DOI: 10.5061/dryad.931zcrjrr
title: Data from: Museum skins enable identification of introgression associated with cytonuclear discordance

description: Increased sampling of genomes and populations across closely related
 species has revealed that levels of genetic exchange during and after
 speciation are higher than previously thought. One obvious manifestation
 of such exchange is strong cytonuclear discordance, where the divergence
 in mitochondrial DNA (mtDNA) differs from that for nuclear genes more (or
 less) than expected from differences between mtDNA and nuclear DNA (nDNA)
 in population size and mutation rate. Given genome-scale datasets and
 coalescent modelling, we can now confidently identify cases of strong
 discordance and test specifically for historical or recent introgression
 as the cause. Using population sampling, combining exon capture data from
 historical museum specimens and recently collected tissues, we showcase
 how genomic tools can resolve complex evolutionary histories in the
 brachyotis group of rock-wallabies (Petrogale). In particular, applying
 population and phylogenomic approaches, we can assess the role of
 demographic processes in driving complex evolutionary patterns and assess
 the role of ancient introgression and hybridisation. We find that
 described species are well supported as monophyletic taxa for nDNA genes,
 but not for mtDNA, with cytonuclear discordance involving at least four
 operational taxonomic units (OTUs) across four species which diverged
 183–278 kya. ABC modelling of nDNA gene trees supports introgression
 during or after speciation for some taxon pairs with cytonuclear
 discordance. Given substantial differences in body size between the
 species involved, this evidence for gene flow is surprising. Heterogenous
 patterns of introgression were identified but do not appear to be
 associated with chromosome differences between species. These and previous
 results suggest that dynamic past climates across the monsoonal tropics
 could have promoted reticulation among related species.
description: This dataset includes ~1000 nuclear loci from a custom-designed
 exon capture approach (SeqCap EZ Developer Library; Roche NimbleGen),
 designed from a yellow-footed rock-wallaby (<em>Petrogale</em>
 <em>xanothpus</em>) transcriptome. The raw sequencing data
 were processed following the workflow of Singhal (2013), and scripts for
 this pipeline are available from 10.5061/dryad.7c99f (see Supplementary
 Materials and Methods here for more detail). The dataset includes samples
 from both modern and historical specimens, and these were processed in
 different pipelines. Modern samples were assembled de novo from the
 cleaned sequencing reads following the workflow described in Bragg et al.
 (2016). The historical samples were assembled using custom scripts https://github.com/CGRL-QB3-UCBerkeley/denovoTargetCapturePhylogenomics) and published methods (Bi et al. 2012; Portik et al. 2016; refer to Supplementary Materials and Methods here for more detail). Data was finally aligned and filtered using the Eaphy (v1.2; Blom 2015) pipeline.  Mitogenomes were assembled following the methods of Hahn et al. (2013) using a docker version for MITObim (https://github.com/chrishah/MITObim). Data were generated in one of two approaches: (1) mapped to the <em>Osphranter</em> <em>robustus</em> mitochondrial genome (Janke et al. 1997), or (2) reconstructed from mitochondrial ND2, COI and Cytb seeds from previously sequenced individuals (Potter et al. 2012, 2014). Final mitochondrial genome assemblies were then aligned using Geneious Prime as well as mafft (Katoh et al. 2002) and edited to protein-coding regions of the genome (~11,500 bp).
description: The files in this repository are either text, Word, Excel or PDF.
 Most software programs can be used to open or view these files. The
 sequence alignments (e.g., .phy or .fasta) can be opened in text
 documents.
