Conservation Genetics

, Volume 10, Issue 1, pp 225–236

Efficiency of markers and methods for detecting hybrids and introgression in stocked populations

  • Nuria Sanz
  • Rosa M. Araguas
  • Raquel Fernández
  • Manuel Vera
  • José-Luis García-Marín
Research Article

Abstract

Detection of hybridization and introgression in wild populations that have been supplemented by hatchery fish is necessary during development of conservation and management strategies. Initially, allozyme data and more recently highly polymorphic microsatellite markers have been used to obtain this information. We used both markers to assess the effectiveness of four assignment methods (Structure, NewHybrids, Baps and GeneClass) to detect hatchery introgression in wild stocked populations. Simulations of hybrid genotypes from real parental data revealed that the number and type of markers used with Structure, NewHybrids and Baps can identify as admixed most first and second generation hybrids as well as first generation backcrosses. In wild populations, introgression rates estimated from different markers and methods were correlated. However, slight disagreements were observed at both population and individual levels. Overall, the fully Bayesian (Structure, NewHybrids and Baps) performed better than partially Bayesian (GeneClass) assignment tests. In wild collections, Baps analyses were limited because of the lack of a native baseline. In all cases, the efficiency of methods was reduced as introgression increased.

Keywords

Allozymes Assignment methods Brown trout Introgression Microsatellites 

References

  1. Allendorf FW, Leary RF, Hitt NP, Knudsen KL, Lundguist LL, Spruell P (2004) Intercrosses and the U.S. endangered species act: should hybridrised populations be included as westslope cutthroat trout? Conserv Biol 18:1203–1213CrossRefGoogle Scholar
  2. Anderson EC, Thompson EA (2002) A model-based method for identifying species hybrids using multilocus genetic data. Genetics 160:1217–1229PubMedGoogle Scholar
  3. Araguas RM, Sanz N, Pla C, García-Marín JL (2004) Breakdown of the brown trout evolutionary history due to hybridization between native and cultivated fish. J Fish Biol 65:28–37CrossRefGoogle Scholar
  4. Arias J, Sánchez L, Martínez P (1995) Low stocking incidence in brown trout populations from north-western Spain monitored by LDH-5* diagnostic marker. J Fish Biol 47:170–176CrossRefGoogle Scholar
  5. Aurelle D, Cattaneo-Berrebi G, Berrebi PL (2002) Natural and artificial secondary contact in brown trout (Salmo trutta L.) in the French western Pyrenees assessed by allozymes and microsatellites. Heredity 89:171–183PubMedCrossRefGoogle Scholar
  6. Barilani M, Deregnaucourt S, Gallego S, Galli L, Mucci N, Piombo R, Puigcerver M, Rimondi S, Rodríguez-Teijeiro JD, Spanò S, Randi E (2005) Detecting hibridization in wild (Coturnix c. coturnix) and domesticated (Coturnix c. japonica) quail populations. Biol Conserv 126:445–455CrossRefGoogle Scholar
  7. Barilani M, Sfougaris A, Giannakopoulos A, Mucci N, Tabarroni C, Randi E (2007) Detecting introgressive hybridization in rock partridge populations (Alectoris graeca) in Greece through Bayesian admixture analyses of multilocus genotypes. Conserv Genet 8:343–354CrossRefGoogle Scholar
  8. Berry O, Tocher MD, Sarre SD (2004) Can assignment tests measure dispersal? Mol Ecol 13:551–561PubMedCrossRefGoogle Scholar
  9. Brown C, Day RL (2002) The future of stock enhancements: lessons for hatchery practice from conservation biology. Fish Fish 3:79–94Google Scholar
  10. Cairney M, Taggart JB, Høyheim B (2000) Characterization of microsatellite and minisatellite loci in Atlantic salmon (Salmo salar L.) and cross-species amplification in other salmonids. Mol Ecol 9:2155–2234CrossRefGoogle Scholar
