Inferences from DNA data: Population histories, evolutionary processes and forensic match probabilities

Journal of the Royal Statistical Society. Series A: Statistics in Society

Volumn 166, Issue 2, 2003, Pages 155-188

  Wilson, Ian J ^a   Weale, Michael E ^b   Balding, David J ^c  

^a UNIVERSITY OF ABERDEEN   (United Kingdom)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

^c IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

Forensic identification; Human history; Markov chain Monte Carlo methods; Population genetics; Statistical genetics

Indexed keywords

EID: 0037503021     PISSN: 09641998     EISSN: None     Source Type: Journal    
DOI: 10.1111/1467-985X.00264     Document Type: Article

References (82)

1. Adcock, G. J., Dennis, E. S., Easteal, S., Huttley, G. A., Jermlin, L. S., Peacock, W. J. and Thorne, A. (2001) Mitochondrial DNA sequences in ancient Australians: implications for modern human origins. Proc. Natn. Acad. Sci. USA, 98, 537-542.
2. Aldous, D. J. (2000) Mixing time for a Markov chain on cladograms. Combin., Probab. Comput., 9, 191-204.
3. Allen, M., Engstrom, A. S., Meyer, S., Handt, O., Saldeen, T., von Haeseler, A., Paabo, S. and Gyllensten, V. (1998) Mitochondrial DNA sequencing of shed hairs and saliva on robbery caps: sensitivity and matching probabilities. J. Forens. Sci., 43, 453-464.
4. e from temporally spaced samples. Genetics, 156, 2109-2118.
5. Bahlo, M. and Griffiths, R. C. (2000) Inference from gene trees in a subdivided population. Theoret. Popln Biol., 57, 79-95.
6. Balding, D. J., Bishop, M. and Cannings, C. (eds) (2001) Handbook of Statistical Genetics. Chichester: Wiley.
7. Balding, D. J. and Donnelly, P. (1995) Inferring identity from DNA profile evidence. Proc. Natn. Acad. Sci. USA, 92, 11741-11745.
8. Bataille, M., Crainic, K., Leterreux, M., Durigon, M. and deMazancourt, P. (1999) Multiplex amplification of mitochondrial DNA for human and species identification in forensic evaluation. Forens. Sci. Int., 99, 165-170.
9. Beaumont, M. (1999) Detecting population expansion and decline using microsatellites. Genetics, 153, 2013-2029.
10. Beaumont, M. (2001) Conservation genetics. In Handbook of Statistical Genetics (eds D. J. Balding, C. Cannings and M. Bishop), ch. 27. Chichester: Wiley.
11. Beerli, P. and Felsenstein, J. (1999) Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. Genetics, 152, 763-773.
12. Beerli, P. and Felsenstein, J. (2001) Maximum-likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proc. Natn. Acad. Sci. USA, 98, 4563-4568.
13. Bianchi, N. O., Catanesi, C. I., Bailliet, G., Martinez-Marignac, V. L., Bravi, C. M., Vidal-Rioja, L. B., Herrera, R. J. and Lopez-Camelo, J. S. (1998) Characterization of ancestral and derived Y-chromosome haplotypes of new world native populations. Am. J. Hum. Genet., 63, 1862-1871.
14. Bonneuil, N. (1998) Population paths implied by the mean number of pairwise nucleotide differences among mitochondrial DNA sequences. Ann. Hum. Genet., 62, 61-73.
15. Brinkmann, B., Klintschar, M., Neuhuber, F., Hühne, J. and Rolf, B. (1998) Mutation rate in human microsatellites: influence of the structure and length of the tandem repeat. Am. J. Hum. Genet., 62, 1408-1415.
16. Cann, R. L., Stoneking, M. and Wilson, A. C. (1987) Mitochondrial DNA and human evolution. Nature, 325, 31-36.
17. Cannings, C. (1974) The latent roots of certain Markov chains arising in genetics: I, Haploid models. Adv. Appl. Probab., 6, 260-290.
