DOI: 10.5061/dryad.41n16
title: Data from: Phylogeographic structure, demographic history, and morph composition in a colour polymorphic lizard

description: In polymorphic species, population divergence in morph composition and
 frequency has the potential to promote speciation. We assessed the
 relationship between geographic variation in male throat colour
 polymorphism and phylogeographic structure in the tawny dragon lizard,
 Ctenophorus decresii. We identified four genetically distinct lineages,
 corresponding to two polymorphic lineages in the Northern Flinders Ranges
 and Southern Flinders Ranges/Olary Ranges regions respectively, and a
 monomorphic lineage in the Mt Lofty Ranges/Kangaroo Island region. The
 degree of divergence between these three lineages was consistent with
 isolation to multiple refugia during Pleistocene glacial cycles, whereas a
 fourth, deeply divergent (at the interspecific level) and monomorphic
 lineage was restricted to western New South Wales. The same four morphs
 occurred in both polymorphic lineages, although populations exhibited
 considerable variation in the frequency of morphs. By contrast, male
 throat coloration in the monomorphic lineages differed from each other and
 from the polymorphic lineages. Our results suggest that colour
 polymorphism has evolved once in the C. decresii species complex, with
 subsequent loss of polymorphism in the Mt Lofty Ranges/Kangaroo Island
 lineage. However, an equally parsimonious scenario, that polymorphism
 arose independently twice within C. decresii, could not be ruled out. We
 also detected evidence of a narrow contact zone with limited genotypic
 admixture between the polymorphic Olary Ranges and monomorphic Mt Lofty
 Ranges regions, yet no individuals of intermediate colour phenotype. Such
 genetic divergence and evidence for barriers to gene flow between lineages
 suggest incipient speciation between populations that differ in morph
 composition.
description: Colour_Pattern_Data_FileData from colour pattern analysis of Ctenophorus decresii male throat coloration from Mt Lofty Ranges (LR), Kangaroo Island (KI), and New South Wales (NSW) populations. ProportionGrey, ProportionRed, ProportionYellow, and ProportionBlue are colour variables, while TotalPower is a measure of overall patterning.Microsatellite_Data_FileComplete microsatellite genotypic data set.StarBEAST_Data_FilesZip file containing nexus files for *BEAST analysis, including one mitochondrial (ND4) and five nuclear loci (BACH1, enol, FSHR, MKL1, SLC8A1). Nuclear sequences were haplotyped using PHASE.STRUCTURE_Input_FilesInput files for STRUCTURE analyses. The "Microsatellite" sheet corresponds to data used in Fig. 2H of the paper, and the "Nuclear Sequence Haplotypes" sheet corresponds to data used in supplementary data Fig. S4.Migrate_Input_FileInput file for Migrate analyses. Data are microsatellite repeat numbers and populations are the adjacent Olary Ranges (OR) and Mt Lofty Ranges (LR) geographic regions.MSVAR_Input_FilesZip file containing input files for MSVAR analyses for two populations from the Southern Flinders Ranges (Aroona and Telowie Gorge), and one from each of the Olary Ranges (Bimbowrie), Mt Lofty Ranges (Morialta), and Kangaroo Island (Snake Lagoon) geographic regions.Sequence_Data_FilesZip file containing fasta files for six loci used in this study.