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 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.

Phylogenomic Analyses Reveal Widespread Gene Flow During the Early Radiation of Oaks and Relatives (Fagaceae: Quercoideae)

“…For hybrid enrichment, we used a set of exonic baits for 100 housekeeping genes designed for use across the rosid clade of angiosperms, but with a focus on the nitrogen-fixing clade, which includes Fagaceae. This locus panel and bait set, the "NitFix loci" reported in Folk et al (2021), Fu et al (2022) and Kates et al (2022), were developed using MarkerMiner (Chamala et al 2015) as universal across the rosids based on 78 phylogenetically representative transcriptomes from the 1KP project (Matasci et al 2014;Leebens-Mack et al 2019). Beyond the default filtering criteria implemented in MarkerMiner, which account for length, copy number, and other criteria (see Chamala et al 2015), loci in the panel had at least 50% species coverage of the included rosid species.…”

Rapid in situ diversification rates in Rhamnaceae explain the parallel evolution of high diversity in temperate biomes from global to local scales

“…(2021). Target enrichment probes (Folk et al ., 2021; Fu et al ., 2022) were used to capture 100 low‐copy nucleotide genes, and hybridization enrichment sequencing (Hyb‐seq) was conducted by Rapid Genomics (Gainesville, FL, USA). Raw sequenced reads were cleaned and filtered as follows: Illumina adapter sequence artifacts were trimmed, low‐quality reads were discarded, and low‐quality read ends were trimmed using T rimmomatic v.0.32 (Bolger et al ., 2014).…”

“…Leaf material was collected from the following herbaria: A, AD, BRI, CAS, F, KUN, MEL, MO, NY, OS, PERTH, TEX, and US as well as from the field (Supporting Information Dataset S1), and total DNA was extracted using a modified CTAB method following the protocol described in Folk et al (2021). Target enrichment probes (Folk et al, 2021;Fu et al, 2022) were used to capture 100 low-copy nucleotide genes, and hybridization enrichment sequencing (Hyb-seq) was conducted by Rapid Genomics (Gainesville, FL, USA). Raw sequenced reads were cleaned and filtered as follows: Illumina adapter sequence artifacts were trimmed, low-quality reads were discarded, and low-quality read ends were trimmed using TRIM-MOMATIC v.0.32 (Bolger et al, 2014).…”

Bioactive Compounds from Natural Sources as Potential Adjuvants in the Treatment of Mild Acne Vulgaris

“…Another notable economic species is the wingceltis (Pteroceltis tatarinowii Maxim. ), prized for its bark fiber, which serves as the primary material in the production of traditional Chinese Xuan paper [24].…”