Conservation Genetics

Handbook of Statistical Genetics: Third Edition

Volumn 2, Issue , 2008, Pages 1021-1066

  Beaumont, M A ^a  

^a UNIVERSITY OF READING   (United Kingdom)

Author keywords

Brownian motion approximation; Constant mutation rate; Drosophila melanogaster; Genetic stock identification; Hardy Weinberg expectation; Identical by descent; Infinite allele model; Isolation drift model; Monte Carlo simulations; Random genetic drift

Indexed keywords

EID: 79955024538     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9780470061619.ch30     Document Type: Chapter

References (178)

1. Anderson, E.C. (2005). An efficient Monte Carlo method for estimating NE from temporally spaced samples using a coalescent-based likelihood. Genetics 170, 955-967.
2. Anderson, E.C. and Thompson, E.A. (2002). A model-based method for identifying species hybrids using multilocus genetic data. Genetics 160, 1217-1229.
3. Anderson, E.C., Williamson, E.G. and Thompson, E.A. (2000). Monte Carlo evaluation of the likelihood for Ne from temporally spaced samples. Genetics 156, 2109-2118.
4. Avise, J.C. (1994). Molecular Markers, Natural History and Evolution. Chapman & Hall, London.
5. Balding, D.J., Carothers, A.D., Marchini, J.L., Cardon, L.R., Vetta, A., Griffiths, B., Weir, B.S., Hill, W.G., Goldstein, D., Strimmer, K., Myers, S., Beaumont, M.A., Glasbey, C.A., Mayer, C.D., Richardson, S., Marshall, C., Durrett, R., Nielsen, R., Visscher, P.M., Knott, S.A., Haley, C.S., Ball, R.D., Hackett, C.A., Holmes, S., Husmeier, D., Jansen, R.C., ter Braak, C.J.F., Maliepaard, C.A., Boer, M.P., Joyce, P., Li, N., Stephens, M., Marcoulides, G.A., Drezner, Z., Mardia, K., McVean, G., Meng, X.L., Ochs, M.F., Pagel, M., Sha, N., Vannucci, M., Sillanpaa, M.J., Sisson, S., Yandell, B.S., Jin, C.F., Satagopan, J.M., Gaffney, P.J., Zeng, Z.B., Broman, K.W., Speed, T.P., Fearnhead, P., Donnelly, P., Larget, B., Simon, D.L., Kadane, J.B., Nicholson, G., Smith, A.V., Jonsson, F., Gustafsson, O., Stefansson, K., Donnelly, P., Parmigiani, G., Garrett, E.S., Anbazhagan, R. and Gabrielson, E. (2002). Discussion on the meeting on 'statistical modelling and analysis of genetic data'. Journal of the Royal Statistical Society, Series B: Statistical Methodology 64, 737-775.
6. Balding, D.J. and Nichols, R.A. (1995). A method for quantifying differentiation between populations at multi-allelic loci and its implications for investigating identity and paternity. Genetica 96, 3-12.
7. Balding, D.J. and Nichols, R.A. (1997). Significant genetic correlations among Caucasians at forensic DNA loci. Heredity 78, 583-589.
8. Balloux, F. (2004). Heterozygote excess in small populations and the heterozygote-excess effective population size. Evolution 58, 1891-1900.
9. Bartley, D., Bagley, M., Gall, G. and Bentley, B. (1992). Use of linkage disequilibrium data to estimate effective size of hatchery and natural fish populations. Conservation Biology 6, 365-375.
10. Beaumont, M.A. (1999). Detecting population expansion and decline using microsatellites. Genetics 153, 2013-2029.
11. Beaumont, M.A. (2003a). Estimation of population growth or decline in genetically monitored populations. Genetics 164, 1139-1160.
12. Beaumont, M.A. (2003b). Recent developments in genetic data analysis: what can they tell us about human demographic history? Heredity 92, 365-379.
13. Beaumont, M.A., 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. Molecular Ecology 10, 319-336.
14. Beaumont, M.A., Zhang, W. and Balding, D.J. (2002). Approximate Bayesian computation in population genetics. Genetics 162, 2025-2035.
