Investigating the Population Genomics of Campylorhynchus in Ecuador Using ddRADseq Data

This study analyzed population genomic patterns in two hybridizing Campylorhynchus species distributed along a precipitation gradient in coastal Ecuador. In total, 112 individuals of C. zonatus and C. fasciatus were sampled and genotyped using double-digest restriction site-associated DNA sequencing (ddRADseq). Multiple population genomic analyses were conducted to elucidate the population structure, isolation by distance, environmental associations, and introgression dynamics between these species. The code provided here documents the analytical workflows, including testing and troubleshooting. These scripts reflect the iterative nature of bioinformatic workflows, rather than presenting finalized pipelines. Please contact the corresponding author for clearer, reproducible versions of any specific analysis. Overall, this study takes a landscape genomic approach to disentangle the drivers of genomic differentiation and introgression between two hybridizing Campylorhynchus species along an environmental gradient in Ecuador!