description: 28 June 2021 GENERAL INFORMATION Title: Museum skins enable identification
 of introgression associated with cytonuclear discordance Principal
 Investigator: Dr Sally Potter, School of Natural Sciences, Macquarie
 University, Sydney, NSW, Australia
 [sally.potter@mq.edu.au](mailto:sally.potter@mq.edu.au) Date of data
 collection: 2013-2023 Geographic location of data collection: northern
 Australia, Kimberley region of Western Australia, Top End region of
 Northern Territory to just across the border into Queensland, Australia
 Keywords: mito-nuclear discordance, introgression, rock-wallabies, museum
 skins, exon capture Citation: Potter S, Moritz C, Piggott MP, Bragg JG,
 Afonso Silva AC, Bi K, McDonald-Spicer C,Turakulov R, Eldridge MDB (2023)
 Museum skins enable identification of introgression associated with
 cytonuclear discordance. Systematic Biology submitted. DATA & FILE
 OVERVIEW These data were generated to investigate the evolutionary
 relationships and divergence history of the brachyotis group of
 rock-wallabies from the Australian Monsoonal Tropics. Exon capture
 sequence data were generated for both modern tissues and historical museum
 samples and both population genomic and phylogenomic approaches used to
 evaluate introgression between species where mito-nuclear discordance was
 detected. Here we have four directories, containing 1) data used in the
 various analyses, 2) design of the exon capture experiment, 3) workflows
 used to assemble and clean the data, and 4) all supplementary material
 pertaining to this paper. 1\. data ------------------------- File 1 Name:
 Metadata_sample_Petrogale_brachyotis File 1 Description: A comma-separated
 (CSV) file of sample information including sample ID, Sequence Read
 Archive (SRA;
 [http://www.ncbi.nlm.nih.gov/sra/](http://www.ncbi.nlm.nih.gov/sra/))
 information - BioProject, BioSample and SRA number, geographical location.
 Directory 1.1 Name: mitochondrial data/ Directory 1.1 Description:
 mitochondrial data files and summary of missing data for mitochondrial
 coding genes for brachyotis group File 1.1.1 Name:
 Concat_mito_coding_genes_brachyotis_ALL_data.phy File 1.1.1 Description:
 phylip file of mitochondrial protein coding genes for brachyotis samples
 File 1.1.2 Name: Concat_mito_coding_genes_brachyotis_50%miss.phyFile 1.1.2
 Description: phylip file of mitochondrial protein coding genes where
 samples have less than 50% missing data File 1.1.3 Name:
 Missing_data_brachyotis_mtDNA.xlsx File 1.1.3 Description: excel file
 summarising the number of missing alleles (N) and the percent of missing
 data for each mitochondrial protein coding gene for each individual
 Directory 1.2 Name: nuclear exon datasets/ Directory 1.2 Description:
 directory of nuclear sequence files Directory 1.2.1 Name:
 phased_h0_nuclear_alignments/Directory 1.2.1 Description: directory of
 phylip sequence files for each phased h0 nuclear exon used in the study,
 including a concatenated alignment of all exons, individuals are labelled
 with their index ID (refer to lib_sample_Petrogale_brachyotis) Directory
 1.2.2 Name: unphased_ambig_nuclear_alignments/Directory 1.2.2 Description:
 directory of phylip sequence files for each unphased nuclear exon used in
 the study (ambiguity codes used), including a concatenated alignment of
 all exons, individuals are labelled with their index ID (refer to
 lib_sample_Petrogale_brachyotis) Directory 1.3 Name: PopGenome analyses/
 Directory 1.3 Description: directory of all the Tajima D coalescent
 simulations and observed estimates from concatenated alignments for each
 OTU in the brachyotis group implemented in PopGenome Directory 1.3.1 Name:
