Estimation of population growth or decline in genetically monitored populations

Genetics

Volumn 164, Issue 3, 2003, Pages 1139-1160

  Beaumont, Mark A ^a  

^a Sch of Anim and Microbial Sciences   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALLELE; ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; BIRD; CALCULATION; COMPARATIVE STUDY; COMPUTER SIMULATION; DROSOPHILA; ESOCIDAE; GENE FREQUENCY; GENE LOCUS; GENE MUTATION; GENEALOGY; GENETICS; MONTE CARLO METHOD; NONHUMAN; PARAMETER; POPULATION DENSITY; POPULATION DYNAMICS; POPULATION GENETICS; POPULATION GROWTH; POPULATION RESEARCH; POPULATION SIZE; PRIORITY JOURNAL; PROBABILITY; SAMPLE SIZE; SAMPLING; SIMULATION; STATISTICAL MODEL; TECHNIQUE;

ALLELES; ANIMALS; BAYES THEOREM; BIRDS; COMPUTER SIMULATION; DROSOPHILA; ESOCIDAE; GENE FREQUENCY; MARKOV CHAINS; MODELS, GENETIC; MONTE CARLO METHOD; POPULATION DYNAMICS; POPULATION GROWTH;

ANIMALIA; AVES; ESOCIDAE;

EID: 0043210659     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (59)

