SEARCH

SEARCH BY CITATION

References

  • 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, 537542.
  • Aldous, D. J. (2000) Mixing time for a Markov chain on cladograms. Combin. Probab. Comput., 9, 191204.
  • 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, 453464.
  • 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, 21092118.
  • Bahlo, M. and Griffiths, R. C. (2000) Inference from gene trees in a subdivided population. Theoret. Popln Biol., 57, 7995.
  • Balding, D. J., Bishop, M. and Cannings, C. (eds) (2001) Handbook of Statistical Genetics. Chichester: Wiley.
  • Balding, D. J. and Donnelly, P. (1995) Inferring identity from DNA profile evidence. Proc. Natn. Acad. Sci. USA, 92, 1174111745.
  • 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, 165170.
  • Beaumont, M. (1999) Detecting population expansion and decline using microsatellites. Genetics, 153, 20132029.
  • Beaumont, M. (2001) Conservation genetics. In Handbook of Statistical Genetics (eds D. J.Balding, C.Cannings and M.Bishop), ch. 27. Chichester: Wiley.
  • 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, 763773.
  • 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, 45634568.
  • 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, 18621871.
  • Bonneuil, N. (1998) Population paths implied by the mean number of pairwise nucleotide differences among mitochondrial DNA sequences. Ann. Hum. Genet., 62, 6173.
  • 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, 14081415.
  • Cann, R. L., Stoneking, M. and Wilson, A. C. (1987) Mitochondrial DNA and human evolution. Nature, 325, 3136.
  • Cannings, C. (1974) The latent roots of certain Markov chains arising in genetics: I, Haploid models. Adv. Appl. Probab., 6, 260290.
  • Cavalli-Sforza, L. L. and Cavalli-Sforza, F. (1995) The Great Human Diasporas: the History of Diversity and Evolution. Reading: Addison-Wesley.
  • Cavalli-Sforza, L. L., Menozzi, P. and Piazza, A. (1994) The History and Geography of Human Genes. Princeton: Princeton University Press.
  • 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, 13471362.
  • Clayton, D. (2000) Linkage disequilibrium mapping of disease susceptibility genes in human populations. Int. Statist. Rev., 68, 2343.
  • Cooper, G., Amos, W., Hoffman, D. and Rubinsztein, D. C. (1996) Network analysis of human Y microsatellite haplotypes. Hum. Molec. Genet., 5, 17591766.
  • 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, 1191611921.
  • Donnelly, P., Nordborg, M. and Joyce, P. (2001) Likelihoods and simulation methods for a class of nonneutral population genetics models. Genetics, 159, 853867.
  • Donnelly, P. and Tavaré, S. (1995) Coalescents and genealogical structure under neutrality. A. Rev. Genet., 29, 410421.
  • Eyre-Walker, A. and Awadalla, P. (2001) Does human mtDNA recombine? J. Molec. Evoln, 53, 430435.
  • Fearnhead, P. and Donnelly, P. (2002) Approximate likelihood methods for estimating local recombination rates. J. R. Statist. Soc. B, 64, 657680.
  • Felsenstein, J. (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Molec. Evoln, 17, 368376.
  • Felsenstein, J. and Churchill, G. A. (1996) A hidden Markov model approach to variation among sites in rate of evolution. Molec. Biol. Evoln, 13, 93104.
  • Forster, P., Röhl, A., Lünnemann, P., Brinkmann, C., Zerjal, T., Tyler-Smith, C. and Brinkmann, B. (2000) A short Tandem Repeat-based phylogeny for the human Y chromosome. Am. J. Hum. Genet., 67, 182196.
  • Fu, Y.-X. and Li, W.-H. (1999) Coalescing into the 21st century: an overview and prospects of coalescent theory. Theoret. Popln Biol., 56, 110.
  • 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, 18051809.
  • Goldstein, D. B. (2001) Islands of linkage disequilibrium. Nat. Genet., 29, 109111.
  • Goldstein, D. B. and Schlötterer, C. (eds) (1999) Microsatellites: Evolution and Applications. Oxford: Oxford University Press.
  • Griffiths, R. C. and Marjoram, P. (1997) An ancestral recombination graph. IMA J. Math. Applic., 87, 257270.
  • Griffiths, R. C. and Tavaré, S. (1994) Simulating probability-distributions in the coalescent. Theoret. Popln Biol., 46, 131159.
  • 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, 749761.
  • Handt, O., Meyer, S. and von Haeseler, A. (1998) Compilation of human mtDNA control region sequences. Nucleic Acids Res., 26, 126129.
  • 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, S133S138.
  • Hartl, D. L. and Clark, A. G. (1997) Principles of Population Genetics, 3rd edn. Sunderland: Sinauer.
  • Hasegawa, M., Kishino, H. and Yano, T. (1985) Dating the human-ape splitting by a molecular clock of mitochondrial DNA. J. Molec. Evoln, 22, 160174.