15. Berthier, P., Beaumont, M.A., Cornuet, J.M. and Luikart, G. (2002). Likelihood-based estimation of the effective population size using temporal changes in allele frequencies: a genealogical approach. Genetics 160, 741-751.
16. Bertorelle, G. and Excoffier, L. (1998). Inferring admixture proportions from molecular data. Molecular Biology and Evolution 15, 1298-1311.
17. Blouin, M.S. (2003). DNA-based methods for pedigree reconstruction and kinship analysis in natural populations. Trends in Ecology and Evolution 18, 503-511.
18. Bucci, G., Vendramin, G.G., Lelli, L. and Vicario, F. (1997). Assessing the genetic divergence of Pinus leucodermis Ant. endangered populations: use of molecular markers for conservation purposes. Theoretical and Applied Genetics 95, 1138-1146.
19. Caballero, A. (1994). Developments in the prediction of effective population size. Heredity 73, 657-679.
20. Calmet, C. (2003). Inférences sur l'histoire des populations a partir de leur diversité genetique: étude de séquences démographiques de type fondation-explosion. Ph.D. thesis, University of Paris.
21. Cannings, C. and Edwards, A.W.F. (1969). Expected genotypic frequencies in a small sample: deviation from Hardy-Weinberg equilibrium. American Journal of Human Genetics 21, 245-247.
22. Carvajal-Rodríguez, A., Rolan-Alvarez, E. and Caballero, A. (2005). Quantitative variation as a tool for detecting human-induced impacts on genetic diversity. Biological Conservation 124, 1-13.
23. Cavalli-Sforza, L.L. and Edwards, A.W.F. (1967). Phylogenetic analysis: models and estimation procedures. Evolution 32, 550-570.
24. Chakraborty, R., Kamboh, M.I., Nwankwo, M. and Ferrell, R.E. (1992). Caucasian genes in American blacks: new data. American Journal of Human Genetics 50, 145-155.
25. Chan, Y.L., Anderson, C.N.K. and Hadly, E.A. (2006). Bayesian estimation of the timing and severity of a population bottleneck from ancient DNA. PLoS Genetics 2, 451-460.
26. Chikhi, L., Bruford, M.W. and Beaumont, M.A. (2001). Estimation of admixture proportions: a likelihood-based approach using Markov chain Monte Carlo. Genetics 158, 1347-1362.
27. Choisy, M., Franck, P. and Cornuet, J.M. (2004). Estimating admixture proportions with microsatellites: comparison of methods based on simulated data. Molecular Ecology 13, 955-968.
28. Ciofi, C., Beaumont, M.A., Swingland, I.R. and Bruford, M.W. (1999). Genetic divergence and units for conservation in the Komodo Dragaon Varanus komodoensis. Proceedings of the Royal Society of London, Series B 266, 2269-2274.
29. Cockerham, C.C. and Weir, B.S. (1977). Digenic descent measures for finite populations. Genetical Research 30, 121-147.
30. Corander, J. and Marttinen, P. (2006). Bayesian identification of admixture events using multilocus molecular markers. Molecular Ecology 15, 2833-2843.
31. Corander, J., Waldmann, P. and Sillanpaa, M.J. (2003). Bayesian analysis of genetic differentiation between populations. Genetics 163, 367-374.
32. Cornuet, J.M. and Luikart, G. (1996). Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144, 2001-2014.
33. 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.
34. Coulon, A., Guillot, G., Cosson, J.F., Angibault, J.M.A., Aulagnier, S., Cargnelutti, B., Galan, M. and Hewison, A.J.M. (2006). Genetic structure is influenced by landscape features: empirical evidence from a roe deer population. Molecular Ecology 15, 1669-1679.
35. Crow, J.F. and Kimura, M. (1970). An Introduction to Population Genetics Theory. Harper & Row, New York.
36. Csillery, K., Johnson, T., Beraldi, D., Clutton-Brock, T., Coltman, D., Hansson, B., Spong, G. and Pemberton, J.M. (2006). Performance of marker-based relatedness estimators in natural populations of outbred vertebrates. Genetics 173, 2091-2101.
