DOI: 10.5061/dryad.14811
title: Data from: Introgression of mtDNA in Urosaurus lizards: historical and ecological processes

description: Introgression of mtDNA appears common in animals but the implications of
 acquiring a novel mitochondrial genome are not well known. This study
 investigates mito-genome introgression between the lizard species
 Urosaurus graciosus, a thermal specialist, and U. ornatus, a species that
 occupies a wider range of thermal environments. As ectotherms, their
 metabolic rate is strongly influenced by the thermal environment; with
 mitochondria being linked to metabolic rates, overall energy budgets could
 be impacted by introgression. I use mitochondrial gene trees, inferred
 from Bayesian analyses of Cyt-B and ND1 gene sequences, along with
 morphology and microsatellites from nineteen populations of these two
 species to address if the direction and location of mito-nuclear
 discordance match predictions of introgression resulting from past
 population expansions. MtDNA is expected to move from resident species
 into expanding or invading species. Second, does having a heterospecific
 form of mitochondria impact body size, a trait strongly associated with
 fitness? Multiple independent introgression events of historic origin were
 detected. All introgression was unidirectional with U. ornatus-type mtDNA
 found in U. graciosus parental type individuals. This result was
 consistent with population expansions detected in U. graciosus but not U.
 ornatus. Females with heterospecific mtDNA were significantly smaller than
 homospecific forms and heterospecific males had a different relationship
 of body mass to body length than those with homospecific mtDNA. These
 changes indicate a potential selective disadvantage for individuals with
 heterospecific mitochondria and are consistent with the theoretical
 expectation that deleterious alleles are more likely to persist in
 expanding populations.
description: Sampling locations and
 sample sizes.Sampling locations and
 initial species designations are provided for each sampling location. Site
 name abbreviations correspond to Figure 3. Sample sizes are given for each
 sampling location with mtDNA given on the first line, microsatellites the
 second, scale morphology the third and the forth row has additional
 individuals from Haenel 2007 and a manuscript that is in preparation
 included in figure 1 and body size analyses.1 Table S1
 locations.docxArlequin input file
 microsatellitesFormatted input file of
 microsatellite data used in Arlequin.Table S2
 microsat_infileALL.arpSTRUCTURE input:
 microsatellitesSTRUCTURE input file of
 microsatellite alleles.Seven Microsatellites are provided in columns. The
 first column has individual Ids.Figure S3a
 project_dataSTRUCTURE summary:
 deltaKGraph of output of
 summary for STRUCTURE analyses. Evanno’s K and individual assignment
 probabilities were used to assess the best value of K (Evanno et al.
 2005). This figure shows the results as DeltaK =
 mean(|L"(K)|)/sd(L(K)).Figure S3b
 deltaK.pngInput file MrBayes mtDNA
 sequences.Input file used to run
 phylogenetic analyses in MrBayes including mtDNA sequences. U. nigricaudus
 included as outgroup. MrBayes block included at bottom of the
 file.4
 Table S4a Uro16_07_25_Un_.txtSummary of MrBayes
 analyses.Table of summary of run
 from MrBayes phylogenetic analyses. This is the .mcmc output
 file.4
 Table S4b
 Uro16_07_25_Un_.txt.mcmcArlequin input U.
 orantus mtDNA sequences.Arlequin input file for
 population genetic analyses of U. orantus mtDNA sequences. Includes
 geographic structure.5 Table S5a
 infileND1CytB6_16_15Uo.arpArlequin input U.
 graciosus mtDNA sequencesArlequin input file for
 population genetic analyses of U. graciosus mtDNA sequences. Includes
 geographic structure.5 Table S5b
 infileND1CytB6_16_15Ug.arpParameter file for
 Bayesian Skyline Plot analyses U. ornatusParameter file for
 Bayesian Skyline Plot analyses of U. ornatus mtDNA sequence data in BEAST
 developed using BEAUti v1.8.2.6 Table S6a
 UomtDNAcodon.xmlBSP analyses log file Uo
 mtDNABSP analyses log file
 generated in BEAST for U. ornatus mtDNA sequence data.6 Table S6b
 UomtDNAcodon.logParameter file for BSP
 U. graciosusParameter file for
 Bayesian Skyline Plot analyses of U. graciosus mtDNA sequence data in
 BEAST developed using BEAUti v1.8.2.6 Table S6c
 Uro16_07_25_UgcodonEBSP.xmlBSP analyses log file U.
 graciosusBSP analyses log file
 generated in BEAST for U. graciosus mtDNA sequence
 data.6
 Table S6d
 Uro16_07_25_UgcodonEBSPcombined.logTable of BAYESASS outputMigration Rates estimated with BAYESASS for U. graciosus and U. ornatus with lowest Bayesian deviances. Each species is a separate tab.7 Table S7 BestBA3out.xlsxScale trait descriptionsDescriptions of scale morphology traits.Table S8a scale trait descriptions.docxDescriminant Function of MorphologySAS code and data input to develop discriminatory function for scale characters of U. graciosus and U. ornatus. Column labels match Table S8a descriptions.Table S8b SAS Descrime Program.txtLizard body size dataBody size data used to compare SVL of parental U. graciosus to heterospecific individuals and to analyze the relations of mass to SVL.Table S9a bodysize.xlsxMass/SVL residuals ANOVAANOVA table generated in SAS comparing residuals of mass to SVL among different population groups.Table S9b MassSVL residulasANOVA.txt