J Syst Evol ›› 2023, Vol. 61 ›› Issue (5): 806-826.DOI: 10.1111/jse.12920

• Research Articles • Previous Articles     Next Articles

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

Xiao-Gang Fu1,2,3†, Shui-Yin Liu2,3†, Robin van Velzen4, Gregory W. Stull2, Qin Tian2,3, Yun-Xia Li2,3, Ryan A. Folk5, Robert P. Guralnick6, Heather R. Kates6, Jian-Jun Jin7, Zhong-Hu Li1, Douglas E. Soltis6,8, Pamela S. Soltis6, and Ting-Shuang Yi2,3*   

  1. 1 Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China;
    2 Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
    3 University of Chinese Academy of Sciences, Beijing 100049, China;
    4 Biosystematics Group, Wageningen University and Research Center, Wageningen 6708 PB, the Netherlands;
    5 Department of Biological Sciences, Mississippi State University, Starkville, MS 39762, USA;
    6 Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA;
    7 Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY 10027, USA;
    8 Department of Biology, University of Florida, Gainesville, FL 32611, USA
    These authors contributed equally to this work.
    *Author for correspondence. E-mail:tingshuangyi@mail.kib.ac.cn
  • Received:2022-06-06 Accepted:2022-09-27 Online:2022-09-30 Published:2023-09-01

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 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 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 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.

Key words: ancient hybridization, Cannabaceae, Celtis, classification, cyto-nuclear discordance, incomplete lineage sorting, phylogenomics, Sparrea