Advertisement

Genetic diversity and population structure of Kichulchoia multifasciata in South Korea

  • Han-Gyu Bae
  • Casey Nightingale
  • Duck Hee Jeoung
  • Sunho Cha
  • Hyung-Bae Jeon
  • Hangkyo Lim
  • Ho Young SukEmail author
Research Article
  • 56 Downloads

Abstract

Kichulchoia multifasciata, a small-sized loach (Family Cobitidae) inhabiting only the Nakdong River on the Korean Peninsula, is generally found around well-oxygenated minor tributaries. Despite the scarcity, this species is not yet a legally protected species in South Korea, and the spatial pattern of genetic diversity, which is essential to create management strategies, has never been studied. In this study, three mitochondrial loci and ten microsatellites were used to analyze the genetic diversity and the structure among eight K. multifasciata populations collected from different tributaries. K. multifasciata populations showed a high level of mitochondrial variability, with above 0.9 of average haplotype diversity in all three loci analyzed. A substantial microsatellite polymorphism was also found. Weak genetic structuring among populations and isolation by distance were clearly revealed in both mitochondrial and microsatellite data, indicating the high levels of gene flow among the tributaries. However, a few of the populations exhibited a genetic signature that they have experienced the historical size decline. Our data suggest that unequal gene flow might be one of the causes; nevertheless, the possibility of effective population size reduction by other factors could not be completely excluded. Our genetic evidence can be the critical information needed to protect the populations from the genetic erosion in the Nakdong River that has been destroyed and fragmented with increasing anthropogenic interferences.

Keywords

Kichulchoia multifasciata Cobitidae Nakdong River Microsatellites Mitochondrial DNA 

Notes

Acknowledgements

Dong-Young Kim, Hari Won, and Seul-Ki Park assisted with field or laboratory work. Research supported by a Grant of the National Institute of Biological Resources (NIBR #201403201) funded by the Ministry of Environment and the grant from the National Research Foundation (2015R1D1A2A01058987) in Republic of Korea.

Compliance with ethical standards

Conflict of interest

The authors declare no conflict of interest.

Supplementary material

10592_2019_1147_MOESM1_ESM.docx (14 kb)
Supplementary material 1 (DOCX 13 KB)

