Phylogenomic analysis of the hemp family (Cannabaceae) reveals deep cyto-nuclear discordance and provides new insights into generic relationships

Cannabaceae are a relatively small family of angiosperms, but they include several species of huge economic and cultural significance: marijuana or hemp (Cannabis sativa) and hops (Humulus lupulus). Previous phylogenetic studies clarified most deep relationships in Cannabaceae, but relationships remain ambiguous among several major lineages. Here, we sampled 83 species representing all genera of Cannabaceae and utilized a new dataset of 90 nuclear genes and 82 chloroplast loci from Hyb-Seq to investigate the phylogenomics of Cannabaceae. Nuclear phylogenetic analyses revealed a robust and consistent backbone for Cannabaceae. We observed nuclear gene-tree conflict at several deep nodes in inferred species trees, also cyto-nuclear discordance concerning the relationship between Gironniera and Lozanella and the relationships among Trema s.l. (including Parasponia), Cannabis + Humulus, and Chaetachme + Pteroceltis. Coalescent simulations and network analyses suggest that observed deep cyto-...

大麻科（Cannabaceae）是一类规模相对较小的被子植物（angiosperms）科，但其内包含多个兼具重大经济与文化价值的物种：大麻（Cannabis sativa，俗称大麻或工业大麻）与啤酒花（Humulus lupulus）。此前的系统发育研究已阐明大麻科内多数深层演化关系，但多个主要谱系间的亲缘关系仍存在歧义。本研究采集了大麻科所有属的83个物种，利用基于杂交捕获测序（Hyb-Seq）获得的包含90个核基因与82个叶绿体基因座的全新数据集，对大麻科开展系统发育基因组学研究。核系统发育分析得到了稳健且一致的大麻科系统发育主干框架。研究发现，在重构的物种树中，多个深层节点存在核基因树冲突；同时，糙叶树属（Gironniera）与洛赞木属（Lozanella）的亲缘关系、广义山黄麻属（Trema s.l.，包含Parasponia）、大麻属+啤酒花属，以及刺枝树属（Chaetachme）+青檀属（Pteroceltis）之间的演化关系均存在质核冲突（cyto-nuclear discordance）。溯祖模拟与网络分析结果表明，观测到的深层质核……