Mosaic tri-lineage secondary contact shapes diverse genomic outcomes in darters

Speciation does not always lead to complete reproductive isolation, which can result in hybrid zones with gene flow. In freshwater fishes, secondary contact and hybridization can arise when river courses shift. Shifting river courses can create physical and ecological dispersal barriers, producing fragmented species distributions within the same stream system. Here, we investigate a secondary contact zone in western New York (USA) between the Tessellated Darter (Etheostoma olmstedi) and the Johnny Darter (Etheostoma nigrum), integrating double digest restriction site associated DNA sequencing (ddRADseq), low-coverage whole genome sequencing (lcWGS), and mtDNA datasets. Our analyses reveal a complex tri-lineage hybrid zone of E. olmstedi and two divergent E. nigrum lineages. lcWGS and ddRADseq approaches yield similar overall results for population genetic structure; however, the two approaches differ in estimates of the magnitude of population differentiation. Several sites with ongoing admixture are proximate to stream confluences and form a temporally stable mosaic of hybridization across the contact zone. We observe active and apparently stable states of hybridization, supporting the hypothesis that niche partitioning by stream size maintains species identity. The species and populations in the contact zone maintain high levels of genome-wide differentiation across streams. Our study provides insight into the dynamic process of secondary contact and highlights the array of possible genomic outcomes of hybridization.