 brachyotis brachyotis EK Directory 1.3.1 Description: directory of input
 and output files from PopGenome for the brachyotis brachyotis EK OTU File
 1.3.1.1 Name: concat_brachEK_h0_TajimaD.phy File 1.3.1.1 Description:
 nuclear phased haplotype (h0) phylip sequence file for brachyotis
 brachyotis EK OTU used an input for PopGenome analysis File 1.3.1.2 Name:
 R Console_brachEK_tajimad.txtFile 1.3.1.2 Description: R output from
 coalescent simulations of Tajima’s D in PopGenome Directory 1.3.2 Name:
 brachyotis brachyotis WK/ Directory 1.3.2 Description: directory of input
 and output files from PopGenome for the brachyotis brachyotis WK OTU File
 1.3.2.1 Name: concat_brachWK_h0_TajimaD.phy File 1.3.2.1 Description:
 nuclear phased haplotype (h0) phylip sequence file for brachyotis
 brachyotis WK OTU used an input for PopGenome analysis File 1.3.2.2 Name:
 R Console_brachWK_tajimad.txtFile 1.3.2.2 Description: R output from
 coalescent simulations of Tajima’s D in PopGenome Directory 1.3.3 Name:
 brachyotis victoriae/ Directory 1.3.3 Description: directory of input and
 output files from PopGenome for the brachyotis victoriae OTU File 1.3.3.1
 Name: concat_bvic_h0_TajimaD.phy File 1.3.3.1 Description: nuclear phased
 haplotype (h0) phylip sequence file for brachyotis victoriae OTU used an
 input for PopGenome analysis File 1.3.3.2 Name: R
 Console_bvic_tajimad.txtFile 1.3.3.2 Description: R output from coalescent
 simulations of Tajima’s D in PopGenome Directory 1.3.4 Name: burbidgei N/
 Directory 1.3.4 Description: directory of input and output files from
 PopGenome for the burbidgei N OTU File 1.3.4.1 Name:
 concat_burbN_h0_TajimaD.phy File 1.3.4.1 Description: nuclear phased
 haplotype (h0) phylip sequence file for burbidgei N OTU used an input for
 PopGenome analysis File 1.3.4.2 Name: R Console_burbN_tajimad.txtFile
 1.3.4.2 Description: R output from coalescent simulations of Tajima’s D in
 PopGenome Directory 1.3.5 Name: concinna canescens/ Directory 1.3.5
 Description: directory of input and output files from PopGenome for the
 concinna canescens OTU File 1.3.5.1 Name: concat_concan_h0_TajimaD.phy
 File 1.3.5.1 Description: nuclear phased haplotype (h0) phylip sequence
 file for concinna canescens OTU used an input for PopGenome analysis File
 1.3.5.2 Name: R Console_concan_tajimad.txtFile 1.3.5.2 Description: R
 output from coalescent simulations of Tajima’s D in PopGenome Directory
 1.3.6 Name: concinna monastria Directory 1.3.6 Description: directory of
 input and output files from PopGenome for the concinna monastria OTU File
 1.3.6.1 Name: concat_conmon_h0_TajimaD.phy File 1.3.6.1 Description:
 nuclear phased haplotype (h0) phylip sequence file for concinna monastria
 OTU used an input for PopGenome analysis File 1.3.6.2 Name: R
 Console_conmon_tajimad.txtFile 1.3.6.2 Description: R output from
 coalescent simulations of Tajima’s D in PopGenome Directory 1.3.7 Name:
 wilkinsi Directory 1.3.7 Description: directory of input and output files
 from PopGenome for the wilkinsi OTU File 1.3.7.1 Name:
 concat_wilk_h0_TajimaD.phy File 1.3.7.1 Description: nuclear phased
 haplotype (h0) phylip sequence file for wilkinsi OTU used an input for
 PopGenome analysis File 1.3.7.2 Name: R Console_wilk_tajimad.txtFile
 1.3.7.2 Description: R output from coalescent simulations of Tajima’s D in
 PopGenome Directory 1.3.8 Name: wilkinsi GULF Directory 1.3.8 Description:
 directory of input and output files from PopGenome for the wilkinsi GULF
 OTU File 1.3.8.1 Name: concat_wilkGU_h0_TajimaD.phy File 1.3.8.1
 Description: nuclear phased haplotype (h0) phylip sequence file for
 wilkinsi GULF OTU used an input for PopGenome analysis File 1.3.8.2 Name:
 R Console_wilkGU_tajimad.txtFile 1.3.8.2 Description: R output from
 coalescent simulations of Tajima’s D in PopGenome File 1.3.9 Name:
 Coalescent_simulations_TajimasD.xlsx File 1.3.9 Description: excel file of
 coalescent simulation data for Tajima’s D values sorted to evaluate 0.05
 significance, comparing the observed Tajima D to the 95%. The highlighted
 section represents the 0.05 cutoff to test for significance. Each tab
 represents a different OTU analysis as outlined in Files 1.3.1-1.3.8
 Directory 1.3.10 Name: nDNA Directory 1.3.10 Description: directory of
 input and output files from PopGenome for the entire nuclear haplotype
 dataset calculating Dxy File 1.3.10.1 Name: Concat_brach_h0.phyFile
 1.3.10.1 Description: Phylip alignment file of all brachyotis individuals
 for nuclear haplotypes File 1.3.10.2 Name: R
 Console_Dxy_brach_nDNA.txtFile 1.3.10.2 Description: R output from Dxy
 analyses of brachyotis group nDNA in PopGenome Directory 1.3.11 Name:
 mtDNA Directory 1.3.11 Description: directory of input and output files
 from PopGenome for the entire mitochondrial dataset calculating Dxy File
 1.3.11.1 Name: 1.1.2 Concat_mito_coding_genes_brachyotis_50%miss.phyFile
 1.3.11.1 Description: Phylip alignment file of all brachyotis individuals
 for mitochondrial data File 1.3.11.2 Name: R
 Console_mtDNA_Dxy_brach.txtFile 1.3.11.2 Description: R output from Dxy
 analyses of brachyotis group mtDNA in PopGenome Directory 1.4 Name:
 rangeExpansion analyses/ Directory 1.4 Description: directory containing
 folders for each OTU with input and output files from rangeExpansion
 analyses Directory 1.4.1 Name: brachbrachEK/ Directory 1.4.1 Description:
 directory containing input and output files for rangeExpansion analysis
 for brachyotis brachyotis EK OTU File 1.4.1.1 Name: bbrachEK_onesnp.snapp
 File 1.4.1.1 Description: input file for rangeExpansion analysis including
 the single nucleotide polymorphisms coded as homozygous 0, heterozygous 1,
 homozygous 2 for alternate allele (missing ?) for each individual. Sample
 ID matches individuals in .csv file which has locality information.
 Outgroups used to call ancestral versus derived allele states are labelled
 as OOG numbers. File 1.4.1.2 Name: bEK_coords.csv File 1.4.1.2
 Description: a csv file used in analysis for rangeExpansion which includes
 sample ID, latitude, longitude, the region name and column for outgroup
 (0=no, 1=yes) File 1.4.1.3 Name: sample_key_bbrachEK_snapp.txt File
 1.4.1.3 Description: a text file which is a key matching the sample ID of
 individuals in this study to the sample code used in rangeExpansion
 analysis (refer to lib_sample_Petrogale_brachyotis for sample information)
 File 1.4.1.4 Name: R Console bEK_PS.txt File 1.4.1.4 Description: a text
 file of the R code and analysis run using rangeExpansion for the
 brachyotis brachyotis EK OTU File 1.4.1.5 Name:
 Rplot_brachEK_expansion.pdf File 1.4.1.5 Description: a pdf file of the
 rangeExpansion output plot showing a map of the samples and the location
 of the source and metrics of the range expansion Directory 1.4.2 Name:
 brachbrachWK/ Directory 1.4.2 Description: directory containing input and
 output files for rangeExpansion analysis for brachyotis brachyotis WK OTU
 File 1.4.2.1 Name: bbrachWK_onesnp.snapp File 1.4.2.1 Description: input
 file for rangeExpansion analysis including the single nucleotide
 polymorphisms coded as homozygous 0, heterozygous 1, homozygous 2 for
 alternate allele (missing ?) for each individual. Sample ID matches
 individuals in .csv file which has locality information. Outgroups used to
 call ancestral versus derived allele states are labelled as OOG numbers.