  11. Corander J, Marttinen P (2006) Bayesian identification of admixture events using multilocus molecular markers. Mol Ecol 15:2833–2843PubMedCrossRefGoogle Scholar
  12. Corujo M, Blanco G, Vázquez E, Sánchez JA (2004) Genetic structure of northwestern Spanish brown trout (Salmo trutta L.) populations, differences between microsatellite and allozyme loci. Hereditas 141:258–271PubMedCrossRefGoogle Scholar
  13. Cortey M, Pla C, García-Marín JL (2004) Historical biogeography of Mediterranean trout. Mol Phylogenet Evol 33:831–844PubMedCrossRefGoogle Scholar
  14. Cowx IG (1999) An appraisal of stocking strategies in the light of developing country constraints. Fish Manag Ecol 6:21–34CrossRefGoogle Scholar
  15. Estoup A, Presa P, Krieg F, Vaiman D, Guyomard R (1993) (CT)n and (GT)n microsatellites: a new class of genetic markers for Salmo trutta L. (brown trout). Heredity 71:488–496PubMedCrossRefGoogle Scholar
  16. Estoup A, Largiader CR, Perrot E, Chourrout D (1996) Rapid one-tube DNA extraction for reliable PCR detection of fish polymorphic markers and transgenes. Mol Mar Biol Biotechnol 5:295–298Google Scholar
  17. Frankham R, Ballou JD, Briscoe DA (2002) Introduction to conservation genetics. Cambridge University Press, UKGoogle Scholar
  18. Ferguson M, Taggart JB, Prodohl PA, McMeel O, Thompson C, Stone C, McGinnity P, Hynes RA (1995) The application of molecular markers to the study and conservation of fish populations, with special reference to Salmo. J Fish Biol 47:103–126CrossRefGoogle Scholar
  19. García-Marín JL, Jorde PE, Ryman N, Utter F, Pla C (1991) Management implications of genetic differentiation between native and hatchery populations of brown trout (Salmo trutta) in Spain. Aquaculture 95:235–249CrossRefGoogle Scholar
  20. García-Marín JL, Sanz N, Pla C (1998) Proportions of native and introduced Brown trout in adjacent fished and unfished Spanish Rivers. Conserv Biol 12:313–319CrossRefGoogle Scholar
  21. Garnier S, Alibert P, Audiot P, Prieur B, Rasplus JY (2004) Isolation by distance and sharp discontinuities in gene frequencies: implications for the phylogeographyy of an alpine insect species, Carabus solieri. Mol Ecol 13:1883–1897PubMedCrossRefGoogle Scholar
  22. Gharbi K, Gautier A, Danzmann RG, Gharbi S, Sakamoto T, Hoyheim B, Taggart JB, Cairney M, Powell R, Krieg F, Okamoto N, Ferguson MM, Holm LE, Guyomard R (2006) A linkage map for brown trout (Salmo trutta): chromosome homeologies and comparative genome organization with other salmonid fish. Genetics 172:2405–2419PubMedCrossRefGoogle Scholar
  23. Goudet J (1995) Fstat version 1.2: a computer program to calculate Fstatistics. J Hered 86:485–486Google Scholar
  24. Hansen MM, Kenchington E, Nielsen EE (2001a) Assigning individuals fish to populations using microsatellite DNA markers. Fish Fish 2:93–112Google Scholar
  25. Hansen MM, Nielsen EE, Bekkevold D, Mensberg KLD (2001b) Admixture analysis and stocking impact assessment in brown trout (Salmo trutta), estimated with incomplete baseline data. Can J Fish Aquat Sci 58:1853–1860CrossRefGoogle Scholar
  26. Hauser L, Seamons TR, Dauer M, Naish KA, Quinn TP (2006) An empirical verification of population assignment methods by marking and parentage data: hatchery and wild steelhead (Oncorhynchus mykiss) in Forks Creek, Washington, USA. Mol Ecol 15:3157–3173PubMedCrossRefGoogle Scholar
  27. Hewitt G (2001) Speciation, hybrid zones and phylogeography—or seeing genes in space and time. Mol Ecol 10:537–549PubMedCrossRefGoogle Scholar
  28. Koskinen MT, Hirvonen H, Landry PA, Primmer CR (2004) The benefits of increasing the number of microsatellites utilized in genetic populations studies: an empirical perspective. Hereditas 141:61–67PubMedCrossRefGoogle Scholar
