DOI QR코드

DOI QR Code

Divergence time estimation of an ancient relict genus Mankyua (Ophioglossaceae) on the young volcanic Jejudo Island in Korea

  • GIL, Hee-Young (Department of Biological Sciences, Sungkyunkwan University) ;
  • KIM, Seung-Chul (Department of Biological Sciences, Sungkyunkwan University)
  • Received : 2017.12.15
  • Accepted : 2018.03.12
  • Published : 2018.03.30

Abstract

Mankyua chejuense is the only member of the monotypic genus Mankyua (Ophioglossaceae) and is endemic to Jejudo Island, Korea. To determine the precise phylogenetic position of M. chejuense, two cpDNA regions of 42 accessions representing major members of lycophytes are obtained from GenBank and analyzed using three phylogenetic analyses (maximum parsimony, maximum likelihood, and Bayesian inference). In addition, the divergence time is estimated based on a relaxed molecular clock using four fossil calibration points. The phylogenetic position of Mankyua still appears to be uncertain, representing either the earliest diverged lineage within Ophioglossaceae or a sister to the clade containing Ophioglossum and Helminthostachys. The most recent common ancestor of Ophioglossaceae and its sister lineage, Psilotum, was estimated to be 256 Ma, while the earliest divergence of Mankyua was estimated to be 195 Ma in the early Jurassic.