37. Dawson, K.J. and Belkhir, K. (2001). A Bayesian approach to the identification of panmictic populations and the assignment of individuals. Genetical Research, Cambridge 78, 59-77.
38. DeSalle, R. and Amato, G. (2004). The expansion of conservation genetics. Nature Reviews Genetics 5, 702-712.
39. Di Rienzo, A., Donnelly, P., Toomajian, C., Sisk, B., Hill, A., Petzl-Erler, M.L., Haines, G.K. and Barch, D.H. (1998). Heterogeneity of microsatellite mutations within and between loci and implications for human demographic histories. Genetics 148, 1269-1284.
40. Di Rienzo, A., Peterson, A.C., Garza, J.C., Valdes, A.M., Slatkin, M. and Freimer, N.B. (1994). Mutational processes of simple sequence repeat loci in human populations. Proceedings of the National Academy of Sciences of the United States of America 91, 3166-3170.
41. Donnelly, P. and Tavaré, S. (1995). Coalescents and genealogical structure under neutrality. Annual Review of Genetics 29, 410-421.
42. Dupanloup, I. and Bertorelle, G. (2001).. Inferring admixture proportions from molecular data: extension to any number of parental populations. Molecular Biology and Evolution 18, 672-675.
43. Elston, R.C. (1971). The estimation of admixture in racial hybrids. Annals of Human Genetics 35, 9-17.
44. Emery, A.M., Wilson, I.J., Craig, S., Boyle, P.R. and Noble, L.R. (2001). Assignment of paternity groups without access to parental genotypes: multiple mating and developmental plasticity in squid. Molecular Ecology 10, 1265-1278.
45. England, P.R., Cornuet, J.M., Berthier, P., Tallmon, D.A. and Luikart, G. (2006). Estimating effective population size from linkage disequilibrium: severe bias in small samples. Conservation Genetics 7, 303-308.
46. Estoup, A., Beaumont, M.A., Sennedot, F., Moritz, C. and Cornuet, J.M. (2004). Genetic analysis of complex demographic scenarios: the case of spatially expanding populations in the cane toad, Bufo marinus. Evolution 58, 2021-2036.
47. Estoup, A., Wilson, I.J., Sullivan, C., Cornuet, J.-M. and Moritz, C. (2001). Inferring population history from microsatellite and enzyme data in serially introduced cane toads Bufo marinus. Genetics 159, 1671-1687.
48. Evanno, G., Regnaut, S. and Goudet, J. (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14, 2611-2620.
49. Ewens, W.J. (1972). The sampling theory of selectively neutral alleles. Theoretical Population Biology 3, 87-112.
50. Ewens, W.J. (2004). Mathematical Population Genetics: Theoretical Introduction, vol. 1. Springer- Verlag, New York.
51. Excoffier, L. and Heckel, G. (2006). Computer programs for population genetics data analysis: a survival guide. Nature Reviews Genetics 7, 745-758.
52. Falush, D., Stephens, M. and Pritchard, J.K. (2003). Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies author(s). Genetics 164, 1567-1587.
53. Felsenstein, J. (1981). Evolutionary trees from gene frequencies and quantitative characters: finding maximum likelihood estimates. Evolution 35, 1229-1242.
54. Frankham, R. (2005). Genetics and extinction. Biological Conservation 126, 131-140.
55. Frankham, R. (1995). Conservation genetics. Annual Review of Genetics 29, 305-327.
56. Fu, Y.-X. (1997). Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147, 915-925.
57. Garza, J.C. and Williamson, E.G. (2001). Detection of reduction in population size using data from microsatellite loci. Molecular Ecology 10, 305-318.
58. Gasbarra, D., Sillanpaa, M.J. and Arjas, E. (2005).. Backward simulation of ancestors of sampled individuals. Theoretical Population Biology 67, 75-83.
59. Gasbarra, D., Pirinen, M., Sillanpáá, M.J., Salmela, E. and Arjas, E. (2007). Estimating genealogies from unlinked marker data: a Bayesian approach. Theoretical Population Biology (Submitted: preprint at http://www.rni.helsinki.fi/dag/genealogy.tar).
