DOI: 10.5061/dryad.tqjq2bwcb
title: Comparative phylogeography of phrynosomatid lizards in Baja California: Asynchronous divergences and expansion of <em>Callisaurus draconoides</em> across the North American deserts

description: This dataset comprises eleven archives containing processed genomic data,
 analysis inputs/outputs, and supporting files from double-digest RAD
 sequencing (ddRAD) and target sequence capture (TSC). Data span four
 genera (Callisaurus, Petrosaurus, Sceloporus, and Urosaurus) and include
 pyRAD assemblies, Admixture clustering, RAxML phylogenies, BPP
 coalescent-with-migration models, phyluce TSC assemblies, BEAST2 and
 StarBEAST2 species trees, and ecoevolity divergence-time inferences across
 Baja California biogeographic breaks. Files are organized by analysis and
 genus, with configuration files, job scripts, summary statistics, and
 outputs in formats such as VCF, structure/geno, Phylip/Nexus alignments,
 phased allele sequences, etc. Geographic coordinates are provided at
 reduced precision (0.01°) to limit exact locality disclosure. These data
 are suitable for reuse in comparative phylogeography, population genomics,
 and phylogenetic method development, enabling replication of published
 analyses or testing of alternative models and pipelines. Collection and
 use of specimens were conducted under relevant permits and institutional
 animal care protocols (see publication for details), and downstream use
 should continue to respect applicable legal and ethical standards.
description: # Comparative phylogeography of phrynosomatid lizards in Baja California:
 Asynchronous divergences and expansion of *Callisaurus draconoides* across
 the North American deserts Dataset DOI:
 [10.5061/dryad.tqjq2bwcb](https://doi.org/10.5061/dryad.tqjq2bwcb) ##
 Summary This dataset is associated with the article titled
 "*Comparative phylogeography of phrynosomatid lizards in Baja
 California: asynchronous divergences and expansion of Callisaurus
 draconoides* across the North American deserts", accepted to *Journal
 of Biogeography* on September 30, 2025 ([DOI:
 10.1111/jbi.70075](https://doi.org/10.1111/jbi.70075)). A preprint is also
 [available
 here](https://www.biorxiv.org/content/10.1101/2025.04.29.650089v1). We did
 our best to thoroughly document every analysis presented in the paper to
 fully enable reproducibility of the key results, but not every
 intermediate file, log file, or job script is included. If you have any
 questions or concerns, please contact the corresponding author, Andrew
 Gottscho ([gottschoa@si.edu](mailto:gottschoa@si.edu) or
 [andrew.gottscho@gmail.com](mailto:andrew.gottscho@gmail.com)). Thank you
 for your interest in this article and dataset! ## Frequently used acronyms
 Throughout this Data Dryad package and the associated paper, you will
 frequently encounter the following acronyms. * BCP = Baja California
 Peninsula * ddRAD = double-digest Restriction-Associated-DNA sequencing *
 TSC = Target Sequence Capture ## Raw data availability Raw sequence data
 (FASTQ format) have been deposited in the NCBI SRA
 ([https://www.ncbi.nlm.nih.gov/sra/PRJNA1242740](https://www.ncbi.nlm.nih.gov/sra/PRJNA1242740)). These FASTQ data are key inputs to the pyRAD (ddRAD) and phyluce (TSC) pipelines. ## Description of the data and file structure Eleven `.zip` files are available to download, roughly following the order they are presented in the manuscript. ### 01_BCP_ddRAD_pyrad.zip This package contains input files, output files, and statistics associated with the pyrad v3.0.6 pipeline, which was used to process the raw FASTQ data (BCP ddRAD) into a variety of output formats. There are four top-level directories, corresponding to the four genera included in the study: `Callisaurus/`, `Petrosaurus/`, `Urosaurus/`, and `Sceloporus/`. Within each of these top-level directories, there are the following files: * `[genus]_params_021017.txt`: The input parameters file (the most important file for reproducibility) * `step2.job`: Example jobscript file for step 2 of the pipeline * `step3_[genus].job`: Example jobscript file for step 3 of the pipeline * `steps5_7_[genus].job`: Example jobscript file for steps 5-7 of the pipeline Within each top-level directory, there are also the following