Environmental Biology of Fishes

, Volume 93, Issue 3, pp 393–402 | Cite as

Mitochondrial DNA reveals low population differentiation in elongate loach, Leptobotia elongata (Bleeker): implications for conservation

  • Guangxun Liu
  • Jian Zhou
  • Dinggang ZhouEmail author


Elongate loach (Leptobotia elongata (Bleeker)), an endemic fish species to China, is a famous ornamental freshwater fish. Here, a comparative study of mtDNA control region (D-loop) (835 bp) sequences was performed to analyze its wild population structure and evaluate the genetic diversity for 110 individuals from five locations in the upper reaches of the Yangtze River, China. A total of 49 polymorphic sites and 45 haplotypes yielded high haplotype diversity (h = 0.952), but low nucleotide diversity (π = 0.00454) as that of many fish species. Sequence divergences between haplotypes ranged from 0.0033 ± 0.0011 to 0.0050 ± 0.0012 in intra-groups, and from 0.0037 ± 0.0.0011 to 0.0050 ± 0.0012 between groups. Significant values of Tajima’s D (−1.86383, P < 0.01) and Fu’s F S (−25.93, P < 0.01), together with uni-modal mismatch distribution, indicated a recent genetic bottleneck or population expansion of the species. Analysis of molecular variance (AMOVA) indicated a small amount of differentiation among groups (1.7%); most of the total variation occurred within groups (98.3%). Also, there was no significant population structure (F ST = 0.017, P > 0.05), and estimates of gene flows among groups were extremely high (Nm = 28.88), suggesting low genetic divergence between populations in the species. The lack of genetic differentiation among groups is most likely due to the combined gene flow from the downstream movement of eggs and larvae with currents and the upstream or downstream migration of adults throughout the distribution. These groups of L. elongata distributed in upper reaches of the Yangtze River should be considered as a single management unit.


Leptobotia elongata (Bleeker) Mitochondrial DNA Genetic diversity Population structure Conservation strategy 



The work was funded by Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, the People’s Republic of China (BM2007-15). English editorial assistance was provided by Jason Scott of Abraham Baldwin Agricultural College, Georgia, USA.


