DOI: 10.5061/dryad.w6m905qwf
title: Data from: Environmental variation influences genome evolution in Hispaniolan trunk anoles (<i>Anolis distichus</i>)

description: Environmental variation often drives evolutionary processes like
 population differentiation, local adaptation, and speciation. We used
 genome-scale data to investigate the contribution of environmental
 variation to evolution of the North Caribbean bark anole (Anolis
 distichus), a widespread common lizard that exhibits impressive phenotypic
 variation across varying habitats on the island of Hispaniola. We obtained
 new double-digest restriction-associated DNA sequence data (ddRADseq) from
 nearly 200 individuals and used 53 GIS data layers representing a range of
 environmental variables. We first asked how environmental variation has
 contributed to genome-wide differentiation across Hispaniola. We found
 that Hispaniola's three major mountain ranges contribute to deep
 genome-wide divergence and patterns of migration, that some deeply
 genomically divergent populations occupy significantly different
 environments, and that environmental variation is broadly capable of
 explaining more range-wide genomic differentiation than geographic
 distance alone. We then asked whether specific loci exhibit evidence of
 local adaptation to environmental variation using genotype-environment
 association (GEA) methods. We initially identified hundreds of loci
 broadly distributed across the genome that are significantly correlated
 with one or more environmental variables, but ultimately found that fewer
 than 100 of these candidate loci are shared across different GEA methods
 applied to our entire dataset, and that only 10 candidate loci are shared
 by independent analyses of two regional subsets of our dataset, suggesting
 parallel evolution is infrequent. Our study shows that abiotic
 environmental variation has played a critical role in explaining the
 evolution and diversity of a widespread and phenotypically diverse
 Caribbean anole species.
description: We sequenced and recovered high-quality genotypes from 191
 specimens of the North Caribbean bark anole (<em>Anolis
 distichus</em>) from the island of Hispaniola. We obtained tissue
 samples from tail tips and livers, extracted genomic DNA, and prepared
 double-digest RADseq (ddRADseq) libraries following the protocol of
 Peterson et al. (2012). We aligned ddRADseq reads to the <em>Anolis
 distichus</em> reference genome and called SNPs using bcftools
 mpileup before filtering with VCFtools.
description: # Data from: Environmental variation influences genome evolution in
 Hispaniolan trunk anoles (*Anolis distichus*) This repository contains
 data associated with the published article "Environmental Variation
 Influences Genome Evolution in Hispaniolan Trunk Anoles (*Anolis
 distichus*)":
 [https://doi.org/10.1111/mec.17622](https://doi.org/10.1111/mec.17622).
 Please see article for details of data collection and analysis. Code
 available for population genomics and ecological niche model analyses
 here:
 [https://github.com/TannerMyers/distichus-population-genomics](https://github.com/TannerMyers/distichus-population-genomics), and here: [https://github.com/TannerMyers/distichus-spatial-variation](https://github.com/TannerMyers/distichus-spatial-variation). ## Description of data and file structure 1. `popgen.tar.gz` - Variant call format files for population genomics analyses (ADMIXTURE, PCA, Mantel tests, EEMS) * `distichus_geno100_filtered_LD_50kb_100_0.1_biallelic_pruned.recode.vcf` - VCF with all samples meeting filters with fully complete linkage-pruned SNPs * `distichus_geno90_filtered_LD_50kb_100_0.1_biallelic_pruned.recode.vcf` - VCF with all samples meeting filters with 90% complete linkage-pruned SNPs * `distichus_geno80_filtered_LD_50kb_100_0.1_biallelic_pruned.recode.vcf` - VCF with all samples meeting filters with 80% complete linkage-pruned SNPs * `south_geno90_50kb_100_0.1_biallelic.recode.vcf` - VCF containing samples mainly from Hispaniola's South Paleo-island used for hierarchical population structure analyses * `north_geno90_50kb_100_0.1_biallelic.recode.vcf` - VCF containing