Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data

Genetics

Volumn 144, Issue 4, 1996, Pages 2001-2014

  Cornuet, Jean Marie ^a,c,d   Luikart, Gordon ^b,c  

^a CNRS   (France)

^b UNIVERSITY OF MONTANA   (United States)

^c LA TROBE UNIVERSITY   (Australia)

^d CEMAGREF   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER SIMULATION; GENE LOCUS; GENETIC VARIABILITY; HETEROZYGOSITY; POPULATION GENETICS; PRIORITY JOURNAL;

ALLELES; ANIMALS; GENE FREQUENCY; GENETICS, POPULATION; HUMANS; MODELS, GENETIC; MODELS, THEORETICAL;

EID: 0030478757     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (64)

1. ALLENDORF, F. W., 1986 Genetic drift and the loss of alleles vs. heterozygosity. Zoo Biol. 5: 181-190.
2. BONNELL, M. L., and R. K. SELANDER, 1974 Elephant seals: genetic variation and near extinction. Science 184: 908-909.
3. BRYANT, E. H., S. A. MCCOMMAS and L. M. COMBS, 1986 The effect of an experimental bottleneck upon quantitative genetic variation in the housefly. Genetics 114: 1191-211.
4. CARSON, H. L., 1959 Genetic conditions which promote or retard the formation of species. Cold Springs Harb. Symp. Quant. Biol. 24: 87-105.
5. CARSON, H. L., 1971 Speciation and the founder principle. Stadler Genet. Symp. 3: 51-70.
6. CARSON, H. L., 1990 Increased genetic variation after a population bottleneck. Trends Ecol. Evol. 5: 228-230.
7. GARSON, H. L., 1992 Genetic changes after colonization. Geojournal 28: 297-302.
8. CHAKRABORTY, R., and L. JIN, 1992 Heterozygote deficiency, population substructure and their implications in DNA fingerprinting. Hum. Genet. 88: 267-272.
9. CHAKRABORTY, R., and M. NEI, 1977 Bottleneck effects on average heterozygosity and genetic distance with the stepwise mutation model. Evolution 31: 347-356.
10. DEKA, R., R. CHAKRABORTY and R. E. FERRELL, 1991 A population genetic study of six VNTR loci in three ethnically defined populations. Genomics 11: 83-92.
11. DENNISTON, C., 1978 Small population size and genetic diversity: implications for endangered species, pp. 281-289 in Endangered Birds: Management Techniques for Presenting Threatened Species, edited by S. A. TEMPLE. University of Wisconsin Press, Madison, WI.
12. DINNERSTEIN, E., and G. F. MCCRACKEN, 1990 Endangered one horned Rhinoceros carry high levels of genetic variation. Conserv. Biol. 4: 417-422.
13. DI RIENZO, A., A. C. PETERSON, J. C. GARZA, A. M. VALDES, M. SLATKIN et al., 1994 Mutational processes of simple sequence repeat loci in human populations. Proc. Natl. Acad. Sci. USA 91: 3166-3170.
14. ESTOUP, A., M. SOLIGNAC, J. M. CORNUET and A. SCHOLL, 1995a Genetic differentiation of continental and island populations of Bombus terrestris (Hymenoptera, Apidae) in Europe. Mol. Ecol. 5: 19-31.
15. ESTOUP, A., C. TAILLEZ, J. M. CORNUET and M. SOLIGNAC, 1995b Size homoplasy and mutational processes of interrupted microsatellites in two bee species, Apis mellifera and Bombus terrestris (Apidae). Mol. Biol. Evol. 12: 1074-1084.
16. ESTOUP, A., L. GARNERY, M. SOLIGNAC and J. M. CORNUET 1995c Microsatellite variation in honey bee (Apis mellifera L.) populations: hierarchical genetic structure and test of the infinite allele and stepwise mutation models. Genetics 140: 679-695.
17. EWENS, W. J., 1972 The sampling theory of selectively neutral alleles. Theor. Popul. Biol. 3: 87-112.
