Comparative evaluation of a new effective population size estimator based on approximate Bayesian computation

Genetics

Volumn 167, Issue 2, 2004, Pages 977-988

  Tallmon, David A ^a,b   Luikart, Gordon ^a   Beaumont, Mark A ^b  

^a UNIVERSITÉ JOSEPH FOURIER   (France)

^b UNIVERSITY OF READING   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTICAL ERROR; ARTICLE; BAYES THEOREM; COMPARATIVE STUDY; CONSERVATION BIOLOGY; EFFECTIVE POPULATION SIZE; EVALUATION; EVOLUTION; GENE FREQUENCY; GENE LOCUS; POPULATION GENETICS; PRIORITY JOURNAL; STATISTICAL MODEL; STATISTICS;

BAYES THEOREM; COMPUTER SIMULATION; LEAST-SQUARES ANALYSIS; MODELS, GENETIC; POPULATION DENSITY; REPRODUCIBILITY OF RESULTS;

MARTES PENNANTI;

EID: 3142749747     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: 10.1534/genetics.103.026146     Document Type: Article

References (34)

1. e from temporally spaced samples. Genetics 156: 2109-2118.
2. BEAUMONT, M. A., 2003 Estimation of population growth or decline in genetically monitored populations. Genetics 164: 1139-1160.
3. BEAUMONT, M. A., W. ZHANG and D. J. BALDING, 2002 Approximate Bayesian computation in population genetics. Genetics 162: 2025-2035.
4. 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.
5. CROW, J. F., and C. DENNISTON, 1988 Inbreeding and variance effective population effective numbers. Evolution 42: 482-495.
6. CROW, J. F., and M. KIMURA, 1970 An Introduction to Population Genetics Theory. Harper & Row, New York.
7. FRANKHAM, R., 1995 Effective population size/adult population size ratios in wildlife: a review. Genet. Res. 16: 95-107.
8. Fu, Y.-X., and W.-H. LI, 1997 Estimating the age of the common ancestor of a sample of DNA sequences. Mol. Biol. Evol. 14: 195-199.
9. HARRIS, R. B., and F. W. ALLENDORF, 1989 Genetically effective population size of large mammals: an assessment of estimators. Conserv. Biol. 3: 181-191.
10. HILL, W. G., 1981 Estimation of effective population size from data on linkage disequilibrium. Genet. Res. 38: 209-216.
11. LANDE, R., 1995 Mutation and conservation. Conserv. Biol. 9: 782-791.
12. LOADER, C. R., 1996 Local likelihood density estimation. Ann. Stat. 24: 1602-1618.
13. LUIKART, G. H., J.-M. CORNUET and F. W. ALLENDORF, 1999 Temporal changes in allele frequencies provide estimators of population bottleneck size. Conserv. Biol. 13: 523-530.
14. LYNCH, M., J. CONERY and R. BURGER, 1995 Mutational meltdowns in sexual populations. Evolution 49: 1067-1080.
15. NEI, M., 1987 Molecular Evolutionary Genetics. Columbia University Press, New York.
16. NEI, M., and F. TAJIMA, 1981 Genetic drift and estimation of effective population size. Genetics 98: 625-640.
17. O'HAGAN, A., 1994 Bayesian Inference. Arnold, London.
18. PRITCHARD, J. K., M. T. SEIELSTAD, A. PEREZ-LEZAUN and M. W. FELDMAN, 1999 Population growth of human Y-chromosomes: a study of Y chromosome microsatellites. Mol. Biol. Evol. 16: 1791-1798.
19. R DEVELOPMENT CORE TEAM, 2003 R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna (http://www.R-project.org).
20. RICHARDS, C., and P. L. LEBERG, 1996 Evaluation of the effects of bottlenecks on changes in allele frequencies. Conserv. Biol. 10: 832-839.
21. SCHWARTZ, M. K., D. A. TALLMON and G. LUIKART, 1998 Review of DNA census and effective population size estimators. Anim. Conserv. 1: 293-299.
22. SHOEMAKER, J. S., I. PAINTER and B. S. WEIR, 1999 Bayesian statistics in genetics. Trends Genet. 15: 354-358.
23. SPENCER, C. C., J. E. NEIGEL and P. L. LEBERG, 2000 Experimental evaluation of the usefulness of microsatellite DNA for detecting demographic bottlenecks. Mol. Ecol. 9: 1517-1528.
24. STORZ, J. F., U. RAMAKRISHNAN and S. C. ALSERTS, 2002 Genetic effective size of a wild primate population: influence of current and historical demography. Evolution 56: 817-829.
25. TAVARÉ, S. J., D. J. BALDING, R. C. GRIFFITHS and P. DONNELLY, 1997 Inferring coalescence times from DNA sequence data. Genetics 145: 505-518.
26. TISHKOFF, S. A., R. VARKONYI, N. CAHINHINAN, S. ABBES and G. ARGYROPOULOS, 2001 Haplotype diversity and linkage disequilibrium at human G6PD: recent origin of alleles that confer malarial resistance. Science 293: 455-462.
27. VITALIS, R., and D. COUVET, 2001 Estimation of effective population size and migration rate from one- and two-locus identity measures. Genetics 157: 911-925.
28. WANG, J., 2001 A pseudo-likelihood method for estimating effective population size from temporally spaced samples. Genet. Res. 78: 243-257.
29. 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.
30. WAPLES, R. S., 1989 A generalized approach for estimating effective population size from temporal changes in allele frequency. Genetics 121: 379-391.
31. WAPLES, R. S., 1991 Genetic methods for estimating the effective size of cetacean populations, pp. 279-300 in Report of the International Whaling Commission, Special Issue 13, edited by A. R. HOEZEL. International Whaling Commission, Cambridge, UK.
32. WEIR, B. S., 1990 Genetic Data Analysis: Methods for Discrete Population Genetic Data. Sinauer, Sunderland, MA.
33. WEISS, G., and A. VON HAESELER, 1998 Inference of population history using a likelihood approach. Genetics 149: 1539-1546.
34. WILLIAMSON, E. G., and M. SLATKIN, 1999 Using maximum likelihood to estimate population size from temporal changes in allele frequencies. Genetics 152: 755-761.