ranges, non-ideal numbers of fragments, and
percentages of repetitive elements. Samples were then processed as per .
Genotyping produced a total of 8649 SNPs, which were then filtered to
remove SNPs with MAF < 1%; call rate < 95%;
technical replicate scores < 95%; and HWE where p
> .05. This resulted in a total of 5007 SNPs that were used
for subsequent analyses. Observed and expected heterozygosity, as well
as the inbreeding coefficient FIS were calculated using
the dartR package , following the same procedure as in .