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Volumn 26, Issue 5, 2009, Pages 1017-1027

Microsatellites are molecular clocks that support accurate inferences about history

Author keywords

Average square distance; Coalescent time; F ST; Microsatellite evolution; Molecular clocks; SNP ascertainment bias

Indexed keywords

AMINO ACID SUBSTITUTION; ARTICLE; CHIMPANZEE; CONTROLLED STUDY; GENE FREQUENCY; GENETIC DISTANCE; GENETIC VARIABILITY; GENOTYPE; HUMAN; MOLECULAR CLOCK; NONHUMAN; SEQUENCE ALIGNMENT; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 65349177267     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msp025     Document Type: Article
Times cited : (61)

References (60)
  • 2
    • 0029684888 scopus 로고    scopus 로고
    • Microsatellites are subject to directional evolution
    • Amos W, Rubinstzein DC. 1996. Microsatellites are subject to directional evolution. Nat Genet. 12:13-14.
    • (1996) Nat Genet , vol.12 , pp. 13-14
    • Amos, W.1    Rubinstzein, D.C.2
  • 5
    • 43249086697 scopus 로고    scopus 로고
    • Caswell JL, Mallick S, Richter DJ, Neubauer J, Schirmer C, Gnerre S, Reich D. 2008. Analysis of chimpanzee history based on genome sequence alignments. PLoS Genet. 4:e1000057.
    • Caswell JL, Mallick S, Richter DJ, Neubauer J, Schirmer C, Gnerre S, Reich D. 2008. Analysis of chimpanzee history based on genome sequence alignments. PLoS Genet. 4:e1000057.
  • 6
    • 0037370384 scopus 로고    scopus 로고
    • The application of molecular genetic approaches to the study of human evolution
    • Cavalli-Sforza LL, Feldman MW. 2003. The application of molecular genetic approaches to the study of human evolution. Nat Genet. 33(Suppl):266-275.
    • (2003) Nat Genet , vol.33 , Issue.SUPPL. , pp. 266-275
    • Cavalli-Sforza, L.L.1    Feldman, M.W.2
  • 7
    • 24344500211 scopus 로고    scopus 로고
    • Initial sequence of the chimpanzee genome and comparison with the human genome
    • Chimpanzee Sequencing and Analysis Consortium
    • Chimpanzee Sequencing and Analysis Consortium. 2005. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature. 437:69-87.
    • (2005) Nature , vol.437 , pp. 69-87
  • 11
    • 13344259999 scopus 로고    scopus 로고
    • Dib C, Faure S, Fizames C, et al. (13 co-authors). 1996. A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature. 380:152-154.
    • Dib C, Faure S, Fizames C, et al. (13 co-authors). 1996. A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature. 380:152-154.
  • 12
    • 84945737762 scopus 로고
    • A leisurely look at the bootstrap, the jackknife, and cross-validation
    • Efron B, Gong G. 1983. A leisurely look at the bootstrap, the jackknife, and cross-validation. Am Stat. 37:36-48.
    • (1983) Am Stat , vol.37 , pp. 36-48
    • Efron, B.1    Gong, G.2
  • 13
    • 0034564097 scopus 로고    scopus 로고
    • Microsatellite mutations in the germline: Implications for evolutionary inference
    • Ellegren H. 2000. Microsatellite mutations in the germline: implications for evolutionary inference. Trends Genet. 16:551-558.
    • (2000) Trends Genet , vol.16 , pp. 551-558
    • Ellegren, H.1
  • 14
    • 3042782819 scopus 로고    scopus 로고
    • Microsatellites: Simple sequences with complex evolution
    • Ellegren H. 2004. Microsatellites: simple sequences with complex evolution. Nat Rev Genet. 5:435-445.
    • (2004) Nat Rev Genet , vol.5 , pp. 435-445
    • Ellegren, H.1
  • 15
    • 0031015402 scopus 로고    scopus 로고
    • Microsatellite genetic distances with range constraints: Analytic description and problems of estimation
    • Feldman MW, Bergman A, Pollock DD, Goldstein DB. 1997. Microsatellite genetic distances with range constraints: analytic description and problems of estimation. Genetics. 145:207-216.