samples mainly from Hispaniola's North Paleo-island used for hierarchical population structure analyses 2. `IBE_GEA.tar.gz` - Input files for GDM, pRDA, and LFMM * `distichus-filt-imp-genind.RData` - 5,746 linkage-pruned SNPs from 90% complete dataset, imputed by population, saved as `genind` object and used as input data for generalized dissimilarity modeling analysis (GDM). * `selected-environmental-variables.tsv` - environmental variables used as predictors for redundancy (RDA) and generalized dissimilarity modeling (GDM) analyses. * `hellinger-transformed-allele-frequencies.RData` - Hellinger-transformed allele frequencies for each population (sampling locality) used as input for RDA. * `hellinger-transformed-quickMEM.RData` - dbMEMs estimated from Hellinger-transformed allele frequencies using the `quickMEM` function available here: [https://raw.githubusercontent.com/zdealveindy/anadat-r/master/scripts/NumEcolR2/quickMEM.R](https://raw.githubusercontent.com/zdealveindy/anadat-r/master/scripts/NumEcolR2/quickMEM.R) * `distichus_imp_LD.vcf` - VCF with 39,427 imputed SNPs across full sampling used for genotype-environment association analyses. * `distichus_imp_LD.lfmm` - `distichus_imp_LD.vcf` in `.lfmm` file format for latent factor mixture model analysis. * `fwd-select-env-pc1-3.tsv` - Principal components 1-3 estimated from `selected-environmental-variables.tsv` used as predictors for latent factor mixture model (LFMM)analysis. 3. `enms.tar.gz` - thinned occurrence records and range polygons from ENMTools analyses * `K2_alpha_poly-thinned-points.csv` - occurrence records for the "K2" population identified by ADMIXTURE. * `K2_alpha_poly.*` (extensions: `.cpg`, `.dbf`, `.prj`, `.shp`, `.shx`) - shapefile for polygon used to thin records of the "K2" population. * `K3_alpha_poly-thinned-points.csv` - occurrence records for the "K3" population identified by ADMIXTURE. * `K3_alpha_poly.*` (extensions: `.cpg`, `.dbf`, `.prj`, `.shp`, `.shx`) - shapefile for polygon used to thin records of the "K3" population. * `K4_alpha_poly-thinned-points.csv` - occurrence records for the "K4" population identified by ADMIXTURE. * `K4_alpha_poly.*` (extensions: `.cpg`, `.dbf`, `.prj`, `.shp`, `.shx`) - shapefile for polygon used to thin records of the "K4" population. * `K5_alpha_poly-thinned-points.csv` - occurrence records for the "K5" population identified by ADMIXTURE. * `K5_alpha_poly.*` (extensions: `.cpg`, `.dbf`, `.prj`, `.shp`, `.shx`) - shapefile for polygon used to thin records of the "K5" population. * `dom14_poly-thinned-points.csv` - occurrence records for the western *Anolis distichus dominicensis* populations identified as a genetically distinct population by ADMIXTURE. * `dom14_poly.cpg.*` (extensions: `.cpg`, `.dbf`, `.prj`, `.shp`, `.shx`) - shapefile for polygon used to thin records of western *Anolis distichus dominicensis* populations. * `fav_poly-thinned-points.csv` - occurrence records for *Anolis distichus favillarum* identified as a genetically distinct population by ADMIXTURE. * `fav_poly.*` (extensions: `.cpg`, `.dbf`, `.prj`, `.shp`, `.shx`) - shapefile for polygon used to thin records of the population corresponding to *Anolis distichus favillarum*. * `tiburon_poly-thinned-points.csv` - occurrence records for the Tiburon *Anolis distichus dominicensis* populations identified as a genetically distinct population by ADMIXTURE. * `tiburon_poly.*` (extensions: `.cpg`, `.dbf`, `.prj`, `.shp`, `.shx`) - shapefile for polygon used to thin records of the population found on Haiti's Tiburon penninsula. 4. `distichus-species-group-Hispaniola-only-popmap-cleaned.tsv` - tab-delimited spreadsheet with locality information for the 191 lizards that were sequenced and met quality filters for this study. 5. `north-island-dataset-master.tsv` - tab-delimited spreadsheet with locality information for the 143 lizards from Hispaniola's North paleo-island that were sequenced and met quality filters for this study. 6. `south-island-dataset-master.tsv` - tab-delimited spreadsheet with locality information for the 48 lizards largely from Hispaniola's South paleo-island that were sequenced and met quality filters for this study.