Demographic inference
We compared four different models to infer the evolutionary history of
this group of S. corvina subspecies in Costa Rica and Panama. We
found one model was preferred over the other three (Table 3). The best
model included the default migration bouts between S. c.
hoffmanni and S. c. hicksii, and between S. c. corvinaand S. c. hicksii only (Model B; Figure 2). This model suggests a
scenario of rapid divergence followed by isolation of the black and pied
lineages until recent gene flow facilitated by secondary contact and is
consistent with reduced hybridization between S. c. corvina andS. c. hoffmanni . Genomic homogenization due to gene flow in
addition to rapid divergence inhibits accurate reconstruction of the
phylogenetic relationship between subspecies, estimates of times of
divergence, and rates of gene flow.
DISCUSSION
We compiled a dataset of 14,839 genome-wide SNPs from 255 individuals
from Costa Rica and Panama to test whether phenotypic traits covary with
population structure and hybridization patterns between S.
corvina subspecies that differ in plumage coloration across three
independent contact zones (Figure 1A). We found three genetic clusters
of moderate genetic differentiation, consistent with subspecies
distributions (Figures 1C and S4), that hybridized extensively across
two of the three contact zones (Figures 3 and 4). Hybridization occurs
despite their differences in plumage coloration, suggesting a limited
role of plumage divergence in reproductive isolation. Across these two
contact zones, subspecies differ in the plumage brightness of a few male
color patches. For these color patches, we found coincident centers with
the respective hybrid index/genetic clines but a sharper transition
(i.e., narrower clines), suggesting limited introgression of these
plumage traits (Figure 5; Table 2). We found no other clear morphometric
variation among subspecies. Finally, our demographic inference supports
our observations of no hybridization between S. c. corvina andS. c. hoffmanni, which recently established secondary contact in
the Central Valley of Costa Rica (Table 3).