Algorithms for selecting informative marker panels for population assignment

Journal of Computational Biology

Volumn 12, Issue 9, 2005, Pages 1183-1201

  Rosenberg, Noah A ^a  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

Ancestry inference; Informativeness; Microsatellites; Population structure

Indexed keywords

ACCURACY; ALGORITHM; ARTICLE; CARP; CAT; CHICKEN; DOG; FLY; GENE FREQUENCY; GENE LOCUS; GENOTYPE; HUMAN; MAIZE; MARKER GENE; MULTIVARIATE ANALYSIS; NONHUMAN; PRIORITY JOURNAL; PROBABILITY; SIMULATION;

ALGORITHMS; ALLELES; ANIMALS; COMPUTATIONAL BIOLOGY; DOGS; GENE FREQUENCY; GENETIC MARKERS; GENETICS, POPULATION; HUMANS; MICROSATELLITE REPEATS; MODELS, GENETIC; MULTIVARIATE ANALYSIS;

CANIS FAMILIARIS; CYPRINUS CARPIO; ZEA MAYS;

EID: 28744455932     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2005.12.1183     Document Type: Article

References (47)

1. Alaska Department of Fish and Game. 2000. SPAM Version 3.2: User's Guide, Alaska Department of Fish and Game, Anchorage.
2. Anderson, E.G., and Thompson, E.A. 2002. A model-based method for identifying species hybrids using multilocus genetic data. Genetics 160, 1217-1229.
3. Ayres, K.L., and Balding, D.J. 1998. Measuring departures from Hardy-Weinberg; A Markov chain Monte Carlo method for estimating the inbreeding coefficient. Heredity 80, 769-777.
4. Bamshad, M.J., Wooding, S., Watkins, W.S., Ostler, C.T., Batzer, M.A., and Jorde, L.B. 2003. Human population genetic structure and inference of group membership. Am. J. Human Genet. 72, 578-589.
5. Banks, M.A., and Eichert, W. 2000. WHICHRUN (version 3.2): A computer program for population assignment of individuals based on multilocus genotype data. J. Hered. 91, 87-89.
6. Banks, M.A., Eichert, W., and Olsen, J.B. 2003. Which genetic loci have greater population assignment power? Bioinformatics 19, 1436-1438.
7. Baudouin, L., Piry, S., and Cornuet, J.M. 2004. Analytical Bayesian approach for assigning individuals to populations. J. Hered. 95, 217-224.
8. Beaumont, M., Barratt, E.M., Gottelli, D., Kitchener, A.C., Daniels, M.J., Pritchard, J.K., and Bruford, M.W. 2001. Genetic diversity and introgression in the Scottish wildcat. Mol. Ecol. 10, 319-336.
9. Bernatchez, L., and Duchesne, P. 2000. Individual-based genotype analysis in studies of parentage and population assignment: How many loci, how many alleles? Can. J. Fish. Aquat. Sci. 57, 1-12.
10. Buchanan, F.C., Adams, L.J., Littlejohn, R.P., Maddox, J.F., and Crawford, A.M. 1994. Determination of evolutionary relationships among sheep breeds using microsatellites. Genomics 22, 397-403.
11. Campbell, D., Duchesne, P., and Bernatchez, L. 2003. AFLP utility for population assignment studies: Analytical investigation and empirical comparison with microsatellites. Mol. Ecol. 12, 1979-1991.
12. Collins-Schramm, H.E., Phillips, C.M., Operario, D.J., Lee, J.S., Weber, J.L., Hanson, R.L., Knowler, W.C., Cooper, R., Li, H., and Seldin, M.F. 2002. Ethnic-difference markers for use in mapping by admixture linkage disequilibrium. Am. J. Human Genet. 70, 737-750.
13. Cornuet, J.-M., Piry, S., Luikart, G., Estoup, A., and Solignac, M. 1999. New methods employing multilocus genotypes to select or exclude populations as origins of individuals. Genetics 153, 1989-2000.
14. David, L., Rosenberg, N.A., Lavi, U., Feldman, M.W., and Hillel, J. 2005. Genetic diversity and population structure inferred from the partially duplicated genome of Cyprinus carpio L. Submitted.
15. Davies, N., Villabianca, F.X., and Roderick, G.K. 1999. Determining the source of individuals: Multilocus genotyping in nonequilibrium population genetics. Trends Ecol. Evol. 14, 17-21.
16. Dean, M., Stephens, J.C., Winkler, C., Lomb, D.A., Ramsburg, M., Boaze, R., Stewart, C., Charbonneau, L., Goldman, D., Albaugh, B.J., Goedert, J.J., Beasley, R.P., Hwang, L.-Y., Buchbinder, S., Weedon, M., Johnson, P.A., Eichelberger, M., and O'Brien, S.J. 1994. Polymorphic admixture typing in human ethnic populations. Am. J. Human Genet. 55, 788-808.
17. Durrett, R. 1996. Probability: Theory and Examples, 2nd ed., Duxbury, Belmont, CA.
18. Edwards, A.W.F. 2003. Human genetic diversity: Lewontin's fallacy. BioEssays 25, 798-801.
19. Gibbons, J.D. 1985. Nonparametric Statistical Inference, 2nd ed., Marcel Dekker, New York.
