DOI: 10.5061/dryad.p2ngf1vtc
title: Data from: Testing assertions of widespread introgressive hybridization in a clade of neotropical toads with low mate selectivity (<em>Rhinella granulosa</em> species group)

description: Discordance between different genomic regions, often identified through
 multi-locus sequencing of selected markers, presents particular
 difficulties in identifying historical processes which drive species
 diversity and boundaries. Mechanisms causing discordance, such as
 incomplete lineage sorting or introgression due to interspecific
 hybridization, are better identified based on population-level genomic
 datasets. In the toads of the Rhinella granulosa species group, patterns
 of mito-nuclear discordance and potential hybridization have been reported
 by several studies. However, these patterns were proposed based on few
 loci, such that alternative mechanisms behind gene-tree heterogeneity
 cannot be ruled out. Using genome-wide ddRADseq loci from a subset of
 species within this clade, we found only partial concordance between
 currently recognized species-level taxon boundaries and patterns of
 genetic structure. While most taxa within the R. granulosa group
 correspond to clades, genetic clustering analyses sometimes grouped
 distinct taxonomic units into a single cluster. Moreover, levels of
 admixture between inferred clusters were limited and restricted to a
 single taxon pair which is best explained by incomplete lineage sorting as
 opposed to introgressive hybridization, according to D-statistics results.
 These findings contradict previous assertions of widespread cryptic
 diversity and gene flow within the R. granulosa clade. Lastly, our
 analyses suggest that diversification events within the Rhinella granulosa
 group mostly dated back to the early Pliocene, being generally younger
 than species divergences in other closely related clades that present high
 levels of cross-species gene flow. This finding uniquely contradicts
 common assertions that this young clade of toads exhibits interspecific
 hybridization.
description: Genomic DNA was extracted, amphified, and sequenced using
 16S-specific primers, and used to generate maximum likelihood and bayesian
 phylogenies using IQTREE and MrBayes. All other data files were generated
 with double-digest restriction site-associated DNA sequence (ddRADseq)
 data. Briefly, ddRADseq libraries were generated using SbfI and MspI
 restriction enzymes, tagging fragments with individual barcodes at the
 University of Texas at Arlington. Libraries were then sequenced on a
 single lane on an Illumina HiSeq 2500 platform. The resulting data was
 demultiplexed using ipyrad, which generated input files for the programs
 used in this analysis.
description: # Data from: Testing assertions of widespread introgressive hybridization
 in a clade of neotropical toads with low mate selectivity (*Rhinella
 granulosa* species group)
 [https://doi.org/10.5061/dryad.p2ngf1vtc](https://doi.org/10.5061/dryad.p2ngf1vtc) ## Contents for dryad_data.zip IMPORTANT: Active Code Repository on GitHub and Zenodo: [https://doi.org/10.5281/zenodo.18683244](https://doi.org/10.5281/zenodo.18683244) All analysis code, data, and documentation are maintained at: [https://github.com/daniellerivera/Rhinella_granulosa](https://github.com/daniellerivera/Rhinella_granulosa) The GitHub repository is the primary, actively maintained source for reproducibility and contains: * All analysis scripts with detailed README files * Software dependencies and installation instructions * Input and output files * Version control for code updates * Issue tracking for user support **We strongly recommend using the GitHub repository rather than the static files archived here.** ### Article Citation Rivera D, Prates I, Caldwell JP, Rodrigues MT, Fujita MK. 2022. Testing assertions of widespread introgressive hybridization in a clade of neotropical toads with low mate selectivity (Rhinella granulosa species group). *Heredity* 130: 14-21. DOI: [https://doi.org/10.1038/s41437-022-00571-9](https://doi.org/10.1038/s41437-022-00571-9) --- ## File Descriptions The input files for this study can be found on Dryad. Please see Zenodo for the scripts and other files needed: [https://doi.org/10.5281/zenodo.18683244](https://doi.org/10.5281/zenodo.18683244) ### Admixture/ Population structure analysis using ADMIXTURE. * `rgran_ref_m65_randomSNP.str` — Genotype data in STRUCTURE format. ### DAPC/ Discriminant Analysis of Principal Components performed in the R package adegenet. * `rgran_ref_m65_randomSNP.str` — Same STRUCTURE-format genotype file as used in Admixture/ ### D-Suite/ Tests of introgression using D-statistics (ABBA-BABA) implemented in D-Suite. * `rgran_ref_1SNP-locus.vcf` — VCF file containing one SNP per locus. * `sets.txt` — Tab-delimited file assigning individuals to populations/taxa for D-Suite analysis. * `plot_order.txt` — Order of populations for output plotting. * `tree.nwk` — Newick-format guide tree specifying population relationships and outgroup for D-Suite. ### G-PhoCS/ Divergence time and migration rate estimation using G-PhoCS. * `gran_ingrps_sub_gphocs.gphocs` — Sequence data file in G-PhoCS format. * `gramir_mercenhum_maj_nomig.ctl` — G-PhoCS control file specifying model parameters, priors, and MCMC settings for the no-migration model. ### SVDQuartets/ Coalescent-based species tree estimation using SVDQuartets as implemented in PAUP*. * `rgran.nex` — NEXUS file containing SNP data and PAUP* block with SVDQuartets analysis settings. ### TESS3r/ Spatial ancestry and population structure estimation using TESS3r. * `rgran_data.geno` — Genotype matrix in .geno format. * `rgran_data.lfmm` — Genotype matrix in LFMM format for the same individuals and SNPs. ## Software Requirements * ADMIXTURE * D-Suite * R (with packages: adegenet, tess3r, and others listed in individual scripts) * G-PhoCS * IQ-TREE * MrBayes * PAUP* * Python (for ADMIXTURE processing) See GitHub repository for detailed installation instructions and dependencies. ## Usage For detailed usage instructions, see the README.md file in the GitHub repository at [https://github.com/daniellerivera/Rhinella_granulosa](https://github.com/daniellerivera/Rhinella_granulosa) Each analysis folder contains input files and scripts. The GitHub repository provides step-by-step instructions for reproducing all analyses. ## Support For questions or issues: * Open an issue on GitHub: [https://github.com/daniellerivera/Rhinella_granulosa/issues](https://github.com/daniellerivera/Rhinella_granulosa/issues) * Contact: Danielle Rivera ## Note on Reproducibility This Dryad entry serves as a permanent DOI for citation purposes. The GitHub repository at [https://github.com/daniellerivera/Rhinella_granulosa](https://github.com/daniellerivera/Rhinella_granulosa) is the definitive source for code and includes version control, making it superior for reproducibility.