 File 1.4.2.2 Name: bbWK_coords.csv File 1.4.2.2 Description: a csv file
 used in analysis for rangeExpansion which includes sample ID, latitude,
 longitude, the region name and column for outgroup (0=no, 1=yes) File
 1.4.2.3 Name: sample_key_bbrachWK_snapp.txt File 1.4.2.3 Description: a
 text file which is a key matching the sample ID of individuals in this
 study to the sample code used in rangeExpansion analysis (refer to
 lib_sample_Petrogale_brachyotis for sample information) File 1.4.2.4 Name:
 R Console bbrachWK_PS.txt File 1.4.2.4 Description: a text file of the R
 code and analysis run using rangeExpansion for the brachyotis brachyotis
 EK OTU Directory 1.4.3 Name: wilkinsi/ Directory 1.4.3 Description:
 directory containing input and output files for rangeExpansion analysis
 for wilkinsi OTU File 1.4.3.1 Name: wilk_onesnp.snapp File 1.4.3.1
 Description: input file for rangeExpansion analysis including the single
 nucleotide polymorphisms coded as homozygous 0, heterozygous 1, homozygous
 2 for alternate allele (missing ?) for each individual. Sample ID matches
 individuals in .csv file which has locality information. Outgroups used to
 call ancestral versus derived allele states are labelled as OOG numbers.
 File 1.4.3.2 Name: wilk_coords.csv File 1.4.3.2 Description: a csv file
 used in analysis for rangeExpansion which includes sample ID, latitude,
 longitude, the region name and column for outgroup (0=no, 1=yes) File
 1.4.3.3 Name: sample_key_wilk_snapp.txt File 1.4.3.3 Description: a text
 file which is a key matching the sample ID of individuals in this study to
 the sample code used in rangeExpansion analysis (refer to
 lib_sample_Petrogale_brachyotis for sample information) File 1.4.3.4 Name:
 R Console_wilk_PS.txt File 1.4.3.4 Description: a text file of the R code
 and analysis run using rangeExpansion for the wilkinsi OTU Directory 1.5
 Name: demographic inference using linked selection/ Directory 1.5
 Description: File 1.5.1 Name: prepareFastaDILS.R File 1.5.1 Description:
 an R script which takes fasta alignments and prepares them into input
 files for DILS analysis and takes a yaml template and information about
 the pairwise comparisons and creates yaml input files for DILS analysis
 File 1.5.2 Name: template.yaml File 1.5.2 Description: the yaml template
 file used in prepareFastaDILS.R to generate yaml input files for DILS
 analysis Directory 1.5.3 Name: fasta files Directory 1.5.3 Description:
 fasta alignment files for each exon of phased h0 haplotype data for all
 individuals in brachyotis group used to generate population input files
 for DILS analysis (used in prepareFastaDILS.R) File 1.5.4 Name:
 samples_lineage.txt File 1.5.4 Description: a text file assigning
 individuals to OTUs for the DILS analysis File 1.5.5 Name:
 ComparisonsOfInterest.txt File 1.5.5 Description: a text file outlining
 the two OTUs and the analysis type used in the DILS analysis, this is
 incorporated into prepareFastaDILS.R and the output files Directory 1.5.6
 Name: dils input fasta files/ Directory 1.5.6 Description: directory of
 fasta files used as input for dils analysis for each pairwise comparison
 of OTUs analysed in dils. The fasta alignment headers include the exon
 name | OTU name | sample ID | and haplotype information Directory 1.5.7
 Name: dils input yaml files/ Directory 1.5.7 Description: a directory of
 yaml input files for replicate runs for each pairwise comparison of OTUs
 analysed in dils. The yaml files indicate the parameter values and priors
 used for the analysis. File 1.5.8 Name: runDILS_SLURM.sh File 1.5.8
 Description: a shell script used to run dils analysis on a cluster
 Directory 1.5.9 Name: output/ Directory 1.5.9 Description: directory of
 .tar.gz output files for each replicate of the dils analysis for each
 pairwise comparison of OTUs. These are the demographic modelling DILS
 results from the paper. File 1.5.10 Name: DILS_plottingResults.Rmd File
 1.5.10 Description: an R mark-down file which processes the output files
 and make plots of the results in R File 1.5.11 Name:
 DILS_plottingResults.html File 1.5.11 Description: an html file with the
 actual outputs from the analysis in R for plotting of dils results
 (produced from DILS_plottingResults.Rmd) Directory 1.6 Name: MIGRATE
 analyses/ Directory 1.6 Description: directory containing input and output
 files for analyses in MIGRATE used to estimate migration and theta values