  1. Beerli P (2008) Migrate version 3.0—a maximum likelihood and Bayesian estimator of gene flow using the coalescent. Distributed over the internet at
  2. Beerli P, Felsentein J (1999) Maximum likelihood estimation of migration rates and effective populations by using a coalescent approach. Proc Natl Acad Sci USA 98:4563–4568CrossRefGoogle Scholar
  3. Brown GG, Gadaleta G, Pepe G, Saccone C, Sbisa E (1986) Structural conservation and variation in the D-loop-containing region of vertebrate mitochondrial DNA. J Mol Biol 192:503–511PubMedCrossRefGoogle Scholar
  4. Cao W, Chang J, Qiao Y, Duan Z (2007) Fish resources of early life history stages in Yangtze River. Beijing: China WaterPower Press, p 252 (in Chinese)Google Scholar
  5. Chen D, Zhang C, Lu C, Zhang X (2006) Polymorphism of D-loop sequence from mitochondrial genomes of different brood-stocks of Gymnocypris przewalskii (Kessler). J Fishery Sci China 13:800–806 (in Chinese)Google Scholar
  6. Ding R (ed) (1994) The fishes of Sichuan, China. Sichuan Publishing House of Science and Technology, Chengdu, Sichuan, China, pp 104–106 (in Chinese)Google Scholar
  7. Excoffier L, Laval G, Schneider S (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinformatics Online 1:47–50Google Scholar
  8. Frankel OH (1983) The place of management in conservation. In: Schonewald-Cox CM, Chambers SM, MacBryde B, Thomas WL (eds) Genetics and Conservation: a reference for managing wild animal and plant Populations. The Benjamin/Cumming Pub Company, Menlo Park, CA, pp 1–14Google Scholar
  9. Frankham R, Ballou JD, Briscoe DA (2003) Introduction to conservation genetics. Cambridge University Press, Cambridge, UKGoogle Scholar
  10. Fu YX (1997) Statistics tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147:915–925PubMedGoogle Scholar
  11. Grant WA, Bowen BW (1998) Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation. J Hered 89:415–426CrossRefGoogle Scholar
  12. Grunwald C, Stabile J, Waldman JR, Gross R, Wirgin I (2002) Population genetics of shortnose sturgeon Acipenser brevirostrum based on mitochondrial DNA control region sequences. Mol Ecol 11:1885–1898PubMedCrossRefGoogle Scholar
  13. Hedrick PW, Dowling TE, Minckley WL, Tibbets CA, Demarais BD, Marsh PC (2000) Establishing a captivebroodstock for the endangered bonytail chub (Gila elegans). J Hered 91:35–39PubMedCrossRefGoogle Scholar
  14. Ku M, Wen X, Luo J, Liu W, Hu Y (1999) A Study on Transplantion and Culture of Leptobotia elongata. J Hubei Agricultural College 19(2):146–148 (in Chinese)Google Scholar
  15. Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150PubMedCrossRefGoogle Scholar
  16. Li Y, Wang D, Fang Y, Liu S, Duan X, Chang Y, Chen D (2008) Genetic diversity in the bronze gudgeon, Coreius heterodon, from the Yangtze River system based on mtDNA sequences of the control region. Environ Biol Fish 82:35–40CrossRefGoogle Scholar
  17. Liang Y, Hu X (2001) Studies on artifical propagation of Leptobotia elongata. Acta Hydro-biol Sinica 25:422–424 (in Chinese)Google Scholar
  18. Liu J (2004) Quantitative Analysis of Yangtze River specific fish threatened and order of priority. China Environ Sci 24(4):395–399 (in Chinese)Google Scholar
  19. Liu HZ, 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 80:569–581CrossRefGoogle Scholar
  20. Liu H, Chen D, Liu S, Duan X (2009) Genetic diversity of Botia superciliaris in the upper Yangtze River. Freshwater Fisheries 39:8–13 (in Chinese)Google Scholar
  21. Mandal A, Kuldeep KL, Vindhya M, Rajeev KS (2009) Evaluation of Genetic Variation in the Clown Knifefish, Chitala chitala, Using Allozymes, RAPD, and Microsatellites. Biochem Genet 47:216–234PubMedCrossRefGoogle Scholar
  22. Nugroho E, Ferrell DJ, Smith P, Taniguchi N (2001) Genetic divergence of kingfish from Japan, Australia and New Zealand inferred by microsatellite DNA and mitochondrial DNA control region markers. Fisheries Sci 67:843–850CrossRefGoogle Scholar
  23. Nyakaana S, Arctander P, Siegismund HR (2002) Population structure of the African savannah elephant inferred from mitochondrial control region sequences and nuclear microsatellite loci. Heredity 89:90–98PubMedCrossRefGoogle Scholar
  24. Richards CM (2000) Inbreeding depression and genetic rescue in a plant metapopulation. Am Nat 155:383–394PubMedCrossRefGoogle Scholar
  25. Rogers AR, Harpending H (1992) Population growth makes waves in the distribution of pairwise genetic differences. Mol Biol Evol 9:552–569PubMedGoogle Scholar
  26. Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496PubMedCrossRefGoogle Scholar
  27. Sambrook J, Russell DW (2001) Molecular cloning: A laboratory manual, 3rd edn. Cold Spring Harbor Laboratory Press, New YorkGoogle Scholar
  28. Sato S, Kojima H, Ando J, Ando H, Wilmot RL, Seeb LW, Efremov V, LeClair L, Buchholz W, Jin DH, Urawa S, Kaeriyama M, Urano A, Abe S (2004) Genetic population structure of chum salmon in the Pacific Rim inferred from mitochondrial DNA sequence variation. Environ Biol Fish 69:37–50CrossRefGoogle Scholar
  29. Song Z, Song J, Yue B (2008) Population genetic diersity of Prenant’s schizothoracin, Schizothorax prenanti, inferred from the mitochondrial DNA contral region. Environ Biol Fish 81(3):247–252CrossRefGoogle Scholar
  30. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585–595PubMedGoogle Scholar
  31. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876PubMedCrossRefGoogle Scholar
  32. Wasko AP, Galetti-Jr PM (2002) RAPD analysis in the Neotropical fish Brycon lundii: genetic diversity and its implications for the conservation of the species. Hydrobiologia 474:131–137CrossRefGoogle Scholar
  33. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370CrossRefGoogle Scholar
  34. Yang J, Hu X, Tang W, Lin H (2008) mtDNA control region sequence variation and genetic diversity of Coilia nasus in Yangtze River estuary and its adjacent waters. Chinese J Zool 43(1):8–15 (in Chinese)Google Scholar
  35. Yue P, Chen Y (1998) Pisces. In: Wang S (ed) China Red Data Book of endangered animals. Science Press, Beijing, pp 203–204 (in Chinese)Google Scholar
  36. Zenger KR, Eldridge MD-B, Johnston PG (2005) Phylogenetics, population structure and genetic diversity of the endangered southern brown bandicoot (Isoodon obesulus) in south-eastern Australia. Conserv Genet 6:93–204CrossRefGoogle Scholar
  37. Zhao K, Duan Z, Peng Z, Guo S, Li J, He S, Zhao X (2009) The youngest split in sympatric schizothoracine fish (Cyprinidae) is shaped by ecological adaptations in a Tibetan Plateau glacier lake. Mol Ecol 18:3616–3628PubMedCrossRefGoogle Scholar
  38. Zhou J, Liang Y, Chen X, Li M (2007) Nursing techniques of Leptobotia elongata larvae. J Aquaculture 28(5):12–13 (in Chinese)Google Scholar

Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  1. 1.College of Animal Science and TechnologySichuan Agricultural UniversityYaanPeople’s Republic of China
  2. 2.Fisheries InstituteSichuan Academy of Agricultural SciencesChengduPeople’s Republic of China

Personalised recommendations