sub-directories: * `outfiles/`: Please see the [pyrad documentation](https://github.com/dereneaton/pyrad) for more details on file formats. Not all output files were used in the manuscript, but are provided here for maximum transparency and utility to anyone interested in reanalyzing this dataset. `[n]` = the MinCov parameter (minimum samples in a final locus). * `output_[genus]_021017_[n]_h5_p75.alleles`: alleles file * `output_[genus]_021017_[n]_h5_p75.excluded_loci`: excluded loci * `output_[genus]_021017_[n]_h5_p75.gphocs`: GPHOCS format * `output_[genus]_021017_[n]_h5_p75.loci`: loci file * `output_[genus]_021017_[n]_h5_p75.nex`: nexus format * `output_[genus]_021017_[n]_h5_p75.phy`: phylip format * `output_[genus]_021017_[n]_h5_p75.phy.partitions`: partitioned phylip format * `output_[genus]_021017_[n]_h5_p75.snps`: single nucleotide polymorphisms (SNPs) * `output_[genus]_021017_[n]_h5_p75.snps.geno`: SNPs in geno format * `output_[genus]_021017_[n]_h5_p75.str`: structure format * `output_[genus]_021017_[n]_h5_p75.unlinked_snps`: unlinked SNPs * `output_[genus]_021017_[n]_h5_p75.usnps.geno`: unlinked SNPs in geno format * `output_[genus]_021017_[n]_h5_p75.vcf`: variant call file * `stats/`: Refer to the [pyrad documentation](https://github.com/dereneaton/pyrad) for more details. * `output_[genus]_021017_[n]_h5_p75.stats`: stats summary file (source for Supplementary Table 4) * `s5.consens.txt`: stats for step 5 * `s3.clusters.txt`: stats for step 3 * `s2.rawedit.txt`: stats for step 2 ### 02_BCP_ddRAD_admixture.zip This package contains the inputs, outputs, and other relevant files for the Admixture analysis of the BCP ddRAD data, presented in Figures 2-5 in the article. For more information, consult the [Admixture website](https://dalexander.github.io/admixture/). * There are four top-level directories for each genus: `callisaurus/`, `petrosaurus/`, `sceloporus/`, and `urosaurus/`. Each directory contains: * `admixture_plot_[genus].R`: R script used to plot results * `CVE_values.txt`: cross-validation errors, used to determine the optimal K value for each genus * `output_[genus]_021017_[n]_h5_p75.usnps.[k].P`: 9 allele frequencies files, one for each K value * `output_[genus]_021017_[n]_h5_p75.usnps.[k].Q`: 9 ancestry proportions files, one for each K value. * `output_[genus]_021017_[n]_h5_p75.usnps.geno`: The input file in `.geno` format * `CVE_table.csv`: A summary of the cross-validation errors for all genera ### 03_BCP_ddRAD_raxml.zip This package contains the inputs, outputs, and other files necessary to reproduce the RAxML analyses for the BCP ddRAD data, presented in Figures 2-5 in the article. To learn more, see the [RAxML website](https://cme.h-its.org/exelixis/web/software/raxml/). * There are four top-level directories for each genus: `callisaurus/`, `petrosaurus/`, `sceloporus/`, and `urosaurus/`. Each directory contains: * `output_[genus]_021017_[n]_h5_p75.phy`: The input file from pyrad * `RAxML_bipartitions.[genus].tre`: The output `.tre` file presented in Figures 2-5 * `raxml_[genus].job`: Jobscript file used to run the analysis * `raxml_[genus].log`: Log file from the analysis ### 04_BCP_ddRAD_bpp.zip This package contains input files for Bayesian Phylogenetics and Phylogeography (BPP) analyses conducted under the Multispecies Coalescent with Migration model (MSC-M). The data include phased genomic data, population/species mapping files, and multiple BPP control (`.ctl`) files for five species complexes. These results are presented in Tables 4-5 and Supplemental Table 6 in the article. For more details, see the [BPP repository on github](https://github.com/bpp/bpp). Each folder corresponds to a focal species and contains: * A data file (`data.txt`) with phased allele sequences formatted for BPP * One or more imap files (`imap.txt`, `imap2.txt`, etc.) that map individuals to populations or species units used in the MSC-M analyses * One or more BPP control files (`bpp1.ctl`, `bpp2.ctl`, etc.), each specifying a different migration scenario These files can be used to replicate the analyses in the associated publication or adapted for additional analyses of gene flow using the MSC-M framework. The package contains folders for each species complex: * `Petrosaurus/` * `Sceloporus_magister/` * `Sceloporus_orcutti/` * `Urosaurus/` * `Callisaurus/` Each