Conservation Genetics

, Volume 8, Issue 3, pp 683–693 | Cite as

Genetic discrimination of middle Mississippi River Scaphirhynchus sturgeon into pallid, shovelnose, and putative hybrids with multiple microsatellite loci

  • A. W. Schrey
  • B. L. Sloss
  • R. J. Sheehan
  • R. C. Heidinger
  • E. J. Heist
Original Paper


The pallid sturgeon (Scaphirhynchus albus), which is protected under the US endangered species act, and shovelnose sturgeon (S. platorhynchus), which is legally harvested in some locations, are sympatric throughout the range of pallid sturgeon. There is considerable morphological overlap between the species making discrimination problematic. The inability to reliably differentiate between species across all life stages has hampered pallid sturgeon recovery efforts. Furthermore, the two species are believed to hybridize. This study used allele frequency data at multiple microsatellite loci to perform Bayesian and likelihood-based assignment testing and morphological measures and meristics to discriminate pallid, shovelnose, and putative hybrid sturgeons from the middle Mississippi River. Bayesian model-based clustering of the genetic data indicated that two natural genetic units occur in the region. These units correspond to morphologically identified pallid and shovelnose sturgeon. Some individuals were morphologically intermediate and many of these failed to strongly assign genetically as either pallid or shovelnose sturgeon, suggesting they may be hybrids. These data indicate that pallid sturgeon and shovelnose sturgeon are genetically distinct in the middle Mississippi River (FST = 0.036, P < 0.0001) and suggest that hybridization between pallid sturgeon and shovelnose sturgeon has occurred in this region with genetic distance estimates indicating the greatest distance is between pallid and shovelnose sturgeon, while hybrid sturgeon are intermediate but closer to shovelnose. This study demonstrates that assignment testing with multiple microsatellite markers can be successful at discriminating pallid sturgeon and shovelnose sturgeon, providing a valuable resource for pallid sturgeon recovery and conservation.


Scaphirhynchus Microsatellite Assignment testing Endangered species Species identification 