References

  1. Bang IC, Kim WJ, Lee IR (2009) Characterization of polymorphic microsatellite loci in the endangered Miho spine loach (Iksookimia choii) and cross-species amplification within the Cobitidae family. Mol Ecol Resour 9(1):281–284CrossRefGoogle Scholar
  2. Brauer CJ, Hammer MP, Beheregaray LB (2016) Riverscape genomics of a threatened fish across a hydroclimatically heterogeneous river basin. Mol Ecol 25(20):5093–5113CrossRefGoogle Scholar
  3. Caldera EJ, Bolnick DI (2008) Effects of colonization history and landscape structure on genetic variation within and among threespine stickleback (Gasterosteus aculeatus) populations in a single watershed. Evol Ecol Res 10:575–598Google Scholar
  4. Castric V, Bonney F, Bernatchez L (2001) Landscape structure and hierarchical genetic diversity in the brook charr, Salvelinus fontinalis. Evolution 55(5):1016–1028CrossRefGoogle Scholar
  5. Chen Y, Chen Y (2005) Revision of the genus Niwaella in China (Pisces, Cobitidae), with description of two new species. J Nat Hist 39(19):1641–1651CrossRefGoogle Scholar
  6. Crispo E, Bentzen P, Reznick DN, Kinnison MT, Hendry AP (2006) The relative influence of natural selection and geography on gene flow in guppies. Mol Ecol 15(1):49–62CrossRefGoogle Scholar
  7. Crookes S, Shaw PW (2016) Isolation by distance and non-identical patterns of gene flow within two river populations of the freshwater fish Rutilus rutilus (L. 1758). Conserv Genet 17(4):861–874CrossRefGoogle Scholar
  8. De Gelas K, Janko K, Volckaert FAM, De Charleroy D, Van Houdt JKJ (2008) Development of nine polymorphic microsatellite loci in the spined loach, Cobitis taenia, and cross-species amplification in the related species C. elongatoides, C. taurica and C. tanaitica. Mol Ecol Resour 8(5):1001–1003CrossRefGoogle Scholar
  9. DeWoody JA, Avise JC (2000) Microsatellite variation in marine, freshwater and anadromous fishes compared with other animals. J Fish Biol 56(3):461–473CrossRefGoogle Scholar
  10. Drummond AJ, Suchard MA, Xie D, Rambaut A (2012) Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 29(8):1969–1973CrossRefGoogle Scholar
  11. Earl DA, vonHoldt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4(2):359–361CrossRefGoogle Scholar
  12. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14(8):2611–2620CrossRefGoogle Scholar
  13. Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10(3):564–567CrossRefGoogle Scholar
  14. Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol 3(5):294–299Google Scholar
  15. Fu Y (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147(2):915–925Google Scholar
  16. Garza J, Williamson E (2001) Detection of reduction in population size using data from microsatellite loci. Mol Ecol 10(2):305–318CrossRefGoogle Scholar
  17. Goudet J (2001) FSTAT, a program to estimate and test gene diversity and fixation indices (version 2.9.3). http://www2.unil.ch/popgen/softwares/fstat.htm
  18. Griffiths AM, Koizumi I, Bright D, Stevens JR (2009) A case of isolation by distance and short-term temporal stability of population structure in brown trout (Salmo trutta) within the River Dart, southwest England. Evol Appl 2(4):537–554CrossRefGoogle Scholar
  19. Guo SW, Thompson EA (1992) Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics 48(2):361–372CrossRefGoogle Scholar
  20. Hand BK, Muhlfeld CC, Wade AA, Kovach RP, Whited DC, Narum SR, Matala AP, Ackerman MW, Garner BA, Kimball JS, Stanford JA, Luikart G (2016) Climate variables explain neutral and adaptive variation within salmonid metapopulations: the importance of replication in landscape genetics. Mol Ecol 25(3):689–705CrossRefGoogle Scholar
  21. Hecht BC, Matala AP, Hess JE, Narum SR (2015) Environmental adaptation in Chinook salmon (Oncorhynchus tshawytscha) throughout their North American range. Mol Ecol 24(22):5573–5595CrossRefGoogle Scholar
  22. Hendry AP (2004) Selection against migrants contributes to the rapid-evolution of reproductive isolation. Evol Ecol Res 6:1219–1236Google Scholar
  23. Jones OR, Wang J (2010) COLONY: a program for parentage and sibship inference from multilocus genotype data. Mol Ecol Resour 10(3):551–555CrossRefGoogle Scholar
  24. Kalinowski ST, Wagner AP, Taper ML (2006) ML-Relate: a computer program for maximum likelihood estimation of relatedness and relationship. Mol Ecol Resour 6(2):576–579CrossRefGoogle Scholar
