Skip to main navigation menu Skip to main content Skip to site footer
Plant Science Today (PST)

Research Articles

Early Access

Molecular phylogenetics and morphological diversification in the genus Gagea (Liliaceae)

DOI
https://doi.org/10.14719/pst.10947
Submitted
29 July 2025
Published
18-12-2025

Abstract

The genus Gagea exhibits high morphological diversity and complex taxonomy. In this study, we analyzed the phylogenetic relationships and morphological differentiation within Gagea using ITS sequences from 32 species across 9 sections. Bayesian analysis revealed 3 main clades, partially congruent with morphological traits. Our results highlight both the value of molecular data for species delimitation and the need for taxonomic revision due to cases of morphological convergence and incongruence. This study contributes to a deeper understanding of evolutionary patterns in Gagea.

References

  1. 1. Kurbaniyazova GT, Levichev IG. History of the study of the genus Gagea Salisb. in the flora of Uzbekistan. Scientific Bulletin of the National Research Institute of Animal Production, Series: Biology of Animals. 2022;4(64):109–15.
  2. 2. Levichev IG. Structural features of shoots in Lloydia, Gagea and Kharkevichia (Liliaceae) as evolutionary variability of mesomic-type modules in monocots. Botanical Journal. 2013;98(4):409–52.
  3. 3. Royal Botanic Gardens, Kew. Plants of the World Online. Facilitated by the Royal Botanic Gardens, Kew. 2025. http://www.plantsoftheworldonline.org
  4. 4. Levichev IG. Zur Morphologie in der Gattung Gagea Salisb. (Liliaceae). I. Die unterirdischen Organe. Flora. 1999;194:379–92.
  5. 5. Levichev IG, Ali SI. New species and their distribution in the genus Gagea. Willdenowia. 2006;36:219–27.
  6. 6. Levichev IG. New species and combinations in the genus Gagea (Liliaceae). Botanical Journal. 2001;86(11):123–8.
  7. 7. Levichev IG, Beshko NYu, Kurbaniyazova GT, Turginov OT, Tajetdinova DM. New records of species of the genus Gagea in Uzbekistan. Turczaninowia. 2023;26(3):184–93. https://doi.org/10.14258/turczaninowia.26.3.17
  8. 8. Peterson A, Levichev IG, Peterson J. Systematics of Gagea and Lloydia (Liliaceae) and infrageneric classification of Gagea based on molecular and morphological data. Molecular Phylogenetics and Evolution. 2008; 46:446–65.
  9. 9. Peruzzi L, Bartolucci F, Frignani F, Minutillo F. Gagea tisoniana, a new species of Gagea Salisb. (Liliaceae) from central Italy. Botanical Journal of the Linnean Society. 2007;155:337–47. https://doi.org/10.1111/j.1095-8339.2007.00648.x
  10. 10. Zarrei M, Zarre S, Wilkin P, Rønsted N, Rudall PJ. Phylogeny of the genus Gagea (Liliaceae) based on morphology and DNA data. Botanical Journal of the Linnean Society. 2011;166:188–211.
  11. 11. Peterson JC, Abbott JT, Griffiths TL. Evaluating (and improving) the correspondence between deep neural network representations and human psychological representations. Cognitive Science. 2018;42(8):2648–69. https://doi.org/10.1111/cogs.12670
  12. 12. Zarrei M, Wilkin P, Zarre S. Phylogenetic relationships in Gagea Salisb. (Liliaceae) inferred from nuclear ribosomal and plastid DNA sequence data. Molecular Phylogenetics and Evolution. 2010;56(2):509–20.
  13. 13. Tison J-M. Typification et statut taxonomique de onze taxons de Gagea Salisb. (Liliaceae) décrits par Achille et Nicola Terracciano et conservés à Napoli (NAP). Candollea. 2004;59(2):325–46.
  14. 14. Zarrei M, Wilkin P, Fay MF, Ingrouille MJ, Zarre S, Chase MW. Molecular systematics of Gagea and Lloydia (Liliaceae; Liliales): Implications of analyses of nuclear ribosomal and plastid sequences for infrageneric classification. Annals of Botany. 2009;104:125–42.
  15. 15. Zhao YZ, Yang QE. Gagea daqingshanensis (Liliaceae), a new species from Inner Mongolia, China. Annales Botanici Fennici. 2006;43(5):379–82.
