The utility of single nucleotide polymorphisms in inferences of population history

Trends in Ecology and Evolution

Volumn 18, Issue 5, 2003, Pages 249-256

  Brumfield, Robb T ^a   Beerli, Peter ^b   Nickerson, Deborah A ^b   Edwards, Scott V ^b  

^a LOUISIANA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EVOLUTION; GENETIC MARKER; GENOME; POLYMORPHISM;

EID: 0037687926     PISSN: 01695347     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0169-5347(03)00018-1     Document Type: Review

References (78)

1. Avise J.C. Molecular Markers, Natural History and Evolution. 1994;Chapman & Hall.
2. Emerson B.C., et al. Revealing the demographic histories of species using DNA sequences. Trends Ecol. Evol. 16:2001;707-716.
3. Hare M.P. Prospects for nuclear gene phylogeography. Trends Ecol. Evol. 16:2001;700-706.
4. Knowles L.L., Maddison W.P. Statistical phylogeography. Mol. Ecol. 11:2002;2623-2635.
5. Takahata N., Satta Y. Pre-speciation coalescence and the effective size of ancestral populations. Slatkin M., Veuille M. Modern Developments in Theoretical Population Genetics. 2002;52-71 Oxford University Press.
6. Edwards S.V., Beerli P. Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution. 54:2000;1839-1854.
7. Rosenberg N., Nordborg M. Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nat. Rev. Genet. 3:2002;380-390.
8. Wakeley J., Hey J. Estimating ancestral population parameters. Genetics. 145:1997;847-855.
9. Kuhner M.K., et al. Usefulness of single nucleotide polymorphism data for estimating population parameters. Genetics. 156:2000;439-447.
10. Harpending H.C., et al. Genetic traces of ancient demography. Proc. Natl. Acad. Sci. U. S. A. 95:1998;1961-1967.
11. Nielsen R. Estimation of population parameters and recombination rates using single nucleotide polymorphisms. Genetics. 154:2000;931-942.
12. Kliman R.M., et al. The population genetics of the origin and divergence of the Drosophila simulans complex species. Genetics. 156:2000;1913-1931.
13. Machado C.A., et al. Inferring the history of speciation from multilocus DNA sequence data: the case of Drosophila pseudoobscura and close relatives. Mol. Biol. Evol. 19:2002;472-488.
14. Sunnucks P. Efficient genetic markers for population biology. Trends Ecol. Evol. 15:2000;199-203.
15. Collins F.S., et al. A DNA polymorphism discovery resource for research on human genetic variation. Genome Res. 8:1998;1229-1231.
16. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature. 409:2001;928-933.
17. Picoult-Newberg L., et al. Mining SNPs from EST databases. Genome Res. 9:1999;167-174.
18. Brookes A.J. The essence of SNPs. Gene. 234:1999;177-186.
19. Sachidanandam R., et al. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature. 409:2001;928-933.
20. Lindblad-Toh K., et al. Large-scale discovery and genotyping of single-nucleotide polymorphisms in the mouse. Nat. Genet. 24:2000;381-386.
21. Hoskins R.A., et al. Single nucleotide polymorphism markers for genetic mapping in Drosophila melanogaster. Genome Res. 11:2001;1100-1113.
22. Cho R.J., et al. Genome-wide mapping with biallelic markers in Arabidopsis thaliana. Nat. Genet. 23:1999;203-207.
23. Wicks S.R., et al. Rapid gene mapping in Caenorhabditis elegans using a high density polymorphism map. Nat. Genet. 28:2001;160-164.
24. Winzeler E.A., et al. Direct allelic variation scanning of the yeast genome. Science. 281:1998;1194-1197.
25. Barnes M.R. SNP and mutation data on the Web: hidden treasures for uncovering. Comp. Funct. Genomics. 3:2002;67-74.
26. Villablanca F.X., et al. Invasion genetics of the Mediterranean fruit fly: variation in multiple nuclear introns. Mol. Ecol. 7:1998;547-560.
