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

Fu, Xiao‐Gang; Liu, Shui‐Yin; van Velzen, Robin; Stull, Gregory W.; Tian, Qin; Li, Yun‐Xia; Folk, Ryan A.; Guralnick, Robert P.; Kates, Heather R.; Jin, Jian‐Jun; Li, Zhong‐Hu; Soltis, Douglas E.; Soltis, Pamela S.; Yi, Ting‐Shuang

doi:10.1111/jse.12920

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

Journal Article · Sun Dec 18 23:00:00 EST 2022 · Journal of Systematics and Evolution

DOI:https://doi.org/10.1111/jse.12920· OSTI ID:2420740

^[1]; Liu, Shui‐Yin ^[2]; ^[3]; Stull, Gregory W. ^[4]; Tian, Qin ^[2]; Li, Yun‐Xia ^[2]; Folk, Ryan A. ^[5]; Guralnick, Robert P. ^[6]; Kates, Heather R. ^[6]; ^[7]; ^[8]; Soltis, Douglas E. ^[9]; Soltis, Pamela S. ^[6]; ^[2]

Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences Northwest University Xi'an 710069 China; Germplasm Bank of Wild Species, Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 China; University of Chinese Academy of Sciences Beijing 100049 China; OSTI
Germplasm Bank of Wild Species, Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 China; University of Chinese Academy of Sciences Beijing 100049 China
Biosystematics Group Wageningen University and Research Center Wageningen 6708 PB the Netherlands
Germplasm Bank of Wild Species, Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 China
Department of Biological Sciences Mississippi State University Starkville MS 39762 USA
Florida Museum of Natural History University of Florida Gainesville FL 32611 USA
Department of Ecology, Evolution, and Environmental Biology Columbia University New York NY 10027 USA
Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences Northwest University Xi'an 710069 China
Florida Museum of Natural History University of Florida Gainesville FL 32611 USA; Department of Biology University of Florida Gainesville FL 32611 USA

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.

Research Organization:: Univ. of Florida, Gainesville, FL (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

DOE Contract Number:: SC0018247

OSTI ID:: 2420740

Journal Information:: Journal of Systematics and Evolution, Journal Name: Journal of Systematics and Evolution Journal Issue: 5 Vol. 61; ISSN 1674-4918

Country of Publication:: United States

Language:: English

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