Species delimitation analysis
We used the SNAPP software (Bryant et al., 2012) to test if species
could be delimited at the molecular level using the Bayes Factors
criteria implemented in BEAST v2.6 (Bouckaert et al., 2019). We
evaluated four competing species models with the BFD* method (Leache et
al., 2014), using as an outgroup the CBS2950 reference strain (group A,
Table S2), and as the interest group we used the strains from B:
Huilo-Huilo, C: Central Plateau, D: Coyhaique and E: Altos de Lircay.
SNAPP analyses were only performed with a subset of individuals per
genetic group for computational feasibility; the total number of SNPs in
the dataset was 218,266. To change the VCF haploid to diploid we used
the java code VcfFilterJdk (Lindenbaum and Redon, 2018). We used the
Marginal likelihood estimation with 12 steps for the dataset to
steppingstone sampling. We used default settings (e.g., Yule prior for
species tree and branch length estimations; gamma distributions for
ancestral theta), with five million burn-in iterations. To ensure
convergence, we confirmed that our runs reached effective sample size
values >500 after burn-in using the program Tracer v1.4
(Rambaut et al., 2018). Maximum credibility trees were generated using
TreeAnnotator in BEAST v2.6, and the posterior distributions of species
trees were visualized using DensiTree (Bouckaert, 2010).