Population structure within Sporophila corvina
We used three complementary methods to estimate patterns of genetic
differentiation and population structure. The Estimated Effective
Migration Surfaces (EEMS) approach found that the continental divide
between Caribbean and Pacific slopes forms the most important barrier
where gene flow is 100 times lower than the average despite relatively
short geographic distance (Fig. 1B). This continental divide extends
from the Central Valley of Costa Rica along the Talamanca mountain range
throughout western Panama, reaching the Canal area in central Panama
(map areas colored dark orange). Conversely, individuals on either side
of both slopes showed high genetic similarity, likely due to strong
connectivity. Our results were consistent among deme densities (200,
300, and 400 demes), and between runs (Figure S2).
Further, we found that S. corvina individuals from Costa Rica and
Panama were best grouped into three genetic clusters (Figure 1C), as
this clustering presented the lowest cross validation error (population
assignments for K = 2–5 are available in Figure S3). The three
genetic groups that we identified were largely consistent with the known
distributions of the three subspecies present in the region (Figures
1A,C and S4). However, we also identified a large proportion of
individuals with mixed ancestries, suggesting pervasive gene flow
between subspecies. From the 255 individuals included, 107 were
identified as pure parental subspecies (53 corvina , 37hoffmanni , and 17 hicksii ) and 148 showed some evidence of
admixture (79 corvina-hicksii , 16 corvina-hoffmanni , 46hoffmanni-hicksii, and 7 three-way hybrids; Figure 1C). We found
relatively low genetic differentiation between subspecies pairs; the
highest differentiation occurred between black and pied subspecies
(corvina vs hicksii : FST = 0.074,corvina vs hoffmanni : FST = 0.066), while
the two pied subspecies showed the lowest genetic differentiation
(hoffmanni vs hicksii : FST = 0.039).
Finally, the PCA analysis identified roughly three genetic clusters; the
first axis of variation explained 4.44% of the genetic variation and
primarily separated corvina individuals from the two pied
subspecies and the second PC axis explained 2.10% of the genetic
variation, and divided hicksii from the other two subspecies
(Figures 3 and S5).