Genetic analysis of invasive Asian Black Carp (Mylopharyngodon piceus) in the Mississippi River Basin: evidence for multiple introductions

Abstract

Invasive Asian Black Carp (Mylopharyngodon piceus) have been present in USA aquaculture facilities since the 1980s and wild Black Carp have been found in the Mississippi River Basin since the early 1990s. This study characterizes the genetic diversity and relatedness of the Basin’s Black Carp and clarifies the introduction history. Analyses focused on three mitochondrial markers (control region, cytochrome-b, and 16S) and seven nuclear microsatellite markers (nDNA), using aquaculture and wild-caught samples collected in the upper and lower Mississippi Basin. Of the three mitochondrial haplotypes, two were shared between the aquaculture and wild populations, while a third was only present in upper Mississippi wild-caught specimens. Due to the presence of diploid and triploid fish, microsatellite markers were scored as pseudodominant and revealed low polymorphism (NA = 4.6, NA Ave = 1.5). Nuclear Bayesian clustering analyses identified two genetically distinct groups and four subclusters, each primarily composed of a unique haplotype. Samples from three aquaculture farms were assigned to group 1, while a fourth farm included samples from both groups 1 and 2. Wild-caught fish from the upper Basin were predominantly group 1, whereas wild samples from the lower Mississippi were assigned to both genetic groups. The presence of divergent haplotypes and distinct nDNA groups, along with geographic distribution patterns, indicate that wild populations in the basin likely resulted from multiple introductions. Genetic similarities between wild and captive populations support claims that aquaculture is the introduction source, but a shortage of samples and a history of repeated transfers among facilities obscure the precise pathway.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3

References

  1. Briolay J, Galtier N, Brito RM, Bouvet Y (1998) Molecular phylogeny of Cyprinidae inferred from cytochrome b DNA sequences. Mol Phylogenet Evol 9:100–108

    CAS  PubMed  Article  Google Scholar 

  2. Burkhead NM (2012) Extinction rates in North American freshwater fishes, 1900–2010. Bioscience 62:798–808

    Article  Google Scholar 

  3. Chapman DC, Hoff MH (2011) Invasive Asian carps in North America. In: American Fisheries Society symposium, vol 74, Bethesda, MD

  4. Chen Q, Wang CH, Lu G, Song X, Xu JW, Yang QL, Li SF (2009) Analysis of genetic variation in grass carp (Ctenopharyngodon idellus) from native and colonized regions using ISSR markers. Biochem Syst Ecol 37:549–555

    CAS  Article  Google Scholar 

  5. Chick JH, Maher RJ, Burr BM, Thomas MR (2003) First black carp captured in U.S. Science 300:1876–1877

    CAS  PubMed  Article  Google Scholar 

  6. Collins TM, Trexler JC, Nico LG, Rawlings TA (2002) Genetic diversity in a morphologically conservative invasive taxon: multiple swamp eel introductions in the southeastern United States. Conserv Biol 16:1024–1035

    Article  Google Scholar 

  7. Drummond AJ, Ashton B, Buxton S, Cheung M, Cooper A, Duran C, Field M, Heled J, Kearse M, Markowitz S, Moir R, Stones-Havas S, Sturrock S, Thierer T, Wilson A (2011) Geneious v5.1. http://wwwgeneious.com

  8. Durand JD, Tsigenopoulos CS, Unlu E, Berrebi P (2002a) Erratum to "Phylogeny and biogeography of the family Cyprinidae in the Middle East inferred from cytochrome b DNA—evolutionary significance of this region" [Mol Phylogenet Evol 22 (2002)]. Mol Phylogenet Evol 25:218

  9. Durand JD, Tsigenopoulos CS, Unlu E, Berrebi P (2002b) Phylogeny and biogeography of the family Cyprinidae in the Middle East inferred from cytochrome b DNA—evolutionary significance of this region. Mol Phylogenet Evol 22:91–100

  10. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620

    CAS  PubMed  Article  Google Scholar 

  11. Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial-DNA restriction data. Genetics 131:479–491

    CAS  PubMed Central  PubMed  Google Scholar 

  12. Ficetola GF, Bonin A, Miaud C (2008) Population genetics reveals origin and number of founders in a biological invasion. Mol Ecol 17:773–782

