Population genetic structure analysis
For individual-based genetic structure analysis, the denovo dataset and
ADMIXTURE program (Alexander et al., 2009) were used, with Kvalues 1–15, as well as 30 iterations per K value, employed for
analysis. The results were visualized using CLUMPAK (Kopelman et al.,
2015), and the K value with the lowest cross-validation (CV)
error was considered the optimal K .
Neighbor-net network analysis on the referenced dataset was conducted
using SplitsTree4 (Huson & Bryant, 2006). Two analyses were performed:
one including the ecotype SH suggested to originate from hybridization,
and one excluding SH.
To reveal phylogenetic relationships, the two individuals with the
highest number of SNPs from each population in the referenced dataset
were selected. A maximum likelihood phylogenetic tree was constructed
using MrBayes ver. 3.2.7 (Ronquist et al., 2012). Model selection was
performed using MrModelTest ver 2.4 (Nylander, 2002) with PAUP*
(Swofford, 2002), employing a general model of DNA substitution (the
GTR) with gamma-distributed rate variation across sites. MrBayes
analysis conditions were as follows: mcmc ngen = 400000; savebrlens =
yes; printfreq = 100; samplefreq = 100; nchains = 4. Similar to
SplitsTree analysis, MrBayes analysis was conducted both with and
without the inclusion of the ecotype SH.