Data from: Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae)
Folk, Ryan A.
Meerow, Alan W.
Gitzendanner, Matthew A.
Oliveira, Renata S. de
Soltis, Douglas E.
Soltis, Pamela S.
Published Apr 11, 2017 on Dryad.
Cite this dataset
García, Nicolás et al. (2017). Data from: Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae) [Dataset]. Dryad. https://doi.org/10.5061/dryad.kg686
Hybridization is a frequent and important force in plant evolution. Next-generation sequencing (NGS) methods offer new possibilities for clade resolution and ambitious sampling of gene genealogies, yet difficulty remains in detecting deep reticulation events using currently available methods. We reconstructed the phylogeny of diploid representatives of Amaryllidaceae tribe Hippeastreae to test the hypothesis of ancient hybridizations preceding the radiation of its major subclade, Hippeastrinae. Through hybrid enrichment of DNA libraries and NGS, we obtained data for 18 nuclear loci through a curated assembly approach and nearly complete plastid genomes for 35 ingroup taxa plus 5 outgroups. Additionally, we obtained alignments for 39 loci through an automated assembly algorithm. These data were analyzed with diverse phylogenetic methods, including concatenation, coalescence-based species tree estimation, Bayesian concordance analysis, and network reconstructions, to provide insights into the evolutionary relationships of Hippeastreae. Causes for gene tree heterogeneity and cytonuclear discordance were examined through a Bayesian posterior predictive approach (JML) and coalescent simulations. Two major clades were found, Hippeastrinae and Traubiinae, as previously reported. Our results suggest the presence of two major nuclear lineages in Hippeastrinae characterized by different chromosome numbers: 1) Tocantinia and Hippeastrum with 2n = 22, and 2) Eithea, Habranthus, Rhodophiala, and Zephyranthes mostly with 2n = 12, 14, and 18. Strong cytonuclear discordance was confirmed in Hippeastrinae, and a network scenario with at least six hybridization events is proposed to reconcile nuclear and plastid signals, along a backbone that may also have been affected by incomplete lineage sorting at the base of each major subclade.
Sequences used to design MYbaits kit.
Curated alignments and gene trees
Includes alignments and partition files, RAxML bootstrap and best tree files for curated nuclear loci.
aTRAM alignments and gene trees
Includes raw alignments for 48 nuclear loci obtained through aTRAM assembly. Also edited alignments and RAxML output files for 39 nuclear loci.
Concatenated alignments and trees
Includes alignments and trees for concatenated analyses of 39 aTRAM nuclear loci, 15 curated nuclear loci (including and excluding noncoding regions), and curated nuclear plus plastid regions.
Includes tree and nexus files used to compute neighbor-net and hybridization networks.
Includes output files from ASTRAL-II analyses of 12 curated nuclear loci and 39 aTRAM nuclear loci.
Includes alignments used in BUCKy and output files for analyses with two different alpha values (1, INFINITY).
Includes xml, log, and species tree files for all runs performed for each analysis.
Includes control and output files for JML analyses of 12 curated nuclear loci and plastid coding sequences. Also collection of *BEAST species trees used in analyses.
Includes simulated gene trees under three branch length scaling factors from ASTRAL species trees inferred from 12 curated loci and 39 aTRAM loci.
Submission script to run Cutadapt, Sickle, Blat, and python script to pull out blat hits.
Transcriptomic reference sequences for 48 nuclear loci.