Contrasting Genomic Outcomes of Secondary Contact in Bornean Bird Lineages: Insights From Barrier Loci, Demographic History and Genomic Features.

Secondary contact before the completion of reproductive isolation can alter speciation trajectories by impeding divergence through gene flow or accelerating it via reinforcement. Using genomic data, we investigated secondary contact between two pairs of Copsychus (Muscicapidae) lineages in Borneo: subspecies of magpie-robins (C. saularis) and two species of shamas (C. malabaricus and C. stricklandii). Although eastern and western lineages in both groups have similar divergence times, they show markedly different phenotypic and genomic outcomes following contact. Magpie-robins exhibit extensive genomic introgression and weak population structure across Borneo, consistent with shallow plumage clines. In contrast, eastern and western shama lineages remain genetically distinct, with little apparent evidence of late-generation hybrids or backcrosses, indicating strong postmating reproductive isolation. The genomic landscape of divergence in shamas contains pronounced peaks, including loci putatively associated with melanism and song learning and production. Mitogenomic data suggest repeated colonization of Borneo by western Sundaland magpie-robin lineages, displacing older Bornean lineages eastward, likely reflecting their greater ability to exploit open habitats that expanded across the Sunda Shelf during glacial periods. In magpie-robin, but not shama, absolute divergence (DXY) is positively associated with recombination rate at the chromosomal level, suggesting a greater role for within-population processes, such as reduced linked selection in high-recombination regions, in shaping genetic diversity, whereas divergence in shama reflects greater accumulation of differences between populations. Elevated introgression of the Z chromosome in magpie-robins suggests a role for sex-biased processes such as dispersal. Our study highlights Sundaland as a natural laboratory for understanding genomic and evolutionary outcomes of secondary contact.