60. Glass, B. and Li, C.C. (1953). The dynamics of racial intermixture-an analysis based on the American Negro. American Journal of Human Genetics 5, 1-20.
61. Goldstein, D.B., Ruiz Linares, A., Cavalli-Sforza, L.L. and Feldman, M.W. (1995).. Genetic absolute dating based on microsatellites and the origin of modern humans. Proceedings of the National Academy of Sciences of the United States of America 92, 6723-6727.
62. Goodman, S.J., Tamate, H.B., Wilson, R., Nagata, J., Tatsuzawa, S., Swanson, G.M., Pemberton, J.M. and McCullough, D.R. (2001). Bottlenecks, drift and differentiation: the population structure and demographic history of sika deer (Cervus nippon) in the Japanese archipelago. Molecular Ecology 10, 1357-1370.
63. Goossens, B., Chikhi, L., Ancrenaz, M., Lackman-Ancrenaz, I., Andau, P. and Bruford, M.W. (2006). Genetic signature of anthropogenic population collapse in orang-utans. PLoS Biology 4, 285-291.
64. Green, P.J. (1995). Reversible jump Markov chain Monte Carlo and Bayesian model determination. Biometrika 82, 711-7732.
65. Griffiths, R.C. and Tavaré, S. (1994). Simulating probability distributions in the coalescent. Theoretical Population Biology 46, 131-159.
66. Guillot, G., Estoup, A., Mortier, F. and Cosson, J.F. (2005). A spatial statistical model for landscape genetics. Genetics 170, 1261-1280.
67. Hadfield, J.D., Richardson, D.S. and Burke, T. (2006). Towards unbiased parentage assignment: combining genetic, behavioural and spatial data in a Bayesian framework. Molecular Ecology 15, 3715-3730.
68. Haig, S.M. (1998). Molecular contributions to conservation. Ecology 79, 413-425.
69. Hanfling, B. and Weetman, D. (2006). Concordant genetic estimators of migration reveal anthropogenically enhanced source-sink population structure in the River Sculpin, Cottus gobio. Genetics 173, 1487-1501.
70. Hedrick, P.W. (2001). Conservation genetics: where are we now? Trends in Ecology and Evolution 16, 629-636.
71. Hey, J. and Nielsen, R. (2004). Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167, 747-760.
72. Hill, W.G. (1981). Estimation of effective population size from data on linkage disequilibrium. Genetical Research 38, 209-216.
73. Hill, W.G. and Robertson, A. (1968). Linkage disequilibrium in finite populations. Theoretical and Applied Genetics 38, 226-231.
74. Hogben, L. (1946). An Introduction to Mathematical Genetics. W. W. Norton, New York.
75. Hudson, R.R. (1985). The sampling distribution of linkage disequilibrium under an infinite allele model without selection. Genetics 109, 611-631.
76. Hudson, R.R. (1991). Gene genealogies and the coalescent process. In Oxford Surveys in Evolutionary Biology, K.J. Futuyama and J. Antonovics, eds. Oxford University Press, Oxford, pp. 1-44.
77. Jorde, P.E. and Ryman, N. (1995). Temporal allele frequency change and estimation of effective size in populations with overlapping generations. Genetics 139, 1077-1090.
78. Kimmel, M., Chakraborty, R., King, J.P., Bamshad, M., Watkins, W.S. and Jorde, L.B. (1998). Signatures of population expansion in microsatellite repeat data. Genetics 148, 1921-1930.
79. King, J.P., Kimmel, M. and Chakraborty, R. (2000). A power analysis of microsatellite-based statistics for inferring past population growth. Molecular Biology and Evolution 17, 1859-1868.
80. Keightley, P.D., Caballero, A. and GarciaDorado, A. (1998). Population genetics: surviving under mutation pressure. Current Biology 8, R235-R239.
81. Krimbas, C.B. and Tsakas, S. (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.
82. Lande, R. (1998). Anthropogenic, ecological and genetic factors in extinction and conservation. Research in Population Economics 40, 259-269.