18. EWENS, W. J., and J. H. GILLESPIE, 1974 Some simulation results for the neutral allele model with interpretations. Theor. Popul. Biol. 6: 35-57.
19. FRANKEL, O. H., and M. E. SOULÉ, 1981 Conservation and Evolution, Cambridge University Press, Cambridge.
20. FRANKHAM, R., 1995a Inbreeding depression: a threshold effect. Conserv. Biol. 9: 792-799.
21. FRANKHAM, R., 1995b Conservation genetics. Annu. Rev. Genet. 29: 305-327.
22. GOODNIGHT, C. J., 1987 On the effect of founder events on epistatic genetic variance. Evolution 41: 80-91.
23. GOTTELLI, D., C. SILLERO ZUBIRI, G. D. APPLEBAUM, M. S. ROY, D. J. GIRMAN et al., 1994 Molecular genetics of the most endangered canid: the Ethiopian wolf. Mol. Ecol. 3: 301-312.
24. HARRISON, R. G., 1991 Molecular changes at speciation. Annu. Rev. Ecol. Syst. 22: 281-308.
25. HEDRICK, R. W., and P. S. MILLER, 1992 Conservation genetics: techniques and fundamentals. Ecol. Appl. 2: 30-46.
26. HOWARD, D. J., 1993 Small populations, inbreeding, and speciation, pp. 118-142 in The Natural History of Inbreeding and Outbreeding, edited by N. W. THORNHILL. University of Chicago Press, Chicago.
27. HUDSON, R. R., 1990 Gene genealogies and the coalescent process, pp. 1-42 in Oxford Survey in Evolutionnary Biology, Vol. 7, edited by D. FUTUYAMA and J. ANTONOVICS. Oxford Uniersity Press, Oxford.
28. JIMINEZ, J. A., D. A. HUGHES, G. ALAKS, G. GRAHAM and R. C. LACY, 1994 An experimental study of inbreeding depression in a natural habitat. Science 266: 271-273.
29. KANESHIRO, K. Y., 1976 Ethological isolation and phylogeny in the planitibia subgroup of Hawaiian drosophila. Evolution 30: 740-745.
30. KANESHIRO, K. Y., 1980 Sexual isolation speciation and the direction of evolution. Evolution 34: 437-444.
31. KARL, S. A., and J. C. AVISE, 1992 Balancing selection at allozyme loci in oysters: implications from nuclear RFLPs. Science 256: 100-102.
32. KIMURA, M., and J. F. CROW, 1964 The number of alleles that can be maintained in a finite population. Genetics 49: 725-738.
33. KIMURA, M., and T. OHTA, 1975 Distribution of allelic frequencies in a finite population under stepwise production of neutral alleles. Proc. Natl. Acad. Sci. USA 72: 2761-2764.
34. LANDE, R., 1994 Risk of population extinction from fixation of new deleterious mutations. Evolution 48: 1460-1469.
35. LYNCH, M., J. CONERY and J. BURGER, 1995 Mutation accumulation and the extinction of small populations. Am. Nat. 146: 489-518.
36. MARUYAMA T., and P. A. FUERST, 1984 Population bottlenecks and non-equilibrium models in population genetics. II. Allele numbers when populations evolve from zero variability. Genetics 111: 675-689.
37. MARUYAMA T., and P. A. FUERST, 1985 Population bottlenecks and non equilibrium models in population genetics. II. Number of alleles in a small population that was formed by a recent bottleneck. Genetics 111: 675-689.
38. MAYR, E., 1954 Change of genetic environment and evolution, pp. 157-180 in Evolution As Process, edited by J. HUXLEY, A. C. HARDY and E. B. FORD. Allen and Unwin, London.
39. MENKIN, S. B. J., 1987 Is extremely low heterozygosity level in Yponomeuta rorellus caused by bottlenecks? Evolution 41: 630-637.
40. MILLS, S. L., and P. E. SMOUSE, 1994 Demographic consequences of inbreeding in remnant populations. Am. Nat. 144: 412-431.
41. NEI, M., 1978 Molecular Evolutionary Genetics. Columbia University Press, New York.
