Skip to main content Skip to main navigation menu Skip to site footer
Type: Article
Published: 2025-10-21
Page range: 1-10
Abstract views: 483
PDF downloaded: 282

A bookend in the Arisaema japonicum (Araceae) taxonomic debate: morphological and genetic evidence for synonymization

Section of Plant Biology and the LH Bailey Hortorium, Cornell University, Ithaca, New York 14853, United States of America
College of Agriculture and Life Sciences, Cornell University, Ithaca, New York 14853, United States of America
College of Agriculture and Life Sciences, Cornell University, Ithaca, New York 14853, United States of America
Section of Plant Biology and the LH Bailey Hortorium, Cornell University, Ithaca, New York 14853, United States of America
Intraspecific variation Monophyly Plant Taxonomy Species Complex Monocots

Abstract

The taxonomic distinction between Arisaema japonicum and A. serratum has long been contentious, with treatments alternating between recognizing them as distinct species or conspecific variants. To resolve their taxonomic status, we conducted an integrative species delimitation analysis combining detailed morphological assessments with genome-wide single nucleotide polymorphism (SNP) data. Morphological investigations revealed continuous trait variation with numerous intermediates, precluding discrete morphological classification. Coalescent-based phylogenetic inference using Singular Value Decomposition Scores (SVDquartets) failed to recover A. japonicum as a monophyletic group, and principal component analysis of SNP data showed no genetic clustering corresponding to species boundaries. Species delimitation using Bayes Factor Delimitation (BFD) overwhelmingly supported a single-species model over competing hypotheses, including those based on previous morphological classifications. Together, these results indicate that A. japonicum does not represent a distinct evolutionary lineage and is best treated as conspecific with A. serratum. Our findings reconcile morphological and genetic data, providing strong support for the synonymization of A. japonicum under A. serratum, thereby resolving a longstanding taxonomic ambiguity within the genus Arisaema.