83. Langley, C.H., Smith, D.B. and Johnson, F.M. (1978). Analysis of linkage disequilibrium between allozyme loci in natural populations of Drosophila melanogaster. Genetical Research 32, 215-229.
84. Laurie-Ahlberg, C.C. and Weir, B.S. (1979). Allozyme variation and linkage disequilibrium in some laboratory populations of Drosophila melanogaster. Genetics 92, 1295-1314.
85. Laval, G. and Excoffier, L. (2004).. SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history. Bioinformatics 20, 2485-2487.
86. Lecis, R., Pierpaoli, M., Biro, Z.S., Szemethy, L., Ragni, B., Vercillo, F. and Randi, E. (2006). Bayesian analyses of admixture in wild and domestic cats (Felis silvestris) using linked microsatellite loci. Molecular Ecology 15, 119-131.
87. Levene, H. (1949). On a matching problem arising in genetics. Annals of Mathematical Statistics 20, 91-94.
88. Long, J.C. (1991). The genetic structure of admixed populations. Genetics 127, 417-428.
89. Luikart, G., Allendorf, F.W., Cornuet, J.M. and Sherwin, W.B. (1998). Distortion of allele frequency distributions provides a test for recent population bottlenecks. The Journal of Heredity 89, 238-247.
90. Luikart, G. and Cornuet, J.M. (1999). Estimating the effective number of breeders from heterozygote excess in progeny. Genetics 151, 1211-1216.
91. Luikart, G. and England, P.R. (1999). Statistical analysis of microsatellite DNA data. Trends in Ecology and Evolution 14, 253-256.
92. Lynch, M., Blanchard, J., Houle, D., Kibota, T., Schultz, S., Vassivlieva, L. and Willis, J. (1999). Perspective: spontaneous deleterious mutation. Evolution 53, 645-663.
93. Lynch, M., Conery, J. and Burger, R. (1995). Mutation accumulation and the extinction of small populations. The American Naturalist 146, 489-518.
94. Lynch, M. and Ritland, K. (1999). Estimation of pairwise relatedness with molecular markers. Genetics 152, 1753-1766.
95. Marjoram, P., Molitor, J., Plagnol, V. and Tavaré, S. (2003).. Markov chain Monte Carlo without likelihoods. Proceedings of the National Academy of Sciences of the United States of America 100, 15324-15328.
96. Miller, N., Estoup, A., Toepfer, S., Bourguet, D., Lapchin, L., Derridj, S., Kim, K.S., Reynaud, P., Furlan, F. and Guillemaud, T. (2005). Multiple transatlantic introductions of the western corn rootworm. Science 310, 992.
97. Milligan, B.G. (2003). Maximum-likelihood estimation of relatedness. Genetics 163, 1153-11167.
98. Mousseau, T.A., Ritland, K. and Heath, D.D. (1998). A novel method for estimating heritability using molecular markers. Heredity 80, 218-224.
99. Nei, M. and Tajima, F. (1981). Genetic drift and estimation of effective population size. Genetics 98, 625-640.
100. Nicholson, G., Smith, A.V., Jonsson, F., Gustafsson, O., Stefansson, K. and Donnelly, P. (2002). Assessing population differentiation and isolation from single-nucleotide polymorphism data. Journal of the Royal Statistical Society, Series B: Statistical Methodology 64, 695-715.
101. Nielsen, R., Mountain, J.L., Huelsenbeck, J.P. and Slatkin, M. (1998). Maximum-likelihood estimation of population divergence times and population phylogeny in models without mutation. Evolution 52, 669-677.
102. Nielsen, R. and Wakeley, J. (2001). Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics 158, 885-896.
103. Nunney, L. (1995). Measuring the ratio of effective population size to adult numbers using genetic and ecological data. Evolution 49, 389-392.
104. Ohta, T. and Kimura, M. (1969). Linkage disequilibrium due to random genetic drift. Genetical Research 13, 47-55.
105. Ohta, T. and Kimura, M. (1973). A model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a finite population. Genetical Research, Cambridge 22, 201-204.
106. Oliehoek, P.A., Windig, J.J., van Arendonk, J.A.M. and Bijma, P. (2006). Estimating relatedness between individuals in general populations with a focus on their use in conservation programs. Genetics 173, 483-496.
