Phylogenomics, introgression, and demographic history of South American true toads (Rhinella)
Creators: name: Rivera, Danielle
name: Prates, Ivan
name: Firneno, Thomas
name: Rodrigues, Miguel
name: Caldwell, Janalee
name: Fujita, Matthew
Publisher: name: Zenodo
Year: 2023
Subjects: demographic modelling
hybridization
introgression
Phylogenomics
Rhinella

description: The effects of genetic introgression on species boundaries and how they affect species' integrity and persistence over evolutionary time have received increased attention. The increasing availability of genomic data has revealed contrasting patterns of gene flow across genomic regions, which impose challenges to inferences of evolutionary relationships and of patterns of genetic admixture across lineages. By characterizing patterns of variation across thousands of genomic loci in a widespread complex of true toads (<em>Rhinella</em>), we assess the true extent of genetic introgression across species thought to hybridize to extreme degrees based on natural history observations and multi-locus analyses. Comprehensive geographic sampling of five large-ranged Neotropical taxa revealed multiple distinct evolutionary lineages that span large geographic areas and, at times, distinct biomes. The inferred major clades and genetic clusters largely correspond to currently recognized taxa; however, we also found evidence of cryptic diversity within taxa. While previous phylogenetic studies revealed extensive mito-nuclear discordance, our genetic clustering analyses uncovered several admixed individuals within major genetic groups. Accordingly, historical demographic analyses supported that the evolutionary history of these toads involved cross-taxon gene flow both at ancient and recent times. Lastly, ABBA-BABA tests revealed widespread allele sharing across species boundaries, a pattern that can be confidently attributed to genetic introgression as opposed to incomplete lineage sorting. These results confirm previous assertions that the evolutionary history of <em>Rhinella</em> was characterized by various levels of hybridization even across environmentally heterogeneous regions, posing exciting questions about what factors prevent complete fusion of diverging yet highly interdependent evolutionary lineages.
description: To read tree files: Figtree <pre>For analyses:<br> - Beast<br> - Admixture<br> - dadi <br> - R<br> - Dsuite</pre>Funding provided by: National Science Foundation<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001<br>Award Number: DEB 1343578Funding provided by: National Science Foundation<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001<br>Award Number: DEB 1754398Funding provided by: National Science Foundation<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001<br>Award Number: GRFPFunding provided by: Fundação de Amparo à Pesquisa do Estado de São Paulo<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001807<br>Award Number: BIOTA 2013/50297-0Funding provided by: Fundação de Amparo à Pesquisa do Estado de São Paulo<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001807<br>Award Number: 2003/10335-8Funding provided by: Fundação de Amparo à Pesquisa do Estado de São Paulo<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001807<br>Award Number: 2011/50146-6Funding provided by: Fundação de Amparo à Pesquisa do Estado de São Paulo<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001807<br>Award Number: 2011/50206‐9Funding provided by: Fundação de Amparo à Pesquisa do Estado de São Paulo<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001807<br>Award Number: 2012/15754-8Funding provided by: Fundação de Amparo à Pesquisa do Estado de São Paulo<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001807<br>Award Number: 2017/08357-6
description: Genomic DNA was extracted, amphified, and sequenced using 16S-specific primers, and used to generate an .xml file to run a time-calibrated phylogeny in BEAST. 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.