Individual-based genotype analysis in studies of parentage and population assignment: How many loci, how many alleles?

Canadian Journal of Fisheries and Aquatic Sciences

Volumn 57, Issue 1, 2000, Pages 1-12

  Bernatchez, Louis ^a   Duchesne, Pierre ^a  

^a UNIVERSITÉ LAVAL   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0034068865     PISSN: 0706652X     EISSN: None     Source Type: Journal    
DOI: 10.1139/f99-271     Document Type: Article

References (44)

1. Amos, B., Schlötterer, C., and Tautz, D. 1993. Social structure of pilot whales revealed by analytical DNA profiling. Science (Washington, D.C.), 260: 670-672.
2. Banks, M.A., Baldwin, B.A., and Hedgecock, D. 1996. Research on chinook salmon (Oncorhynchus tshawytscha) stock structure using microsatellite data. Bull. Natl. Res. Inst. Aquacult. 2(Suppl.): 5-9.
3. Bernatchez, L. 1995. A role for molecular systematics in defining evolutionarily significant units in fishes. In Evolution and aquatic ecosystem: defining units in population conservation. Edited by J.L. Nielsen. Am. Fish. Soc. Symp. 17: 114-132.
4. Bernatchez, L., and Wilson, C.C. 1998. Comparative phylogeography of nearctic and palearctic fishes. Mol. Ecol. 7: 465-452.
5. Bernatchez, L., Chouinard, A., and Lu, L. 1999. Integrating molecular genetics and ecology in studies of adaptive radiation: whitefish, Coregonus sp., as a case study. Biol. J. Linn. Soc. 68: 173-197.
6. Bowen, B.W., and Avise, J.C. 1995. Conservation genetics of marine turtles. In Conservation genetics: case histories from nature. Edited by J.C. Avise and J.L. Hamrick. Chapman and Hall, New York. pp. 190-237.
7. Carvalho, G.R., and Hauser, L. 1994. Molecular genetics and the stock concept in fisheries. Rev. Fish Biol. Fish. 4: 326-350.
8. Clapham, P.J., and Palsbøll, P.J. 1997. Molecular analysis of paternity shows promiscuous mating in female humpback whales (Megaptera novaeangliae, Borowski). Proc. R. Soc. Lond. Ser. B, Biol. Sci. 264: 95-98.
9. Colbourne, J.K., and Hebert, P.D.N. 1996. The systematics of North American Daphnia (Crustacea: Anomopoda): a molecular phylogenetic approach. Philos. Trans. R. Soc. Lond. B, Biol. Sci. 351: 349-360.
10. Davies, N., Villablanca, F.X., and Roderick, G.K. 1999. Determining the source of individuals: multilocus genotyping in nonequilibrium population genetics. Trends Ecol. Evol. 14: 17-21.
11. Dizon, A.E., Lockyer, C., Perrin, W.F., Demaster, D.P., and Sisson, J. 1992. Rethinking the stock concept: a phylogeographic approach. Conserv. Biol. 6: 24-36.
12. Estoup, A., and Angers, B. 1998. Microsatellites and minisatellites for molecular ecology: theoretical and empirical considerations. In Advances in molecular ecology. Edited by G.R. Carvalho. NATO Sciences Series, IOS Press, Amsterdam, The Netherlands, pp. 55-79.
13. Estoup, A., Gharbi, K., SanCristobal, M., Chevalet, C., Haffrey, P., and Guyomard, R. 1998. Parentage assignment using microsatellites in turbot (Scophtalmus maximus) and rainbow trout (Oncorhynchus mykiss) hatchery populations. Can. J. Fish. Aquat. Sci. 55: 715-725.
14. Ferguson, M.M., and Danzmann, R.G. 1998. Role of genetic markers in fisheries and aquaculture: useful tools or stamp collecting? Can. J. Fish. Aquat. Sci. 55: 1553-1563.
15. Foltz, D.W., and Hoogland, D.W. 1981. Analysis of the mating system in the black-tailed prairie dog (Cynomis ludovicianus) by likelihood of paternity. J. Mammal. 62: 706-712.
16. Fontaine, P.M., and Dodson, J.J. 1999. An analysis of the distribution of juvenile Atlantic salmon (Salmo salar) in nature as a function of relatedness using microsatellites. Mol. Ecol. 8: 189-198.
17. Hanken, J., and Sherman, P.W 1981. Multiple paternity in Belding's ground squirrel litters. Science (Washington, D.C.), 212: 351-353.
18. Herbinger, C.M., Doyle, R.W., Taggart, C.T., Lochmann, S.E., Wright, J.M., Brooker, A.L., and Cook, D. 1997. Family relationships and effective population size in a natural cohort of cod larvae. Can. J. Fish. Aquat. Sci. 54: 11-18.
19. Jones, A.G., and Avise, J.C. 1997. Microsatellite analysis of maternity and the mating system in the Gulf pipefish Syngnathus scovelli, a species with male pregnancy and sex-role inversal. Mol. Ecol. 6: 203-213.
20. Jones, A.G., Kvarnemo, C., Moore, G.I., Simmons, L.W., and Avise, J.C. 1998. Microsatellite evidence for monogamy and sex-biased recombinaition in the Western Australian seahorse Hippocampus angustus. Mol. Ecol. 7: 1497-1505.