107. O'Ryan, C., Harley, E.H., Bruford, M.W., Beaumont, M., Wayne, R.K. and Cherry, M.I. (1998). Microsatellite analysis of genetic diversity in fragmented South African buffalo populations. Animal Conservation 1, 85-94.
108. Paetkau, D., Calvert, W., Stirling, I. and Strobeck, C. (1995). Microsatellite analysis of population structure in Canadian polar bears. Molecular Ecology 4, 347-354.
109. Paetkau, D., Shields, G.F. and Strobeck, C. (1998). Gene flow between insular, coastal and interior populations of brown bears in Alaska. Molecular Ecology 7, 1283-1292.
110. Painter, I. (1997). Sibship reconstruction without parental information. Journal of Agricultural Biological and Environmental Statistics 2, 212-229.
111. Palo, J.U., Makinen, H.S., Helle, E., Stenman, O. and Vainola, R. (2001). Microsatellite variation in ringed seals (Phoca hispida): genetic structure and history of the Baltic Sea population. Heredity 86, 609-617.
112. Parra, E.J., Marcini, A., Akey, J., Martinson, J., Batzer, M.A., Cooper, R., Forrester, T., Allison, D.B., Deka, R., Ferrell, R.E. and Shriver, M.D. (1998). Estimating African American admixture proportions by use of population-specific alleles. American Journal of Human Genetics 63, 1839-1851.
113. Pella, J. and Masuda, M. (2001). Bayesian methods for analysis of stock mixtures from genetic characters. Fishery Bulletin 99, 151-167.
114. Piry, S., Luikart, G. and Cornuet, J.M. (1999). BOTTLENECK: a computer program for detecting recent reductions in the effective population size using allele frequency data. The Journal of Heredity 90, 502-503.
115. Pollak, E. (1983). A new method for estimating the effective population size from allele frequency changes. Genetics 104, 531-548.
116. Pritchard, J.K., Seielstad, M.T., Perez-Lezaun, A. and Feldman, M.W. (1999). Population growth of human Y chromosomes: a study of Y chromosome microsatellites. Molecular Biology and Evolution 16, 1791-1798.
117. Pritchard, J.K., Stephens, M. and Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics 155, 945-959.
118. Pudovkin, A.I., Zaykin, D.V. and Hedgecock, D. (1996). On the potential for estimating the effective number of breeders from heterozygote-excess in progeny. Genetics 144, 383-387.
119. Queller, D.C. and Goodnight, K.F. (1989). Estimating relatedness using genetic markers. Evolution 43, 258-275.
120. Ramos-Onsins, S.E. and Rozas, J. (2002). Statistical properties of new neutrality tests against population growth. Molecular Biology and Evolution 19, 2092-2100.
121. Rannala, B. and Hartigan, J.A. (1996). Estimating gene flow in island populations. Genetical Research, Cambridge 67, 147-158.
122. Rannala, B. and Mountain, J.L. (1997). Detecting immigration by using multilocus genotypes. Proceedings of the National Academy of Sciences of the United States of America 94, 9197-9201.
123. Regnaut, S., Christe, P., Chapuisat, M. and Fumagalli, L. (2006). Genotyping faeces reveals facultative kin association on capercaillie's leks. Conservation Genetics 7, 665-674.
124. Reich, D.E., Feldman, M.W. and Goldstein, D.B. (1999). Statistical properties of two tests that use multilocus data sets to detect population expansions. Molecular Biology and Evolution 16, 453-466.
125. Reich, D.E. and Goldstein, D.B. (1998). Genetic evidence for a Paleolithic human population expansion in Africa. Proceedings of the National Academy of Sciences of the United States of America 95, 8119-8123.
126. Ritland, K. (1996). Estimators for pairwise relatedness and individual inbreeding coefficients. Genetical Research 67, 175-185.
127. Robert, C.P. (1996). Mixtures of distributions: inference and estimation. In Markov Chain Monte Carlo in Practice, W.R. Gilks, S. Richarson and D.J. Spiegelhalter, eds. Chapman & Hall, London, pp. 441-464.