18. Cavalli-Sforza, L. L. and Cavalli-Sforza, F. (1995) The Great Human Diasporas: the History of Diversity and Evolution. Reading: Addison-Wesley.
19. Cavalli-Sforza, L. L., Menozzi, P. and Piazza, A. (1994) The History and Geography of Human Genes. Princeton: Princeton University Press.
20. 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.
21. Clayton, D. (2000) Linkage disequilibrium mapping of disease susceptibility genes in human populations. Int. Statist. Rev., 68, 23-43.
22. Cooper, G., Amos, W., Hoffman, D. and Rubinsztein, D. C. (1996) Network analysis of human Y microsatellite haplotypes. Hum. Molec. Genet., 5, 1759-1766.
23. Cooper, G., Burroughs, N. J., Rand, D. A., Rubinsztein, D. C. and Amos, W. (1999) Markov Chain Monte Carlo analysis of human Y-chromosome microsatellites provides evidence of biased mutation. Proc. Natn. Acad Sci. USA, 96, 11916-11921.
24. Donnelly, P., Nordborg, M. and Joyce, P. (2001) Likelihoods and simulation methods for a class of nonneutral population genetics models. Genetics, 159, 853-867.
25. Donnelly, P. and Tavaré, S. (1995) Coalescents and genealogical structure under neutrality. A. Rev. Genet., 29, 410-421.
26. Eyre-Walker, A. and Awadalla, P. (2001) Does human mtDNA recombine? J. Molec. Evoln, 53, 430-435.
27. Fearnhead, P. and Donnelly, P. (2002) Approximate likelihood methods for estimating local recombination rates. J. R. Statist. Soc. B, 64, 657-680.
28. Felsenstein, J. (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Molec. Evoln, 17, 368-376.
29. Felsenstein, J. and Churchill, G. A. (1996) A hidden Markov model approach to variation among sites in rate of evolution. Molec. Biol Evoln, 13, 93-104.
30. Forster, P., Röhl, A., Lünnemann, P., Brinkmann, C., Zerjal, T., Tyler-Smith, C. and Brinkmann, B. (2000) A short Tandem Repeat-based phytogeny for the human Y chromosome. Am. J. Hum. Genet., 67, 182-196.
31. Fu, Y.-X. and Li, W.-H. (1999) Coalescing into the 21st century: an overview and prospects of coalescent theory. Theoret. Popln Biol., 56, 1-10.
32. Fullerton, S. M., Harding, R. M., Boyce, A. J. and Clegg, J. B. (1994) Molecular and population genetic analysis of allelic sequence diversity at the human β-globin locus. Proc. Natn. Acad. Sci. USA, 91, 1805-1809.
33. Goldstein, D. B. (2001) Islands of linkage disequilibrium. Nat. Genet., 29, 109-111.
34. Goldstein, D. B. and Schlötterer, C. (eds) (1999) Microsatellites: Evolution and Applications. Oxford: Oxford University Press.
35. Griffiths, R. C. and Marjoram, P. (1997) An ancestral recombination graph. IMA J. Math. Applic., 87, 257-270.
36. Griffiths, R. C. and Tavaré, S. (1994) Simulating probability-distributions in the coalescent. Theoret. Popln Biol., 46, 131-159.
37. Hammer, M. F. (1994) A recent insertion of an Alu element on the Y chromosome is a useful marker for human population studies. Molec. Biol. Evoln, 11, 749-761.
38. Handt, O., Meyer, S. and von Haeseler, A. (1998) Compilation of human mtDNA control region sequences. Nucleic Acids Res., 26, 126-129.
39. Harding, R. M., Fullerton, S. M., Griffiths, R. C. and Clegg, J. B. (1997) A gene tree for β-globin sequences from Melanesia. J. Molec. Evoln, 44, suppl. 1, S133-S138.
40. Hartl, D. L. and Clark, A. G. (1997) Principles of Population Genetics, 3rd edn. Sunderland: Sinauer.
41. Hasegawa, M., Kishino, H. and Yano, T. (1985) Dating the human-ape splitting by a molecular clock of mitochondrial DNA. J. Molec. Evoln, 22, 160-174.
