Replicate contact zones suggest a limited role of plumage in reproductive isolation among subspecies of the variable seedeater (Sporophila corvina)

Abstract

After establishing secondary contact, recently diverged populations may remain reproductively isolated or may hybridize to a varying extent depending on factors such as hybrid fitness and the strength of assortative mating. Here, we used genomic and phenotypic data from three independent contact zones between subspecies of the variable seedeater (Sporophila corvina) to examine how coloration and genetic divergence shape patterns of hybridization. We found that differences in plumage coloration are probably maintained by divergent selection across contact zones; however, the degree of plumage differentiation does not match overall patterns of hybridization. Across two parallel contact zones between populations with divergent phenotypes (entirely black vs. pied plumage), populations hybridized extensively across one contact zone but not the other, suggesting that plumage divergence is not sufficient to maintain reproductive isolation. Where subspecies hybridized, hybrid zones were wide and formed by later-generation hybrids, suggesting frequent reproduction and high survivorship for hybrid individuals. Moreover, contemporary gene flow has played an important role in shaping patterns of genetic structure between populations. Replicated contact zones between hybridizing taxa offer a unique opportunity to explore how different factors interact to shape patterns of hybridization. Overall, our results demonstrate that divergence in plumage coloration is important in reducing gene flow but insufficient in maintaining reproductive isolation in this clade, and that other factors such as divergence in song and time since secondary contact may also play an important role in driving patterns of reduced hybridization and gene flow.

Genomic islands of speciation harbor genes underlying coloration differences in a pair of Neotropical seedeaters

“…Whole-genome sequencing of Sporophila beltoni and Sporophila plumbea revealed little genetic differentiation between this species pair despite their marked phenotypic differences, similar to what has been found in other Sporophila species [14,26,32]. The highest levels of differentiation were concentrated in three narrow peaks, containing only six genes, which are candidates for mediating the phenotypic differences between our focal taxa.…”

“…Taken together, these regions show evidence of having undergone selection and experiencing reduced migration compared to other areas in the genome, especially when analyzing allopatric samples which may be more representative of historical processes (see Discussion). Whole-genome sequencing of Sporophila beltoni and Sporophila plumbea revealed little genetic differentiation between this species pair despite their marked phenotypic differences, similar to what has been found in other Sporophila species [14,26,32]. The highest levels of differentiation were concentrated in three narrow peaks, containing only six genes, which are candidates for mediating the phenotypic differences between our focal taxa.…”

“…These genes likely mediate the different coloration phenotypes observed across males from different species [14,20,30], which in turn, impact species recognition [20]. Similarly, the Variable Seedeater superspecies complex ( S. corvina , S. intermedia , S. murallae , and S. americana ) and Morelet’s Seedeater ( S. morelletti ) represent additional cases of plumage diversity, yet shallow genetic differentiation within Sporophila [26,27,31,32]. Overall, these examples suggest that localized genetic differences may mediate divergence in coloration traits, contributing to reproductive isolation and speciation [20].…”

triangulaR:an R package for identifying AIMs and building triangle plots using SNP data from hybrid zones

“…thousands) SNPs from which AIMs can be identified, but practices for sampling parental populations and identifying AIMs vary widely (e.g. Del-Rio et al, 2022; Ocampo et al, 2023; Preckler-Quisquater et al, 2023). The sample size needed for each parental group is an important consideration because any method for identifying AIMs depends on identifying genomic sites that reliably show differentiation between the parental groups (Rosenberg et al, 2003).…”