3RAD Data
For the 157 specimens sampled throughout the distribution of theA. unicolor species complex, 234,116,852 raw reads were obtained
ranging from 365,011 to 4,698,473 and averaging 1,491,190 reads per
sample (Table 1). Table 1 outlines the number of loci and SNPs generated
in each dataset with different min_sample_locus parameter values.
Additional clustering thresholds (0.85, 0.88, 0.90) were tested as well,
but there were minimal differences in the number of retained loci/SNPs
across these thresholds; therefore, we chose the threshold value of 0.85
in ipyrad for generating our data matrices. When min_sample_locus
values are lower for both the full dataset (All_samples) and the subset
with A. unicolor B samples only (A.unicolorB_only), more loci and
SNPs are retained compared to higher min_sample_locus values, which
have a lower yield of loci and SNPs.