42. Heyer, E., Puymirat, J., Dieltjes, P., Bakker, E. and de Knijff, P. (1997) Estimating Y-chromosome specific microsatellite mutation frequencies using deep rooting phytogenies. Hum. Molec. Genet., 6, 799-803.
43. Hudson, R. R. (1991) Gene genealogies and the coalescent process. In Oxford Surveys in Evolutionary Biology (eds D. J. Futuyama and J. Antonovics). Oxford: Oxford University Press.
44. Jorde, L. B., Watkins, W. S. and Bamshad, M. J. (2001) Population genomics: a briidge from evolutionary history to genetic medicine. Hum. Molec. Genet., 10, 2199-2207.
45. Jukes, T. H. and Cantor, C. R. (1969) Evolution of protein molecules. In Mammalian Protein Metabolism (ed. H. N. Munro), pp. 21-132. New York: Academic Press.
46. Kayser, M., Roewer, L., Hedman, M., Henke, L., Henke, J., Brauer, S., Kruger, C., Krawczak, M., Nagy, M., Dobosz, T., Szibor, R., de Kniff, P., Stoneking, M. and Sajantila, A. (2000) Characteristics and frequency of germline mutations at microsatellite loci from the human Y-chromosome, as revealed by direct observation in father/son pairs. Am. J. Hum. Genet., 66, 1580-1588.
47. Kingman, J. F. C. (1982) The coalescent. Stock Process. Applic., 13, 235-248.
48. Krings, M., Stone, A., Schmitz, R. W, Krainitzki, H., Stoneking, M. and Paabo, S. (1997) Neandertal DNA sequences and the origin of modern humans. Cell, 90, 19-30.
49. Kuhner, M. K., Yamato, J. and Felsenstein, J. (1995) Estimating effective population size from sequence data using Metropolis-Hastings sampling. Genetics, 140, 1421-1430.
50. Kuhner, M. K., Yamato, J. and Felsenstein, J. (1998) Maximum likelihood estimation of population growth rates based on the coalescent. Genetics, 149, 429-434.
51. Kuhner, M. K., Yamato, J. and Felsenstein, J. (2000) Maximum likelihood estimation of recombination rates from population data. Genetics, 156, 1393-1401.
52. Liu, J. S. (2002) Monte Carlo Strategies in Scientific Computing. New York: Springer.
53. Marjoram, P. and Donnelly, P. (1994) Pairwise comparisons of Mitochondrial DNA sequences in subdivided populations and implications for early human evolution. Genetics, 136, 673-683.
54. Markovtsova, L., Marjoram, P. and Tavaré, S. (2000a) The age of a unique event polymorphism. Genetics, 156, 401-409.
55. Markovtsova, L., Marjoram, P. and Tavaré, S. (2000b) The effects of rate variation on ancestral inference in the coalescent. Genetics, 156, 1427-1436.
56. Mau, B., Newton, M. A. and Larget, B. (1999) Bayesian phylogenetic inference via Markov Chain Monte Carlo methods. Biometrics, 55, 1-12.
57. Meyer, S., Weiss, G. and von Haeseler, A. (1999) Pattern of nucleotide substitution and rate heterogeneity in the hypervariable regions I and II of human mtDNA. Genetics, 152, 1103-1110.
58. Nielsen, R. (2000) Estimation of population parameters and recombination rates from single nucleotide polymorphisms. Genetics, 154, 931-942.
59. Nielsen, R. and Wakeley, J. (2001) Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics, 158, 885-896.
60. Nordborg, M. (2001) Coalescent theory. In Handbook of Statistical Genetics (eds D. J. Balding, C. Cannings and M. Bishop), ch. 7. Chichester: Wiley.
61. Ovchinnikov, I. V., Gotherstrom, A., Romanova, G. P., Kharitonov, V. M., Liden, K. and Goodwin, W. (2000) Molecular analysis of Neanderthal DNA from the northern Caucasus. Nature, 404, 490-493.
