2.4 | Population genetic analyses
We selected high-quality SNPs which contained no more than 20% missing
data, and thinned the sites such that no two sites were within the same
2000-bp region. Thereby, we eliminated the potential effects of physical
linkage among variants. We then conducted a phylogenetic analysis with
the final SNP set using the IQ-TREE software (version 1.6.9). We
constructed a maximum likelihood (ML)-based phylogenetic tree using the
GTR + F + R5 model, and ran 1000 rapid bootstrap replicates to determine
the confidence values of phylogenetic branches.
To visualize patterns of genetic variation, we conducted a principal
component analysis (PCA) of the final SNP set using PLINK (version
1.90), and plotted the resultant principal components against one
another using the software R (version 3.4). we also used the final SNP
set for a population structure analysis using ADMIXTURE (version 1.3),
which was ran with K values (the number of assumed ancestral components)
ranging from 1 to 10.