    CAS  PubMed  Article  Google Scholar 

  13. Glover KA, Skilbrei OT, Skaala O (2008) Genetic assignment identifies farm of origin for Atlantic salmon Salmo salar escapees in a Norwegian fjord. ICES J Mar Sci 65:912–920

    Article  Google Scholar 

  14. Guo S, Zou G, Yang G (2009) Development of microsatellite DNA markers of grass carp (Ctenopharyngodon idella) and their cross-species application in black carp (Mylopharyngodon piceus). Conserv Genet 10:1515–1519

    CAS  Article  Google Scholar 

  15. Haag WR (2009) Past and future patterns of freshwater mussel extinctions in North America during the Holocene. In: Turvey S (ed) Holocene extinctions. Oxford University Press, Oxford, pp 107–128

    Google Scholar 

  16. Hammer Ø, Harper DAT, Ryan PD (2001) PAST: paleontological statistics software package for education and data analysis. Palaeontol Electron 4:9

    Google Scholar 

  17. He SP, Chen YY, Tsuneo N (2001) Sequences of cytochrome b gene for primitive cyprinid fishes in East Asia and their phylogenetic concerning. Chin Sci Bull 46:661–665

    CAS  Article  Google Scholar 

  18. He S, Gu X, Mayden RL, Chen W-J, Conway KW, Chen Y (2008) Phylogenetic position of the enigmatic genus Psilorhynchus (Ostariophysi: Cypriniformes): evidence from the mitochondrial genome. Mol Phylogenet Evol 47:419–425

    PubMed  Article  Google Scholar 

  19. Hillis DM, Mable BK, Larson A, Davis SK, Zimmer EA (1996) Nucleic acids IV: sequencing and cloning. In: Hillis DM, Moritz C, Mable BK (eds) Molecular systematics. Sinauer Associates, Inc., Sunderland, pp 321–381

    Google Scholar 

  20. Hunter ME, Mignucci-Giannoni AA, Tucker KP, King TK, Bonde RK, Gray BA, McGuire PM (2012) Puerto Rico and Florida manatees represent genetically distinct groups. Conserv Genet 13:1623–1635

    Article  Google Scholar 

  21. Israel JA, May B (2010) Indirect genetic estimates of breeding population size in the polyploid green sturgeon (Acipenser medirostris). Mol Ecol 19:1058–1070

    CAS  PubMed  Article  Google Scholar 

  22. Israel JA, Bando KJ, Anderson EC, May B (2009) Polyploid microsatellite data reveal stock complexity among estuarine North American green sturgeon (Acipenser medirostris). Can J Fish Aquat Sci 66:1491–1504

    CAS  Article  Google Scholar 

  23. Jenkins JA, Thomas RG (2007) Use of eyeballs for establishing ploidy of Asian carp. N Am J Fish Manag 27:1195–1202

    Article  Google Scholar 

  24. Jung J, Song KH, Lee E, Kim W (2009) Mitochondrial genetic variations in fishes of the genus Carassius from South Korea: proximity to northern China rather than Japanese Islands? Hydrobiologia 635:95–105

    Article  Google Scholar 

  25. King TL, Eackles MS, Chapman DC (2011) Tools for assessing kinship, population structure, phylogeography, and interspecies hybridization in Asian carps invasive to the Mississippi River, USA: isolation and characterization of novel tetranucleotide microsatellite DNA loci in silver carp Hypophthalmichthys molitrix. Conserv Genet Resour 3:397–401

    Article  Google Scholar 

  26. Kolbe JJ, Glor RE, Schettino LR, Lara AC, Larson A, Losos JB (2007) Multiple sources, admixture, and genetic variation in introduced Anolis lizard populations. Conserv Biol 21:1612–1625

    PubMed  Article  Google Scholar 

  27. Li SF, Lu GQ (1998) Diversity of mitochondrial DNA in the populations of silver carp, bighead carp, grass carp and black carp in the middle and lower reaches of the Yangtze River. Acta Zool Sin 44:82–93

    Google Scholar 

  28. Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452

    CAS  PubMed  Article  Google Scholar 

  29. Liu ZJ, Cordes JF (2004) DNA marker technologies and their applications in aquaculture genetics. Aquaculture 242:735–736

    Article  Google Scholar 

  30. Lu G, Li S, Bernatchez L (1997) Mitochondrial DNA diversity, population structure, and conservation genetics of four native carps within the Yangtze River, China. Can J Fish Aquat Sci 54:47–58

