DOI: 10.5061/dryad.kg686
title: Data from: Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae)

description: 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.
description: bait-120-60-selectionSequences used to design MYbaits kit.Curated alignments and gene treesIncludes alignments and partition files, RAxML bootstrap and best tree files for curated nuclear loci.curated_alignments&trees.zipaTRAM alignments and gene treesIncludes raw alignments for 48 nuclear loci obtained through aTRAM assembly. Also edited alignments and RAxML output files for 39 nuclear loci.aTRAM_alignments&trees.zipConcatenated alignments and treesIncludes 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.concatenated_alignments&trees.zipNetworksIncludes tree and nexus files used to compute neighbor-net and hybridization networks.networks.zipASTRALIncludes output files from ASTRAL-II analyses of 12 curated nuclear loci and 39 aTRAM nuclear loci.BUCKyIncludes alignments used in BUCKy and output files for analyses with two different alpha values (1, INFINITY).*BEASTIncludes xml, log, and species tree files for all runs performed for each analysis.BEAST.zipJMLIncludes 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.Coalescent simulationsIncludes simulated gene trees under three branch length scaling factors from ASTRAL species trees inferred from 12 curated loci and 39 aTRAM loci.coalescent simulations.ziprun_cut_trim_blat.qsubSubmission script to run Cutadapt, Sickle, Blat, and python script to pull out blat hits.get_reads_w_blat_hit_pePython scriptReference sequencesTranscriptomic reference sequences for 48 nuclear loci.references_Illumina_9XII2016.fasta