27. Primmer C.R., et al. Single-nucleotide polymorphism characterization in species with limited available sequence information: high nucleotide diversity revealed in the avian genome. Mol. Ecol. 11:2002;603-612.
28. Friesen V.L., et al. PCR primers for the amplification of five nuclear introns in vertebrates. Mol. Ecol. 8:1999;2147-2149.
29. Dietrich W.F., et al. Identification and analysis of DNA polymorphisms. Birren B., et al. Genome Analysis: A Laboratory Manual. 1999;135-186 Cold Spring Harbor Laboratory Press.
30. Karl S.A., Avise J.C. PCR-based assays of Mendelian polymorphisms from anonymous single-copy nuclear DNA: techniques and applications for population genetics. Mol. Biol. Evol. 10:1993;342-361.
31. 2 locus to a simple, codominant, PCR-based marker form. Theor. Appl. Genet. 97:1998;960-967.
32. McLenachan P.A., et al. Markers derived from amplified fragment length polymorphism gels for plant ecology and evolution studies. Mol. Ecol. 9:2000;1899-1903.
33. Fisher R.A. The effects of methods of ascertainment upon the estimation of frequencies. Ann. Hum. Genet. 6:1934;13-25.
34. Wakeley J., et al. The discovery of single-nucleotide polymorphisms- and inferences about human demographic history. Am. J. Hum. Genet. 69:2001;1332-1347.
35. Schlötterer C., Harr B. Single nucleotide polymorphisms derived from ancestral populations show no evidence for biased diversity estimates in Drosophila melanogaster. Mol. Ecol. 11:2002;947-950.
36. Prodohl P.A., et al. Genetic maternity and paternity in a local population of armadillos assessed by microsatellite DNA markers and field data. Am. Nat. 151:1998;7-19.
37. Giordano M., et al. Identification by denaturing high-performance liquid chromatography of numerous polymorphisms in a candidate region for multiple sclerosis susceptibility. Genomics. 56:1999;247-253.
38. Kruglyak L. The use of a genetic map of biallelic markers in linkage studies. Nat. Genet. 17:1997;21-24.
39. Macaubas C., et al. The complex mutation pattern of a microsatellite. Genome Res. 7:1997;635-641.
40. Hedrick P.W. Perspective: highly variable loci and their interpretation in evolution and conservation. Evolution. 53:1999;313-318.
41. Charlesworth B. Measures of divergence between populations and the effect of forces that reduce variability. Mol. Biol. Evol. 15:1998;538-543.
42. Allendorf F.W., Seeb L.W. Concordance of genetic divergence among sockeye salmon populations at allozyme, nuclear DNA, and mitochondrial DNA markers. Evolution. 54:2000;640-651.
43. Wang D.G., et al. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science. 280:1998;1077-1082.
44. Congdon B.C., et al. Mechanisms of population differentiation in marbled murrelets: historical versus contemporary processes. Evolution. 54:2000;974-986.
45. Pluzhnikov A., Donnelly P. Optimal sequencing strategies for surveying molecular genetic diversity. Genetics. 144:1996;1247-1262.
46. Nachman M.W. Single nucleotide polymorphisms and recombination rate in humans. Trends Genet. 17:2001;481-485.
47. Harris E.E., Hey J. X chromosome evidence for ancient human histories. Proc. Natl. Acad. Sci. U. S. A. 96:1999;3320-3324.
48. Kaessmann H., et al. Extensive nuclear DNA sequence diversity among chimpanzees. Science. 286:1999;1159-1162.
49. Yu N., et al. Global patterns of human DNA sequence variation in a 10-kb region on chromosome 1. Mol. Biol. Evol. 18:2001;214-222.
50. Aquadro C.F., et al. Selection, recombination and DNA polymorphism in Drosophila. Golding B., et al. Non-Neutral Evolution: Theories and Molecular Data. 1994;46-56 Chapman & Hall.