    CAS  Article  Google Scholar 

  31. Lundrigan TA, Reist JD, Ferguson MM (2005) Microsatellite genetic variation within and among Arctic charr (Salvelinus alpinus) from aquaculture and natural populations in North America. Aquaculture 244:63–75

    CAS  Article  Google Scholar 

  32. Lynch M, Milligan B (1994) Analysis of population genetic structure using RAPD markers. Mol Ecol 3:91–99

    CAS  PubMed  Article  Google Scholar 

  33. Lysne SJ, Perez KE, Brown KM, Minton RL, Sides JD (2008) A review of freshwater gastropod conservation: challenges and opportunities. J N Am Benthol Soc 27:463–470

    Article  Google Scholar 

  34. Mahon AR, Jerde CL, Galaska M, Bergner JL, Chadderton WL, Lodge DM, Hunter ME, Nico LG (2013) Validation of eDNA surveillance sensitivity for detection of Asian carps in controlled and field experiments. PLoS ONE 8:e58316. doi:10.1371/journal.pone.0058316

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  35. McPhee MV, Turner TF (2009) Genealogical diversity suggests multiple introductions of white suckers (Catostomus commersonii) into the Rio Grande, New Mexico. Southwest Nat 54:485–492

    Article  Google Scholar 

  36. Muirhead JR, Gray DK, Kelly DW, Ellis SM, Heath DD, MacIsaac HJ (2008) Identifying the source of species invasions: sampling intensity vs. genetic diversity. Mol Ecol 17:1020–1035

    CAS  PubMed  Article  Google Scholar 

  37. Nico LG, Jelks HL (2011) The black carp in North America: an update. In: Chapman DC, Hoff MH (eds) Invasive Asian carps in North America, American Fisheries Society symposium, vol 74, pp 89–104, Bethesda, MD

  38. Nico LG, Williams JD, Jelks HL (2005) Black carp: biological synopsis and risk assessment of an introduced fish. American Fisheries Society, Bethesda

    Google Scholar 

  39. Nico LG, Demopoulos A, Gualtieri D, Wieser C (2011) Use of stable isotopes and mercury to assess trophic positions of black carp and other large fishes in the Red–Atchafalaya River system, Louisiana, USA. In: Chapman DC, Hoff MH (eds) Invasive Asian carps in North America, American Fisheries Society symposium, vol 74, pp 105–119, Bethesda, MD

  40. Papoulias DM, Candrl J, Jenkins JA, Tillitt DE (2011) Verification of ploidy and reproductive potential in triploid black carp and grass carp. In: Chapman DC, Hoff MH (eds) Invasive Asian carps of North America, American Fisheries Society symposium, vol 74, pp 251–266, Bethesda, MD

  41. Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295

    Article  Google Scholar 

  42. Pitlick J (1997) A regional perspective of the hydrology of the 1993 Mississippi River Basin flood. Ann Assoc Am Geogr 87:135–151

  43. Pritchard J, Wen X, Falush D (2010) Documentation for Structure software: version 2.3. http://pritchardlab.stanford.edu/structure_software/release_versions/v2.3.4/html/structure

  44. Rodzen JA, Famula TR, May B (2004) Estimation of parentage and relatedness in the polyploid white sturgeon (Acipenser transmontanus) using a dominant marker approach for duplicated microsatellite loci. Aquaculture 232:165–182

    Article  Google Scholar 

  45. Ryman N, Palm S (2006) POWSIM: a computer program for assessing statistical power when testing for genetic differentiation. Mol Ecol Notes 6:600–602

    Article  Google Scholar 

  46. Simon C, Franke A, Martin A (1991) The polymerase chain reaction: DNA extraction and amplification. In: Hewitt GM, Johnson A, Young JPW (eds) Molecular techniques in taxonomy. Springer, Berlin, pp 329–355

    Google Scholar 

  47. Simon A, Britton R, Gozlan R, Oosterhout C, Volchaert FAM, Hanfling B (2011) Invasive cyprinid fish in Europe originate from the single introduction of an admixed source population followed by a complex pattern of spread. PLoS ONE 6:e18560