128. Roberts, D. and Hiorns, R. (1965). Methods of analysis of the genetic composition of a hybrid population. Human Biology 37, 38-43.
129. Robertson, A. (1965). The interpretation of genotypic ratios in domestic animal populations. Animal Production 7, 319-324.
130. Rogers, A.R. (1995). Genetic evidence for a Pleistocene population explosion. Evolution 49, 608-615.
131. Rogers, A.R. and Harpending, H. (1992). Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution 9, 552-569.
132. Roy, M.S., Geffen, E., Smith, D., Ostrander, E.A. and Wayne, R.K. (1994). Patterns of differentiation and hybridization in North American wolf-like canids, revealed by analysis of microsatellite loci. Molecular Biology and Evolution 11, 553-570.
133. Ruppert, D. and Wand M.P., (1994).. Multivariate locally weighted least squares regression. Annals of Statistics, 22, 1346-1370.
134. Saccheri, I., Kuussaari, M., Kankare, M., Vikman, P., Fortelius, W. and Hanski, I. (1998). Inbreeding and extinction in a butterfly metapopulation. Nature 392, 491-494.
135. Saccheri, I.J., Wilson, I.J., Nichols, R.A., Bruford, M.W. and Brakefield, P.M. (1999). Inbreeding of bottlenecked butterfly populations: estimation using the likelihood of changes in marker allele frequencies. Genetics 151, 1053-1063.
136. Schneider, S. and Excoffier, L. (1999). Estimation of past demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: application to human mitochondrial DNA. Genetics 152, 1079-1089.
137. Schwartz, M.K., Tallmon, D.A. and Luikart, G. (1998). Review of DNA-based census and effective population size estimators. Animal Conservation 1, 293-299.
138. Slatkin, M. (1996). Gene genealogies within mutant allelic classes. Genetics 145, 579-587.
139. Spielman, D., Brook, B.W. and Frankham, R. (2004). Most species are not driven to extinction before genetic factors impact them. Proceedings of the National Academy of Sciences of the United States of America 101, 15261-15264.
140. Steel, M. and Hein, J. (2006). Reconstructing pedigrees: a combinatorial perspective. Journal of Theoretical Biology 240, 360-367.
141. Storfer, A. (1996). Quantitative genetics: a promising approach for the assessment of genetic variation in endangered species. Trends in Ecology and Evolution 11, 343-348.
142. Tajima, F. (1983). Evolutionary relationship of DNA sequences in finite populations. Genetics 105, 437-460.
143. Tajima, F. (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585-595.
144. Tavaré, S. (1984). Lines-of-descent and genealogical processes, and their application in population genetics models. Theoretical Population Biology 26, 119-164.
145. Taylor, A.C., Sherwin, W.B. and Wayne, R.K. (1994). Genetic variation of microsatellite loci in a bottlenecked species: the northern hairy-nosed wombat. Molecular Ecology 3, 277-290.
146. Thomas, S.C. (2005). The estimation of genetic relationships using molecular markers and their efficiency in estimating heritability in natural populations. Philosophical Transactions of the Royal Society of London, Series B 360, 1457-1467.
147. Thomas, S.C. and Hill, W.G. (2002). Sibship reconstruction in hierarchical population structures using Markov chain Monte Carlo techniques. Genetical Research 79, 227-234.
148. Thompson, E.A. (1973). The Icelandic admixture problem. Annals of Human Genetics 37, 69-80.
149. Thompson, E.A. (1975a). Human Evolutionary Trees. Cambridge University Press, Cambridge.
150. Thompson, E.A. (1975b). The estimation of pairwise relationships. Annals of Human Genetics 39, 173-188.
151. Verardi, A., Lucchini, V. and Randi, E. (2006). Detecting introgressive hybridization between free-ranging domestic dogs and wild wolves (Canis lupus) by admixture linkage disequilibrium analysis. Molecular Ecology 15, 2845-2855.
152. Vitalis, R. and Couvet, D. (2001). Estimation of effective population size and migration rate from one-and two-locus identity measures. Genetics 157, 911-925.
