Impact of a putative riverine barrier on genomic population structure and gene flow in the presence of sexual selection

Gene flow connects populations and facilitates the exchange of alleles, impacting speciation and adaptation. In western Panama, lekking golden-collared and white-collared manakins (Manacus vitellinus and M. candei, respectively) interbreed in a narrow hybrid zone across which males’ brilliant yellow collar plumage, principally controlled by the carotenoid metabolism gene BCO2,  has introgressed from vitellinus into candei under sexual selection. Plumage introgression is sharply limited across the lower reaches of the widest river in the region, but both color morphs occur on both riverbanks at its headwaters. Previous authors have speculated that the river may be a strong barrier to gene flow, preventing further plumage color introgression, but this hypothesis has never been tested. In this study, we used between ~10,000 and 14,000 single nucleotide polymorphisms (SNPs) to test this hypothesis by assessing genetic differentiation and estimating gene flow across the river. The data ..., , # Impact of a putative riverine barrier on genomic population structure and gene flow in the presence of sexual selection

Dataset DOI: [10.5061/dryad.6hdr7src2](10.5061/dryad.6hdr7src2)

## Description of the data and file structure

The data contained in this repository, along with methods descriptions in the paper and data associated with NCBI BioProject PRJNA951544 are sufficient to reproduce all analyses from the related paper, published in Evolution and with the same title as this dataset.

### Code

#### Data processing

raw-to-gstacks.sh - Shell commands to demultiplex raw reads (not needed if downloading reads from NCBI), align to the M. vitellinus reference (available from NCBI at [ASM171598v3](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_001715985.3/)), merge bams where the same individual was sequenced multiple times, then assemble contigs using gstacks.

snp-filtering.sh - Shell commands to call SNPs with Stacks populations then filter with VCFtools, creating two VCF fi...,