Maximum-likelihood and Markov chain Monte Carlo approaches to estimate inbreeding and effective size from allele frequency changes

Genetics

Volumn 164, Issue 3, 2003, Pages 1189-1204

  Laval, Guillaume ^a   SanCristobal, Magali ^b   Chevalet, Claude ^b  

^a UNIVERSITY OF BERN   (Switzerland)

^b CEMAGREF   (France)

Author keywords

[No Author keywords available]

Indexed keywords

MICROSATELLITE DNA;

ACCURACY; ALGORITHM; ALLELE; ANALYTIC METHOD; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; COMPUTER SIMULATION; EFFECTIVE POPULATION SIZE; EVALUATION; FOUNDER EFFECT; GENE FREQUENCY; GENE LOSS; GENETIC DRIFT; GENETIC SELECTION; GENETIC VARIABILITY; GENETICS; GENOME ANALYSIS; INBREEDING; MARKER GENE; MAXIMUM LIKELIHOOD METHOD; MONTE CARLO METHOD; NONHUMAN; POPULATION DENSITY; POPULATION GENETICS; POPULATION MODEL; POPULATION RESEARCH; PRIORITY JOURNAL; PROBABILITY; SAMPLE SIZE; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL MODEL; TECHNIQUE;

GENE FREQUENCY; GENETICS, POPULATION; INBREEDING; LIKELIHOOD FUNCTIONS; MARKOV CHAINS; MICROSATELLITE REPEATS; MODELS, GENETIC; MONTE CARLO METHOD; POPULATION DENSITY;

ANIMALIA;

EID: 0041707968     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (35)

1. ANDERSON, E. C., E. G. WILLIAMSON and E. A. THOMPSON, 2000 Monte Carlo evaluation of the likelihood for N from temporally spaced samples. Genetics 156: 2109-2118.
2. BALDING, D. J., and R. A. NICHOLS, 1995 A method for quantifing differentiation between populations at multi-allelic loci and its implications for investigating identity and paternity. Genetica 96: 3-12.
3. BARKER, J. S. F., W. G. HILL, D. BRADLEY, M. NEI, R. FRIES et al., 1998 Measurement of Domestic Animal Diversity (MoDAD): Original Working Group Report. FAO, Rome.
4. BEAUMONT, M. A., 1999 Detecting population expansion and decline using microsatellites. Genetics 153: 2013-2029.
5. 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.
6. CHEVALET, C., 2000 The number of lines of descent and fixation probabilities of alleles in the pure genetic drift process: analytical approximations, Theor. Popul. Biol. 57: 167-175.
7. EXCOFFIER, L., and M. SLATKIN, 1995 Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol. Biol. Evol. 12: 921-927.
8. EWENS, W. J., 1972 The sampling theory of selectively neutral alleles. Theor. Popul. Biol. 3: 87-112.
9. FOULLEY, J. L., and W. G. HILL, 1999 On the precision of estimation of genetic distance. Genet. Sel. Evol. 31: 457-464.
10. HASTING, W. K., 1970 Monte Carlo sampling methods using Markov chains and their application. Biometrika 57: 97-109.
11. HOLSINGER, K. E., 1999 Analysis of genetic diversity in geographically structured populations: a Bayesian perspective. Hereditas 130: 245-255.
12. KANTANEN,J., I. OLSAKER, S. ADALSTEINSSON, K. SANDBERG, E. EYTHORSDOTTIR et al., 1999 Temporal changes in genetic variation of north European cattle breeds. Anim. Genet. 30: 16-27.
13. FIMURA, M., 1955 Process of random genetic drift with a continuous model. Proc. Natl. Acad. Sci. USA 41: 144-150.
14. KITADA, S., T. HAYASHI and H. KISHINO, 2000 Empirical Bayes procedure for estimating genetic distance between populations and effective population size. Genetics 156: 2063-2079.
15. 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.
16. LAVAL, G., N. IANNUCCELLI, C. LEGAULT, D. MILAN, M. A. M. GROENEN et al., 2000 Genetic diversity of eleven European pig breeds. Genet. Sel. Evol. 32: 187-203.
17. LAVAL, G., M. SANCRISTOBAL and C. CHEVALET, 2002 Measuring genetic distances between breeds: use of some distances in various short term evolution models. Genet. Sel. Evol. 34: 481-507.
18. MACHUGH, D. E., M. D. SHRIVER, R. T. LOFTUS, P. CUNNINGHAM and D. G. BRADLEY, 1997 Microsatellite DNA variation and the evolution, domestication and phylogeography of taurine and zebu cattle (Bos taurus and Bos indicus). Genetics. 146: 1071-1086.
19. MADEC, L., C. DESBUQUOIS and M. A. COUTELLEC-VRETO, 2000 Phenotypic plasticity in reproductive traits: importance in the life history of Helix aspersa (Mollusca: Helicidae) in a recently colonized habitat. Biol. J. Linn. Soc. 69: 25-39.
20. MALÉCOT, G., 1948 Les Mathematiques de l'Heredite. Masson, Paris.
21. METROPOLIS, N., A. W. ROSENBLUTH, M. N. ROSENBLUTH, A. H. TELLER and E. TELLER, 1953 Equation of state calculations by fast computing machines. J. Chem. Phys. 21: 1087-1092.
22. MOAZAMI-GOUDARZI, K., D. LALOE, J. P. FURET and F. GROSCLAUDIE, 1997 Analysis of genetic relationships between 10 cattle breeds with 17 microsatellites. Anim. Genet. 28: 338-345.
23. NEI, M., 1978 Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89: 583-590.
24. NEI, M., and F. TAJIMA, 1981 Genetic drift and estimation of effective population size. Genetics 98: 625-640.
25. POLLAK, E., 1983 A new method for estimating the effective population size from allele frequency changes. Genetics 104: 531-548.
26. REYNOLDS,J., B. S. WEIR and C. C. COCKERHAM, 1983 Estimation of the coancestry coefficient: basis for a short-term genetic distance. Genetics 105: 767-779.
27. ROBERT, C., 1996 Methodes de Monte Carlo par Chaines de Markov. Economica, Paris.
28. SCHNEIDER, S., D. ROESSLI and L. EXCOFIER, 2000 A software for population genetics data analysis. http://anthro.unige.ch/arlequin.
29. TAVARE, S., 1984 Line-of-descent and genealogical processes, and their applications in population genetics models. Theor. Popul. Biol. 26: 119-164.
30. VIGNAL, A., D. MILAN, M. SANCRISTOBAL and A. EGGEN, 2002 A review on SNP and other types of molecular markers and their use in animal genetics. Genet. Sel. Evol. 34: 275-305.
31. WAPLES, R. S, 1990 Temporal changes of allele frequency in Pacific salmon: implications for mixed-stock fishery analysis. Can. J. Fish. Aquat. Sci. 47: 968-976.
32. WILLIAMSON, E. G., and M. SLATKIN, 1999 Using maximum likelihood to estimate population size from temporal changes in allele frequencies. Genetics 152: 755-761.
33. WILSON, I. J., and D. J. BALDING, 1998 Genealogical inference from microsatellite data. Genetics 150: 499-510.
34. WRIGHT, S., 1931 Evolution in Mendeleian populations. Genetics 16: 97-159.
35. WRIGHT, S., 1951 The genetical structure of populations. Ann. Eugen. 15: 323-354.