Phylogenetics of Cannabis
More actions
Phylogenetics of Cannabis is the reconstruction of the evolutionary relationships of the genus Cannabis from molecular data. It addresses three questions: the placement of Cannabis among the genera of the family Cannabaceae, the genetic structure within the genus, and the genomic signatures left by domestication.[1] Successive methods resolve these relationships at different depths, and the picture has sharpened as whole-genome sequencing has replaced the biochemical and marker-based approaches used earlier.
Molecular evidence informs the long-running dispute over how many species the genus contains, but has not settled it; recent genomic reviews lean toward a single species while treating the question as open, and the rank debate itself is covered in Cannabis taxonomy.[2] How much phylogenetic structure can be recovered is limited by two features of the plant: the genus is fully interfertile, so gene flow between lineages is easy, and four decades of intentional hybridisation between drug-type populations have overwritten much of the older structure in cultivated material.[3]
Phylogenetic position within Cannabaceae
Cannabis is one of about ten genera in Cannabaceae, a family of the order Rosales. Its sister genus is Humulus, the hops, and the two herbaceous genera form a strongly supported clade nested among the family's otherwise woody members.[4][1] Molecular-clock analysis places the divergence of Cannabis and Humulus at roughly 28 million years ago.[1] The relationships among the ten genera, and the plastid and nuclear evidence that resolved them, are set out in the article on Cannabaceae; the phylogenetics of Cannabis proper begins below the genus boundary.
Molecular markers and methods
The earliest population-level work used biochemical and chemical markers. Hillig scored allozyme variation at 17 loci across a worldwide accession set in 2005, having the year before analysed the ratio of the two principal cannabinoids as a chemotype marker with Mahlberg; both studies pointed to a small number of broad gene pools rather than a continuum.[5][6]
Genomic methods followed the first reference sequences. van Bakel and colleagues published a draft genome and transcriptome of Cannabis sativa in 2011, and Laverty and colleagues added a chromosome-scale physical and genetic map in 2019 that placed the THCA and CBDA synthase genes in a heavily rearranged, repeat-rich region, which complicates their assembly and comparison.[7][8] Reduced-representation genotyping then made population samples affordable: Sawler and colleagues scored 14,031 single-nucleotide polymorphisms across 81 drug-type and 43 hemp accessions in 2015.[9]
Whole-genome resequencing widened the sample again. Ren and colleagues resequenced 110 accessions of worldwide origin in 2021, and Lynch and colleagues assembled a Cannabis pan-genome from wild, feral and cultivated plants in 2025.[10][11] Target-capture sequencing has extended the reach to herbarium material: Balant and colleagues combined sequence capture from historical collections with fresh whole genomes in 2025 to reconstruct the phylogeography of wild-growing and cultivated cannabis across Eurasia.[12] Chemical and allozyme markers resolve the broad gene pools, marker panels resolve population differentiation, and whole-genome data resolve the finer structure of domestication and the rearranged cannabinoid-synthase region.
Gene pools and intraspecific structure
The recurring result across methods is a division into two principal gene pools, a hemp or fibre type and a drug type, with a wild or ruderal element at the margin.[6][5] Hillig and Mahlberg's chemotype survey separated accessions into two pools corresponding to the traditional sativa and indica groupings, and Hillig's allozyme analysis recovered the same broad division while proposing a finer set of putative taxa within it.[6][5] Sawler and colleagues found significant genome-wide differentiation between hemp and drug accessions, consistent with the two-pool picture.[9]
Within the drug type, genome data recover a further split between a narrow-leaflet group of South Asian origin and a broad-leaflet group of Central Asian origin.[10][13] These correspond to the narrow-leaflet and broad-leaflet drug biotypes of the NLD/BLD classification and to the varieties indica and afghanica of the conservation treatment of McPartland and Small.[13] Their mapping onto the vernacular labels "Sativa" and "Indica" is looser and is treated in Sativa vs Indica. The gene-pool structure is clearest in landrace and wild-derived material and is largely obscured in modern hybrid cultivars.[9][3]
Domestication and evolutionary history
Whole-genome data have given the domestication of Cannabis its firmest treatment. Ren and colleagues resequenced 110 accessions and resolved four groups: a basal group, a hemp type, a drug type and a feral group.[10] The basal group, closest to the ancestral gene pool, now survives as feral plants and landraces in China, and from its position the authors inferred a single domestication in East Asia in the early Neolithic, about 12,000 years ago.[10] This revised a long-standing assumption of a Central Asian origin: on the genomic evidence the wild-growing populations of Central and South Asia are feral escapes rather than the source stock, and the pure wild progenitor is probably extinct, surviving only as feral and landrace relicts.[10]
The hemp and drug lineages diverged later, roughly 4,000 years ago, under selection at genes governing branching architecture, cellulose and lignin synthesis in the fibre type and the cannabinoid synthases in the drug type.[10] The pan-genome of Lynch and colleagues set this in a longer perspective: domestication simplified cannabinoid-synthase variation within a much older and more diverse genomic background, so cannabinoid chemistry is a recent overlay on the genome rather than a deep phylogenetic signal.[11] The geographic reading of these origins, and the older Vavilovian framework it revises, are treated in Centre of origin.