 File 1.6.1 Name: brachyotis_migrate_input.phy File 1.6.1 Description:
 input file used for MIGRATE analyses of Petrogale brachoytis group
 (excluding Petrogale wilkinsi OTUs) with sequences in phylip format and in
 format required by MIGRATE File 1.6.2 Name: brachyotis_migrate_output.pdf
 File 1.6.2 Description: output file generated from MIGRATE analysis with
 details of input parameters and output values for Petrogale brachyotis
 group excluding Petrogale wilkinsi OTUs File 1.6.3 Name:
 wilkinsi_migrate_input.phy File 1.6.3 Description: input file used for
 MIGRATE analyses of Petrogale wilkinsi OTUs with sequences in phylip
 format and in format required by MIGRATE File 1.6.4 Name:
 wilkinsi_migrate_output.pdf File 1.6.4 Description: output file generated
 from MIGRATE analysis with details of input parameters and output values
 for Petrogale wilkinsi OTUs File 1.6.5 Name: bv_w_migrate_input.phy File
 1.6.5 Description: input file used for MIGRATE analyses of Petrogale
 brachyotis victoriae and P. wilkinsi Top End OTUs with sequences in phylip
 format and in format required by MIGRATE File 1.6.6 Name: bv_w_out1.pdf
 File 1.6.6 Description: output file generated from MIGRATE analysis with
 details of input parameters and output values for Petrogale brachyotis
 victoriae and P. wilkinsi Top End OTUs Directory 1.7 Name: Chromosomes/
 Directory 1.7 Description: directory containing directories of nuclear
 loci separated into known chromosome location and phylip sequences for
 each locus mapped tot that chromosome. Also directories for rearranged (R)
 and non-rearranged (NR) loci based on known chromosomal variation from
 karyotypes. Outputs of analyses are also stored in a directory. Directory
 1.7.1 Name: Chr1/ Directory 1.7.1 Description: directory of sequence
 alignments in phylip format which were mapped to chromosome 1 of the
 Petrogale penicillata genome Directory 1.7.2 Name: Chr2/ Directory 1.7.2
 Description: directory of sequence alignments in phylip format which were
 mapped to chromosome 2 of the Petrogale penicillata genome Directory 1.7.3
 Name: Chr3/ Directory 1.7.3 Description: directory of sequence alignments
 in phylip format which were mapped to chromosome 3 of the Petrogale
 penicillata genome Directory 1.7.4 Name: Chr4/ Directory 1.7.4
 Description: directory of sequence alignments in phylip format which were
 mapped to chromosome 4 of the Petrogale penicillata genome Directory 1.7.5
 Name: Chr5/ Directory 1.7.5 Description: directory of sequence alignments
 in phylip format which were mapped to chromosome 5 of the Petrogale
 penicillata genome Directory 1.7.6 Name: Chr6/ Directory 1.7.6
 Description: directory of sequence alignments in phylip format which were
 mapped to chromosome 6 of the Petrogale penicillata genome Directory 1.7.7
 Name: Chr7/ Directory 1.7.7 Description: directory of sequence alignments
 in phylip format which were mapped to chromosome 7 of the Petrogale
 penicillata genome Directory 1.7.8 Name: Chr8/ Directory 1.7.8
 Description: directory of sequence alignments in phylip format which were
 mapped to chromosome 8 of the Petrogale penicillata genome Directory 1.7.9
 Name: Chr9/ Directory 1.7.9 Description: directory of sequence alignments
 in phylip format which were mapped to chromosome 9 of the Petrogale
 penicillata genome Directory 1.7.10 Name: Chr10/ Directory 1.7.10
 Description: directory of sequence alignments in phylip format which were
 mapped to chromosome 10 of the Petrogale penicillata genome Directory
 1.7.11 Name: ChrX/ Directory 1.7.11 Description: directory of sequence
 alignments in phylip format which were mapped to the X chromosome of the
 Petrogale penicillata genome Directory 1.7.12 Name: NR_Chr/ Directory
 1.7.12 Description: a concatenated sequence alignment in phylip format of
 exons on non-rearranged chromosomes Directory 1.7.13 Name: R_Chr/
 Directory 1.7.13 Description: a concatenated sequence alignment in phylip
 format of exons on rearranged chromosomes Directory 1.7.14 Name:
 Summary_outputs/ Directory 1.7.14 Description: directory of R console
 outputs from PopGenome analysis of Dxy in R for each chromosome as well as
 an excel file summarising the average Dxy between OTUs File 1.7.14.1 Name:
 OTU_Dxy_RvNR.xlsx File 1.7.14.1 Description: an Excel file summarising the
 average Dxy between OTUs for rearranged (R) and non-rearranged (NR) loci.