42. NEI, M., T. MARUYAMA and R. CHAKRABORTY, 1975 The bottleneck effect and genetic variability in populations. Evolution 29: 1-10.
43. O'BRIEN, S. J., and J. F. EVERMAN, 1988 Interactive influences of infectious disease and genetic diversity in natural populations. Trends Ecol. Evol. 3: 254-259.
44. O'BRIEN, S. J., D. E. WILDT, M. BUSH, T. M. CARO, C. FITZGIBBON et al., 1987 East African cheetahs: evidence for two population bottlenecks? Proc. Natl. Acad. Sci. USA 84: 508-511.
45. OHTA, T., and M. KIMURA, 1973 A model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a finite population. Genet. Res. Camb. 22: 201-204.
46. PEMBERTON, J. M., and R. H. SMITH, 1985 Lack of biochemical polymorphism in British fallow deer. Heredity 55: 199-207.
47. PIMM, S. L., J. L. GITTLEMAN, G. F. MCCRACKEN and M. E. GILPIN, 1989 Plausible alternatives to bottlenecks to explain reduced genetic diversity. Trends Ecol. Evol. 4: 176-178.
48. POGSON, G. H., K. A. MESA and R. G. BOUTILIER, 1995 Genetic population structure and gene flow in the Atlantic cod: a comparison of allozyme and nuclear RFLP loci. Genetics 139: 375-385.
49. RALLS, K., J. D. BALLOU and A. TEMPLETON, 1988 Estimates of lethal equivalents and the cost of inbreeding in mammals. Conserv. Biol. 2: 185-193.
50. RANDI, E., and M. APOLLONIO, 1988 Low biochemical variability in European fallow deer (Dama dama L.): natural bottlenecks and the effects of domestication. Heredity 61: 405-410.
51. ROGERS, A. R., and H. HARPENDING, 1992 Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol. 9: 552-569.
52. SHRIVER, M. D., L. JIN, R. CHAKRABORTY and E. BOERWINKLE, 1993 VNTR allele frequency distributions under the stepwise mutation model a computer simulation approach. Genetics 134: 983-993.
53. SING, C. F., G. J. BREWER and B. THIRTLE, 1973 Inherited biochemical variation in Drosophila melanogaster: noise or signal? Genetics 75: 381-404.
54. TAJIMA, F., 1983 Evolutionary relationship of DNA sequences in finite populations. Genetics 105: 437-460.
55. TAYLOR, A. C., W. B. SHERWIN and R. K. WAYNE, 1994 Genetic variation of microsatellite loci in a bottlenecked species: the hairy nosed wombat (Lasiorhinus krefftii). Mol. Ecol. 3: 277-290.
56. TEMPLETON, A. R., 1980 Modes of speciation and inferences based on genetic distances. Evolution 34: 719-729.
57. THORNTON, I. W. B., 1992 Krakatau: a century of changes. GeoJournal 28: 83-102.
58. VALDES, A. M., M. SLATKIN and N. B. FREINER, 1993 Allele frequencies at microsatellite loci: the stepwise mutation model revisited. Genetics 133: 737-749.
59. VRIJENHOEK, R. C., 1994 Genetic diversity and fitness in small populations, pp. 37-53 in Conservation Genetics, edited by V. LOESCHCKE, J. TOMIUK and S. K. JAIN. Switzerland Birkhauser Verlag, Basel.
60. WATT, W. B., 1977 Adaptation at specific loci. II. Demographic and biochemical elements in the maintenance of the Colias PGI polymorphism. Genetics 103: 691-724.
61. WATTERSON, G. A., 1978 The homozygosity test of neutrality. Genetics 88: 405-417.
62. WATTERSON, G. A., 1984 Allele frequencies after a bottleneck. Theor. Popul. Biol. 26: 387-407.
63. WATTERSON, G. A., 1986 The homozygosity test after a change in population size. Genetics 112: 899-907.
64. ZOUROS, E., 1979 Mutation rates, population sizes and amounts of electrophoretic variation of enzyme loci in natural populations. Genetics 92: 623-646.