153. Wakeley, J. (1999). Nonequilibrium migration in human history. Genetics 153, 1863-1871.
154. Wakeley, J. (2001). The coalescent in an island model of population subdivision with variation among demes. Theoretical Population Biology 59, 133-144.
155. Wakeley, J., Nielsen, R., Liu-Cordero, S.N. and Ardlie, K. (2001). The discovery of singlenucleotide polymorphisms-and inferences about human demographic history. American Journal of Human Genetics 69, 1332-1347.
156. Wang, J. (2001). A pseudo-likelihood method for estimating effective population size from temporally spaced samples. Genetical Research, Cambridge 78, 243-257.
157. Wang, J. (2002). An estimator for pairwise relatedness using molecular markers. Genetics 160, 1203-1215.
158. Wang, J.L. (2003). Maximum-likelihood estimation of admixture proportions from genetic data. Genetics 164, 747-765.
159. Wang, J.L. (2004). Sibship reconstruction from genetic data with typing errors. Genetics 166, 1963-1979.
160. Wang, J.L. (2005). Estimation of effective population sizes from data on genetic markers. Philosophical Transactions of the Royal Society of London, Series B 360, 1395-1409.
161. Wang, J.L. (2006). A coalescent-based estimator of admixture from DNA sequences. Genetics 173, 1679-1692.
162. Wang, J.L. and Whitlock, M.C. (2003). Estimating effective population size and migration rates from genetic samples over space and time. Genetics 163, 429-446.
163. Waples, R.S. (1989). A generalized approach for estimating effective population size from temporal changes in allele frequency. Genetics 121, 379-392.
164. Waples, R.S. (1991). Genetic methods for estimating the effective size of Cetacean populations. Genetic Ecology of Whales and Dolphins, (special issue 13). Report of the International Whaling Commission, pp. 279-300.
165. Waples, R.S. (2006). A bias correction for estimates of effective population size based on linkage disequilibrium at unlinked gene loci. Conservation Genetics 7, 167-184.
166. Waser, P.M. and Strobeck, C. (1998). Genetic signatures of interpopulation dispersal. Trends in Ecology and Evolution 13, 43-44.
167. Wasser, S.K., Shedlock, A.M., Comstock, K., Ostrander, E.A., Mutayoba, B. and Stephens, M. (2004). Assigning African elephant DNA to geographic region of origin: applications to the ivory trade. Proceedings of the National Academy of Sciences of the United States of America 101, 14847-14852.
168. Watterson, G.A. (1975). On the number of segregating sites in genetical models without recombination. Theoretical Population Biology 7, 256-276.
169. Watterson, G.A. (1978). The homozygosity test of neutrality. Genetics 88, 405-417.
170. Weir, B.S. (1996). Genetic Data Analysis, 2nd edition. Sinauer Associates, Sunderland.
171. Weir, B.S. and Hill, W.G. (1980). Effect of mating structure on variation in linkage disequilibrium. Genetics 95, 477-488.
172. Weiss, G. and von Haeseler, A. (1998). Inference of population history using a likelihood approach. Genetics 149, 1539-1546.
173. Whitlock, M.C., Griswold, C.K. and Peters, A.D. (2003). Compensating for the meltdown: the critical effective size of a population with deleterious and compensatory mutations. Annales Zoologici Fennici 40, 169-183.
174. Williamson, E.G. and Slatkin, M. (1999). Using maximum likelihood to estimate population size from temporal changes in allele frequencies. Genetics 152, 755-761.
175. Wilson, I.J. and Balding, D.J. (1998). Genealogical inference from microsatellite data. Genetics 150, 499-510.
176. Wilson, G.A. and Rannala, B. (2003). Bayesian inference of recent migration rates using multilocus genotypes. Genetics 163, 1177-1191.
177. Wilson, I.J., Weale, M.E. and Balding, D.J. (2003). Inferences from DNA data: population histories, evolutionary processes, and forensic match probabilities. Journal of the Royal Statistical Society, Series A 166, 155-188.
178. Wright, S. (1931). Evolution in Mendelian populations. Genetics 16, 97-159.