DOI: 10.5061/dryad.brv15dv7k
title: Contrasting signatures of introgression in North American box turtle (Terrapene spp.) contact zones

description: Hybridization occurs differentially across the genome in a balancing act
 between selection and migration. With the unprecedented resolution of
 contemporary sequencing technologies, selection and migration can now be
 effectively quantified such that researchers can identify genetic elements
 involved in introgression. Furthermore, genomic patterns can now be
 associated with ecologically relevant phenotypes, given availability of
 annotated reference genomes. We do so in North American box turtles
 (Terrapene) by deciphering how selection affects hybrid zones at the
 interface of species-boundaries and identifying genetic regions
 potentially under selection that may relate to thermal adaptations. Such
 genes may impact physiological pathways involved in temperature-dependent
 sex determination, immune system functioning, and hypoxia tolerance. We
 contrasted these patterns across inter- and intra-specific hybrid zones
 that differ temporally and biogeographically. We demonstrate hybridization
 is broadly apparent in Terrapene, but with observed genomic cline patterns
 corresponding to species boundaries at loci potentially associated with
 thermal adaptation. These loci display signatures of directional
 introgression within intra-specific boundaries, despite a genome-wide
 selective trend against intergrades. In contrast, outlier loci for
 inter-specific comparisons exhibited evidence of being under selection
 against hybrids. Importantly, adaptations coinciding with
 species-boundaries in Terrapene overlap with climatic boundaries and
 highlight the vulnerability of these terrestrial ectotherms to
 anthropogenic pressures.
description: Samples were sequenced on an Illumina Hi-Seq 4000 at
 1x100 bp. Reads were demultiplexed and aligned using
 ipyrad. The "scaffold alignment" (AKA
 "fulldataset") was mapped to the <em>Terrapene mexicana
 triunguis</em> reference genome (scaffold-level; GenBank Accession:
 GCA_002925995.2). The "transcriptome
 alignment" (AKA "genes") was mapped to the <em>T. m.
 triunguis</em> reference transcriptome to obtain annotation
 information.
description: See the <em>readme.txt</em> file for comments on each
 of the directories and files. The <em>Terrapene
 </em>population codes are as follows: 
 <em>Terrapene carolina</em> 
 <em>T. carolina carolina</em> - Woodland box turtle
 (EA) <em>T. carolina major</em> - Gulf
 Coast box turtle (GU) 
 <em>Terrapene mexicana</em> <em>T.
 mexicana triunguis - </em>Three-toed box turtle (TT)
 <em>Terrapene ornata</em>
 <em>T. ornata ornata  </em>- Ornate box
 turtle (ON)  Input
 files are included for the following analyses: 
 ADMIXTURE (via the AdmixPipe pipeline) 
 https://github.com/stevemussmann/admixturePipeline)
 NewHybrids (via HybridDetective and
 parallelnewhybrid) 
 https://github.com/bwringe/hybriddetective
 https://github.com/bwringe/parallelnewhybrid)
 TESS3 (via tess3r)
 Genomic clines BGC (Bayesian Genomic
 Clines) INTROGRESS 
 RDA - Redundancy Analysis Input
 files are either in VCF or GENEPOP format. Additionally, the VCF files
 have been filtered for missing data (50%), limited to 1 SNP per ddRAD
 locus, and including only bi-allelic sites. For the
 RDA, missing data per were imputed per population in one of the included R
 scripts, as RDA requires no missing data. NewHybrids
 was run via the hybridDetective and parallelnewhybrid pipelines in R. The
 scripts to do so are located at:
 https://github.com/btmartin721/R_scripts.