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Genetic Diversity and Population Genetic Structure of Black-spotted Pond Frog (Pelophylax nigromaculatus) Distributed in South Korean River Basins

  • Park, Jun-Kyu (Department of Biological Science, Kongju National University) ;
  • Yoo, Nakyung (National Institute of Ecology, Research Center for Endangered Species) ;
  • Do, Yuno (Department of Biological Science, Kongju National University)
  • 투고 : 2021.03.25
  • 심사 : 2021.04.07
  • 발행 : 2021.05.01

초록

The objective of this study was to analyze the genotype of black-spotted pond frog (Pelophylax nigromaculatus) using seven microsatellite loci to quantify its genetic diversity and population structure throughout the spatial scale of basins of Han, Geum, Yeongsan, and Nakdong Rivers in South Korea. Genetic diversities in these four areas were compared using diversity index and inbreeding coefficient obtained from the number and frequency of alleles as well as heterozygosity. Additionally, the population structure was confirmed with population differentiation, Nei's genetic distance, multivariate analysis, and Bayesian clustering analysis. Interestingly, a negative genetic diversity pattern was observed in the Han River basin, indicating possible recent habitat disturbances or population declines. In contrast, a positive genetic diversity pattern was found for the population in the Nakdong River basin that had remained the most stable. Results of population structure suggested that populations of black-spotted pond frogs distributed in these four river basins were genetically independent. In particular, the population of the Nakdong River basin had the greatest genetic distance, indicating that it might have originated from an independent population. These results support the use of genetics in addition to designations strictly based on geographic stream areas to define the spatial scale of populations for management and conservation practices.

키워드

과제정보

This research was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (No. 2018R1C1B3008645).