    • (1997) Genetics , vol.145 , pp. 207-216
    • Feldman, M.W.1    Bergman, A.2    Pollock, D.D.3    Goldstein, D.B.4
  • 17
    • 38949170720 scopus 로고    scopus 로고
    • The genetic structure of Pacific Islanders. PLoS Genet
    • 11 coauthors
    • Friedlaender JS, Friedlaender FR, Reed FA, et al. (11 coauthors). 2008. The genetic structure of Pacific Islanders. PLoS Genet. 4:e19.
    • (2008) , vol.4
    • Friedlaender, J.S.1    Friedlaender, F.R.2    Reed, F.A.3
  • 18
    • 0030983892 scopus 로고    scopus 로고
    • Launching microsatellites: A review of mutation processes and methods of phylogenetic interference
    • Goldstein DB, Pollock DD. 1997. Launching microsatellites: a review of mutation processes and methods of phylogenetic interference. J Hered. 88:335-342.
    • (1997) J Hered , vol.88 , pp. 335-342
    • Goldstein, D.B.1    Pollock, D.D.2
  • 21
    • 0036184745 scopus 로고    scopus 로고
    • Generating samples under a Wright-Fisher neutral model of genetic variation
    • Hudson RR. 2002. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics. 18:337-338.
    • (2002) Bioinformatics , vol.18 , pp. 337-338
    • Hudson, R.R.1
  • 22
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • International Human Genome Sequencing Consortium
    • International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature. 409:860-921.
    • (2001) Nature , vol.409 , pp. 860-921
  • 23
    • 58149151065 scopus 로고    scopus 로고
    • Accelerated genetic drift on chromosome X during the human dispersal out of Africa
    • Keinan A, Mullikin JC, Patterson N, Reich D. 2008. Accelerated genetic drift on chromosome X during the human dispersal out of Africa. Nat Genet. 41:66-70.
    • (2008) Nat Genet , vol.41 , pp. 66-70
    • Keinan, A.1    Mullikin, J.C.2    Patterson, N.3    Reich, D.4
  • 24
    • 34748819978 scopus 로고    scopus 로고
    • Measurement of the human allele frequency spectrum demonstrates greater genetic drift in East Asians than in Europeans
    • Keinan A, Mullikin JC, Patterson N, Reich D. 2007. Measurement of the human allele frequency spectrum demonstrates greater genetic drift in East Asians than in Europeans. Nat Genet. 39:1251-1255.
    • (2007) Nat Genet , vol.39 , pp. 1251-1255
    • Keinan, A.1    Mullikin, J.C.2    Patterson, N.3    Reich, D.4
  • 25
    • 0030447670 scopus 로고    scopus 로고
    • Measures of variation at DNA repeat loci under a general stepwise mutation model
    • Kimmel M, Chakraborty R. 1996. Measures of variation at DNA repeat loci under a general stepwise mutation model. Theor Popul Biol. 50:345-367.
    • (1996) Theor Popul Biol , vol.50 , pp. 345-367
    • Kimmel, M.1    Chakraborty, R.2
  • 27
    • 0032168989 scopus 로고    scopus 로고
    • Equilibrium distributions of microsatellite repeat length resulting from a balance between slippage events and point mutations
    • Kruglyak S, Durrett RT, Schug MD, Aquadro CF. 1998. Equilibrium distributions of microsatellite repeat length resulting from a balance between slippage events and point mutations. Proc Natl Acad Sci USA. 95:10774-10778.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 10774-10778
    • Kruglyak, S.1    Durrett, R.T.2    Schug, M.D.3    Aquadro, C.F.4
  • 28
    • 0023649836 scopus 로고
    • High frequencies of short frameshifts in poly-CA/TG tandem repeats borne by bacte-riophage M13 in Escherichia coli K-12
    • Levinson G, Gutman GA. 1987. High frequencies of short frameshifts in poly-CA/TG tandem repeats borne by bacte-riophage M13 in Escherichia coli K-12. Nucleic Acids Res. 15:5323-5338.
