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-nuclear discordances likeliest stem from incomplete lineage sorting
(ILS); nuclear gene-tree conflict might be caused by both ILS and gene
flow between species. All genera of Cannabaceae were recovered as
monophyletic, except for Celtis, which consisted of two distinct clades:
Celtis I (including most Celtis species) and Celtis II (including Celtis
gomphophylla and Celtis schippii). We suggest that Celtis II should be
recognized as the independent genus Sparrea based on both molecular and
morphological evidence. Our work provides the most comprehensive and
reliable phylogeny to date for Cannabaceae, enabling further exploration
of evolutionary patterns across this family and highlighting the necessity
of comparing nuclear with chloroplast data to examine the evolutionary
history of plant groups.