DOI: 10.5061/dryad.fn2z34v68
title: Data from: Replicate geographic transects across a hybrid zone reveal parallelism and differences in the genetic architecture of reproductive isolation

description: Determining the genetic architecture of traits involved in adaptation and
 speciation is one of the key components of understanding the evolutionary
 mechanisms behind biological diversification. Hybrid zones provide a
 unique opportunity to use genetic admixture to identify traits and loci
 contributing to partial reproductive barriers between taxa. Many studies
 have focused on temporal dynamics of hybrid zones, but geographical
 variation in hybrid zones that span distinct ecological contexts has
 received less attention. We address this knowledge gap by analyzing
 hybridization and introgression between black-capped and Carolina
 chickadees in two geographically remote transects across their extensive
 hybrid zone, one located in eastern and one in central North America.
 Previous studies demonstrated that this hybrid zone is moving northward as
 a result of climate change, but is staying consistently narrow due to
 selection against hybrids. In addition, the hybrid zone is moving ~5x
 slower in central North America compared to more eastern regions,
 reflecting continent-wide variation in the rate of climate change. We use
 whole genome sequencing of 259 individuals to assess whether variation in
 the rate of hybrid zone movement is reflected in patterns of hybridization
 and introgression, and which genes and genomic regions show consistently
 restricted introgression in distinct ecological contexts. Our results
 highlight substantial similarities between geographically remote transects
 and reveal large Z-linked chromosomal rearrangements that generate
 measurable differences in the degree of gene flow between transects. We
 further use simulations and analyses of climatic data to examine potential
 factors contributing to continental-scale nuances in selection pressures.
 We discuss our findings in the context of speciation mechanisms and the
 importance of sex chromosome inversions in chickadees and other species.
description: # Data from: Replicate geographic transects across a hybrid zone reveal
 parallelism and differences in the genetic architecture of reproductive
 isolation Dataset DOI: [10.5061/dryad.fn2z34v68](10.5061/dryad.fn2z34v68)
 ## Description of the data and file structure ### ASAPH "ASAPH"
 directory contains R script and input files for analysis of chromosomal
 rearrangements. ASAPH plotting.R script specifies input files for each
 analysis. All input files for these analyses are located in the ASAPH
 directory. There are two types of files with `.eigneval` and `.eigenvec`
 extensions used for each analysis of chromosomal rearrangements (please
 refer to ASAPH manual for further details). "allo_bcch" =
 comparison between allopatric population of black-capped chickadees.
 "allo_cach" = comparison between allopatric populations of
 Carolina chickadees. Further, four comparisons are made for PCA ASAPH
 analysis: "bcch_pca" = comparison between allopatric
 black-capped chickadees, "cach_pca" = comparison between
 allopatric Carolina chickadees, "mo_pca" = comparison for the
 Missouri transect. "pa_pca" = comparison for the Pennsylvania
 transect. ### BGC analysis "BGC analysis" directory contains
 input files and R scripts for Bayesian Genomic Cline
 analysis. `MO.big.code.R` and `PA.big.code.R` specify steps for the
 analysis of Missouri and Pennsylvania transects
 respectively. `MO.big.Rdata` and `PA.big.Rdata `contain input files for
 Missouri and Pennsylvania transects respectively.  **MO.big.Rdata file
 structure:** * gc1 -- the gghybrid output object containing results of
 Bayesian Genomic Cline analysis for Missouri transect's test run *
 gc.MO.long -- the gghybrid output object containing results of Bayesian
 Genomic Cline analysis for Missouri transect's final run * dat --
 gghybrid object containing information on input SNP table for hybrid index
 estimates * prepdata -- an intermediate gghybrid object used to prepare
 input data for analysis (see gghybrid manual)  * hindlabel -- gghybrid
 object containing posterior hybrid index estimates used for plotting
 **PA.big.Rdata file structure:** * gc1 -- the gghybrid output object
 containing results of Bayesian Genomic Cline analysis for Pennsylvania
 transect's test run * gc.PA.long -- the gghybrid output object
 containing results of Bayesian Genomic Cline analysis for Missouri
 transect's final run * dat -- gghybrid object containing information
 on input SNP table for hybrid index estimates * prepdata -- an
 intermediate gghybrid object used to prepare input data for analysis (see
 gghybrid manual)  * hind label -- gghybrid object containing posterior
 hybrid index estimates used for plotting ### Climate "Climate"
 directory contains R script `Climate analysis.R` used for analysis of
 climatic differences between Missouri and Pennsylvania transects. ###
 Hybrid index "Hybrid index" directory contains R script and
 input files for analysis of heterozygosity and hybrid
 index. `MO.new.ref.hybrid.index.heteroz.R`and `PA.new.ref.hybrid.index.heteroz.R` outline analysis steps for Missouri and Pennsylvania transects and specify input files. All input files for these analyses are located in the Hybrid index directory. All files that have MO and PA in their naming refer to Missouri and Pennsylvania transects respectively. * meta.hiho -- data tables containing metadata (Order in VCF file, ID, sampling region) * hybrid.index.and.hiho.*.W.mtdna - output files containing information on hybrid index and heterozygosity for each transect and information on MtDNA haplotype (0=Black-capped chickadee , 1=Carolina chickadee) * for.hybr.index.012* -- input file in 012 VCFtools format with SNPs. ### PCA "PCA" directory contains R script and input data for the Principal Component Analysis of genomic data. `pca.both.transect.new.reference.R` specifies input files used for Missouri and Pennsylvania transects.  * pca.meta.new.ref.txt -- metadata (Order in VCF file, ID, sampling region) * final.filtered.combined.new.reference..thin10000.012 -- input file in 012 VCFtools format with SNPs filtered to retain sites fixed between allopatric Black-capped and Carolina chickadees and thinned to retain only 1 SNP per 10,000bp window. ### VCF table "VCF table" directory contains filtered panel of SNPs final.filtered.combined.new.reference.recode.vcf used in all downstream analyses: final.filtered.combined.new.reference.recode.vcf -- Filtered dataset in VCFTools format containing SNP table used in all downstream analyses DRYAD_Submission.zip contains all directories in the compressed format