    • (1987) Nucleic Acids Res , vol.15 , pp. 5323-5338
    • Levinson, G.1    Gutman, G.A.2
  • 29
    • 39749181521 scopus 로고    scopus 로고
    • Li JZ, Absher DM, Tang H, et al. (10 co-authors). 2008. Worldwide human relationships inferred from genome-wide patterns of variation. Science. 319:1100-1104.
    • Li JZ, Absher DM, Tang H, et al. (10 co-authors). 2008. Worldwide human relationships inferred from genome-wide patterns of variation. Science. 319:1100-1104.
  • 30
    • 0030070216 scopus 로고    scopus 로고
    • Constraints on allele size at microsatellite loci: Implications for genetic differentiation
    • Nauta MJ, Weissing FJ. 1996. Constraints on allele size at microsatellite loci: implications for genetic differentiation. Genetics. 143:1021-1032.
    • (1996) Genetics , vol.143 , pp. 1021-1032
    • Nauta, M.J.1    Weissing, F.J.2
  • 31
    • 0034764307 scopus 로고    scopus 로고
    • SSAHA: A fast search method for large DNA databases
    • Ning Z, Cox AJ, Mullikin JC. 2001. SSAHA: a fast search method for large DNA databases. Genome Res. 11:1725-1729.
    • (2001) Genome Res , vol.11 , pp. 1725-1729
    • Ning, Z.1    Cox, A.J.2    Mullikin, J.C.3
  • 32
    • 0015765702 scopus 로고
    • A model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a finite population
    • Ohta T, Kimura M. 1973. A model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a finite population. Genet Res. 22:201-204.
    • (1973) Genet Res , vol.22 , pp. 201-204
    • Ohta, T.1    Kimura, M.2
  • 33
    • 0030782517 scopus 로고    scopus 로고
    • An empirical evaluation of genetic distance statistics using microsatellite data from bear (Ursidae) populations
    • Paetkau D, Waits LP, Clarkson PL, Craighead L, Strobeck C. 1997. An empirical evaluation of genetic distance statistics using microsatellite data from bear (Ursidae) populations. Genetics. 147:1943-1957.
    • (1997) Genetics , vol.147 , pp. 1943-1957
    • Paetkau, D.1    Waits, L.P.2    Clarkson, P.L.3    Craighead, L.4    Strobeck, C.5
  • 35
    • 33745591114 scopus 로고    scopus 로고
    • Genetic evidence for complex speciation of humans and chimpanzees
    • Patterson N, Richter DJ, Gnerre S, Lander ES, Reich D. 2006. Genetic evidence for complex speciation of humans and chimpanzees. Nature. 441:1103-1108.
    • (2006) Nature , vol.441 , pp. 1103-1108
    • Patterson, N.1    Richter, D.J.2    Gnerre, S.3    Lander, E.S.4    Reich, D.5
  • 36
    • 27644509150 scopus 로고    scopus 로고
    • Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa
    • Ramachandran S, Deshpande O, Roseman CC, Rosenberg NA, Feldman MW, Cavalli-Sforza LL. 2005. Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. Proc Natl Acad Sci USA. 102:15942-15947.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 15942-15947
    • Ramachandran, S.1    Deshpande, O.2    Roseman, C.C.3    Rosenberg, N.A.4    Feldman, M.W.5    Cavalli-Sforza, L.L.6
  • 37
    • 55949085425 scopus 로고    scopus 로고
    • Population differentiation and migration: Coalescence times in a two-sex island model for autosomal and X-linked loci
    • Ramachandran S, Rosenberg NA, Feldman MW, Wakeley J. 2008. Population differentiation and migration: coalescence times in a two-sex island model for autosomal and X-linked loci. Theor Popul Biol. 74:291-301.