1. e from temporally spaced samples. Genetics 156: 2109-2118.
2. AUSTERLITZ, F., and E. HEYER, 1998 Social transmission of reproductive behavior increases frequency of inherited disorders in a young-expanding population. Proc. Natl. Acad. Sci. USA 95: 15140-15144.
3. BEAUMONT, M. A., 1999 Detecting population expansion and decline using microsatellites. Genetics 153: 2013-2029.
4. BEAUMONT, M. A., 2001 Conservation genetics, pp. 779-812 in The Handbook of Statistical Genetics, edited by D. J. BALDING, M. BISHOP and C. CANNINGS. Wiley, Chichester, UK.
5. BEERLI, P., and J. FELSENSTEIN, 2001 Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proc. Natl. Acad. Sci. USA 98: 4563-4568.
6. BEGON, M., C. B. KRIMBAS and M. LOUKAS, 1980 The genetics of Drosophila subobscura populations. XV. Effective size of a natural population estimated by three independent methods. Heredity 45: 335-350.
7. BERTHIER, P., M. A. BEAUMONT, J.-M. CORNUET and G. LUIKART, 2002 Likelihood-based estimation of the effective population size using temporal changes in allele frequencies: a genealogical approach. Genetics 160: 741-751.
8. CABALLERO, A., 1994 Developments in the prediction of effective population size. Hereditary 73: 657-679.
9. CHIKHI, L., M. W. BRUFORD and M. A. BEAUMONT, 2001 Estimation of admixture proportions: a likelihood-based approach using Markov chain Monte Carlo. Genetics 158: 1347-1362.
10. CIOFI, C., M. A. BEAUMONT, I. R. SWINGLAND and M. W. BRUFORD, 1999 Genetic divergence and units for conservation in the Komodo dragon Varanus komodoensis. Proc. R. Soc. Lond. Ser. B 266: 2269-2274.
11. DONNELLY, P., and S. TAVARÉ, 1995 Coalescents and genealogical structure under neutrality. Annu. Rev. Genet. 29: 410-421.
12. DRUMMOND, A. J., G. K. NICHOLLS, A. G. RODRIGO and W. SOLOMON, 2002 Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 161: 1307-1320.
13. FEARNHEAD, P., and P. DONNELLY, 2001 Estimating recombination rates from population genetic data. Genetics 159: 1299-1318.
14. FRANKHAM, R., 1995 Conservation genetics. Annu. Rev. Genet. 29: 305-327.
15. Fu, Y. X., 2001 Estimating mutation rate and generation time from longitudinal samples of DNA sequences. Mol. Biol. Evol. 18: 620-626.
16. GELMAN, A., J. B. CARLIN, H. S. STERN and D. B. RUBIN, 1995 Bayesian Data Analysis. Chapman & Hall, London.
17. GREEN, P. J., 1995 Reversible jump Markov chain Monte Carlo computation and Bayesian model determination. Biometrika 82: 711-732.
18. GRIFFITHS, R. C., and S. TAVARÉ, 1994a Simulating probability distributions in the coalescent. Theor. Popul. Biol. 46: 131-159.
19. GRIFFITHS, R. C., and S. TAVARÉ, 1994b Sampling theory for neutral alleles in a varying environment. Philos. Trans. R. Soc. Lond. Ser. B Biol. Sci. 344: 403-410.
20. GRIFFITHS, R. C., and S. TAVARÉ, 1994c Ancestral inference in population genetics. Stat. Sci. 9: 307-319.
21. GROOMBRIDGE, J. J., C. G. JONES, M. W. BRUFORD and R. A. NICHOLS, 2000 'Ghost' alleles of the Mauritius kestrel. Nature 403: 616.
22. HILL, W. G., 1981 Estimation of effective population size from data on linkage disequilibrium. Genet. Res. 38: 209-216.
23. KRIMBAS, C. B., and S. TSAKAS, 1971 The genetics of Dacus oleae. V. Changes of esterase polymorphism in a natural population following insecticide control - Selection or drift? Evolution 25: 454-460.
24. KUHNER, M. K., J. YAMATO and J. FELSENSTEIN, 1995 Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling. Genetics 140: 1421-1430.
25. LANDE, R., 1998 Anthropogenic, ecological and genetic factors in extinction and conservation. Res. Popul. Ecol. 40: 259-269.
26. LANGLEY, C. H., D. B. SMITH and F. M. JOHNSON, 1978 Analysis of linkage disequilibrium between allozyme loci in natural populations of Drosophila melanogaster. Genet. Res. 32: 215-229.
27. LAURIE-ALHLBERG, C. C., and B. S. WEIR, 1979 Allozyme variation and linkage disequilibrium in some laboratory populations of Drosophila melanogaster. Genetics 92: 1295-1314.
28. LEWONTIN, R. C., and J. KRAKAUER, 1973 Distribution of gene frequency as a test of the theory of selective neutrality of polymorphisms. Genetics 74: 175-195.
29. LUIKART, G., and J. M. CORNUET, 1999 Estimating the effective number of breeders from heterozygote excess in progeny. Genetics 151: 1211-1216.
30. LYNCH, M., J. CONERY and R. BURGER, 1995 Mutation accumulation and the extinction of small populations. Am. Nat. 146: 489-518.