  1. Allendorf FW, Leary RF, Spruell P, Wenburg JK (2001) The problems with hybrids: setting conservation guidelines. TREE 16:613–622Google Scholar
  2. Bailey RM, Cross FB (1954) River sturgeons of the American genus Scaphirhynchus: characters, distribution, and synonymy. Pap Mich Acad Sci Arts & Lett 36:169–208, 54Google Scholar
  3. Birstein VJ (1993) Sturgeons and paddlefishes: threatened fishes in need of conservation. Conserv Biol 7:773–787CrossRefGoogle Scholar
  4. Bischof R, Szalanski AL (2000) Mitochondrial-DNA variation in pallid and shovelnose sturgeons, Scaphirhynchus (Pisces: Acipenseridae). Trans Nebr Acad Sci 26:19–21Google Scholar
  5. Campton DE, Bass AL, Chapman FA, Bowen BW (2000) Genetic distinction of pallid, shovelnose, and Alabama sturgeon: emerging species and the US Endangered Species Act. Conserv Genet 1:17–32CrossRefGoogle Scholar
  6. Chakraborty R, Jin L (1993) A unified approach to study hypervariable polymorphisms: statistical considerations of determining relatedness and population distances. In: Chakraborty R, Epplen JT (eds) DNA fingerprinting: state of the science. AJ Jefferys Birkhauser, VerlagGoogle Scholar
  7. Carlson DM, Pflieger WL, Trial L, Haverland PS (1985) Distribution, biology and hybridization of Scaphirhynchus albus and S. platorhynchus in the Missouri and Mississippi Rivers. Environ Biol Fish 14:51–59CrossRefGoogle Scholar
  8. Dryer MP, Sandoval AJ (1993) Recovery plan for the pallid sturgeon (Scaphirhynchus albus). US Fish and Wildlife Service, Denver, 55 ppGoogle Scholar
  9. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software structure: a simulation study. Mol Ecol 14:2611–2620PubMedCrossRefGoogle Scholar
  10. Forbes SA, Richardson RE (1905) On a new shovelnose sturgeon from the Mississippi River. Bull Illinois State Lab Nat Hist 7:37–44Google Scholar
  11. Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567–1587PubMedGoogle Scholar
  12. Goudet J (2001) FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3). Available from fstat.html. Updated from Goudet (1995). Cited Feb 2002Google Scholar
  13. Goudet J (1995) FSTAT (vers. 1.2): a computer program to calculate F-statistics. J Hered 86:485–486Google Scholar
  14. Goudet J, Raymond M, Demeeus T, Rousset F (1996) Testing differentiation in diploid populations. Genetics 144:1933–1940PubMedGoogle Scholar
  15. Hansen MM, Kenchington E, Nielsen EE (2001) Assigning individual fish to populations using microsatellite DNA markers. Fish Fish 2:93–121Google Scholar
  16. Keenlyne KD (1997) Life history and status of the shovelnose sturgeon, Scaphirhynchus platorhynchus. Environ Biol Fish 48:291–298CrossRefGoogle Scholar
  17. Kuhajda BR, Mayden RL (2001) Morphological comparisons of hatchery-reared specimens of Scaphirhynchus albus, S. platorhynchus, and S. albus  ×  S. platorhynchus hybrids. Final Report US Fish and Wildlife Service Bismarck, North Dakota, 119 ppGoogle Scholar
  18. Langella O (2002) Populations 1.2.28 (available at = en#ancre-bibliographie. Cited 5 Dec 2002Google Scholar
  19. Lewis PO, Zaykin D (2001) Genetic data analysis: computer program for the analysis of allelic data. Version 1.0 (d16c). Free program distributed by the authors over the internet from software.html. Cited 2001Google Scholar
  20. Manel S, Gaggiotti OE, Waples RS (2005) Assignment methods: matching biological questions with appropriate techniques. TREE 20:136–142PubMedGoogle Scholar
  21. Miller LM, Kapuscinski AR (2003) Genetic guidelines for hatchery supplementation programs. In: Hallerman EM (ed) Population genetics: principles and applications for fisheries scientists. American Fisheries Society, Bethesda, MDGoogle Scholar
  22. McQuown EC, Sloss BL, Sheehan RJ, Rodzen J, Tranah GJ, May B (2000) Microsatellite analysis of genetic variation in sturgeon: new primer sequences for Scaphirhynchus and Acipenser. Trans Am Fish Soc 129:1380–1388CrossRefGoogle Scholar
  23. Paetkau D, Slade R, Burden M, Estoup A (2004) Genetic assignment methods for direct, real-time estimation of migration rate: a simulation-based exploration of accuracy and power. Mol Ecol 13:55–65PubMedCrossRefGoogle Scholar
  24. Paetkau D, Calvert W, Stirling I, Strobeck C (1995) Microsatellite analysis of population structure in Canadian polar bears. Mol Ecol 4:347–354PubMedGoogle Scholar
  25. Phelps SR, Allendorf FW (1983) Genetic identity of pallid and shovelnose sturgeon (Scaphirhynchus albus and S. platorhynchus). Copeia 1983:696–700Google Scholar
  26. Piry S, Alapetite A, Cornuet J-M, Paetkau D, Baudouin L, Estoup A (2004) GeneClass2. A software for genetic assignment and first-generation migrant detection. J Hered 95:536–539PubMedCrossRefGoogle Scholar
  27. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedGoogle Scholar
  28. Rannala B, Mountain J (1997) Detecting immigration using multilocus genotypes. Proc Natl Acad Sci USA 94: 9197–9201PubMedCrossRefGoogle Scholar
  29. Rice WR(1989) Analyzing tables of statistical tests. Evolution 43:223–225CrossRefGoogle Scholar
  30. Rhymer JM, Simberloff D (1996) Extinction by hybridization and introgression. Annu Rev Ecol Syst 27:83–109CrossRefGoogle Scholar
  31. Straughan DJ, Burnham-Curtis ME, Fain SR (2002) Experimental search for forensically useful markers in the genus Scaphirhynchus. J App Ichthyol 18: 621–628CrossRefGoogle Scholar
  32. Tranah G, Campton DE, May B (2004) Genetic evidence for hybridization of pallid and shovelnose sturgeon. J Hered 95:474–480PubMedCrossRefGoogle Scholar
  33. Tranah GJ, Kincaid HL, Krueger CC, Campton DE, May B (2001) Reproductive isolation in sympatric populations of pallid and shovelnose sturgeon. N Am J Fish Manage 21:367–373CrossRefGoogle Scholar
  34. Vaha JP, Primmer CR (2006) Efficiency of model-based Bayesian methods for detecting hybrid individuals under different hybridization scenarios and with different numbers of loci. Mol Ecol 15:63–72PubMedCrossRefGoogle Scholar
  35. Weir BS, Cockerham CS (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1258–1370CrossRefGoogle Scholar
  36. Wills PS, Sheehan RJ, Heidinger R, Sloss BL, Clevenstine R (2002) Differentiation of pallid sturgeon and shovelnose sturgeon using an index based on meristics and morphometrics. Am Fish Soc Symp 28:249–258Google Scholar
  37. Wirgin II, Stabile JE, Waldman JR (1997) Molecular analysis in the conservation of sturgeons and paddlefish. Environ Biol Fish 48:385–398CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, Inc. 2006

Authors and Affiliations

  • A. W. Schrey
    • 1
  • B. L. Sloss
    • 2
  • R. J. Sheehan
    • 1
  • R. C. Heidinger
    • 1
  • E. J. Heist
    • 1
  1. 1.Fisheries and Illinois Aquaculture Center and Department of ZoologySouthern Illinois University CarbondaleCarbondaleUSA
  2. 2.US Geological Survey, Wisconsin Cooperative Fisheries Research UnitCollege of Natural Resources, University of Wisconsin-Stevens PointStevens PointUSA

Personalised recommendations