Keywords

References

  1. Anderson, F. E. and D. L. Swofford. 2004. Should we be worried about long-branch attraction in real data sets? Investigations using metazoan 18S rDNA. Molecular Phylogenetics and Evolution 33: 440-451. https://doi.org/10.1016/j.ympev.2004.06.015
  2. Bouckaert, R., J. Heled, D. Kuhnert, T. Vaughan, C.-H. Wu, D. Xie, M. A. Suchard, A. Rambaut and A. J. Drummond. 2014. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Computational Biology 10: e1003537.
  3. Brauner, S., D. J. Crawford and T. F. Stuessy. 1992. Ribosomal DNA and RAPD variation in the rare plant family Lactoridaceae. American Journal of Botany 79: 1436-1439. https://doi.org/10.1002/j.1537-2197.1992.tb13755.x
  4. Chang, C.-S., D. Y. Choi, H. Kim, T. Y. Park and Y.-S. Kim. 2005. Patterns of allozyme variation in relation to population size of the threatened plant Megaleranthis saniculifolia (Ranunculaceae) in Korea. Journal of Plant Biology 48: 339-350. https://doi.org/10.1007/BF03030575
  5. Chang, C.-S., H. Kim and G. S. Chang. 2011. Illustrated Encyclopedia of Fauna & Flora of Korea Vol. 43. Woody Plants. Ministry of Education, Seoul, 511 pp.
  6. Chang, C.-S., H. Kim, S. Son and Y.-S. Kim. 2016. The Red List of Selected Vascular Plants in Korea. Korea National Arboretum and Korean Plant Specialist Group, Pocheon, 50 pp.
  7. Chung, M. G. 1999. Allozyme diversity in the endangered shrub Abeliophyllum distichum (Oleaceae): a monotypic Korean genus. International Journal of Plant Sciences 160: 553-559. https://doi.org/10.1086/314149
  8. Chung, M. G., M. Y. Chung and B. K. Epperson. 2001. Conservation genetics of an endangered herb, Hanabusaya asiatica (Campanulaceae). Plant Biology 3: 42-49. https://doi.org/10.1055/s-2001-11744
  9. Chung, M. Y., J. D. Nason, B.-Y. Sun, M.-O. Moon, J. M. Chung, C.-W. Park and M. G. Chung. 2010. Extremely low levels of genetic variation in the critically endangered monotypic fern genus Mankyua chejuense (Ophioglossaceae) from Korea: implications for conservation. Biochemical Systematics and Ecology 38: 888-896.
  10. Crawford, D. J., T. F. Stuessy, M. B. Cosner, D. W. Haines, D. Wiens and P. Penaillo. 1994. Lactoris fernandeziana (Lactoridaceae) on the Juan Fernandez Islands: allozyme uniformity and field observations. Conservation Biology 8: 277-280. https://doi.org/10.1046/j.1523-1739.1994.08010277.x
  11. Crawford, D. J., M. Tago-Nakazawa, T. F. Stuessy, G. J. Anderson, G. Bernardello, E. Ruiz, R. J. Jensen, C. Baeza, A. D. Wolfe and M. Silva O. 2001. Intersimple sequence repeat (ISSR) variation in Lactoris fernandeziana (Lactoridaceae), a rare endemic of the Juan Fernandez Archipelago, Chile. Plant Species Biology 16: 185-192. https://doi.org/10.1046/j.1442-1984.2001.00065.x
  12. Darriba, D., G. L. Taboada, R. Doallo and D. Posada. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9: 772.
  13. Drummond, A. J., S. Y. W. Ho, M. J. Phillips and A. Rambaut. 2006. Relaxed phylogenetics and dating with confidence. PLoS Biology 4: e88. https://doi.org/10.1371/journal.pbio.0040088
  14. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x
  15. Friis, E. M., K. R. Pedersen and P. R. Crane. 1994. Angiosperm floral structures from the early Cretaceous of Portugal. Plant Systematics and Evolution 8(Supplement): 31-49.
  16. Friis, E. M., K. R. Pedersen and P. R. Crane. 1999. Early angiosperm diversification: the diversity of pollen associated with angiosperm reproductive structures in early Cretaceous floras from Portugal. Annals of the Missouri Botanical Garden 86: 259-296. https://doi.org/10.2307/2666179
  17. Hyeon, H.-J., C.-H. Kang, K.-M. Song, M.-O. Moon, G.-P. Song and M.-H. Kim. 2010. Flora and the conditions of Mankyua chejuense habitats. Korean Journal of Plant Resources 23: 350-359. (in Korean)
  18. Hyeon, H.-J., M.-O. Moon and M.-H. Kim. 2011. Vegetation characteristics of Mankyua chejuense habitats. Korean Journal of Plant Resources 24: 395-403. https://doi.org/10.7732/kjpr.2011.24.4.395
  19. Hyun, H.-J., M.-O. Moon, H.-S. Choi and C.-S. Kim. 2014. Growth pattern and phenology of Mankyua chejuense B.-Y. Sun, M.H. Kim & C.H. Kim. Korean Journal of Plant Resources 27: 95-101. (in Korean) https://doi.org/10.7732/kjpr.2014.27.1.095
  20. Jeong, J. H., E. H. Kim, W. Guo, K. O. Yoo, D. G. Jo and Z. S. Kim. 2010. Genetic diversity and structure of the endangered species Megaleranthis saniculifolia in Korea as revealed by allozyme and ISSR markers. Plant Systematics and Evolution 289: 67-76. https://doi.org/10.1007/s00606-010-0333-y
  21. Kang, U., C.-S. Chang and Y. S. Kim. 2000. Genetic structure and conservation considerations of rare endemic Abeliophyllum distichum Nakai (Oleaceae) in Korea. Journal of Plant Research 113: 127-138. https://doi.org/10.1007/PL00013923
  22. Kearse, M., R. Moir, A. Wilson, S. Stones-Havas, M. Cheung, S. Sturrock, S. Buxton, A. Cooper, S. Markowitz, C. Duran, T. Thierer, B. Ashton, P. Meintjes and A. Drummond. 2012. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28: 1647-1649.