31. MARJORAM, P., and P. DONNELLY, 1997 Human demography and the time since mitochondrial Eve, pp. 107-131 in Progress in Population Genetics and Human Evolution, edited by P. DONNELLY and S. TAVARÉ. Springer-Verlag, New York.
32. MILLER, L. M., and A. R. KAPUSCINSKI, 1997 Historical analysis of genetic variation reveals low effective population size in a northern pike (Esox lucius) population. Genetics 147: 1249-1258.
33. NEI, M., and F. TAJIMA, 1981 Genetic drift and estimation of effective population size. Genetics 98: 625-640.
34. NICHOLS, R. A., M. W. BRUFORD and J. J. GROOMBRIDGE, 2001 Sustaining genetic variation in a small population: evidence from the Mauritius kestrel. Mol. Ecol. 10: 593-602.
35. NIELSEN, R., and J. WAKELEY, 2001 Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics 158: 885-896.
36. NIELSEN, R., J. L. MOUNTAIN, J. P. HUELSENBECK and M. SLATKIN, 1998 Maximum-likelihood estimation of population divergence times and population phylogeny in models without mutation. Evolution 52: 669-677.
37. NORDBORG, M., 1997 Structured coalescent processes on different time scales. Genetics 146: 1501-1514.
38. O'NEILL, P. D., D. J. BALDING, N. G. BECKER, M. EEROLA and D. MOLLISON, 2000 Analyses of infections disease data from household outbreaks by Markov chain Monte Carlo methods. Appl. Stat. 49: 517-542.
39. O'RYAN, C., E. H. HARLEY, M. W. BRUFORD, M. BEAUMONT, R. K. WAYNE et al., 1998 Microsatellite analysis of genetic diversity in fragmented South African buffalo populations. Anim. Conserv. 1: 85-94.
40. POLLAK, E., 1983 A new method for estimating the effective population size from allele frequency changes. Genetics 104: 531-548.
41. PRITCHARD, J. K., M, STEPHENS and P. DONNELLY, 2000 Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
42. PUDOVKIN, A. I., D. V. ZAYKIN and D. HEDGECOCK, 1996 On the potential for estimating the effective number of breeders from heterozygote-excess in progeny. Genetics 144: 383-387.
43. RICE, J. A., 1995 Mathematical Statistics and Data Analysis. Duxbury Press, Belmont, CA.
44. RODRIGO, A. G., E. G. SHPAER, E. L. DELWART, A. K. N. IVERSEN, M. V. GALLO et al., 1999 Coalescent estimates of HIV-1 generation time in vivo. Proc. Natl. Acad. Sci. USA 96: 2187-2191.
45. SACCHERI, I., M. KUUSSAARI, M. KANKARE, P. VIKMAN, W. FORTELIUS et al., 1998 Inbreeding and extinction in a butterfly metapopulation. Nature 392: 491-494.
46. SACCHERI, I. J., I. J. WILSON, R. A. NICHOLS, M. W. BRUFORD and P. M. BRAKEFIELD, 1999 Inbreeding of bottlenecked butterfly populations: estimation using the likelihood of changes in marker allele frequencies. Genetics 151: 1053-1063.
47. SLATKIN, M., 1996 Gene genealogies within mutant allelic classes. Genetics 145: 579-587.
48. STEPHENS, M., 2001 Inference under the coalescent, pp. 213-238 in The Handbook of Statistical Genetics, edited by D. J. BALDING, M. BISHOP and C. CANNINGS. Wiley, Chichester, UK.
49. STEPHENS, M., and P. DONNELLY, 2000 Inference in molecular population genetics (with discussion). J. R. Stat. Soc. B 62: 605-655.
50. STORZ, J. F., and M. A. BEAUMONT, 2002 Testing for genetic evidence of population expansion and contraction: an empirical analysis of microsatellite DNA variation using a hierarchical Bayesian model. Evolution 56: 154-166.
51. TAVARÉ, S., 1984 Lines-of-descent and genealogical processes, and their application in population genetics models. Theor. Popul. Biol. 26: 119-164.
52. TIERNEY, L., 1996 Introduction to general state-space Markov chain theory, pp. 59-74 in Markov Chain Monte Carlo in Practice, edited by W. R. GILKS, S. RICHARDSON and D. J. SPIEGELHALTER. Chapman & Hall, London.
53. WAKELEY, J., 1999 Nonequilibrium migration in human history. Genetics 153: 1863-1871.
54. WAKELEY, J., and N. ALIACAR, 2001 Gene genealogies in a metapopulation. Genetics 159: 893-905.
55. WANG, J., 2001 A pseudo-likelihood method for estimating effective population size from temporally spaced samples. Genet. Res, 78: 243-257.
56. WANG, J., and M. C. WHITLOCK, 2003 Estimating effective population size and migration rates from genetic samples over space and time. Genetics 163: 429-446.
57. WAPLES, R. S., 1989 A generalized approach for estimating effective population size from temporal changes in allele frequency. Genetics 121: 379-392.
58. WILLIAMSON, E. G., and M. SLATKIN, 1999 Using maximum likelihood to estimate population size from temporal changes in allele frequencies. Genetics 152: 755-761.
59. WILSON, I. J., and D. J. BALDING, 1998 Genealogical inference from microsatellite data. Genetics 150: 499-510.