species complex has the following files: * `data.txt` * Phased ddRADseq data formatted for BPP input * Each data file contains two alleles per individual, and is ready for direct use in MSC-M analyses * `imap.txt`, `imap2.txt`, etc. * These files define the mapping of individuals (allele pairs) to species or population units * Multiple `imap` files are provided where alternative grouping hypotheses were tested * `bpp1.ctl`, `bpp2.ctl`, etc. * Control files for BPP, each specifying model parameters, file paths, and the migration scenario being analyzed * Each `.ctl` file corresponds to a specific analysis or migration model (e.g., different gene flow model, different population assignments) Species folder details: * `Petrosaurus/`: * `data.txt`: Phased alleles for all individuals * `imap.txt`, `imap2.txt`: Two different population/species groupings tested * `bpp1.ctl`, `bpp2.ctl`, `bpp3.ctl`: Three different migration scenarios * `Sceloporus_magister/`: * `data.txt`: Input data for analysis * `imap.txt`: Single grouping * `bpp1.ctl`: One migration scenario * `Sceloporus_orcutti/`: * `data.txt`: Input data for analysis * `imap.txt`, `imap2.txt`, `imap3.txt`: Three different groupings tested * `bpp1.ctl`, `bpp2.ctl`, `bpp3.ctl`: Three migration scenarios tested * `Urosaurus/`: * `data.txt`: Input data for analysis * `imap.txt`, `imap2.txt`: Two groupings tested * `bpp1.ctl`, `bpp2.ctl`: Two migration scenarios * `Callisaurus/`: * `data.txt`: Input data for analysis * `imap.txt`: Single grouping * `bpp1.ctl` through `bpp9.ctl`: Nine different migration models tested ### 05_BCP_TSC_phyluce.zip This package contains input files, jobscripts, logs, and a complete set of final output files for the phyluce pipeline, which was used to process the TSC data. For more details, please see the [phyluce documentation](https://phyluce.readthedocs.io/en/latest/). * `assembly.conf`: configuration file used for assembly * `illumiprocessor.conf`: configuration file used for Illumiprocessor * `illumiprocessor.log`: log file used for Illumiprocessor * `lizard_probes_edit.fasta`: probe files used in the TSC workflow * `mafft-nexus-internal-trimmed-gblocks-clean-75p/`: output files for 75% complete data in nexus format * 549 nexus files provided, one for each locus, following the format `[locus_name].nexus` * `mafft-nexus-internal-trimmed-gblocks-clean-75p-raxml/`: output file for 75% complete data in phylip format * a single concatenated file is provided * `mafft-nexus-internal-trimmed-gblocks-clean-90p/`: output files for 90% complete data in nexus format * 310 nexus files provided, one for each locus, following the format `[locus_name].nexus` * `mafft-nexus-internal-trimmed-gblocks-clean-90p-raxml/`: output file for 90% complete data in phylip format * a single concatenated file is provided * `phyluce_assembly_assemblo_trinity.log`: log file for phyluce assembly * `phyluce_assembly_get_match_counts.log`: log file for phyluce assembly * `phyluce_assembly_match_contigs_to_probes.log`: log file for phyluce assembly * `step2_illumiprocessor.job/.log`: jobscript/log files for step 2 (Illumiprocessor) * `step3_trinity.job/.log`: jobscript/log files for step 3 (Trinity) * `step4_fasta_lengths.job/.log`: jobscript/log files for step 4 * `step5_assembly_match_contigs_probes.job/.log`: jobscript/log files for step 5 * `step6_get_match_counts_baja.job/.log`: jobscript/log files for step 6 * `step6_get_match_counts.job/.log`: jobscript/log files for step 6 * `step7_get_fastas_from_match_counts.job/.log`: jobscript/log files for step 7 * `step8_explode_get_fastas_file.job/.log`: jobscript/log files for step 8 * `step9_get_fasta_lengths.job/.log`: jobscript/log files for step 9 * `step10_align_seqcap_align.job/.log`: jobscript/log files for step 10 * `step11_get_align_summary_data.job/.log`: jobscript/log files for step 11 * `step12_align_seqcap_align.job/.log`: jobscript/log files for step 12 * `step13_get_gblocks_trimmed_alignments_from_untrimmed.job/.log`: jobscript/log files for step 13 * `step14_get_align_summary_data.job/.log`: jobscript/log files for step 14 * `step15_remove_locus_name_from_nexus_lines.job/.log`: jobscript/log files for step 15 * `step16_get_only_loci_with_min_taxa.job/.log`: jobscript/log