    • (2008) Theor Popul Biol , vol.74 , pp. 291-301
    • Ramachandran, S.1    Rosenberg, N.A.2    Feldman, M.W.3    Wakeley, J.4
  • 38
    • 0032493379 scopus 로고    scopus 로고
    • Genetic evidence for a Paleolithic human population expansion in Africa
    • Reich DE, Goldstein DB. 1998. Genetic evidence for a Paleolithic human population expansion in Africa. Proc Natl Acad Sci USA. 95:8119-8123.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 8119-8123
    • Reich, D.E.1    Goldstein, D.B.2
  • 39
    • 59249102648 scopus 로고    scopus 로고
    • Reich D, Nalls MA, Kao WHL, et al. (20 co-authors). 2009. Reduced neutrophil count in people of African descent is due to a regulatory variant in the Duffy Antigen Receptor for Chemokines gene. PLoS Genetics. 5, e1000360.
    • Reich D, Nalls MA, Kao WHL, et al. (20 co-authors). 2009. Reduced neutrophil count in people of African descent is due to a regulatory variant in the Duffy Antigen Receptor for Chemokines gene. PLoS Genetics. 5, e1000360.
  • 41
    • 0036515730 scopus 로고    scopus 로고
    • The probability of topological concordance of gene trees and species trees
    • Rosenberg NA. 2002. The probability of topological concordance of gene trees and species trees. Theor Popul Biol. 61:225-247.
    • (2002) Theor Popul Biol , vol.61 , pp. 225-247
    • Rosenberg, N.A.1
  • 42
    • 33749575795 scopus 로고    scopus 로고
    • Standardized subsets of the HGDP - CEPH Human Genome Diversity Cell Line Panel, accounting for atypical and duplicated samples and pairs of close relatives
    • Rosenberg NA. 2006. Standardized subsets of the HGDP - CEPH Human Genome Diversity Cell Line Panel, accounting for atypical and duplicated samples and pairs of close relatives. Ann Hum Genet. 70:841-847.
    • (2006) Ann Hum Genet , vol.70 , pp. 841-847
    • Rosenberg, N.A.1
  • 43
    • 33845994051 scopus 로고    scopus 로고
    • Rosenberg NA, Mahajan S, Gonzalez-Quevedo C, et al. (12 coauthors). 2006. Low levels of genetic divergence across geographically and linguistically diverse populations from India. PLoS Genet. 2:e215.
    • Rosenberg NA, Mahajan S, Gonzalez-Quevedo C, et al. (12 coauthors). 2006. Low levels of genetic divergence across geographically and linguistically diverse populations from India. PLoS Genet. 2:e215.
  • 46
    • 5144224893 scopus 로고    scopus 로고
    • Micro-satellite mutation models: Insights from a comparison of humans and chimpanzees
    • Sainudiin R, Durrett RT, Aquadro CF, Nielsen R. 2004. Micro-satellite mutation models: insights from a comparison of humans and chimpanzees. Genetics. 168:383-395.
    • (2004) Genetics , vol.168 , pp. 383-395
    • Sainudiin, R.1    Durrett, R.T.2    Aquadro, C.F.3    Nielsen, R.4
  • 48
    • 0028816747 scopus 로고
    • A measure of population subdivision based on microsatellite allele frequencies
    • Slatkin M. 1995. A measure of population subdivision based on microsatellite allele frequencies. Genetics. 139:457-462.
    • (1995) Genetics , vol.139 , pp. 457-462
    • Slatkin, M.1
  • 49
    • 0026050476 scopus 로고
    • Inbreeding coefficients and coalescence times
    • Slatkin M. 1991. Inbreeding coefficients and coalescence times. Genet Res. 58:167-175.
    • (1991) Genet Res , vol.58 , pp. 167-175
    • Slatkin, M.1
  • 50
    • 54949147974 scopus 로고    scopus 로고
    • ADZE: A rarefaction approach for counting alleles private to combinations of populations
    • Szpiech ZA, Jakobsson M, Rosenberg NA. 2008. ADZE: a rarefaction approach for counting alleles private to combinations of populations. Bioinformatics. 24:2498-2504.
    • (2008) Bioinformatics , vol.24 , pp. 2498-2504
    • Szpiech, Z.A.1    Jakobsson, M.2    Rosenberg, N.A.3
  • 51
    • 0027474097 scopus 로고
    • Allele frequencies at microsatellite loci: The stepwise mutation model revisited
    • Valdes AM, Slatkin M, Freimer NB. 1993. Allele frequencies at microsatellite loci: the stepwise mutation model revisited. Genetics. 133:737-749.