  16. 16. Zhao YZ, Zhao LQ. A new species of Gagea (Liliaceae) from Nei Mongol, China. Acta Phytotaxonomica Sinica. 2003;41(4):393–4.
  17. 17. Peterson A, John H, Koch E, Peterson J. A molecular phylogeny of the genus Gagea (Liliaceae) in Germany inferred from non-coding chloroplast and nuclear DNA sequences. Plant Systematics and Evolution. 2004;245(3):145–62. https://doi.org/10.1007/s00606-003-0114-y
  18. 18. Peterson A, Levichev IG, Peterson J, Harpke D, Schnittler M. New insights into the phylogeny and taxonomy of Chinese species of Gagea (Liliaceae) – speciation through hybridization. Organisms Diversity & Evolution. 2011;11(5):387–407. https://doi.org/10.1007/s13127-011-0059-x
  19. 19. Doyle JJ, Doyle JL. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin. 1987;19:11–5.
  20. 20. Aronesty E. Comparison of sequencing utility programs. The Open Bioinformatics Journal. 2013;7:1–8. https://doi.org/10.2174/1875036201307010001
  21. 21. White TJ, Bruns T, Lee S, Taylor J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ, editors. PCR Protocols: A Guide to Methods and Applications. New York: Academic Press; 1990. p. 315–22.
  22. 22. Wörz A, Hohmann N, Thiv M. Morphological and molecular diversity of some populations of Gagea (Liliaceae) in Southwest Germany. Stuttgarter Beiträge zur Naturkunde, Serie A (Biologie), Neue Serie. 2012;5:1–11.
  23. 23. Bolger AM, Lohse M, Usadel B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20. https://doi.org/10.1093/bioinformatics/btu170
  24. 24. Rognes T, Flouri T, Nichols B, Quince C, Mahé F. VSEARCH: A versatile open source tool for metagenomics. PeerJ. 2016;4:e2584. https://doi.org/10.7717/peerj.2584
  25. 25. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 2018;35:1547–9.
  26. 26. GenBank [Internet]. Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information; [cited 2025 Jul 7]. https://www.ncbi.nlm.nih.gov/genbank/
  27. 27. Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, Lanfear R. IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Molecular Biology and Evolution. 2020;37(5):1530–4. https://doi.org/10.1093/molbev/msaa015
  28. 28. Rambaut A. FigTree v1.4.4: Tree Figure Drawing Tool. Institute of Evolutionary Biology, University of Edinburgh; 2014. http://tree.bio.ed.ac.uk/software/figtree/
  29. 29. Ali SI. Two new species of Gagea Salisb. (Liliaceae) from Pakistan. Pak J Bot. 2006;38:43–46.
  30. 30. Hamzaoğlu E, Koç M, Babaç MT. New species from the section Gagea. Turkish Journal of Botany. 2008;32(5):373–8.
  31. 31. Henker H. A new classification of Gagea species. Feddes Repert. 2005;116(7–8):487–512.
  32. 32. IPNI. International Plant Name Index. [cited 2025 Jul 7]. https://www.ipni.org
  33. 33. Russian Academy of Sciences. Historia Gagearum. [cited 2025 Jul 7]. https://www.binran.ru/resources/archive/gagearum/nameslist-rus.html
  34. 34. Ridgway KP, Duck JM, Young JPW. Identification of roots from grass swards using PCR-RFLP and FFLP of the plastid trnL (UAA) intron. BMC Ecology and Evolution. 2003;3:8. https://doi.org/10.1186/1472-6785-3-8
  35. 35. Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP. MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology. 2012;61(3):539–42. https://doi.org/10.1093/sysbio/sys029
  36. 36. Peruzzi L, Tison JM, Peterson A, Peterson J. On the phylogenetic position and taxonomic value of Gagea trinervia (Viv.) Greuter and Gagea sect. Anthericoides A. Terracc. (Liliaceae). Taxon. 2008;57:1201–14. https://doi.org/10.1002/tax.574013
  37. 37. Peterson A, Harpke D, Levichev IG, Beisenova S, Schnittler M, Peterson J. Morphological and molecular investigations of Gagea (Liliaceae) in southeastern Kazakhstan with special reference to putative altitudinal hybrid zones. Plant Systematics and Evolution. 2016;302:985–1007. https://doi.org/10.1007/s00606-016-1313-7

Downloads

Download data is not yet available.