DOI: 10.5061/dryad.wwpzgmss1
title: Data from: Understanding species boundaries that arise from complex histories: Gene flow across the speciation continuum in the spotted whiptail lizards

description: Gene flow between diverging lineages challenges the resolution of species
 boundaries and the understanding of evolutionary history in recent
 radiations. Here, we integrate phylogenetic and coalescent tools to
 resolve reticulate patterns of diversification and use a perspective
 focused on evolutionary mechanisms to distinguish interspecific and
 intraspecific taxonomic variation. We use this approach to resolve the
 systematics for one of the most intensively studied but difficult to
 understand groups of reptiles: the spotted whiptail lizards of the genus
 Aspidoscelis (A. gularis complex). Whiptails contain the largest number of
 unisexual species known within any vertebrate group and the spotted
 whiptail complex has played a key role in the generation of this diversity
 through hybrid speciation. Understanding lineage boundaries and the
 evolutionary history of divergence and reticulation within this group is
 therefore key to understanding the generation of unisexual diversity in
 whiptails. Despite this importance, long-standing confusion about their
 systematics has impeded understanding of which gonochoristic species have
 contributed to the formation of unisexual lineages. Using reduced
 representation genomic data, we resolve patterns of divergence and gene
 flow within the spotted whiptails and clarify patterns of hybrid
 speciation. We find evidence that biogeographically structured ecological
 and environmental variation has been important in morphological and
 genetic diversification, as well as the maintenance of species boundaries
 in this system. Our study elucidates how gene flow among lineages and the
 continuous nature of speciation can bias the practice of species
 delimitation and lead taxonomists operating under different frameworks to
 different conclusions (here we propose that a two species arrangement best
 reflects our current understanding). In doing so, this study provides
 conceptual and methodological insights into approaches to resolving
 diversification patterns and species boundaries in rapid radiations with
 complex histories, as well as long-standing taxonomic challenges in the
 field of systematic biology.
description: The primary data associated with this research is restriction
 site associated DNA genotyping data sequenced from tissue samples of
 lizards. Data were processed and analyzed using a variety of bioinformatic
 tools for genome assembly and evolutionary analyses. These are described
 in detail in the associated manuscript.
description: # Understanding Species Boundaries that Arise from Complex Histories: Gene
 Flow Across the Speciation Continuum in the Spotted Whiptail Lizards
 [https://doi.org/10.5061/dryad.wwpzgmss1](https://doi.org/10.5061/dryad.wwpzgmss1) ## Appendices Appendix 1: Details of taxonomic sampling Supplementary Information: Taxonomic discussion and supplementary figures and tables ## Description of the data and file structure ADMIXTOOLS.vcf: Dataset used in ADMIXTOOLS analysis BayesAss.immanc: Genotypes used in BayesAss analysis BPP.ctl: Control file used in BPP analysis bpp.txt: Dataset used in BPP analysis Imap.txt: Map file for BPP analysis colossus_coords.txt: coordinates for conStruct analysis (colossus lineage) colossus_distances.txt: geographic distances for conStruct analysis (colossus lineage) colossus_frequencies.txt: genotype data for conStruct analysis (colossus lineage) scalaris_coords.txt: coordinates for conStruct analysis (scalaris lineage) scalaris_distances.txt: geographic distances for conStruct analysis (scalaris lineage) scalaris_frequencies.txt: genotype data for conStruct analysis (scalaris lineage) colossus-gularis.sfs: Site frequency spectrum for dadi analysis colossus-scalaris.sfs: Site frequency spectrum for dadi analysis gularis-scalaris.sfs: Site frequency spectrum for dadi analysis Dsuite.vcf: Genetic dataset for Dsuite analysis gularis.coord: coordinates for EEMS analysis gularis.diffs: diffs file for EEMS analysis gularis.outer: outer file for EEMS analysis colossus_ENMcoords.csv: coordinates used for niche modeling in Maxent (colossus lineage) gularis_ENMcoords.csv: coordinates used for niche modeling in Maxent (gularis lineage) scalaris_ENMcoords.csv: coordinates used for niche modeling in Maxent (scalaris lineage) FixedDiffs.vcf: Genetic data used in Fixed Differences analysis Fst_unisexuals.vcf: SNP dataset used to calculate pairwise Fst between gularis complex taxa and unisexual taxa BEAST.xml: XML dataset used for BEAST analysis ND2.phy: Alignment of mtDNA data for phylogenetic analysis PhyloNetworks_CFs.csv: Concordance factors calculated for PhyloNetworks analysis of gonochoristic taxa PhyloNet_gularis.nex: Dataset used in PhyloNet analysis of gonochoristic taxa PhyloNet_unisexual.nex: Dataset used in PhyloNet analysis with unisexual taxa RAxML.phy: Dataset used in RAxML analysis STRUCURE.ustr: Dataset used in STRUCTURE analysis ## Code/Software ADMIXTOOLS.R: R code for running ADMIXTOOLS analyses conStruct.R: R code for running conStruct analyses dadi_Models.py: Python code for running coalescent modeling analyses in dadi FixedDiffs.R: R code for performing analysis of fixed differences gmyc.R: R code for running GMYC analysis rase.R: R code for running rase analysis extraparams: extraparams file for running STRUCTURE analysis mainparams: mainparams file for running STRUCTURE analysis