참고문헌

  1. Banks, S.C., Cary, G.J., Smith, A.L., Davies, I.D., Driscoll, D.A., Gill, A.M., et al. (2013). How does ecological disturbance influence genetic diversity? Trends in Ecology and Evolution, 28, 670-679. doi:10.1016/j.tree.2013.08.005
  2. Beebee, T.J.C. (1996). Ecology and conservation of amphibians. Berlin: Springer Science & Business Media.
  3. Beebee, T.J.C. (2005). Conservation genetics of amphibians. Heredity , 95, 423-427. doi:10.1038/sj.hdy.6800736
  4. Dufresnes, C., Litvinchuk, S.N., Borzee, A., Jang, Y., Li, J.T., Miura, I., et al. (2016). Phylogeography reveals an ancient cryptic radiation in East-Asian tree frogs (Hyla japonica group) and complex relationships between continental and island lineages. BMC Evolutionary Biology, 16, 253. doi:10.1186/s12862-016-0814-x
  5. Earl, D.A., and Vonholdt, B.M. (2012). STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources, 4, 359-361. doi:10.1007/s12686-011-9548-7
  6. Evanno, G., Regnaut, S., and Goudet, J. (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology, 14, 2611-2620. doi:10.1111/j.1365-294X.2005.02553.x
  7. Excoffier, L., and Lischer, H.E.L. (2010). Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources, 10, 564-567. doi:10.1111/j.1755-0998.2010.02847.x
  8. Finn, D.S., Encalada, A.C., and Hampel, H. (2016). Genetic isolation among mountains but not between stream types in a tropical high-altitude mayfly. Freshwater Biology, 61, 702-714. doi:10.1111/fwb.12740
  9. Finn, D.S., Theobald, D.M., Black, W.C., and Poff, N.L. (2006). Spatial population genetic structure and limited dispersal in a Rocky Mountain alpine stream insect. Molecular Ecology , 15, 3553-3566. doi:10.1111/j.1365-294X.2006.03034.x
  10. Garcia, V.O.S., Ivy, C., and Fu, J. (2017). Syntopic frogs reveal different patterns of interaction with the landscape: A comparative landscape genetic study of Pelophylax nigromaculatus and Fejervarya limnocharis from central China. Ecology and Evolution, 7, 9294-9306. doi:10.1002/ece3.3459
  11. Garris, A.J., Tai, T.H., Coburn, J., Kresovich, S., and McCouch, S. (2005). Genetic structure and diversity in Oryza sativa L. Genetics, 169, 1631-1638. doi:10.1534/genetics.104.035642
  12. Gong, J., Lan, H., Fang, S.G., and Wan, Q.H. (2013). Development and characterization of 13 polymorphic microsatellite DNA markers for the pond green frog (Rana nigromaculata). Journal of Genetics, 92, 7-10. doi:10.1007/s12041-011-0004-y
  13. Hammer, O., Harper, D.A.T., and Ryan, P.D. (2001). PAST: Paleontological statistics software package for education and data analysis. Palaeontologia Electronica, 4, 1-9.
  14. Hatmaker, E.A., Staton, M.E., Dattilo, A.J., Hadziabdic, D., Rinehart, T.A., Schilling, E.E., et al. (2018). Population structure and genetic diversity within the endangered species Pityopsis ruthii (Asteraceae). Frontiers in Plant Science, 9, 943. doi:10.3389/fpls.2018.00943
  15. Hughes, A.R., and Stachowicz, J. (2004). Genetic diversity enhances the resistance of a seagrass ecosystem to disturbance. Proceedings of the National Academy of Sciences of United States of America, 101, 8998-9002. doi:10.1073/pnas.0402642101
  16. Jeong, H., and Lee, Y.I. (2000). Late Cambrian biogeography: conodont bioprovinces from Korea. Palaeogeography, Palaeoclimatology, Palaeoecology, 162, 119-136. doi:10.1016/S0031-0182(00)00108-5
  17. Jombart, T., Devillard, S., and Balloux, F. (2010). Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genetics, 11, 94. doi:10.1186/1471-2156-11-94
  18. Lam, A., Toussaint, E.F., Kindler, C., Van Dam, M.H., Panjaitan, R., Roderick, G.K., et al. (2018). Stream flow alone does not predict population structure of diving beetles across complex tropical landscapes. Molecular Ecology, 27, 3541-3554. doi:10.1111/mec.14807
  19. Luikart, G., and England, P.R. (1999). Statistical analysis of microsatellite DNA data. Trend in Ecology and Evolution , 14, 253-256. doi:10.1016/S0169-5347(99)01632-8
  20. Ma, D., Liu, H.T., Ji, Y.J., Shi, C.M., Yang, Y.H., and Zhang, D.X. (2015). Black-spotted pond frog (Pelophylax nigromaculatus) on the Chinese Loess Plateau represents a cryptic species: Evidence from molecular phylogeny and ecological niche modeling. Journal of Systematics and Evolution, 53, 339-350. doi:10.1111/jse.12156
  21. Mullen, L.B., Woods, H.A., Schwartz, M.K., Sepulveda, A.J., and Lowe, W.H. (2010). Scale-dependent genetic structure of the Idaho giant salamander (Dicamptodon aterrimus) in stream networks. Molecular Ecology, 19, 898-909. doi:10.1111/j.1365-294X.2010.04541.x
  22. Peakall, R., and Smouse, P.E. (2012). GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics, 28, 2537-2539. doi:10.1093/bioinformatics/bts460
  23. Pritchard, J.K., Stephens, M., and Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics, 155, 945-959.
  24. Rousset, F. (2008). Genepop'007: a complete re-implementation of the genepop software for Windows and Linux. Molecular Ecology Resources, 8, 103-106. doi:10.1111/j.1471-8286.2007.01931.x
  25. Spielman, D., Brook, B.W., Briscoe, D.A., and Frankham, R. (2004). Does inbreeding and loss of genetic diversity decrease disease resistance? Conservation Genetics, 5, 439-448. doi:10.1023/B:COGE.0000041030.76598.cd
  26. Sunnucks, P. (2000). Efficient genetic markers for population biology. Trends in Ecology and Evolution, 15, 199-203. doi:10.1016/S0169-5347(00)01825-5
  27. Wang, S., Zhu, W., Gao, X., Li, X., Yan, S., Liu, X., et al. (2014). Population size and time since island isolation determine genetic diversity loss in insular frog populations. Molecular Ecology, 23, 637-648. doi: 10.1111/mec.12634
  28. Waraniak, J.M., Fisher, J.D., Purcell, K., Mushet, D.M., and Stockwell, C.A. (2019). Landscape genetics reveal broad and fine-scale population structure due to landscape features and climate history in the northern leopard frog (Rana pipiens) in North Dakota. Ecology and Evolution, 9, 1041-1060. doi:10.1002/ece3.4745
  29. Watanabe, K., Tominaga, K., Nakajima, J., Kakioka, R., and Tabata, R. (2017). Japanese freshwater fishes: biogeography and cryptic diversity. In M. Motokawa, and H. Kajihara (Eds.), Species Diversity of Animals in Japan (pp. 183-227). Tokyo: Springer. doi:10.1007/978-4-431-56432-4_7
  30. Willoughby, J.R., Fernandez, N.B., Lamb, M.C., Ivy, J.A., Lacy, R.C., and DeWoody, J.A. (2015). The impacts of inbreeding, drift and selection on genetic diversity in captive breeding populations. Molecular Ecology, 24, 98-110. doi:10.1111/mec.13020128 https://doi.org/10.22920/PNIE.2021.2.2.120
  31. Yoon, J.D., Jang, M.H., Kim, H.W., and Joo, G.J. (2012). Fish biodiversity monitoring in rivers of South Korea. In S. Nakano, et al. (Eds.), The Biodiversity Observation Network in the Asia-Pacific Region (pp. 175-191). Tokyo: Springer. doi:10.1007/978-4-431-54032-8_13
  32. Young, A., Boyle, T., and Brown, T. (1996). The population genetic consequences of habitat fragmentation for plants. Trends in Ecology and Evolution, 11, 413-418. doi:10.1016/0169-5347(96)10045-8
  33. Zane, L., Bargelloni, L., and Patarnello, T. (2002). Strategies for microsatellite isolation: a review. Molecular Ecology , 11, 1-16. doi:10.1046/j.0962-1083.2001.01418.x