References

  1. Beckman Coulter. (2012) SPRI based size selection. Brea, California, pp. 1–14.
  2. Blume, C.L. (1836) Commentationes botanicæ imprimis de plantis Indiae orientalis. Rumphia 1: 106. https://doi.org/10.5962/bhl.title.51502
  3. Bouckaert, R., Heled, J., Kühnert, D., Vaughan, T., Wu, C., Xie, D., Suchard, M., Rambaut, A. & Drummond, A. (2014) BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Computational Biology 10: e1003537. https://doi.org/10.1371/journal.pcbi.1003537
  4. Boyce, P.C. & Croat, T. (2011) The Überlist of Araceae, totals for published and estimated number of species in Aroid genera. Available from: https://www.researchgate.net/publication/369741356_Uberlist_-_April_2023 (accessed 10 June 2024)
  5. Catchen, J., Hohenlohe, P., Bassham, S., Amores, A. & Cresko, W. (2013) Stacks: an analysis tool set for population genomics. Molecular Ecology 22: 3124–3140. https://doi.org/10.1111/mec.12354
  6. Cervantes, C.R., Montes, J.R., Rosas, U. & Arias, S. (2023) Phylogenetic discordance and integrative species delimitation in the Mammillaria haageana species complex (Cactaceae). Molecular Phylogenetics and Evolution 187: 107891. https://doi.org/10.1016/j.ympev.2023.107891
  7. Chang, C., Chow, C., Tellier, L., Vattikuti, S., Purcell, S. & Lee, J. (2015) Second-generation PLINK: rising to the challenge of larger and richer datasets. GigaScience 4: s13742-015-0047-8. https://doi.org/10.1186/s13742-015-0047-8
  8. Chen, S. (2023) Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp. iMeta 2: e107. https://doi.org/10.1002/imt2.107
  9. Chifman, J. & Kubatko, L. (2014) Quartet inference from SNP data under the coalescent. Bioinformatics 30: 3317–3324. https://doi.org/10.1093/bioinformatics/btu530
  10. Cook, J. (2004) Disease, pollinator, and resource limitation influences on the reproductive biology and growing season of Arisaema triphyllum, Jack-in-the-Pulpit. Michigan State University, East Lansing, 144 pp.
  11. Danecek, P., Bonfield, J., Liddle, J., Marshall, J., Ohan, V., Pollard, M., Whitwham, A., Keane, T., McCarthy, S., Davies, R. & Li, H. (2021) Twelve years of SAMtools and BCFtools. GigaScience 10: giab008. https://doi.org/10.1093/gigascience/giab008
  12. DeRaad, D. (2022) SNPfiltR: an R package for interactive and reproducible SNP filtering. Molecular Ecology Resources 22: 1–15. https://doi.org/10.1111/1755-0998.13618
  13. Doyle, J.J. & Doyle, J.L. (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19: 11–15.
  14. Engler, A. (1879) Araceae. In: Candolle, A.de & Candolle, C. (Ed.) Monographiæ phanerogamarum: Prodromi nunc continuatio, nunc revisio. Sumptibus G. Masson, Paris, pp. 541.
  15. Franchet, A. & Savatier, L. (1878) Enumeratio plantarum: in Japonia sponte crescentium hucusque rite cognitarum, adjectis descriptionibus specierum pro regione novarum, quibus accedit determinatio herbarum in libris japonicis So mokou zoussetz xylographice delineatarum. F. Savy, Paris, 507 pp.
  16. Govaerts, R. (1995) World Checklist of Seed Plants. 1 (1–2). Anversa (Deurne): MIM.
  17. Gusman, G. & Gusman, L. (2006) The Genus Arisaema: A Monograph for Botanists and Nature Lovers. (Ed. 2). Timber Press, Oregon, pp. 1–474.
  18. Gusman, G. & Gusman, L. (2008) Validation of new infrageneric taxa in Arisaema (Araceae). Systematics and Geography of Plants 78: 231.
  19. Jussieu, A.L. (1789) Genera plantarum, secundum ordines naturales disposita, juxta methodum in Horto regio parisiensi exaratam, anno M.DCC.LXXIV. Apud viduam Herissant et Theophilum Barrois, Paris, 23 pp. https://doi.org/10.5962/bhl.title.284
  20. Knaus, B. & Grunwald, N. (2017) VCFR: a package to manipulate and visualize variant call format data in R. Molecular Ecology Resources 17: 44–53. https://doi.org/10.1111/1755-0998.12549
  21. Leaché, A., Fujita, M., Minin, V. & Bouckaert, R. (2014) Species delimitation using genome-wide SNP Data. Systematic Biology 63: 534–542. https://doi.org/10.1093/sysbio/syu018
  22. Li, H. & Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754–1760. https://doi.org/10.1093/bioinformatics/btp324
  23. Linnaeus, C. (1754) Genera Plantarum: Eorumque Characteres Naturales Secundum Numerum, Figuram, Situm, et Proportionem Omnium Fructificationis Partium. (Ed. 5). Impensis Laurentii Salvii, Stockholm, 557 pp. https://doi.org/10.5962/bhl.title.746
  24. Makino, T. (1901) Observations on the Flora of Japan. Shokubutsugaku zasshi 15: 128–130. https://doi.org/10.15281/jplantres1887.15.167_10