    • (1993) Genetics , vol.133 , pp. 737-749
    • Valdes, A.M.1    Slatkin, M.2    Freimer, N.B.3
  • 52
    • 37349025758 scopus 로고    scopus 로고
    • Genetic variation and population structure in native Americans. PLoS Genet
    • 26 co-authors
    • Wang S, Lewis CM, Jakobsson M, et al. (26 co-authors). 2007. Genetic variation and population structure in native Americans. PLoS Genet. 3:e185.
    • (2007) , vol.3
    • Wang, S.1    Lewis, C.M.2    Jakobsson, M.3
  • 53
    • 41949133594 scopus 로고    scopus 로고
    • Wang S, Ray N, Rojas W, et al. (27 co-authors). 2008. Geographic patterns of genome admixture in Latin American Mestizos. PLoS Genet. 4:e1000037.
    • Wang S, Ray N, Rojas W, et al. (27 co-authors). 2008. Geographic patterns of genome admixture in Latin American Mestizos. PLoS Genet. 4:e1000037.
  • 54
    • 0035228946 scopus 로고    scopus 로고
    • Genotyping for human whole-genome scans: Past, present, and future
    • Weber JL, Broman KW. 2001. Genotyping for human whole-genome scans: past, present, and future. Adv Genet. 42:77-96.
    • (2001) Adv Genet , vol.42 , pp. 77-96
    • Weber, J.L.1    Broman, K.W.2
  • 55
    • 0030950735 scopus 로고    scopus 로고
    • Human whole-genome shotgun sequencing
    • Weber JL, Myers EW. 1997. Human whole-genome shotgun sequencing. Genome Res. 7:401-409.
    • (1997) Genome Res , vol.7 , pp. 401-409
    • Weber, J.L.1    Myers, E.W.2
  • 56
    • 0027161022 scopus 로고
    • Mutation of human short tandem repeats
    • Weber JL, Wong C. 1993. Mutation of human short tandem repeats. Hum Mol Genet. 2:1123-1128.
    • (1993) Hum Mol Genet , vol.2 , pp. 1123-1128
    • Weber, J.L.1    Wong, C.2
  • 57
    • 0034111151 scopus 로고    scopus 로고
    • The direction of microsatellite mutations is dependent upon allele length
    • Xu X, Peng M, Fang Z. 2000. The direction of microsatellite mutations is dependent upon allele length. Nat Genet. 24:396-399.
    • (2000) Nat Genet , vol.24 , pp. 396-399
    • Xu, X.1    Peng, M.2    Fang, Z.3
  • 58
    • 0035042266 scopus 로고    scopus 로고
    • Estimating divergence time with the use of microsatellite genetic distances: Impacts of population growth and gene flow
    • Zhivotovsky LA. 2001. Estimating divergence time with the use of microsatellite genetic distances: impacts of population growth and gene flow. Mol Biol Evol. 18:700-709.
    • (2001) Mol Biol Evol , vol.18 , pp. 700-709
    • Zhivotovsky, L.A.1
  • 59
    • 0038744254 scopus 로고    scopus 로고
    • Features of evolution and expansion of modern humans, inferred from genomewide microsatellite markers
    • Zhivotovsky LA, Rosenberg NA, Feldman MW. 2003. Features of evolution and expansion of modern humans, inferred from genomewide microsatellite markers. Am J Hum Genet. 72:1171-1186.
    • (2003) Am J Hum Genet , vol.72 , pp. 1171-1186
    • Zhivotovsky, L.A.1    Rosenberg, N.A.2    Feldman, M.W.3
  • 60
    • 0002331493 scopus 로고
    • Molecular disease, evolution, and genetic heterogeneity
    • Kasha M, Pullman B, editors, New York: Academic Press. p
    • Zuckerkandl E, Pauling L. 1962. Molecular disease, evolution, and genetic heterogeneity. In: Kasha M, Pullman B, editors. Horizons in biochemistry. New York: Academic Press. p. 189-225.
    • (1962) Horizons in biochemistry , pp. 189-225
    • Zuckerkandl, E.1    Pauling, L.2


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