files for step 16 * `step17_format_nexus_files_for_raxml.job/.log`: jobscript/log files for step 17 * `taxon-set-baja.conf`: taxon set file ### 06_BCP_TSC_beast2.zip This package contains input files, selected output files, and jobscripts used to generate a phylogeny of the concatenated BCP TSC data, presented in Supplemental Figure 1 in the article. For more details, see the [BEAST2 web page](https://www.beast2.org/). * `mafft-nexus-internal-trimmed-gblocks-clean-75p.phylip`: concatenated data used as input, directly from phyluce * `baja_TSC_75p.xml`: Input file for the analysis * `baja_TSC_mafft-nexus-internal-trimmed-gblocks-clean-75p_run1.trees`: Trees from the first run (run 1) * `baja_TSC_mafft-nexus-internal-trimmed-gblocks-clean-75p_run3.trees`: Trees from the second run (run 3) * `BEAST_TSC.job`: job file used to run BEAST * `combined_trees2.trees`: combined trees across two runs, after discarding burn-in * `max_clade_cred.tre`: The final maximum clade consensus tree used to generate Supplemental Figure 1 ### 07_BCP_TSC_starbeast2.zip This package contains the input files, selected output files, and jobscript used to run the StarBEAST analysis, presented in Figure 6 in the article. For more details, please see the [StarBEAST tutorial](https://beast2-dev.github.io/beast-docs/beast2/STARBEAST/StarBEAST_tutorial.html). * `starbeast.job`: jobscript file used to run the analysis * `combined_species.trees`: combined species trees resulting from three independent runs, after discarding burn-in * `species_run1.trees`: species trees resulting from the first run * `species_run3.trees`: species trees resulting from the second run * `species_run4.trees`: species trees resulting from the third run * `species.tree`: maximum clade consensus tree, presented in Figure 6 * `SpeciesTreeUCLN_26exons_HKY_500million_2.4.5.xml`: input file used to run the analysis ### 08_BCP_ecoevolity.zip This archive contains input files for ecoevolity analyses conducted on two types of genomic data: ddRAD and TSC. The data are organized to reflect two separate biogeographic tests across the Baja California peninsula: the La Paz and Vizcaíno biogeographic breaks. These results are presented in Figures 7 & 8 in the article. For more details, see the [ecoevolity repository on github](https://github.com/phyletica/ecoevolity). The base directory contains two main subdirectories: * `BCP_ddRAD/` * `TSC/` Each of these directories contains two subfolders, representing the two biogeographic regions tested: * `lapaz/` * `vizcaino/` Within each biogeographic subfolder (`lapaz` and `vizcaino`), there are three key directories: * `data/ ` * Contains the sequence data in NEXUS format. Each file corresponds to a population pair used in the ecoevolity analysis. The filenames include species identifiers and dataset parameters (e.g., filtering thresholds, and region). * `Independent_prior/ ` * Contains a single file: `configuration.yml` * This YAML file specifies the ecoevolity run configuration using an *independent prior* for each divergence event across population pairs. * `Shared_prior/` * Contains a single file: `configuration.yml` * This YAML file specifies the ecoevolity run configuration using a *shared prior* across divergence events. Contents Overview: ``` Baja_phryno_ecoevolity/ ├── ddRAD/ │ ├── lapaz/ │ │ ├── data/ │ │ ├── Independent_prior/ │ │ └── Shared_prior/ │ └── vizcaino/ │ ├── data/ │ ├── Independent_prior/ │ └── Shared_prior/ ├── uce/ │ ├── lapaz/ │ │ ├── uce/ │ │ ├── Independent_prior/ │ │ └── Shared_prior/ │ └── vizcaino/ │ ├── uce/ │ ├── independent_prior/ │ ├── shared_prior/ ``` ### 09_callisaurus_rangewide_pyrad.zip This package contains input files, output files, and statistics associated with the pyrad v3.0.66 pipeline, which was used to process the raw FASTQ data (range-wide *Callisaurus*, ddRAD) into a variety of output formats. * `steps2-7.job`: Example jobscript file for steps 2-7 of the pipeline * `callisaurus_params_051917.txt`: The input parameters file (the most important file for reproducibility) This package also contains the following directories: * `outfiles/`: Please see the [pyrad documentation](https://github.com/dereneaton/pyrad) for more details on file formats. Not all output files were used in the manuscript, but