DOI: 10.5061/dryad.47d7wm3rz
title: Hybrid zone analysis using coalescent-based estimates of introgression and migration in plateau fence lizards (Sceloporus tristichus)

description: Coalescent modeling of hybrid zones can provide novel insights into the
 historical demography of populations, including divergence times,
 population sizes, introgression proportions, migration rates, and the
 timing of hybrid zone formation. We used coalescent analysis to determine
 whether the hybrid zone between phylogeographic lineages of the Plateau
 Fence Lizard (Sceloporus tristichus) in Arizona formed recently due to
 human-induced landscape changes, or if it originated during Pleistocene
 climatic shifts. Given the presence of mitochondrial DNA from another
 species in the hybrid zone (Southwestern Fence Lizard, S. cowlesi), we
 tested for the presence of S. cowlesi nuclear DNA in the hybrid zone as
 well as reassess the species boundary between S. tristichus and S.
 cowlesi. The data files supplied here include mtDNA sequences and nuclear
 DNA collected using ddRADseq for both study species. Files for
 phylogeographic and hybrid zone analysis are provided.
description: Mitochondrial DNA: The mitochondrial <em>ND1</em>
 protein-coding gene (969 bp) was amplified and sequenced using standard
 PCR methods. New sequences were combined with previously published data,
 which included additional hybrid zone samples and broad-scale sampling of
 other species. Genbank numbers for each sample are listed in the
 supplemental table associated with the manuscript.
 Nuclear DNA: The nuclear data was collected using double
 digestion restriction site associated DNA sequencing (ddRADseq). All
 samples collected from 2002, 2012, and 2022 were assembled together (335
 hybrid zone samples). For the phylogeographic analysis, a total of 56
 samples were used with species assignments determined using mtDNA-based
 phylogenetic placement.
description: # Hybrid zone analysis using coalescent-based estimates of introgression
 and migration in plateau fence lizards (Sceloporus tristichus) Dataset
 DOI: [10.5061/dryad.47d7wm3rz](10.5061/dryad.47d7wm3rz) ## Description of
 the data and file structure Data includes mtDNA sequences and ddRADseq
 data. ### Files and variables #### File: hzar.csv **Description:** Hybrid
 zone data for conducting spatial cline analysis in HZAR. ##### Variables *
 locationID: Population * distance: Distance from northern population in km
 * snp2002.Q: 2002 SNP admixture Q value (under K=2) * snp2002.N: 2002
 sample size * snp2012.Q: 2012 SNP admixture Q value (under K=2) *
 snp2012.N: 2012 sample size * snps2022.Q: 2022 SNP admixture Q value
 (under K=2) * snps2022.N: 2022 sample size * snpsAll.Q: all years combined
 SNP admixture Q value (under K=2) * snpsAll.N: all years combined sample
 size * mtdna2022.N: 2022 sample size * mtdna2022.F: 2022 mtDNA frequency
 of northern haplotype (vs. southern) * mtdna2002.F: 2002 mtDNA frequency
 of northern haplotype (vs. southern) * mtdna2002.N: 2002 sample size *
 mtdna2012.F:  2012 mtDNA frequency of northern haplotype (vs. southern) *
 mtdna2012.N: 2012 sample size * mtdnaALL.N: all years combined sample size
 * mtdnaALL.F:  all years combined mtDNA frequency of northern haplotype
 (vs. southern) #### File: mtDNA_775.phy **Description:**  MtDNA sequence
 alignment (ND1 gene).  #### File: phylogeography.vcf **Description:**  SNP
 data for the phylogeographic analysis of *S. tristichus* and *S. cowlesi*.
 #### File: phylogeography_concatenated.phy **Description:** concatenated
 ddRADseq data for the phylogenetic analysis of *S. tristichus* and *S.
 cowlesi*. Sites with &gt;10% missing data are removed. #### File:
 hybridzone.vcf **Description:** SNP data for the hybrid zone analysis of
 *S. tristichus*, all years combined. #### File: BPP.zip
 **Description:** ddRADseq data, imap, control files for BPP analyses of
 introgression and migration separated into seven folders (6 MSC-I; 1
 MSC-M). The six MSC-I folders correspond to the six hybrid populations.
 Each of these six folders contains the files necessary to run the MSC-I
 model in BPP. The MSC-M folder corresponds to the migration analysis of
 the parental populations. ## Code/software **Phylogenetic analysis with
 iqtree** *.phy files are ready to run in iqtree: `iqtree -s ND1_775.phy
 -alrt 1000 -bb 1000` `iqtree -s phylogeography_concatenated.phy -alrt 1000
 -bb 1000` **Admixture analysis of population structure** *.vcf files are
 used to run admixture. Filtering is required (we used vcftools), then
 covert to bed using plink2: `vcftools --vcf *.vcf --max-missing 0.5
 --max-alleles 2 --maf 0.01 --thin 50 --recode --out filtered` `plink2
 --vcf filtered.recode.vcf --allow-extra-chr --make-bed --out final`
 admixture run: `for k in {1..8}; do` ` admixture final.bed --seed=$RANDOM
 --cv=50 -C 0.0001 $k &gt;results$k.txt` ` done`; **BPP analysis of
 introgression and migration** `bpp --cfile bpp.ctl` ## Access information
 Other publicly accessible locations of the data: * Mitochondrial DNA
 sequences: Genbank accessions PQ901620–PQ901697 and PV462017–PV462129. *
 Nuclear ddRADseq data: NCBI SRA Accession PRJNA1211730