 The OTUs are abbreviated as follows: wGR (wilkinsi GROOTE), w (wilkinsi
 Top End), wGU (wilkinsi GULF), bS (burbidgei South), bN (burbidgei North),
 cc (concinna canescens), cm (concinna monastria), bbWK (brachyotis
 brachyotis West Kimberley), bbEK (brachyotis brachyotis East Kimberley),
 and bv (brachyotis victoriae). Directory 1.7.14.2 Name: Outputs_PopGenome/
 Directory 1.7.14.2 Description: directory of R console outputs from
 PopGenome analysis of Dxy for each chromosome between OTUs Directory 1.8
 Name: SVDquartets/ Directory 1.8 Description: directory containing data
 files and code for SVDquartet analyses to estimate a species tree and
 divergence times in PAUP File 1.8.1 Name: brach_wOG_concat_ambig_SVD.nex
 File 1.8.1 Description: input file used for SVDquartets analyses of
 Petrogale brachoytis group with sequences in nexus format File 1.8.2 Name:
 brach_SVD_OTUs.tre File 1.8.2 Description: output file from SVDquartets
 species tree analysis of Petrogale brachoytis group, also used as input
 for qage divergence analyses in PAUP File 1.8.3 Name:
 code_svdquartets_qage.txt File 1.8.3 Description: a text file showing the
 results from SVDquartets species tree analysis in coalescent units and
 some equations used to convert this to real divergence dates in years for
 Petrogale brachoytis group File 1.8.4 Name:
 divergence_dating_qage_brach.xlsx File 1.8.4 Description: an excel file
 showing the divergence outputs from SVDquartets qage analysis and the
 conversion to time in years based on a mutation rate and generation time
 File 1.9 Name: brachyotis_individual_He.csv File 1.9 Description: CSV file
 containing the individual heterozygosity estimates from nuclear exon data
 for all individuals in brachyotis study
 \------------------------------------- 2\. design -----------------------
 Information on the sequence capture kit \# Transcriptome sequence of
 Petrogale xanthous used for target identification is available in Dryad
 (doi: 10.5061/dryad.5606t) File 1 Name: targetExons.fa File 1 Description:
 the list of target exons used for probe design
 \------------------------------------- 3\. workflow --------------------
 \# folder of perl scripts used to clean raw sequence data and assembling
 \# External dependencies including bowtie2, samtools and GATK Directory
 3.1 Name: clean/-- Directory 3.1 Description: script used to clean reads
 (adaptor/duplicate/contamination removal), trimming File 1 Name:
 scrubReads.pl File 1 Description: copy of script used for cleaning reads,
 see also [https://github.com/MVZSEQ](https://github.com/MVZSEQ), SCPP
 directory Directory 3.2 Name: assembly/ Directory 3.2 Description: scripts
 used to assemble exon capture data using a series of Perl scripts that are
 linked with shell wrapper scripts. It accepts three main datasets: target
 exon sequences, the reference proteome used during annotation, and
 captured sequence reads from each sample. Pipeline details can be found at