are provided here for maximum transparency and utility to anyone interested in reanalyzing this dataset. * `output_callisaurus_051917_n102_h5_p75.alleles`: alleles file * `output_callisaurus_051917_n102_h5_p75.excluded_loci`: excluded loci * `output_callisaurus_051917_n102_h5_p75.gphocs`: GPHOCS format * `output_callisaurus_051917_n102_h5_p75.loci`: loci file * `output_callisaurus_051917_n102_h5_p75.nex`: nexus format * `output_callisaurus_051917_n102_h5_p75.phy`: phylip format * `output_callisaurus_051917_n102_h5_p75.phy.partitions`: partitioned phylip format * `output_callisaurus_051917_n102_h5_p75.snps`: single nucleotide polymorphisms (SNPs) * `output_callisaurus_051917_n102_h5_p75.snps.geno`: SNPs in geno format * `output_callisaurus_051917_n102_h5_p75.str`: structure format * `output_callisaurus_051917_n102_h5_p75.unlinked_snps`: unlinked SNPs * `output_callisaurus_051917_n102_h5_p75.usnps.geno`: unlinked SNPs in geno format * `output_callisaurus_051917_n102_h5_p75.vcf`: variant call file * An identical set of files with the suffix `_ex_outgr` mirrors the files above, but excludes the outgroups (*Holbrookia*). * `stats/`: Refer to the [pyrad documentation](https://github.com/dereneaton/pyrad) for more details. * `output_callisaurus_051917_n102_h5_p75_ex_outgr.stats`: stats summary file * `output_callisaurus_051917_n102_h5_p75.stats` * `s2.rawedit.txt`: stats for step 2 * `s3.clusters.txt`: stats for step 3 * `s5.consens.txt`: stats for step 5 ### 10_callisaurus_rangewide_admixture.zip This package contains the inputs, outputs, and other relevant files for the Admixture analysis of the range-wide *Callisaurus* ddRAD data, presented in Figure 9 in the article. For more information, consult the [Admixture website](https://dalexander.github.io/admixture/). * `data_conversion/`: As described in the article, plink and PGDSpider were used to convert data from pyRAD into a format usable by the newer version of Admixture (v1.3.0). * `output_callisaurus_051917_n102_h5_p75_ex_outgr_plink.log`: log file from plink * `output_callisaurus_051917_n102_h5_p75_ex_outgr_plink.nosex`: a PLINK output that flags individuals with missing or ambiguous sex information * `output_callisaurus_051917_n102_h5_p75_ex_outgr.map`: SNP map information (chromosome, SNP ID, position) * `output_callisaurus_051917_n102_h5_p75_ex_outgr.ped`: genotype data in a large text table (individual IDs + genotypes) * `plink-calli_020625.log`: log file from plink * `plink.job`: jobscript file used to run plink * `inputs/` * `admix-calli_K5-12.log`: log file from Admixture * `admixture.job`: jobscript used to run Admixture * `output_callisaurus_051917_n102_h5_p75_ex_outgr_plink.bed`: input file for Admixture; binary genotype data * `output_callisaurus_051917_n102_h5_p75_ex_outgr_plink.bim`: input file for Admixture; extended SNP map * `output_callisaurus_051917_n102_h5_p75_ex_outgr_plink.fam`: input file for Admixture; family/individual information (sample IDs, sex, phenotype) * `results_plotting/` * `admixture_on_map_callisaurus_020825.R`: R script used to plot Admixture results on a map * `admixture_plot_callisaurus_rangewide.R`: R script used to generate barplots * `callisaurus_K12_run2.data`: output data for K=12 * `callisaurus_rangewide_gps.data`: GPS coordinates for range-wide *Callisaurus*. Rounded to a precision of two decimal degrees for the purposes of this archive. * `CVE.csv`: cross-validation errors, used to determine optimal K * `output_callisaurus_051917_n102_h5_p75_ex_outgr_plink.[k].P`: allele frequencies output by Admixture * `output_callisaurus_051917_n102_h5_p75_ex_outgr_plink.[k].Q`: ancestry proportions estimated by Admixture ### 11_callisaurus_rangewide_raxml.zip This package contains the inputs, outputs, and other files necessary to reproduce the RAxML analyses for the range-wide *Callisaurus* ddRAD data, presented in Figure 9 in the article. To learn more, see the [RAxML website](https://cme.h-its.org/exelixis/web/software/raxml/). * `output_callisaurus_051917_n102_h5_p75.phy`: The input file from pyrad * `RAxML_bipartitions.output_callisaurus_051917_n102_h5_p75_raxml.tre`: The output `.tre` file presented in Figure 9 * `raxml_callisaurus.log`: Log file from the analysis * `raxml-jobscript.job`: Jobscript file used to run the analysis