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  48. Stepien CA, Tumeo MA (2006) Invasion genetics of Ponto-Caspian gobies in the Great Lakes: a ‘cryptic’ species, absence of founder effects, and comparative risk analysis. Biol Invasions 8:61–78

    Article  Google Scholar 

  49. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  50. Thai BT, Burridge CP, Phan PD, Austin CM (2005) Using mitochondrial nucleotide sequences to investigate diversity and genealogical relationships within common carp (Cyprinus carpio). Anim Genet 36:23–28

    CAS  PubMed  Article  Google Scholar 

  51. Thai BT, Si VN, Phan PD, Austin CM (2007) Phylogenetic evaluation of subfamily classification of the Cyprinidae focusing on Vietnamese species. Aquat Living Resour 20:143–153

    Article  Google Scholar 

  52. Thomas RG, Jenkins JA, David J (2011) Occurrence and distribution of Asian carps in Louisiana. In: Chapman DC, Hoff MH (eds) Invasive Asian carps in North America, American Fisheries Society symposium, vol 74, pp 239–250, Bethesda, MD

  53. Thorgaard GH, Allen SK (1987) Chromosome manipulation and markers in fishery management. In: Tyman N, Utter F (eds) Population genetics and fishery management, pp 319–331, Washington Sea Grant Program, Seattle

  54. Tiwary BK, Kirubagaran R, Ray AK (2004) The biology of triploid fish. Rev Fish Biol Fish 14:391–402

    Article  Google Scholar 

  55. Vidal O, García-Berthou E, Tedesco PA, García-Marín JL (2010) Origin and genetic diversity of mosquitofish (Gambusia holbrooki) introduced to Europe. Biol Invasions 12:841–851

    Article  Google Scholar 

  56. Wang CH, Wang J, Yang JQ, Lu GQ, Song X, Chen Q, Xu JW, Yang QL, Li SF (2012) Complete mitogenome sequence of black carp (Mylopharyngodon piceus) and its use for molecular phylogeny of leuciscine fishes. Mol Biol Rep 39:6337–6342

    CAS  PubMed  Article  Google Scholar 

  57. Zhao JL, Li SF (1996) Isoenzyme analysis of population divergence of silver carp, bighead carp, grass carp and black carp in the middle and lower stream of Changjiang River. J Fisher China 20:104–110

    Google Scholar 

  58. Zigler SJ, Dewey MR, Knights BC, Runstrom AL, Steingraeber MT (2004) Hydrologic and hydraulic factors affecting passage of paddlefish through dams in the Upper Mississippi River. Trans Am Fish Soc 133:160–172

    Article  Google Scholar 

Download references

Acknowledgments

We thank the following commercial fishers for procuring wild-caught specimens and sharing knowledge: Rusty Kimble, James Gaspard, Dwayne Dibble, Ronnie Watters, Aaron Pierce, Gary Shaw, and Preston Terrell. Others assisting in our hunt for specimen samples, included Mike Freeze, Jody David, Rob Maher, Greg Whitledge, Jacob Norman, James Candrl, Duane Chapman, and Jill Jenkins. Tim King and Michael Eackles provided microsatellite marker sequences and labeled aliquots for testing. Jill Jenkins and Rob Maher shared ploidy data. We are grateful to Jonathan Saunders, Theresa Floyd, and Gaia Meigs-Friend for assisting with sample processing. Rob Robins (Florida Museum of Natural History), Hank Bart and Justin Mann (Tulane University Museum of Natural History) cataloged museum vouchers. Howard Jelks and Mary Brown contributed time and help. Amy Benson and Matthew Neilson kindly reviewed manuscript drafts. The U.S. Fish and Wildlife Service Invasive Species office and the U.S. Geological Survey Invasive Species Program provided funding. Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

Author information

Affiliations

Authors

Corresponding author

Correspondence to Margaret E. Hunter.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 29 kb)

Supplementary material 2 (DOCX 55 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Hunter, M.E., Nico, L.G. Genetic analysis of invasive Asian Black Carp (Mylopharyngodon piceus) in the Mississippi River Basin: evidence for multiple introductions. Biol Invasions 17, 99–114 (2015). https://doi.org/10.1007/s10530-014-0708-z

Download citation

Keywords

  • Cyprinidae
  • Nuclear microsatellite marker
  • Mitochondrial marker
  • Phylogenetic population structure
  • Polyploidy
  • Pseudodominant loci