Population structure of S. corvina subspecies
We assessed genetic structure between individuals of S. corvinausing three complementary approaches. First, we estimate spatial genetic
structure between samples using estimated effective migration surfaces
(EEMS; Petkova et al., 2015). This software superposes a triangular grid
of a predetermined number of demes (i.e., nodes) within the geographic
area of interest and assigns the georeferenced samples to the closest
deme. Then, EEMS estimates pairwise genetic distances between demes to
identify paths of above- or below-average genetic similarity, while
correcting for geographic distance. Deviations from the average genetic
distance for a given geographic distance are inferred to result from
increased or reduced gene flow. Therefore, EEMS finds geographic regions
that act as barriers or corridors to gene flow. We explored the spatial
structure using an arbitrary number of 200, 300, and 400 demes, and
completed three independent runs per number of demes with different
seeds to assess consistency and the effect of demes density (Petkova et
al., 2015).
Second, we used the program ADMIXTURE (Alexander et al., 2009) to test
for the most likely number of genetically distinct population clusters
(K ) within Costa Rica and Panama, and we evaluated different
population assignments and ancestry by identifying pure and admixed
individuals. We ran ADMIXTURE for 100 iterations (-C), 200 bootstraps
(-B), and 10 cross validations (-cv), with K values from 1 to 10.
We found that K = 3 (see Results) was the most likely number of
genetic populations and that they matched, in general, the three
recognized subspecies. We therefore refer to pure individuals withq values > 0.95 by their respective subspecies’ name
(i.e., corvina , hoffmanni , and hicksii ). Then, we
classified hybrids as those individuals with q < 0.02
from the third genetic cluster and in which q from the second
genetic cluster was at least 2x the value from the third genetic
cluster. Admixed individuals with q > 0.1 from the
third cluster were considered three-way hybrids (as in Scordato et al.,
2017) and were removed from further analyses, together with the
remaining individuals in which q from the second and third
populations were similar, because they cannot be confidently assigned
for pairwise comparisons. We calculated average Weir and Cockerham’sFST per SNP between pure individuals (i.e.,corvina vs hicksii , hoffmanni vs hicksii , corvina vs
hoffmanni ) in VCFTOOLS to estimate genomic differentiation between
subspecies pairs. Finally, we decomposed the genetic variation by a
principal component analysis using the R package ADEGENET (Jombart,
2008), and visualized individuals based on the pure and hybrids
categories described above based on q values from ADMIXTURE.