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

Abstract 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 have clarified the most deep relationships in Cannabaceae, but relationships remain ambiguous among several major lineages. Here, we sampled 82 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 betweenGironnieraandLozanellaand the relationships amongTremas.l. (includingParasponia),Cannabis + Humulus, andChaetachme + Pteroceltis. Coalescent simulations and network analyses suggest that observed deep cyto‐nuclear discordances were most likely to 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 forCeltis, which consisted of two distinct clades:CeltisI (including mostCeltisspecies) andCeltisII (includingCeltis gomphophyllaandCeltis schippii). We suggest thatCeltisII should be recognized as the independent genusSparreabased 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.