DOI: 10.5061/dryad.h44j0zpqx
title: Data from: Gene flow and isolation in the arid Nearctic revealed by genomic analyses of desert spiny lizards

description: The opposing forces of gene flow and isolation are two major processes
 shaping genetic diversity. Understanding how these vary across space and
 time is necessary to identify the environmental features that promote
 diversification. The detection of considerable geographic structure in
 taxa from the arid Nearctic has prompted research into the drivers of
 isolation in the region. Several geographic features have been proposed as
 barriers to gene flow, including the Colorado River, Western Continental
 Divide, and a hypothetical Mid-Peninsular Seaway in Baja California.
 However, recent studies suggest that the role of barriers in genetic
 differentiation may have been overestimated when compared to other
 mechanisms of divergence. In this study, we infer historical and spatial
 patterns of connectivity and isolation in Desert Spiny Lizards (Sceloporus
 magister) and Baja Spiny Lizards (S. zosteromus), which together form a
 species complex composed of parapatric lineages with wide distributions in
 arid western North America. Our analyses incorporate mitochondrial
 sequences, genomic-scale data, and past and present climatic data to
 evaluate the nature and strength of barriers to gene flow in the region.
 Our approach relies on estimates of migration under the multispecies
 coalescent to understand the history of lineage divergence in the face of
 gene flow. Results show that the S. magister complex is geographically
 structured, but we also detect instances of gene flow. The Continental
 Divide is a strong barrier to gene flow, while the Colorado River is more
 permeable. Analyses yield conflicting results for the catalyst of
 differentiation of peninsular lineages in S. zosteromus. Our study shows
 how large-scale genomic data for thoroughly sampled species can shed new
 light on biogeography. Furthermore, our approach highlights the need for
 the combined analysis of multiple sources of evidence to adequately
 characterize the drivers of divergence.
description: We provide several input data files for the various analyses that were
 performed. We also provide documents containing Supplementary Methods,
 Tables and Figures. **Specific file information** Smagister_mtDNA77.phy =
 alignment of mtDNA data. magister_all.phy = alignment of nuclear data.
 magister_all_BPP.phy = nuclear alignments for BPP.
 magister_BPP_SpeciesTree.phy = nuclear alignments for species tree
 inference in BPP. magister_pruned_BPP_IM.phy = pruned nuclear alignments
 for IM analysis in BPP. zosteromus_only.ugeno = genotype data for *S.
 zosteromus* for use in sNMF. ingroup_only.ugeno = genotype data for all
 ingroup individuals for use in sNMF. magister_only.ugeno = genotype data
 for all *S. magister* individuals for use in sNMF. magister_all_SVDq.nexus
 = input nuclear alignment for SVDquartets analysis.
 SupplementaryMaterialsAndMethods-Final.docx = Online Supplementary
 Materials and Methods. SupplementaryTablesGB-Final.xlsx = Online
 Supplementary Tables. SupplementaryFigures-Final.docx = Online
 Supplementary Figures.