  29. Latch EK, Dharmarajan G, Glaubitz JC, Rhodes OE Jr (2006) Relative performance of Bayesian clustering software for inferring population substructure and individual assignment at low levels of population differentiation. Conserv Genet 7:295–302CrossRefGoogle Scholar
  30. Lerceteau-Kohler E, Weiss S (2006) Development of a multiplex PCR microsatellite assay in brown trout Salmo trutta, and its potential application for the genus. Aquaculture 258:641–645CrossRefGoogle Scholar
  31. Manel S, Berthier P, Luikart G (2002) Detecting wildlife poaching: identifying the origin of individuals with Bayesian assignment tests and multilocus genotypes. Conserv Biol 16:650–659CrossRefGoogle Scholar
  32. McMeel OM, Hoey EM, Ferguson A (2001) Partial nucleotide sequences, and routine typing by polymerase chain reaction-restriction fragment length polymorphism, of the brown trout (Salmo trutta) lactate dehydrogenase, LDH-C1*90 and *100 alleles. Mol Ecol 10:29–34PubMedCrossRefGoogle Scholar
  33. Nielsen EE, Bach LA, Kotlicki P (2006) Hybridlab (version 1.0): a program for generating simulated hybrids from population samples. Mol Ecol Notes 6:971–973CrossRefGoogle Scholar
  34. O’Reilly PT, Hamilton LC, McConnell SK, Wright JM (1996) Rapid analysis of genetic variation in Atlantic salmon (Salmo salar) by PCR multiplexing of dinucleotids and tetranucleotide microsatellites. Can J Fish Aquat Sci 53:2292–2298CrossRefGoogle Scholar
  35. Paetkau D, Slade R, Burden M, Estoup A (2004) Genetic assignment methods for the direct, real-time estimation of migration rate: a simulation-based exploration of accuracy and power. Mol Ecol 13:55–65PubMedCrossRefGoogle Scholar
  36. Paterson S, Piertney SB, Knox D, Gilbey J, Verspoor E (2004) Characterization and PCR multiplexing of novel highly variable tetranucleotide Atlantic salmon (Salmo salar L.) microsatellites. Mol Ecol Notes 4:160–162CrossRefGoogle Scholar
  37. Piry S, Alapetite A, Cornuet JM, Paetkau D, Baudouin L, Estoup A (2004) GeneClass2: a software for genetic assignment and first-generation migrant detection. J Hered 95:536–539PubMedCrossRefGoogle Scholar
  38. Poteaux C, Berrebi P, Bonhomme J (2001) Allozymes, mtDNA and microsatellites study introgression in a stocked trout population in France. Rev Fish Biol Fisher 10:281–292CrossRefGoogle Scholar
  39. Presa P, Guyomard R (1996) Conservation of microsatellites in three species of salmonids. J Fish Biol 49:1326–1329Google Scholar
  40. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedGoogle Scholar
  41. Rannala B, Mountain JL (1997) Detecting immigration by using multilocus genotypes. Proc Natl Acad Sci USA 94:9197–9201PubMedCrossRefGoogle Scholar
  42. Raymond M, Rousset F (1995) Genepop (ver. 3.3): a population genetics software for exact test and ecumenicism. J Hered 86:248–249Google Scholar
  43. Rhymer JM, Simberloff D (1996) Extinction by hybridization and introgression. Annu Rev Ecol Syst 27:83–109CrossRefGoogle Scholar
  44. Slettan A, Olsaker I, Lie Ø (1995) Atlantic salmon, Salmo salar, microsatellites at the SSOSL25, SSOSL85, SSOSL311, SSOSL417 loci. Anim Genet 26:281–282PubMedGoogle Scholar
  45. Slettan A, Olsaker I, Lie Ø (1996) Polymorphic Atlantic salmon (Salmo salar L.) microsatellites at the SSOSL438, SSOSL439 and SSOSL444 loci. Anim Genet 27:57–58PubMedCrossRefGoogle Scholar
  46. Vähä 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
  47. Ward RD, Woodwark M, Skibinski DOF (1994) A comparison of genetic diversity levels in marine, fresh-water, and anadromous fishes. J Fish Biol 44:213–232CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  • Nuria Sanz
    • 1
  • Rosa M. Araguas
    • 1
  • Raquel Fernández
    • 1
  • Manuel Vera
    • 1
  • José-Luis García-Marín
    • 1
  1. 1.Laboratori d’Ictiologia GenèticaUniversitat de GironaGironaSpain

Personalised recommendations