 [https://github.com/jasongbragg/exon-capture-phylo/](https://github.com/jasongbragg/exon-capture-phylo/) Directory 3.2.1 Name: pl/ Directory 3.2.1 Description: perl scripts for assembly workflow Directory 3.2.2 Name: sh/ Directory 3.2.2 Description: shell scripts for assembly workflow File 1 Name: exon_capture_phylo.sh File 1 Description: main script for assembly workflow, run the exon_capture_phylo.sh script to run the assembly and bash scripts in the sh/ and pl/ directory (3.2.1 and 3.2.2) File 2 Name: rw.all.config File 2 Description: example configuration script Directory 3.3 Name: GATK_docker_info/ Directory 3.3 Description: folder containing information about the GATK docker # this docker is available at [https://hub.docker.com/r/trust1/gatk](https://hub.docker.com/r/trust1/gatk) File 1 Name: Overview_GATK_docker.txt File 1 Description: text file outlining the GATK docker, instructions and background File 2 Name: callingpipe_GATK.pl File 2 Description: perl script used to run GATK from the docker Directory 3.4 Name: SNP_filtering/ Directory 3.4 Description: folder containing code and readme files for filtering SNP dataset File 1 Name: process.vcf.1.sh File 1 Description: shell script used to filter snps, it does this by calling vcftools. It also contains calls to scripts for comparing genotypes of technical replicates, largely using R code from /r file Directory 3.4.1 Name: r/    Directory 3.4.1 Description: contains r code for opening vcf files, and comparing technical replicates \#Scripts in the workflow directory are provided here primarily for archival purposes. For updated versions, see: [https://github.com/MVZSEQ](https://github.com/MVZSEQ) [https://github.com/jasongbragg/exon-capture-phylo](https://github.com/jasongbragg/exon-capture-phylo) [https://github.com/CGRL-QB3-UCBerkeley/denovoTargetCapturePhylogenomics](https://github.com/CGRL-QB3-UCBerkeley/denovoTargetCapturePhylogenomics) [https://github.com/MozesBlom/EAPhy](https://github.com/MozesBlom/EAPhy) 4\. Supplementary Materials -------------------- \# folder of supplementary figures, tables and materials and methods used in this paper Directory 4.1 Name: Supplementary materials and methods/ -- Directory 4.1 Description: Directory for word file of supplementary materials and methods 4.1.1 Name: Supplementary Materials and Methods 4.1.1 Description: word file outlining the detailed materials and methods to go together with the main text of the paper, including the figure and table legends of supplementary material. Directory 4.2 Name: SuppFigs/ -- Directory 4.2 Description: Directory for pdf of supplementary figures outlined in the paper 4.2.1 Name: Supp_Figs_1-7 4.2.1 Description: pdf file of supplementary figures of the paper in order from one to seven Directory 4.3 Name: SuppTables/ -- Directory 4.3 Description: Directory for supplementary tables outlined in the paper in comma-separated (CSV) format 4.3.1 Name: Supp_Table1 4.3.1 Description: CSV file of supplementary table 1 of the paper outlining sample information including sample id, OTU and locations and latitude and longitude, and the year the sample was collected. The short read archive (SRA) number is also given to obtain raw sequencing data from NCI. 4.3.2 Name: Supp_Table2 4.3.2 Description: CSV file of supplementary table 2 of the paper outlining the missing data for each mitochondrial gene and the total across the 13 loci analysed 4.3.3 Name: Supp_Table3 4.3.3 Description: CSV file of supplementary table 3 of the paper outlining the divergence dates between lineages 4.3.4 Name: Supp_Table4 4.3.3 Description: CSV file of supplementary table 4 of the paper outlining the statistics of the mitochondrial tree comparisons 4.3.5 Name: Supp_Table5 4.3.3 Description: CSV file of supplementary table 5 of the paper outlining the theta and migration values from the MIGRATE analysis 4.3.6 Name: Supp_Table6 4.3.3 Description: CSV file of supplementary table 6 of the paper outlining the Tajima D statistics for each lineage