DOI: 10.5061/dryad.x0k6djhrs
title: The explosive radiation of the Neotropical Tillandsia subgenus Tillandsia (Bromeliaceae) has been accompanied by pervasive hybridization

description: The recent rapid radiation of Tillandsia subgenus Tillandsia
 (Bromeliaceae) provides an attractive system to study the drivers and
 constraints of species diversification. This species-rich Neotropical
 monocot clade includes predominantly epiphytic species displaying vast
 phenotypic diversity. Recent in-depth phylogenomic work revealed that the
 subgenus originated within the last 7 MY, with one major expansion from
 South into Central America within the last 5 MY. However, disagreements
 between phylogenies and lack of resolution at shallow nodes suggest that
 hybridization may have occurred throughout the radiation, together with
 frequent incomplete lineage sorting and rapid gene family evolution. We
 used whole-genome resequencing data to explore the evolutionary history of
 representative ingroup species employing both tree-based and network
 approaches. Our results indicate that lineage co-occurrence does not
 predict relatedness and confirm significant deviations from a tree-like
 structure, coupled with pervasive gene tree discordance. Focusing on
 hybridization, ABBA-BABA and related statistics were used to infer the
 rates and relative timing of events, while topology weighting uncovered
 high heterogeneity of the phylogenetic signal along the genome. High rates
 of hybridization within and among subclades suggest that, contrary to
 previous hypotheses, the expansion of subgenus Tillandsia into Central
 America proceeded through several dispersal events, punctuated by episodes
 of diversification and gene flow. Network analysis revealed reticulation
 as a plausible propeller during radiation and establishment across
 different ecological niches. This work contributes a plant example of
 prevalent hybridization during rapid species diversification, supporting
 the hypothesis that interspecific gene flow facilitates explosive
 diversification.
description: # The explosive radiation of the Neotropical Tillandsia subgenus
 Tillandsia (Bromeliaceae) has been facilitated by pervasive hybridization
 [https://doi.org/10.5061/dryad.x0k6djhrs](https://doi.org/10.5061/dryad.x0k6djhrs) ## List of files in the dataset sample_id_dict.list - a dictionary containing accession codes used in analysis (column 1) and corresponding full accession name, species and code (column 2).  all_gene_partitions_alignments.fasta.gz - per-gene FASTA alignments used for partitioned maximum-likelihood tree construction with IQ-TREE v.2. gen_wins_10kb.all.treefile.gz - contains the 15,791 maximum-likelihood trees (in newick format) generated on non-overlapping genomic windows of 10 kb (without pruning). Only alignments containing at least 40 variable site (SNPs) were considered. all_windows_phylip.tar.gz - an archive containing 15,791 alignments in phylip format, produced from from 10 kb non-overlapping genomic windows. Only windows containing at least 40 variable sites (SNPs) are included. phylip_per_chr.tar.gz - concatenated multi-sample alignments for each chromosome of the *T. fasciculata* reference, in phylip format. Supporting_Dstats_all_run6_j2ksnp - Output of genome-wide D-statistics (ABBA-BABA) for all possible trios of species in the data - see Supporting_table_S1 for collection data. PhyloNet_18taxa_tree_input.nwk.gz - Trees in newick format inferred on 10 kb non-overlapping genomic windows and used as input for PhyloNet analysis, on a data-set reduced to 18 taxa.