Data From: Estimation of genome-wide coupling in rattlesnake hybrids provides insight into the process of speciation and its progress

Genomic coupling theory predicts that progress towards speciation involves a transition from the dominant effects of selection on individual barrier loci to the aggregate effects of direct and indirect selection across loci that collectively produce stronger barriers to gene flow through genetic associations. However, our ability to test this prediction and to understand the factors that lead to the buildup and maintenance of these associations has been limited by a lack of methods to estimate variation in coupling across the genome. Here we develop approaches to quantify coupling using window-based estimates of Barton’s coupling coefficient and apply these to a dataset of 118 genomes from a rattlesnake hybrid zone. Our results provide empirical evidence for genomic coupling that is consistent with the predicted relationships of coupling with recombination, linkage, and inferences of selection. Applying these approaches, we find evidence for coupling within and among chromosomes, and hi..., , # Estimation of genome-wide coupling in rattlesnake hybrids provides insight into the process of speciation and its progress

Dataset DOI: [10.5061/dryad.kh18932k9](10.5061/dryad.kh18932k9)

## Description of the data and file structure

This dataset contains all the processed data required to run genomic coupling analysis that relates to the Francioli et al. (2025) study.

### Files and variables

#### File: chromosomes.txt

**Description:** 

##### Variables

* Chrom: Chromosome names
* size: size of chromosomes (number of bp)
* type: chromosome category: macro- or microchromosome, or sex chromosome (Z)

#### File: ancestry_blocks_ScutVir.vcf

**Description:** vcf of the ancestry blocks (continuous blocks of the genome that are inherited from either parental species) for the *C. viridis* x *C. scutulatus* hybrids

#### File: Cvv_GTF_to_converted_names.txt

**Description:** This table contains the gene names as it is in the *C. viridis* reference genome annotation, and there correspond...,