Genomic data support interspecific divergence but reveal limited population structure and cryptic hybridization in <i>Rallus elegans</i> (King Rail) and <i>R. crepitans</i> (Clapper Rail)

Abstract Coastal ecosystems across the globe are threatened due to anthropogenic activities and human-mediated climate change. Sea level rise and altered hydrology may lead to increased secondary contact between closely related freshwater and saltwater species, such as Rallus elegans (King Rail) and R. crepitans (Clapper Rail). The 2 rallid species are secretive marsh birds with declining populations and largely uncharacterized population structure. Rallus elegans and R. crepitans are known to hybridize, but the extent of hybridization and introgression have not been studied using modern genomics. Hence, to increase our understanding of the connectivity of R. crepitans populations and their hybridization with R. elegans, we adopted a genomic approach using restriction site-associated DNA sequencing (RAD-seq) to examine intra- and interspecific variation in single nucleotide polymorphisms (SNPs) from populations along the east coast of North America. We obtained 154 R. crepitans samples from Connecticut, Delaware, North Carolina, South Carolina, and Louisiana and 50 R. elegans samples from North Carolina and Louisiana. In addition, we included 15 putative hybrids collected in Louisiana. Using 8,834 SNPs across the genome, we found that some individuals had been misidentified in the field, including 5 cryptic hybrids from Delaware salt marshes classified as R. crepitans and 16 individuals from Louisiana. There was evidence of hybridization across all sampled populations with more than 20% of sampled individuals having some degree of introgression based on 142 SNPs found to be fixed between the parental species. Our results suggest that R. crepitans is panmictic, and we found no support for the currently described subspecies in the sampling regions. The 2 R. elegans populations show some evidence of differentiation, albeit with weak support.