DOI: 10.5061/dryad.tb2rbp09n
title: Rampant Reticulation in a Rapid Radiation of Tropical Trees - Insights from <i>Inga</i> (Fabaceae)

description: Evolutionary radiations underlie much of the species diversity of life on
 Earth, particularly within the world’s most species-rich tree flora – that
 of the Amazon rainforest. Hybridisation occurs in many radiations, with
 effects ranging from homogenisation of species to generation of genetic
 and phenotypic novelty that fuels speciation, but the influence of
 hybridisation on Amazonian tree radiations has been little studied. We
 address this using the ubiquitous, species-rich, neotropical tree genus
 Inga, which typifies rapid radiations of rainforest trees. We assess
 patterns of gene tree incongruence to ascertain whether hybridisation was
 associated with rapid radiation in Inga. Given the importance of insect
 herbivory in structuring rainforest tree communities (and hence the
 potential for hybridisation to promote adaptation through admixture of
 defence traits), we also test whether introgression of loci underlying
 chemical defences against herbivory occurred during the radiation of Inga.
 Our phylogenomic analyses of 189/288 Inga species using &gt;1300
 target capture loci showed widespread introgression in Inga. Specifically,
 we found widespread phylogenetic incongruence explained by introgression,
 with phylogenetic networks recovering multiple introgression events across
 Inga and up to 20% of shared, likely introgressed, genetic variation
 between some species. In addition, most defence chemistry loci showed
 evidence of positive selection and marginally higher levels of
 introgression. Overall, our results suggest that introgression has
 occurred widely over the course of Inga’s history, likely facilitated by
 extensive dispersal across Amazonia, and that in some cases, introgression
 of chemical defence loci may influence adaptation in Inga.
description: # Rampant Reticulation in a Rapid Radiation of Tropical Trees - Insights
 from <i>Inga</i> (Fabaceae)
 [https://doi.org/10.5061/dryad.tb2rbp09n](https://doi.org/10.5061/dryad.tb2rbp09n) ## Description of the data and file structure ### **Data (Available on Dryad)** * **Data 1 -** MAFFT alignments for all loci and all 3 datasets (Singlesp (one *Inga* accession per species only), Outgroup (A few *Inga* species, mostly Ingoid clade outgroups), and PPD (Singlesp dataset with paralogs removed)). Folder structure and file naming convention details dataset (e.g. Outgroup), hybseq locus (compxxxxxx) and alignment treatment (xxx_realigned). * **Data 2** - VCF files used in Dsuite analyses for all 3 datasets (Singlesp, Outgroup, PPD). File naming convention details genus, method, dataset and filtering details (e.g. Inga_Dsuite_singlesp_DP8_Q20_filtered.vcf.gz) * **Data 3** - Codon-aware alignments generated with OMM_MACSE for three subclade subsets within Inga, used for BUSTED analysis. Naming convention matches that of Data 1. * **Data 4** - IQtrees generated for all locus alignments from all 3 datasets (Singlesp, Outgroup, PPD). Naming convention matches that of Data 1. ### Supplementary Figures and Tables (Held as Supplemental Information on Zenodo) **Figures** * Figure S1: Clade definitions for taxon subsets used in *f dM *and BUSTED analyses * Figure S2: Recovery success heatmaps * Figure S3ai: *Inga* single-accession-per-species ASTRAL tree * Figure S3aii: *Inga* single-accession-per-species concatenated IQtree * Figure S3b: Outgroup ASTRAL tree * Figure S3c: PPD ASTRAL tree * Figure S4a: *Inga* single-accession-per-species SplitsTree * Figure S4b: Outgroup SplitsTree * Figure S4c: PPD SplitsTree * Figure S5: PPD QC and DiscoVista plot * Figure S6a: *Inga* single-accession-per-species QD tree * Figure S6b: Outgroup QD tree * Figure S6c: PPD QD tree * Figure S7: *Inga* PPD D-statistic & F4 ratio plot * Figure S8a: *Inga* single-accession-per-species Fbranch * Figure S8b: Outgroup Fbranch * Figure S9ai: -loglikelihood h-value plot for single-accession-per-species PhyloNetworks run * Figure S9aii: -loglikelihood h-value plots for single-accession-per-species PhyloNetworks per-subclade run * Figure S9aiii: Inferred networks for single-accession-per-species per-subclade run * Figure S9b: -loglikelihood h-value plot for Outgroup PhyloNetworks run * Figure S10: Boxplots of *f dM* grouped by locus class and selection result for subclade subsets * Figure S11: Correlation plots of selection results grouped by locus class for subclade subsets **Tables** * Table S1: Voucher information * Table S2: DiscoVista clade definitions * Table S3: Locus recovery success and alignment summaries * Table S4: -loglikelihood values per value of *h* for PhyloNetworks analyses * Table S5: BUSTED selection χ2 results * Table S6: ANCOVA BUSTED *f dM* results