Data_Sheet_2_Phylogenomics of the Andean Tetraploid Clade of the American Amaryllidaceae (Subfamily Amaryllidoideae): Unlocking a Polyploid Generic Radiation Abetted by Continental Geodynamics.PDF

One of the two major clades of the endemic American Amaryllidaceae subfam. Amaryllidoideae constitutes the tetraploid-derived (n = 23) Andean-centered tribes, most of which have 46 chromosomes. Despite progress in resolving phylogenetic relationships of the group with plastid and nrDNA, certain subclades were poorly resolved or weakly supported in those previous studies. Sequence capture using anchored hybrid enrichment was employed across 95 species of the clade along with five outgroups and generated sequences of 524 nuclear genes and a partial plastome. Maximum likelihood phylogenetic analyses were conducted on concatenated supermatrices, and coalescent-based species tree analyses were run on the gene trees, followed by hybridization network, age diversification and biogeographic analyses. The four tribes Clinantheae, Eucharideae, Eustephieae, and Hymenocallideae (sister to Clinantheae) are resolved in all analyses with > 90 and mostly 100% support, as are almost all genera within them. Nuclear gene supermatrix and species tree results were largely in concordance; however, some instances of cytonuclear discordance were evident. Hybridization network analysis identified significant reticulation in Clinanthus, Hymenocallis, Stenomesson and the subclade of Eucharideae comprising Eucharis, Caliphruria, and Urceolina. Our data support a previous treatment of the latter as a single genus, Urceolina, with the addition of Eucrosia dodsonii. Biogeographic analysis and penalized likelihood age estimation suggests an origin in the Cauca, Desert and Puna Neotropical bioprovinces for the complex in the mid-Oligocene, with more dispersals than vicariances in its history, but no extinctions. Hymenocallis represents the only instance of long-distance vicariance from the tropical Andean origin of its tribe Hymenocallideae. The absence of extinctions correlates with the lack of diversification rate shifts within the clade. The Eucharideae experienced a sudden lineage radiation ca. 10 Mya. We tie much of the divergences in the Andean-centered lineages to the rise of the Andes, and suggest that the Amotape—Huancabamba Zone functioned as both a corridor (dispersal) and a barrier to migration (vicariance). Several taxonomic changes are made. This is the largest DNA sequence data set to be applied within Amaryllidaceae to date.

原产于美洲的石蒜科（Amaryllidaceae）石蒜亚科（Amaryllidoideae）的两大主要演化支（clade）之一，是以安第斯山脉为分布中心的四倍体起源类群，其单倍染色体数为23，多数类群的体细胞染色体数为46。尽管此前借助质体（plastid）与核糖体DNA（nrDNA）解析该类群系统发育关系的研究已取得一定进展，但部分演化支在过往研究中仍分辨率不足或支持率较弱。本研究采用锚定杂交富集（anchored hybrid enrichment）技术对该演化支的95个物种及5个外类群（outgroups）开展序列捕获，获得了524个核基因序列与部分质体基因组（plastome）。基于拼接的超级矩阵（concatenated supermatrices）开展最大似然法（maximum likelihood）系统发育分析，同时基于基因树（gene trees）进行基于溯祖理论的物种树分析，随后开展杂交网络分析（hybridization network analysis）、分化时间分析（age diversification analysis）与生物地理分析（biogeographic analysis）。所有分析均高度支持克林族（Clinantheae）、优卡百合族（Eucharideae）、尤斯特菲族（Eustephieae）以及与克林族互为姊妹群的水鬼蕉族（Hymenocallideae）这四个族的单系性，支持率均大于90%，多数节点支持率达100%；族内绝大多数属的单系性也得到了一致支持。核基因超级矩阵与物种树的分析结果整体一致，但也存在少量核质体冲突（cytonuclear discordance）的现象。杂交网络分析显示，克林花属（Clinanthus）、水鬼蕉属（Hymenocallis）、狭叶蒜属（Stenomesson）以及包含优卡百合属（Eucharis）、Caliphruria属和瓮蕊花属（Urceolina）的优卡百合族演化支存在显著的网状进化事件。本研究数据支持此前将该优卡百合族演化支处理为单一的瓮蕊花属（Urceolina），并加入Eucrosia dodsonii的分类处理方案。生物地理分析与惩罚似然法（penalized likelihood）年龄估计结果显示，该类群复合体起源于渐新世中期的新热带界考卡、荒漠与普纳生物省，其演化历史中扩散事件多于隔离分化（vicariance）事件，且未发生类群灭绝。水鬼蕉属是其所在的水鬼蕉族中唯一出现自热带安第斯起源发生远距离隔离分化的类群。未检测到类群灭绝的现象，与该演化支内未发生分化速率变化的结果相符。优卡百合族在约1000万年前（ca. 10 Mya）经历了快速的谱系辐射（lineage radiation）。本研究将安第斯分布类群的多数分化事件与安第斯山脉的隆升相关联，并提出阿莫塔佩-万卡班巴带（Amotape—Huancabamba Zone）同时充当了物种扩散的廊道与迁移阻隔的屏障。本研究共提出多项分类学修订。本数据集是目前石蒜科内应用的规模最大的DNA序列数据集。