  25. Kim IS, Lee WO (1995) Niwaella brevifasciata, a new cobitid fish (Cypriniformes: Cobitidae) with a revised key to the species of Niwaella. Jap J Ichthyol 42(3/4):285–290Google Scholar
  26. Kim HS, Yang H (2016) Spawning period and spawning characteristics of Kichulchoia multifasciata (Pisces: Cobitidae) in the Yugokcheon (stream) of Nakdonggang (river) from Korea. Kor J Ichthyol 28(2):93–99Google Scholar
  27. Kwan YS, Ko MH, Won YJ (2014) Genomic replacement of native Cobitis lutheri with introduced C. tetralineata through a hybrid swarm following the artificial connection of river systems. Ecol Evol 4(8):1451–1465CrossRefGoogle Scholar
  28. Laroche J, Durand JD (2004) Genetic structure of fragmented populations of a threatened endemic percid of the Rhône river: Zingel asper. Heredity 92(4):329–334CrossRefGoogle Scholar
  29. Leigh JW, Bryant D (2015) POPART: full-feature software for haplotype network construction. Methods Ecol Evol 6(9):1110–1116CrossRefGoogle Scholar
  30. Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25(11):1451–1452CrossRefGoogle Scholar
  31. Liu H, Tzeng CS, Teng HY (2002) Sequence variations in the mitochondrial DNA control region and their implications for the phylogeny of the Cypriniformes. Can J Zool 81(12):1938–1946CrossRefGoogle Scholar
  32. Luikart G, Allendorf F, Cornuet J, Sherwin W (1998) Distortion of allele frequency distributions provides a test for recent population bottlenecks. J Hered 89(3):238–247CrossRefGoogle Scholar
  33. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New YorkGoogle Scholar
  34. Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update. Bioinformatics 28(19):2537–2539CrossRefGoogle Scholar
  35. Perdices A, Bohlen J, Šlechtová V, Doadrio I (2016) Molecular evidence for multiple origins of the European spined loaches (Teleostei, Cobitidae). PLoS ONE 11(1):e0144628CrossRefGoogle Scholar
  36. Piry S, Luikart G, Cornuet J (1999) BOTTLENECK: a computer program for detecting recent reductions in the effective population size using allele frequency data. J Hered 90(4):502–503CrossRefGoogle Scholar
  37. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155(2):945–959Google Scholar
  38. Raymond M, Rousset F (1995) GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J Hered 86(3):248–249CrossRefGoogle Scholar
  39. Reed DH, Frankham R (2003) Correlation between fitness and genetic diversity. Conserv Biol 17(1):230–237CrossRefGoogle Scholar
  40. Rogers AR, Harpending H (1992) Population growth makes waves in the distribution of pairwise genetic differences. Mol Biol Evol 9(3):552–569Google Scholar
  41. Schluter D (2000) The ecology of adaptive radiation. Oxford University Press, OxfordGoogle Scholar
  42. Schönhuth S, Blum MJ, Lozano-Vilano L, Neely DA, Varela-Romero A, Espinosa H, Perdices A, Mayden RL (2011) Inter-basin exchange and repeated headwater capture across the Sierra Madre Occidental inferred from the phylogeography of Mexican stonerollers. J Biogeogr 38(7):1406–1421CrossRefGoogle Scholar
  43. Schönhuth S, Hillis DA, Neely DA, Lozano-Vilano L, Perdices A, Mayden RL (2012) Phylogeny, diversity, and species delimitation of the North American round-nosed minnow (Teleostei: Dionda) as inferred from mitochondrial and nuclear DNA sequences. Mol Phylogenet Evol 62(1):427–446CrossRefGoogle Scholar
  44. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123(3):585–595Google Scholar
  45. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30(12):2725–2729CrossRefGoogle Scholar
  46. Ward RD, Woodwark M, Skibinski DOF (1994) A comparison of genetic diversity levels in marine, freshwater, and anadromous fishes. J Fish Biol 44(2):213–232CrossRefGoogle Scholar
  47. Xiao W, Zhang Y, Liu H (2001) Molecular systematics of Xenocyprinae (Teleostei: Cyprinidae): taxonomy, biogeography, and coevolution of a special group restricted in East Asia. Mol Phylogenet Evol 18(2):163–173CrossRefGoogle Scholar
  48. Yoon JD, Kim JH, Park SH, Jang MH (2018) The distribution and diversity of freshwater fishes in Korean Peninsula. Kor J Ecol Environ 51(1):71–85Google Scholar

Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Department of Life SciencesYeungnam UniversityGyeongsanSouth Korea
  2. 2.Department of BiologyUniversity of St. ThomasSt. PaulUSA
  3. 3.GenoTech CorporationDaejeonSouth Korea
  4. 4.Department of BiologyNotre Dame of Maryland UniversityBaltimoreUSA
  5. 5.Department of BiologyConcordia UniversityMontrealCanada

Personalised recommendations