  25. Makino, T. (1912) Karashu-tishaku. In: Iinuma, C. (Ed.) Sōmoku-Dzusetsu. Seibido, Tokyo, pp. 1229.
  26. Martius, K.F.P. (1831) Ueber die Art der Befruchtung bei einigen Aroideen und über die Charakteristik mehrerer Gattungen dieser Familie. Flora oder allgemeine botanische Zeitung 14: 449–464.
  27. McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M. & DePristo, M. (2010) The genome analysis toolkit: a mapreduce framework for analyzing next-generation DNA sequencing data. Genome Research 20: 1297–1303. https://doi.org/10.1101/gr.107524.110
  28. Montes, J.R., Peláez, P., Willyard, A., Moreno-Letelier, M., Piñero, D. & Gernandt, D. (2019) Phylogenetics of Pinus subsection Cembroides Engelm. (Pinaceae) inferred from low‐copy nuclear gene sequences. Systematic Botany 44: 501–518. https://doi.org/10.1600/036364419X15620113920563
  29. Montes, J.R., Peláez, P., Moreno‐Letelier, A. & Gernandt, D. (2022) Coalescent‐based species delimitation in North American pinyon pines using low‐copy nuclear genes and plastomes. American Journal of Botany 109: 706–726. https://doi.org/10.1002/ajb2.1847
  30. Murata, J. & Ohashi, H. (2009) Taxonomic history of Arisaema serratum and A.japonicum. Bunrui 9: 37–45.
  31. Murata, J. (2011) The Picture Book of Plant Systematics in Color: Arisaema in Japan. Hokuryukan Publishing Co., Tokyo, pp. 81–85.
  32. Murata, J., Ohno, J., Koeayashi, T. & Ohi-Toma, T. (2018) The Genus Arisaema in Japan. Hokuryukan Publishing Co., Tokyo, pp. 263–277.
  33. Nakai, T. (1918) Noulae ad Plantas Japoniae et Koreae XVIII. Shokubutsugaku zasshi 32: 215–233. https://doi.org/10.15281/jplantres1887.32.382_215
  34. Nakai, T. (1929) Conspectus specierum arisaematis Japono-Koreanarum. Shokubutsugaku zasshi 43: 524–540. https://doi.org/10.15281/jplantres1887.43.524
  35. Nakai, T. (1934) Notlæ ad Plantas Japoniæ & Korea XLIV. Shokubutsugaku zasshi 48: 773–792. https://doi.org/10.15281/jplantres1887.48.773
  36. Nakai, T. (1935) Notulae ad Plantas Japoniae & Koreae XLVI. Shokubutsugaku zasshi 49: 417–424. https://doi.org/10.15281/jplantres1887.49.417
  37. Nakai, T. (1940) Notlæ ad Plantas Asiæ Orietnales. XIII. Shokubutsugaku zasshi 54: 61–81.
  38. Ohi-Toma, T., Wu, S., Murata, H. & Murata, J. (2016) An updated genus-wide phylogenetic analysis of Arisaema (Araceae) with reference to sections. Botanical Journal of the Linnean Society 182: 100–114. https://doi.org/10.1111/boj.12459
  39. Ortiz, E. (2019) vcf2phylip v2.0: convert a VCF matrix into several matrix formats for phylogenetic analysis. (v2.0). Zenodo.
  40. Royer, D., Meyerson, L., Robertson, K. & Adams, J. (2009) Phenotypic plasticity of leaf shape along a temperature gradient in Acer rubrum. PLoS One 4: e7653. https://doi.org/10.1371/journal.pone.0007653
  41. Schott, H.W. & Endlicher, S. (1832) Meletemata botanica. Typis C. Gerold, Vienna, 17 pp. https://doi.org/10.5962/bhl.title.40101
  42. Schott, H.W. (1856) Synopsis Aroidearum. Typis Congregationis Mechitharisticae, Vienna, 5 pp.
  43. Scholten, J. & Specht, C.D. (2025) Arisaema species from Shikoku Island, Japan [dataset]. Dryad. https://doi.org/10.5061/dryad.7pvmcvf4q
  44. Thunberg, C. (1794) Botanical observations on the Flora Japonica. Transactions of the Linnean Society of London 2: 326–342. https://doi.org/10.1111/j.1096-3642.1794.tb00268.x
  45. Tran, V.T., Hoang, T., Croat, T., Ma, Z., Liu, B., Nguyen, V.D. & Le, C.T. (2022) Reconstruction of the evolutionary biogeography reveals the origin and diversification of Arisaema (Araceae). Acta Botanica Brasilica 36: e2021abb0253. https://doi.org/10.1590/0102-33062021abb0253
  46. Wickham, H., Averick, M., Bryan, J., Chang, W., Mcgowan, L.D., Francois, R., Grolemund, G., Hayes, A., Henry, L., Hester, J., Kuhn, M., Pedersen, T.L., Miller, E., Bache, S.M., Muller, K., Ooms, J., Robinson, D., Seidel, D.P., Spinu, V., Takahashi, K., Vaughan, D., Wilke, C., Woo, K. & Yutani, H. (2019) Welcome to the tidyverse. Journal of Open Source Software 4: 1686. https://doi.org/10.21105/joss.01686
  47. Yamashiro, F. & Wada, N. (2002) Size-dependent leaf emergence and expansion pattern in a perennial understory herb Arisaema serratum (Araceae). Journal of Phytogeography and Taxonomy 50: 55–61.

How to Cite

Scholten, J., Sprenger, A., Hullihen, O. & Specht, C.D. (2025) A bookend in the Arisaema japonicum (Araceae) taxonomic debate: morphological and genetic evidence for synonymization. Phytotaxa 725 (1): 1–10. https://doi.org/10.11646/phytotaxa.725.1.1