Data from: Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae)

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.

杂交是植物演化中常见且关键的演化动力。下一代测序（Next-generation sequencing, NGS）技术为提升支系分辨率、实现基因谱系的海量采样提供了新可能，但现有方法仍难以检测深层网状演化事件。本研究对石蒜科（Amaryllidaceae）朱顶红族（Hippeastreae）的二倍体代表类群构建系统发育树，以验证其主要亚族朱顶红亚族（Hippeastrinae）辐射演化前曾发生古老杂交事件的假说。通过DNA文库杂交富集与NGS技术，本研究经质控优化的组装流程获得了18个核基因位点的数据，并为35个内群类群及5个外群类群获取了近乎完整的质体基因组。此外，本研究还通过自动化组装算法获得了39个基因位点的序列比对矩阵。本研究采用多种系统发育分析方法对上述数据进行解析，包括串联法、基于溯祖理论的物种树推断、贝叶斯一致性分析及网状演化重建，以阐明朱顶红族的演化关系。本研究通过贝叶斯后验预测方法（JML）与溯祖模拟，探究了基因树异质性与核质基因组冲突的成因。如既往研究报道，本研究共检出两个主要支系：朱顶红亚族（Hippeastrinae）与特劳比阿亚族（Traubiinae）。研究结果显示，朱顶红亚族存在两个以不同染色体数为特征的主要核谱系：1）Tocantinia属与朱顶红属（Hippeastrum），其染色体数多为2n=22；2）Eithea属、Habranthus属、Rhodophiala属及Zephyranthes属，其染色体数多为2n=12、14及18。本研究证实朱顶红亚族存在显著的核质基因组冲突，并提出至少包含6次杂交事件的网状演化框架，以协调核基因组与质体基因组的信号差异；该演化框架的主干在两个主要亚族的基部可能亦受不完全谱系分选的影响。