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Volumn 19, Issue 11, 2009, Pages 1929-1941

Phylogenomics of primates and their ancestral populations

Author keywords

[No Author keywords available]

Indexed keywords

DNA SEQUENCE; GENOMICS; HUMAN; MUTATIONAL ANALYSIS; NATURAL SELECTION; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENY; POPULATION DYNAMICS; PRIMATE; PRIORITY JOURNAL; REVIEW; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SPECIES DIFFERENTIATION;

EID: 70350714430     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.084228.108     Document Type: Review
Times cited : (51)

References (104)
  • 1
    • 0042208362 scopus 로고    scopus 로고
    • Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites
    • Anisimova M, Nielsen R, Yang Z. 2003. Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics 164: 1229-1236. (Pubitemid 36935693)
    • (2003) Genetics , vol.164 , Issue.3 , pp. 1229-1236
    • Anisimova, M.1    Nielsen, R.2    Yang, Z.3
  • 2
    • 55449127787 scopus 로고    scopus 로고
    • Predicting functional gene links from phylogenetic-statistical analyses of whole genomes
    • doi: 10.1371/journal.pcbi.0010003
    • Barker D, Pagel M. 2005. Predicting functional gene links from phylogenetic-statistical analyses of whole genomes. PLoS Comput Biol 1: e3. doi: 10.1371/journal.pcbi.0010003.
    • (2005) PLoS Comput Biol , vol.1
    • Barker, D.1    Pagel, M.2
  • 3
    • 33747180898 scopus 로고    scopus 로고
    • Evolutionary biology: How did the human species form?
    • Barton NH. 2006. Evolutionary biology: How did the human species form? Curr Biol 16: R647-R650.
    • (2006) Curr Biol , vol.16
    • Barton, N.H.1
  • 4
    • 0035836728 scopus 로고    scopus 로고
    • Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach
    • DOI 10.1073/pnas.081068098
    • Beerli P, Felsenstein J. 2001. Maximumlikelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proc Natl Acad Sci 98: 4563-4568. (Pubitemid 32295016)
    • (2001) Proceedings of the National Academy of Sciences of the United States of America , vol.98 , Issue.8 , pp. 4563-4568
    • Beerli, P.1    Felsenstein, J.2
  • 5
    • 0242418246 scopus 로고    scopus 로고
    • Phylogenetic shadowing of primate sequences to find functional regions of the human genome
    • DOI 10.1126/science.1081331
    • Boffelli D, McAuliffe J, Ovcharenko D, Lewis KD, Ovcharenko I, Pachter L, Rubin EM. 2003. Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science 299: 1391-1394. (Pubitemid 36254651)
    • (2003) Science , vol.299 , Issue.5611 , pp. 1391-1394
    • Boffelli, D.1    McAuliffe, J.2    Ovcharenko, D.3    Lewis, K.D.4    Ovcharenko, I.5    Pachter, L.6    Rubin, E.M.7
  • 6
    • 49749142953 scopus 로고    scopus 로고
    • Estimation of hominoid ancestral population sizes under bayesian coalescent models incorporating mutation rate variation and sequencing errors
    • Burgess R, Yang Z. 2008. Estimation of hominoid ancestral population sizes under bayesian coalescent models incorporating mutation rate variation and sequencing errors. Mol Biol Evol 25: 1979-1994.
    • (2008) Mol Biol Evol , vol.25 , pp. 1979-1994
    • Burgess, R.1    Yang, Z.2
  • 8
    • 0027305597 scopus 로고
    • The effect of deleterious mutations on neutral molecular variation