  23. Kenrick, P. and P. R. Crane. 1997. The Origin and Early Diversification of Land Plants: A Cladistic Study. Smithsonian Press, Washington, D.C., 441 pp.
  24. Kim, C. H. 2004. Conservation status of the endemic fern Mankyua chejuense (Ophioglossaceae) on Cheju Island, Republic of Korea. Oryx 38: 217-219.
  25. Kim, C. H. and J. H. Park. 2013. Endemic Species of Korea: Plantae. National Institute of Biological Resources, Incheon, 912 pp.
  26. Kim, H.-R., J.-H. Shin, H.-M. Jeon and Y.-H. You. 2014. Effects of environmental factors on the growth response of above- and below-ground parts of Mankyua chejuense, endangered endemic plant to Jeju province, in Korea. Journal of Ecology and Environment 37: 61-67.
  27. Kim, K.-J., H.-L. Lee and Y.-D. Kim. 2000. Phylogenetic position of Abeliophyllum (Oleaceae) based on nuclear ITS sequence data. Korean Journal of Plant Taxonomy 30: 235-250. https://doi.org/10.11110/kjpt.2000.30.3.235
  28. Kim, Y. K., C. W. Park and K. J. Kim. 2009. Complete chloroplast DNA sequence from a Korean endemic genus, Megaleranthis saniculifolia, and its evolutionary implications. Molecules and Cells 27: 365-381. https://doi.org/10.1007/s10059-009-0047-6
  29. Larkin, M. A., G. Blackshields, N. P. Brown, R. Chenna, P. A. McGettigan, H. McWilliam, F. Valentin, I. M. Wallace, A. Wilm, R. Lopez, J. D. Thompson, T. J. Gibson and D. G. Higgins. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948. https://doi.org/10.1093/bioinformatics/btm404
  30. Lee, C. and S.-P. Hong. 2011. Phylogenetic relationships of the rare Korean monotypic endemic genus Pentactina Nakai in the tribe Spiraeeae (Rosaceae) based on molecular data. Plant Systematics and Evolution 294: 159-166. https://doi.org/10.1007/s00606-011-0457-8
  31. Lee, W. K., T. Tokuoka and K. Heo. 2004. Molecular evidence for the inclusion of the Korean endemic genus "Echinosophora" in Sophora (Fabaceae), and embryological features of the genus. Journal of Plant Research 117: 209-219.
  32. Miller, C. N. 1971. Evolution of the fern family Osmundaceae based on anatomical studies. Contributions from the Museum of Paleontology The University of Michigan 23: 105-169.
  33. Miller, C. N. 1999. Implications of fossil conifers for the phylo genetic relationships of living families. The Botanical Review 65: 239-277.
  34. Park, C.-W. 2005. Recent progress in floristic research in Korea. Progress in Botany 67: 345-360.
  35. Pryer, K. M., E. Schuettpelz, P. G. Wolf, H. Schneider, A. R. Smith and R. Cranfill. 2004. Phylogeny and evolution of ferns (Monilophytes) with a focus on the early leptosporangiate divergences. Amercan Journal of Botany 91: 1582-1598. https://doi.org/10.3732/ajb.91.10.1582
  36. Roquet, C., L. Saez, J. Jose Aldasoro, A. Susanna, M. L. Alarcon and N. Garcia-Jacas. 2008. Natural delineation, molecular phylogeny and floral evolution in Campanula. Systematic Botany 33: 203-217. https://doi.org/10.1600/036364408783887465
  37. Sanderson, M. J., M. F. Wojciechowski, J. M. Hu, T. S. Khan and S. G. Brady. 2000. Error, bias, and long-branch attraction in data for two chloroplast photosystem genes in seed plants. Molecular Biology and Evolution 17: 782-797. https://doi.org/10.1093/oxfordjournals.molbev.a026357
  38. Shinohara, W., N. Nakato, Y. Yatabe-Kakugawa, T. Oka, J. K. Kim, N. Murakami, H. Noda and N. Sahashi. 2013. The use of matK in Ophioglossaceae phylogeny and the determination of Mankyua chromosome number shed light on chromosome number evolution in Ophioglossaceae. Systematic Botany 38: 564-570. https://doi.org/10.1600/036364413X670232
  39. Silvestro, D. and I. Michalak. 2012. RaxmlGUI: a graphical frontend for RAxML. Organisms Diversity & Evolution 12: 335-337. https://doi.org/10.1007/s13127-011-0056-0
  40. Stamatakis, A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30: 1312-1313. https://doi.org/10.1093/bioinformatics/btu033
  41. Stuessy, T. F., K. Takayama, P. Lopez-Sepulveda and D. J. Crawford. 2014. Interpretation of patterns of genetic variation in endemic plant species of oceanic islands. Botanical Journal of the Linnean Society 174: 276-288. https://doi.org/10.1111/boj.12088
  42. Sun, B.-Y., T. G. Baek, Y.-D. Kim and C. S. Kim. 2009. Phylogeny of the family Ophioglossaceae with special emphasis on genus Mankyua. Korean Journal of Plant Taxonomy 39: 135-142. https://doi.org/10.11110/kjpt.2009.39.3.135
  43. Sun, B.-Y., M. H. Kim, C. H. Kim and C.-W. Park. 2001. Mankyua (Ophioglossaceae): a new fern genus from Cheju Island, Korea. Taxon 50: 1019-1024. https://doi.org/10.2307/1224718
  44. Swofford, D. L. 2002. PAUP*: phylogenetic analysis using parsimony (*and other methods), version 4.0b10. Sinauer Associates, Sunderland, MA.
  45. Woo, K., Y. Sohn, U. Ahn, S. Yoon and A. Spate. 2013. Geology of Jeju Island. In Jeju Island Geopark: A Volcanic Wonder of Korea. Vol. 1. Geoparks of the World (closed) (Development and Management). Spriner, Berlin, Heidelberg. Pp. 13-14.