Genetic structure among subspecies
In a previous study, we found evidence for reduced gene flow near the
contact zone between the all-black S. c. corvina and the piedS. c. hicksii and S. c. hoffmanni subspecies (Ocampo et
al., 2022a). Here, we have extended the genomic aspect of our previous
study by increasing sample size and spatial resolution of this region
and adding phenotypic data. We found an important barrier to gene flow
that is partially concordant with the Talamanca mountain range and with
the range limits between the black and pied subspecies (Figure 1).
Consistent with the Talamancas acting as a geographic barrier, high
genetic divergence between Caribbean and southern Pacific populations
have been found in other lowland taxa in this region (e.g., in frogs
[Crawford et al., 2003, Robertson & Zamudio, 2009], snakes
[Zamudio & Greene, 1997], caimans [Venegas-Anaya et al., 2008],
beetles [Kohlmann & Wilkinson, 2007], and birds [Hackett, 1996;
Marks et al., 2002]). Moreover, the South Pacific region of Costa Rica
is considered an important climate refuge (Haffer, 1974), harboring high
biological richness and endemism in plants and animals (Crain &
Fernandez, 2020; Kohlmann et al., 2010; Pareira & Barrantes, 2009).Sporophila corvina subspecies established secondary contact at
both ends of the Talamanca mountain range (Figure 1A, no. 1 & 3), and
we found significant gene flow between the Pacific and Caribbean
populations at the Canal in central Panama (Figure 1B, blue shades). In
contrast, there is reduced gene flow between S. c. corvina andS. c. hoffmanni in the Central Valley of Costa Rica. These
observations suggest that levels of gene flow differed between the two
contact zones despite similar degrees of phenotypic plumage divergence
(black vs. pied plumage). Importantly, from the six individuals
collected in Central Valley contact zone (San Ramón [SRA]; Table
S1), two individuals showed the genetic makeup of the Pacific
subspecies, while four individuals showed the genetic makeup of the
Caribbean subspecies, which confirms that the two subspecies are in
contact but are likely not hybridizing or doing so at levels we cannot
detect in this study.
When determining genetic structure among individuals, our samples were
best clustered into three genetic groups. Clusters are consistent, in
general, with the subspecies assignments, suggesting that described
subspecies correspond to recognizable lineages. However, we found
evidence of admixture between clusters (Figure 1C), between pairs of
clusters, and even a few individuals with signatures of ancestry from
the three subspecies (Figure 3). We found that corvina is the
most differentiated subspecies, with paired FSTvalues that are twice the value between hoffmanni andhicksii. This pattern is consistent with our expectations of
stronger differentiation between phenotypically differentiated
subspecies and with the hierarchical population structure identified
previously (Ocampo et al., 2022a).