21. Jordan, W.C., and Youngson, A.F. 1992. The use of genetic marking to assess the reproductive success of mature male Atlantic salmon parr (Salmo salar L.) under natural spawning conditions. J. Fish Biol. 41: 613-618.
22. Lu, G., and Bernatchez, L. 1999. Correlated trophic specialization and genetic divergence in sympatric lake whitefish ecotypes (Coregonus clupeaformis): support for the ecological speciation hypothesis. Evolution, 53: 1491-1505.
23. Marshall, T.C., Slate, J., Kruuk, L.E.B., and Pemberton, J.M. 1998. Statistical confidence for likelihood-based paternity inference in natural populations. Mol. Ecol. 7: 639-655.
24. Mayden, R.L. 1995. In Evolution and aquatic ecosystem: defining units in population conservation. Edited by J.L. Nielsen. Am. Fish. Soc. Symp. 17: 114-132.
25. Meagher, T.R., and Thompson, E. 1986. The relationship between single parent and parent pair genetic likelihoods in genealogy reconstruction. Theor. Popul. Biol. 29: 87-106.
26. Nielsen, E.E., Hansen, M.M., and Loeschcke, V. 1997. Analysis of microsatellite DNA from old scale samples of Atlantic salmon Salmo salar: a comparison of genetic composition over 60 years. Mol. Ecol. 6: 487-492.
27. O'Reilly, P.T., Herbinger, C., and Wright, J.M. 1998. Analysis of parentage determination in Atlantic salmon (Salmo salar) using microsatellites. Anim. Genet. 29: 363-370.
28. Paetkau, D., Calvert, W., Stirling, I., and Strobeck, C. 1995. Microsatellite analysis of population structure in Canadian polar bears. Mol. Ecol. 4: 347-354.
29. Palsbøll, P.J, Allen, J., Bérubé, M., Clapham, P.J., Feddersen, T.P., Hammond, P.S., Hudson, R.R., Jørgensen, H., Katona, S., Larsen, A.H., Larsen, F., Lien, J., Mattila, D.K., Sigurjònsson, J., Sears, R., Smith, T., Sponer, R., Stevick, P., and Øien, N. 1997. Genetic tagging of humpback whales. Nature (Lond.), 388: 767-769.
30. Rico, C., Kuhnlein, U., and Fitzgerald, G.J. 1992. Male reproductive tactics in the threespine stickleback - an evaluation by DNA fingerprinting. Mol. Ecol. 1: 79-87.
31. Roques, S., Duchesne, P., and Bernatchez, L. 1999. Potential of microsatellites for individual assignment: the North Atlantic redfish (genus Sebastes) species complex as a case study. Mol. Ecol. 8: 1703-1718.
32. Sancristobal, M., and Chevalet, C. 1997. Error tolerant parent identification from a finite set of individuals. Genet. Res. 70: 53-62.
33. Shriver, M.D., Smith, M.W., Jin, L., Marcini, A., Akey, J.M., Deka, R., and Ferrell, R.E. 1997. Ethnic-affiliation estimation by use of population-specific DNA markers. Am. J. Hum. Genet. 60: 957-964.
34. Smouse, P.E., and Chakraborty, R. 1986. The use of restriction fragmment length polymorphisms in paternity analysis. Am. J. Hum. Genet. 38: 918-939.
35. Smouse, P.E., and Chevillon, C. 1998. Analytical aspects of population-specific DNA fingerprinting for individuals. J. Hered. 89: 143-150.
36. Smouse, P.E., Spielman, R.S., and Park, M.-H. 1982. Multiple-locus allocation of individuals to groups as a function of the genetic variation within and differences among human populations. Am. Nat. 119: 445-463.
37. Stanley, H.F., Casey, S., Carnahan, J.M., Goodman, S., Harwood, J., and Wayne, R.K. 1996. Worldwide patterns of mitochondrial DNA differentiation in the harbor seal (Phoca vitulina). Mol. Biol. Evol. 13: 368-382.
38. Taylor, E.B., and Bentzen, P. 1993. Evidence for multiple origins and sympatric divergence of trophic ecotypes of smelt (Osmerus) in northeastern North America. Evolution, 47: 813-832.
39. Taylor, E.B., and McPhail, J.D. 1999. Evolutionary history of an adaptive radiation in sticklebacks (Gasterosteus) inferred from mitochondrial DNA variation. Biol. J. Linn. Soc. 66: 271-291.
40. Tessier, N., and Bernatchez, L. 1998. Contribution des differentes populations de ouananiches à la pêche sportive en lac pour les années 1994 à 1996. Rapport présenté par l'Université Laval à la Corporation de l'Activité Pêche Lac Saint-Jean (CLAP). Université Laval, Sainte-Foy, Qué.
41. Turgeon, J., Estoup, A., and Bernatchez, L. 1999. Species flock in the North American Great Lakes: molecular ecology of lake Nipigon ciscoes (Teleotei: Coregonidae: Coregonus). Evolution, 53: 1857-1871.
42. Utter, F., and Ryman, N. 1993. Genetic markers and mixed fisheries. Fisheries (Bethesda), 18: 11-21.
43. Ward, R.D., and Grewe, P.M. 1994. Appraisal of molecular genetic techniques in fisheries. Rev. Fish Biol. Fish. 4: 300-325.
44. Waser, P.M., and Strobeck, C. 1998. Genetic signatures of inter-population dispersal. Trends Ecol. Evol. 13: 43-44.