DOI: 10.5061/dryad.kh18932k9
title: Data From: Estimation of genome-wide coupling in rattlesnake hybrids provides insight into the process of speciation and its progress

description: 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 highlight the roles of coupling in complex barrier effects, including
 the Large-Z effect, cytonuclear incompatibilities, and incompatibilities
 related to venom resistance. Together, our findings demonstrate the
 mechanism by which coupling is predicted to lead to speciation, and
 highlight how genome-wide quantification of coupling presents a promising
 framework for understanding progress towards speciation and the processes
 that underlie this progress.
description: # 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 corresponding standardized gene symbols. ##### Variables * gtf_gene:
 *C. viridis* gene IDs as in the reference genome annotation *
 gtf_gene_trimmed: shorter gene IDs (as in the reference genome annotation)
 * crovir_transcript: transcript IDs (as in the reference genome
 annotation) * converted_id: standardized gene symbols *
 converted_id_no_dups: standardized gene symbols (with numbers added in
 case of duplicates) #### File: ClineParameters_bgchm.txt **Description:**
 Cline parameters for all variants in the VCF provided ##### Variables *
 Chrom: Chromosome name * Pos: position * v.med: cline slope * v.lb: cline
 slope lower 95%CI * v.ub: cline slope upper 95%CI * c.med: cline center *
 c.lb: cline center lower 95%CI * c.ub: cline center upper 95%CI #### File:
 hybrid.txt **Description:** List of putative hybrid IDs #### File:
 mito_haplotypes.txt **Description:** mitochondrial haplotypes for all
 individuals in this study ##### Variables * sample_ID: Individual ID *
 mtDNA_nad4: mitochondrial haplotype (based on NADH4) #### File:
 parental.vir.txt **Description:** list of individuals belonging to the
 parental species *C. viridis* #### File: parental.scut.txt
 **Description:** list of individuals belonging to the parental species *C.
 scutulatus* #### File:
 Scut.Vir.Hybrid.combined.cohort.118.samples.snps.g.phased.vcf
 **Description:** VCF containing all biallelic variants that passed
 filtration steps for parental species individuals and hybrids. ##
 Code/software Code and scripts are available on GitHub:
 [https://github.com/yzfranci/GenomicCoupling](https://github.com/yzfranci/GenomicCoupling) ## Access information Other publicly accessible location of the data: Raw genomic data is available on SRA (BioProject: PRJNA1137891)