    • Charlesworth B, Morgan MT, Charlesworth D. 1993. The effect of deleterious mutations on neutral molecular variation. Genetics 134: 1289-1303. (Pubitemid 23220050)
    • (1993) Genetics , vol.134 , Issue.4 , pp. 1289-1303
    • Charlesworth, B.1    Morgan, M.T.2    Charlesworth, D.3
  • 9
    • 0035130163 scopus 로고    scopus 로고
    • Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees
    • Chen F-C, Li W-H. 2001. Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. Am J Hum Genet 68: 444-456.
    • (2001) Am J Hum Genet , vol.68 , pp. 444-456
    • Chen, F.-C.1    Li, W.-H.2
  • 13
    • 22244452677 scopus 로고    scopus 로고
    • Distribution and intensity of constraint in mammalian genomic sequence
    • DOI 10.1101/gr.3577405
    • Cooper GM, Stone EA, Asimenos G, Green ED, Batzoglou S, Sidow A. 2005. Distribution and intensity of constraint in mammalian genomic sequence. Genome Res 15: 901-913. (Pubitemid 40994210)
    • (2005) Genome Research , vol.15 , Issue.7 , pp. 901-913
    • Cooper, G.M.1    Stone, E.A.2    Asimenos, G.3    Green, E.D.4    Batzoglou, S.5    Sidow, A.6
  • 14
    • 59249106248 scopus 로고    scopus 로고
    • Copy number variation of CCL3-like genes affects rate of progression to simian-AIDS in Rhesus Macaques (Macaca mulatta)
    • doi: 10.1371/journal.pgen.1000346
    • Degenhardt JD, de Candia P, Chabot A, Schwartz S, Henderson L, Ling B, Hunter M, Jiang Z, Palermo RE, Katze M, et al. 2009. Copy number variation of CCL3-like genes affects rate of progression to simian-AIDS in Rhesus Macaques (Macaca mulatta). PLoS Genet 5: e1000346. doi: 10.1371/journal.pgen.1000346.
    • (2009) PLoS Genet , vol.5
    • Degenhardt, J.D.1    De Candia, P.2    Chabot, A.3    Schwartz, S.4    Henderson, L.5    Ling, B.6    Hunter, M.7    Jiang, Z.8    Palermo, R.E.9    Katze, M.10
  • 15
    • 33646928341 scopus 로고    scopus 로고
    • Discordance of species trees with their most likely gene trees
    • doi: 10.1371/ journal.pgen.0020068
    • Degnan JH, Rosenberg NA. 2006. Discordance of species trees with their most likely gene trees. PLoS Genet 2: e68. doi: 10.1371/ journal.pgen.0020068.
    • (2006) PLoS Genet , vol.2
    • Degnan, J.H.1    Rosenberg, N.A.2
  • 16
    • 0038518196 scopus 로고    scopus 로고
    • Phylogenomics: Intersection of evolution and genomics
    • Eisen JA, Fraser CM. 2003. Phylogenomics: Intersection of evolution and genomics. Science 300: 1706-1707.
    • (2003) Science , vol.300 , pp. 1706-1707
    • Eisen, J.A.1    Fraser, C.M.2
  • 18
    • 34250305146 scopus 로고    scopus 로고
    • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    • The ENCODE Project Consortium
    • The ENCODE Project Consortium. 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816.
    • (2007) Nature , vol.447 , pp. 799-816
  • 19
    • 33645310990 scopus 로고    scopus 로고
    • Protein molecular function prediction by Bayesian phylogenomics
    • doi: 10.1371/journal.pcbi.0010045
    • Engelhardt BE, Jordan MI, Muratore KE, Brenner SE. 2005. Protein molecular function prediction by Bayesian phylogenomics. PLoS Comput Biol 1: e45. doi: 10.1371/journal.pcbi.0010045.
    • (2005) PLoS Comput Biol , vol.1
    • Engelhardt, B.E.1    Jordan, M.I.2    Muratore, K.E.3    Brenner, S.E.4
  • 20
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences
    • Felsenstein J. 1981. Evolutionary trees from DNA sequences. J Mol Evol 17: 368-376.
    • (1981) J Mol Evol , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 21
    • 0002918460 scopus 로고
    • On the problem of discovering the most parsimonious tree
    • Fitch W. 1977. On the problem of discovering the most parsimonious tree. Am Nat 111: 223-257.
    • (1977) Am Nat , vol.111 , pp. 223-257
    • Fitch, W.1
  • 22
    • 0037357461 scopus 로고    scopus 로고
    • Estimation of divergence times for major lineages of primate species
    • DOI 10.1093/molbev/msg050
    • Glazko GV, Nei M. 2003. Estimation of divergence times for major lineages of primate species. Mol Biol Evol 20: 424-434. (Pubitemid 36427177)
    • (2003) Molecular Biology and Evolution , vol.20 , Issue.3 , pp. 424-434
    • Glazko, G.V.1    Nei, M.2
  • 23
    • 0033360816 scopus 로고    scopus 로고
    • The genomic record of humankind's evolutionary roots
    • DOI 10.1086/302218
    • Goodman M. 1999. The genomic record of Humankind's evolutionary roots. Am J Hum Genet 64: 31-39. (Pubitemid 30428954)
    • (1999) American Journal of Human Genetics , vol.64 , Issue.1 , pp. 31-39
    • Goodman, M.1
  • 24
    • 23644459637 scopus 로고    scopus 로고
    • Moving primate genomics beyond the chimpanzee genome
    • DOI 10.1016/j.tig.2005.06.012, PII S0168952505001897
    • Goodman M, Grossman LI, Wildman DE. 2005. Moving primate genomics beyond the chimpanzee genome. Trends Genet 21: 511-517. (Pubitemid 41132586)
    • (2005) Trends in Genetics , vol.21 , Issue.9 , pp. 511-517
    • Goodman, M.1    Grossman, L.I.2    Wildman, D.E.3
  • 25
    • 0030498194 scopus 로고    scopus 로고
    • Ancestral inference from samples of DNA sequences with recombination
    • Griffiths RC, Marjoram P. 1996. Ancestral inference from samples of DNA sequences with recombination. J Comput Biol 3: 479-502.
    • (1996) J Comput Biol , vol.3 , pp. 479-502
    • Griffiths, R.C.1    Marjoram, P.2
  • 26
    • 0000557367 scopus 로고    scopus 로고
    • An ancestral recombination graph
    • eds. P Donnelly and S Tavaré Springer Verlag, New York
    • Griffiths R, Marjoram P. 1997. An ancestral recombination graph. In Progress in population genetics and human evolution (eds. P Donnelly and S Tavaré), pp. 257-270. Springer Verlag, New York.
    • (1997) Progress in Population Genetics and Human Evolution , pp. 257-270
    • Griffiths, R.1    Marjoram, P.2
  • 27
    • 33645979674 scopus 로고    scopus 로고
    • Using multiple alignments to improve gene prediction
    • Gross SS, Brent MR. 2006. Using multiple alignments to improve gene prediction. J Comput Biol 13: 379-393.
    • (2006) J Comput Biol , vol.13 , pp. 379-393
    • Gross, S.S.1    Brent, M.R.2
  • 28
    • 23744452485 scopus 로고    scopus 로고
    • Estimating the tempo and mode of gene family evolution from comparative genomic data
    • DOI 10.1101/gr.3567505
    • Hahn MW, De Bie T, Stajich JE, Nguyen C, Cristianini N. 2005. Estimating the tempo and mode of gene family evolution from comparative genomic data. Genome Res 15: 1153-1160. (Pubitemid 41126871)
    • (2005) Genome Research , vol.15 , Issue.8 , pp. 1153-1160
    • Hahn, M.W.1    De Bie, T.2    Stajich, J.E.3    Nguyen, C.4    Cristianini, N.5
  • 29
    • 52949083951 scopus 로고    scopus 로고
    • Sex-biased evolutionary forces shape genomic patterns of human diversity