  • Heyer, E., Puymirat, J., Dieltjes, P., Bakker, E. and de Knijff, P. (1997) Estimating Y-chromosome specific microsatellite mutation frequencies using deep rooting phylogenies. Hum. Molec. Genet., 6, 799803.
  • 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.
  • Jorde, L. B., Watkins, W. S. and Bamshad, M. J. (2001) Population genomics: a bridge from evolutionary history to genetic medicine. Hum. Molec. Genet., 10, 21992207.
  • Jukes, T. H. and Cantor, C. R. (1969) Evolution of protein molecules. In Mammalian Protein Metabolism (ed. H. N.Munro), pp. 21132. New York: Academic Press.
  • 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, 15801588.
  • Kingman, J. F. C. (1982) The coalescent. Stoch. Process. Applic., 13, 235248.
  • 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, 1930.
  • Kuhner, M. K., Yamato, J. and Felsenstein, J. (1995) Estimating effective population size from sequence data using Metropolis-Hastings sampling. Genetics, 140, 14211430.
  • Kuhner, M. K., Yamato, J. and Felsenstein, J. (1998) Maximum likelihood estimation of population growth rates based on the coalescent. Genetics, 149, 429434.
  • Kuhner, M. K., Yamato, J. and Felsenstein, J. (2000) Maximum likelihood estimation of recombination rates from population data. Genetics, 156, 13931401.
  • Liu, J. S. (2002) Monte Carlo Strategies in Scientific Computing. New York: Springer.
  • Marjoram, P. and Donnelly, P. (1994) Pairwise comparisons of Mitochondrial DNA sequences in subdivided populations and implications for early human evolution. Genetics, 136, 673683.
  • Markovtsova, L., Marjoram, P. and Tavaré, S. (2000a) The age of a unique event polymorphism. Genetics, 156, 401409.
  • Markovtsova, L., Marjoram, P. and Tavaré, S. (2000b) The effects of rate variation on ancestral inference in the coalescent. Genetics, 156, 14271436.
  • Mau, B., Newton, M. A. and Larget, B. (1999) Bayesian phylogenetic inference via Markov Chain Monte Carlo methods. Biometrics, 55, 112.
  • 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, 11031110.
  • Nielsen, R. (2000) Estimation of population parameters and recombination rates from single nucleotide polymorphisms. Genetics, 154, 931942.
  • Nielsen, R. and Wakeley, J. (2001) Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics, 158, 885896.
  • Nordborg, M. (2001) Coalescent theory. In Handbook of Statistical Genetics (eds D. J.Balding, C.Cannings and M.Bishop), ch. 7. Chichester: Wiley.
  • 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, 490493.
  • 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, 309313.
  • 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, 17911798.
  • Relethford, J. (1998) Genetics of modern human origins and diversity. A. Rev. Anthropol., 27, 123.
  • 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, 3143.
  • Rubin, D. B. and Schenker, N. (1986) Efficiently simulating the coverage properties of interval estimates. Appl. Statist., 35, 159167.
  • Ruiz Linares, A., Nayar, K., Goldstein, D. B., Hebert, J. M., Seielstad, M. T., Underhill, 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, 401408.
  • 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 microsatellite loci on Drosophila Melanogaster. Molec. Evoln, 7, 5770.
  • 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, 19771982.
  • 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, 15991609.
  • 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.
  • Stephens, M. and Donnelly, P. (2000) Inference in molecular population genetics (with discussion). J. R. Statist. Soc. B, 62, 605635.
  • Sykes, B. (1999) The molecular genetics of European ancestry. Phil. Trans. R. Soc. Lond. B, 354, 131139.
  • 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, 73607365.
  • 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, 651658.
  • 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, 8391.
  • 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, 107113.
  • Weber, J. L. and Wong, C. (1993) Mutation of human short tandem repeats. Hum. Molec. Genet., 2, 11231128.
  • Weir, B. S. and Cockerham, C. C. (1984) Estimating F-statistics for the analysis of population structure. Evolution, 38, 13581370.
  • Wilkinson-Herbots, H. M. (1998) Genealogy and subpopulation differentiation under various models of population structure. J. Math. Biol., 37, 535585.
  • Wilson, I. J. and Balding, D. J. (1998) Genealogical inference from microsatellite data. Genetics, 150, 499510.
  • Wright, S. (1931) Evolution in Mendelian populations. Genetics, 16, 97159.