Hybridisation and modern accessions
Intentional hybridisation between drug-type populations of different geographic origin, carried out by breeders in North America and Europe from the late 1970s onward, has made the relationships among modern cultivars reticulate rather than tree-like.[3][9] Commercial "strain" names correspond poorly to genomic clusters, and neither morphology nor marker data assign hybrid accessions reliably to the underlying gene pools.[3][2] Reliable phylogenetic structure is therefore recovered mainly from pre-hybridisation landraces and from wild and feral material, which retain the older signal that recent crossing has erased in the commercial pool.[11][10]
Implications for taxonomy and conservation
Phylogenetic evidence bears on the number of species in Cannabis without deciding it. Genome-wide data are consistent with a division into two groups but do not distinguish a single species with two subspecies from two separate species; recent genomic reviews lean toward a single-species treatment while noting that the question remains open.[2][14] The rank debate itself is set out in Cannabis taxonomy.
For conservation the same data have a clearer use. Because domestication and later hybridisation have overwritten much of the genus's structure, genomic markers are used to identify surviving landrace and wild gene pools and to monitor their integrity.[13] McPartland and Small named four endangered drug-type varieties and their wild relatives to bring them under a formal treatment, and landrace genome studies, such as the association analysis of Iranian accessions by Babaei and Torkamaneh, characterise the diversity that survives in situ.[13][15] The link between phylogenetic structure and the conservation of landrace populations is developed in that article.
See also
References
- ↑ 1.0 1.1 1.2 McPartland, J.M. (2018). "Cannabis systematics at the levels of family, genus, and species". Cannabis and Cannabinoid Research. 3 (1): 203–212. doi:10.1089/can.2018.0039.
- ↑ 2.0 2.1 2.2 Lapierre, É.; Monthony, A.S.; Torkamaneh, D. (2023). "Genomics-based taxonomy to clarify cannabis classification". Genome. 66 (8): 202–211. doi:10.1139/gen-2023-0005.
- ↑ 3.0 3.1 3.2 3.3 McPartland, J.M.; Guy, G.W. (2017). "Models of cannabis taxonomy, cultural bias, and conflicts between scientific and vernacular names". Botanical Review. 83 (4): 327–381. doi:10.1007/s12229-017-9187-0.
- ↑ Yang, M.Q.; van Velzen, R.; Bakker, F.T.; Sattarian, A.; Li, D.Z.; Yi, T.S. (2013). "Molecular phylogenetics and character evolution of Cannabaceae". Taxon. 62 (3): 473–485. doi:10.12705/623.9.
- ↑ 5.0 5.1 5.2 Hillig, K.W. (2005). "Genetic evidence for speciation in Cannabis (Cannabaceae)". Genetic Resources and Crop Evolution. 52 (2): 161–180. doi:10.1007/s10722-003-4452-y.
- ↑ 6.0 6.1 6.2 Hillig, K.W.; Mahlberg, P.G. (2004). "A chemotaxonomic analysis of cannabinoid variation in Cannabis (Cannabaceae)". American Journal of Botany. 91 (6): 966–975. doi:10.3732/ajb.91.6.966.
- ↑ van Bakel, H.; Stout, J.M.; Cote, A.G.; Tallon, C.M.; Sharpe, A.G.; et al. (2011). "The draft genome and transcriptome of Cannabis sativa". Genome Biology. 12 (10) R102. doi:10.1186/gb-2011-12-10-r102.
- ↑ Laverty, K.U.; Stout, J.M.; Sullivan, M.J.; Shah, H.; Gill, N.; et al. (2019). "A physical and genetic map of Cannabis sativa identifies extensive rearrangements at the THC/CBD acid synthase loci". Genome Research. 29 (1): 146–156. doi:10.1101/gr.242594.118.
- ↑ 9.0 9.1 9.2 9.3 Sawler, J.; Stout, J.M.; Gardner, K.M.; Hudson, D.; Vidmar, J.; et al. (2015). "The genetic structure of marijuana and hemp". PLOS ONE. 10 (8) e0133292. doi:10.1371/journal.pone.0133292.
- ↑ 10.0 10.1 10.2 10.3 10.4 10.5 10.6 Ren, G.; Zhang, X.; Li, Y.; Ridout, K.; Serrano-Serrano, M.L.; et al. (2021). "Large-scale whole-genome resequencing unravels the domestication history of Cannabis sativa". Science Advances. 7 (29) eabg2286. doi:10.1126/sciadv.abg2286.
- ↑ 11.0 11.1 11.2 Lynch, R.C.; Padgitt-Cobb, L.K.; Garfinkel, A.R.; Knaus, B.J.; Hartwick, N.T.; et al. (2025). "Domesticated cannabinoid synthases amid a wild mosaic cannabis pangenome". Nature. doi:10.1038/s41586-025-09065-0.
- ↑ Balant, M.; Vitales, D.; Wang, Z.; Barina, Z.; Fu, L.; et al. (2025). "Integrating target capture with whole genome sequencing of recent and natural history collections to explain the phylogeography of wild-growing and cultivated cannabis". Plants, People, Planet. 7 (6): 1771–1788. doi:10.1002/ppp3.70043.
- ↑ 13.0 13.1 13.2 13.3 McPartland, J.M.; Small, E. (2020). "A classification of endangered high-THC cannabis (Cannabis sativa subsp. indica) domesticates and their wild relatives". PhytoKeys. 144: 81–112. doi:10.3897/phytokeys.144.46700.
- ↑ Small, E. (2015). "Evolution and classification of Cannabis sativa (marijuana, hemp) in relation to human utilization". Botanical Review. 81 (3): 189–294. doi:10.1007/s12229-015-9157-3.
- ↑ Babaei, M.; Torkamaneh, D. (2026). "Genetic architecture of phenological, morphological, and phytochemical traits in Cannabis landraces". The Plant Genome. 19 (2) e70243. doi:10.1002/tpg2.70243.