51. Lercher M.J., Hurst L.D. Human SNP variability and mutation rate are higher in regions of high recombination. Trends Genet. 18:2002;337-340.
52. Nei M. Molecular Evolutionary Genetics. 1987;Columbia University Press.
53. Hare M.P., et al. Genetic evidence on the demography of speciation in allopatric dolphin species. Evolution. 56:2002;804-816.
54. Watterson G.A. On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7:1975;256-276.
55. Friesen V.L., et al. Intron variation in marbled murrelets detected using analysis of single-stranded conformational polymorphism. Mol. Ecol. 6:1997;1047-1058.
56. Shi L., et al. Comparative DNA sequence analysis of genetic variation in the African grey parrot, Psittacus erythacus. Genetica. 110:2001;227-230.
57. Nei M., Li W. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. U. S. A. 76:1979;5269-5273.
58. Schneider K., et al. SNP frequency and allelic haplotype structure of Beta vulgaris expressed genes. Mol. Breed. 8:2001;63-74.
59. Koufopanou V., et al. Concordance of gene genealogies reveals reproductive isolation in the pathogenic fungus Coccidioides immitis. Proc. Natl. Acad. Sci. U. S. A. 94:1997;5478-5482.
60. Ewing B., et al. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8:1998;175-185.
61. Gordon D., et al. Consed: a graphical tool for sequence finishing. Genome Res. 8:1998;195-202.
62. Marth G.T., et al. A general approach to single-nucleotide polymorphism discovery. Nat. Genet. 23:1999;452-456.
63. Nickerson D.A., et al. PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing. Nucleic Acids Res. 25:1997;2745-2751.
64. Rieder M.J., et al. Automating the identification of DNA variations using quality-based fluorescence re-sequencing: analysis of the human mitochondrial genome. Nucleic Acids Res. 26:1998;967-973.
65. Buetow K.H., et al. Reliable identification of large numbers of candidate SNPs from public EST data. Nat. Genet. 21:1999;323-325.
66. Gasper J.S., et al. Songbird genomics: analysis of 45 kb upstream of a polymorphic MHC class II gene in red-winged blackbirds (Agelaius phoeniceus). Genomics. 75:2001;26-34.
67. Ortí G., et al. Detection and isolation of nuclear haplotypes by PCR-SSCP. Mol. Ecol. 6:1997;575-580.
68. Hare M.P., Palumbi S.R. The accuracy of heterozygous base calling from diploid sequence and resolution of haplotypes using allele-specific sequencing. Mol. Ecol. 8:1999;1750-1752.
69. Clark A.G. Inference of haplotypes from PCR-amplified samples of diploid populations. Mol. Biol. Evol. 7:1990;111-122.
70. Excoffier L., Slatkin M. Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol. Biol. Evol. 12:1995;921-927.
71. Stephens M., et al. A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet. 68:2001;978-989.
72. Kuhner M.K., Felsenstein J. Sampling among haplotype resolutions in a coalescent-based genealogy sampler. Genet. Epidemiol. 19:2000;S15-S21.
73. Nielsen, R. and Signorovitch, J. Correcting for ascertainment biases when analyzing SNP data: applications to the estimation of linkage disequilibrium. Theor. Popul. Biol. (in press).
74. Kuhner M.K., et al. Maximum likelihood estimation of recombination rates from population data. Genetics. 156:2000;1393-1401.
75. Klicka J., Zink R.M. The importance of recent ice ages in speciation: a failed paradigm. Science. 277:1997;1666-1669.
76. Brumfield R.T., et al. Evolutionary implications of divergent clines in an avian (Manacus: Aves) hybrid zone. Evolution. 55:2001;2070-2087.
77. Pluzhnikov A., et al. Inferences about human demography based on multilocus analyses of noncoding sequences. Genetics. 161:2002;1209-1218.
78. Przeworski M., et al. Adjusting the focus on human variation. Trends Genet. 16:2000;296-302.