20. Goldstein, D.B., and Schlötterer, C., eds. 1999. Microsatellites: Evolution and Applications, Oxford University Press, Oxford, UK.
21. Guinand, B., Topchy, A., Page, K.S., Burnham-Curtis, M.K., Punch, W.F., and Scribner, K.T. 2002. Comparisons of likelihood and machine learning methods of individual classification. J. Hered. 93, 260-269.
22. Hansen, M.M., Kenchington, E., and Nielsen, E.E. 2001. Assigning individual fish to populations using microsatellite DNA markers. Fish Fish. 2, 93-112.
23. Irion, D.N., Schaffer, A.L., Famula, T.R., Eggleston, M.L., Hughes, S.S., and Pedersen, N.C. 2003. Analysis of genetic variation in 28 dog breed populations with 100 microsatellite markers. J. Hered. 94, 81-87.
24. Kauer, M., Dieringer, D., and Schlötterer, C. 2003. Nonneutral admixture of immigrant genotypes in African Drosophila melanogaster populations from Zimbabwe. Mol. Biol. Evol. 20, 1329-1337.
25. Koskinen, M.T., Nilsson, J., Veselov, A., Potutkin, A.G., Ranta, E., and Primmer, C.R. 2002. Microsatellite data resolve phylogeographic patterns in European grayling, Thymallus thymallus, Salmonidae. Heredity 88, 391-401.
26. Lewis, P.O., and Zaykin, D. 2001. GDA (Genetic Data Analysis): Computer program for the analysis of allelic data (version 1.0 d16c). hydrodidyon.eeb.uconn.edu/people/plewis
27. Lowe, A.L., Urquhart, A., Foreman, L.A., and Evett, I.W. 2001. Inferring ethnic origin by means of an STR profile. Forensic Sci. Int. 119, 17-22.
28. Manel, S., Berthier, P., and Luikart, G. 2002. Detecting wildlife poaching: Identifying the origin of individuals with Bayesian assignment tests and multilocus genotypes. Conserv. Biol. 16, 650-659.
29. Manel, S., Gaggiotti, O.E., and Waples, R.S. 2005. Assignment methods: Matching biological questions with appropriate techniques. Trends Ecol. Evol. 20, 136-142.
30. Matsuoka, Y., Vigouroux, Y., Goodman, M.M., Sanchez, G.J., Buckler, E., and Doebley, J. 2002. A single domestication for maize shown by multilocus microsatellite genotyping. Proc. Natl. Acad. Sci. USA 99, 6080-6084.
31. Nei, M. 1987. Molecular Evolutionary Genetics, Columbia University Press, New York.
32. Paetkau, D., Calvert, W., Stirling, I., and Strobeck, C. 1995. Microsatellite analysis of population structure in Canadian polar bears. Mol. Ecol. 4, 347-354.
33. Paetkau, D., Slade, R., Burden, M., and 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, 55-65.
34. Pfaff, C.L., Barnholtz-Sloan, J., Wagner, J.K., and Long, J.C. 2004. Information on ancestry from genetic markers. Genet. Epidemiol. 26, 305-315.
35. Primmer, C.R., Koskinen, M.T., and Piironen, J. 2000. The one that did not get away: Individual assignment using microsatellite data detects a case of fishing competition fraud. Proc. R. Soc. Lond. B 267, 1699-1704.
36. Pritchard, J.K., Stephens, M., and Donnelly, P. 2000. Inference of population structure using multilocus genotype data. Genetics 155, 945-959.
37. Risch, N., Burchard, E., Ziv, E., and Tang, H. 2002. Categorization of humans in biomedical research: Genes, race and disease. Genome Biol. 3, comment2007.
38. Rosenberg, N.A., Burke, T., Elo, K., Feldman, M.W., Freidlin, P.J., Groenen, M.A.M., Hillel, J., Mäki-Tanila, A., Tixier-Boichard, M., Vignal, A., Wimmers, K., and Weigend, S. 2001. Empirical evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds. Genetics 159, 699-713.
39. Rosenberg, N.A., Li, L., Ward, R., and Pritchard, J.K. 2003. Informativeness of genetic markers for inference of ancestry. Am. J. Human Genet. 73, 1402-1422.
40. Rosenberg, N.A., Pritchard, J.K., Weber, J.L., Cann, H.M., Kidd, K.K., Zhivotovsky, L.A., and Feldman, M.W. 2002. Genetic structure of human populations. Science 298, 2381-2385.
41. Rudin, W. 1976. Principles of Mathematical Analysis, 3rd ed., McGraw-Hill, New York.
42. Serfling, R.J. 1980. Approximation Theorems of Mathematical Statistics, Wiley, New York.
43. 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. Human Genet. 60, 957-964.
44. Turakulov, R., and Easteal, S. 2003. Number of SNPS loci needed to detect population structure. Human Hered. 55, 37-45.
45. Waser, P.M., and Strobeck, C. 1998. Genetic signatures of interpopulation dispersal. Trends Ecol. Evol. 13, 43-44.
46. Weir, B.S. 1996. Genetic Data Analysis II, Sinauer, Sunderland, MA.
47. Ziv, E., and Burchard, E.G. 2003. Human population structure and genetic association studies. Pharmacogenomics 4, 431-441.