62. Pfeiffer, H., Steighner, R., Fisher, R., Mornstad, H., Yoon, C. L. and Holland, M. M. (1998) Mitochondrial DNA extraction and typing from isolated dentin - experimental evaluation in a Korean population. Int. J. Leg. Med., 111, 309-313.
63. 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. Molec. Biol. Evoln, 16, 1791-1798.
64. Relethford, J. (1998) Genetics of modern human origins and diversity. A. Rev. Anthropol, 27, 1-23.
65. Roewer, L., Kayser, M., de Knijff, P., Anslinger, K. and Betz, A. (2000) A new method for the evaluation of matches in non-recombining genomes: application to Y-chromosomal short tandem repeat (STR) haplotypes in European males. Forens. Sci. Int., 114, 31-43.
66. Rubin, D. B. and Schenker, N. (1986) Efficiently simulating the coverage properties of interval estimates. Appl. Statist., 35, 159-167.
67. Ruiz Linares, A., Nayar, K., Goldstein, D. B., Hebert, J. M., Seielstad, M. T., Underbill, P. A., Lin, A. A., Feldman, M. W. and Cavalli-Sforza, L. L. (1996) Geographic clustering of human Y-chromosome haplotypes. Ann. Hum. Genet., 60, 401-408.
68. Schug, M. D., Wetterstrand, K. A., Gaudette, M. S., Lim, R. H., Hutter, C. M. and Aquadro, C. F. (1998) The distribution and frequency of micro satellite loci on Drosophila Melanogaster. Molec. Evoln, 7, 57-70.
69. Sherry, S. T., Harpending, H. C., Batzer, M. A. and Stoneking, M. (1997) Alu evolution in human populations: using the coalescent to estimate effective population size. Genetics, 147, 1977-1982.
70. Siguroardottir, S., Helgason, A., Gulcher, J. R., Stefansson, K. and Donnelly, P. (2000) The mutation rate in the human mtDNA control region. Am. J. Hum. Genet., 66, 1599-1609.
71. Stephens, M. (2001) Inference under the coalescent. In Handbook of Statistical Genetics (eds D. J. Balding, C. Cannings and M. Bishop), ch. 8. Chichester: Wiley.
72. Stephens, M. and Donnelly, P. (2000) Inference in molecular population genetics (with discussion). J. R. Statist. Soc. B, 62, 605-635.
73. Sykes, B. (1999) The molecular genetics of European ancestry. Phil. Trans. R. Soc. Lond. B, 354, 131-139.
74. Thomson, R., Pritchard, J. K., Shen, P., Oefner, P. J. and Feldman, M. W. (2000) Recent common ancestry of human Y chromosomes: evidence from DNA sequence data. Proc. Natn, Acad. Sci. USA, 97, 7360-7365.
75. Tremblay, M. and Vézina, H. (2000) New estimates of intergenerational time intervals for the calculation of age and origins of mutations. Am. J. Hum. Genet., 66, 651-658.
76. Tully, G, Bär, W, Brinkmann, B., Carracedo, A., Gill, P., Morling, N, Parson, W. and Schneider, P. (2001) Considerations by the European DNA Profiling (EDNAP) Group on the working practices, nomenclature and interpretation of mitochondrial DNA profiles. Forens. Sci. Int., 124, 83-91.
77. Tully, G., Sullivan, K. M., Nixon, P., Stones, R. E. and Gill, P. (1996) Rapid detection of mitochondrial sequence polymorphisms using multiplex solid-phase fluorescent minisequencing. Genomics, 34, 107-113.
78. Weber, J. L. and Wong, C. (1993) Mutation of human short tandem repeats. Hum. Molec. Genet., 2, 1123-1128.
79. Weir, B. S. and Cockerham, C. C. (1984) Estimating F-statistics for the analysis of population structure. Evolution, 38, 1358-1370.
80. Wilkinson-Herbots, H. M. (1998) Genealogy and subpopulation differentiation under various models of population structure. J. Math. Biol, 37, 535-585.
81. Wilson, I. J. and Balding, D. J. (1998) Genealogical inference from microsatellite data. Genetics, 150, 499-510.
82. Wright, S. (1931) Evolution in Mendelian populations. Genetics, 16, 97-159.