    • doi: 10.1371/journal.pgen.1000202
    • Hammer MF, Mendez FL, Cox MP, Woerner AE, Wall JD. 2008. Sex-biased evolutionary forces shape genomic patterns of human diversity. PLoS Genet 4: e1000202. doi: 10.1371/journal.pgen.1000202.
    • (2008) PLoS Genet , vol.4
    • Hammer, M.F.1    Mendez, F.L.2    Cox, M.P.3    Woerner, A.E.4    Wall, J.D.5
  • 31
    • 46449121800 scopus 로고    scopus 로고
    • Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals
    • DOI 10.1101/gr.074187.107
    • Hellmann I, Mang Y, Gu Z, Li P, de la Vega FM, Clark AG, Nielsen R. 2008. Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals. Genome Res 18: 1020-1029. (Pubitemid 351931153)
    • (2008) Genome Research , vol.18 , Issue.7 , pp. 1020-1029
    • Hellmann, I.1    Mang, Y.2    Gu, Z.3    Li, P.4    De La Vega, F.M.5    Clark, A.G.6    Nielsen, R.7
  • 32
    • 33847253862 scopus 로고    scopus 로고
    • Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model
    • DOI 10.1371/journal.pgen.0030007
    • Hobolth A, Christensen OF, Mailund T, Schierup MH. 2007. Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model. PLoS Genet 3: e7. doi: 10.1371/journal.pgen.0030007. (Pubitemid 46318408)
    • (2007) PLoS Genetics , vol.3 , Issue.2 , pp. 294-304
    • Hobolth, A.1    Christensen, O.F.2    Mailund, T.3    Schierup, M.H.4
  • 33
    • 0000424609 scopus 로고
    • Testing the constant-rate neutral allele model with protein sequence data
    • Hudson R. 1983a. Testing the constant-rate neutral allele model with protein sequence data. Evolution 37: 203-217.
    • (1983) Evolution , vol.37 , pp. 203-217
    • Hudson, R.1
  • 34
    • 0020744702 scopus 로고
    • Properties of a neutral allele model with intragenic recombination
    • Hudson RR. 1983b. Properties of a neutral allele model with intragenic recombination. Theor Popul Biol 23: 183-201.
    • (1983) Theor Popul Biol , vol.23 , pp. 183-201
    • Hudson, R.R.1
  • 35
    • 0030902563 scopus 로고    scopus 로고
    • Phylogenetic methods come of age: Testing hypotheses in an evolutionary context
    • DOI 10.1126/science.276.5310.227
    • Huelsenbeck J, Rannala B. 1997. Phylogenetic methods come of age: Testing hypotheses in an evolutionary context. Science 276: 227-232. (Pubitemid 27172674)
    • (1997) Science , vol.276 , Issue.5310 , pp. 227-232
    • Huelsenbeck, J.P.1    Rannala, B.2
  • 36
    • 4644300141 scopus 로고    scopus 로고
    • Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution
    • DOI 10.1073/pnas.0404142101
    • Hwang D, Green P. 2004. Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution. Proc Natl Acad Sci 101: 13994-14001. (Pubitemid 39305018)
    • (2004) Proceedings of the National Academy of Sciences of the United States of America , vol.101 , Issue.39 , pp. 13994-14001
    • Hwang, D.G.1    Green, P.2
  • 37
    • 33646555436 scopus 로고    scopus 로고
    • The effect of gene flow on the coalescent time in the human-chimpanzee ancestral population
    • DOI 10.1093/molbev/msj109
    • Innan H, Watanabe H. 2006. The effect of gene flow on the coalescent time in the human-chimpanzee ancestral population. Mol Biol Evol 23: 1040-1047. (Pubitemid 43726069)
    • (2006) Molecular Biology and Evolution , vol.23 , Issue.5 , pp. 1040-1047
    • Innan, H.1    Watanabe, H.2
  • 39
    • 0035565654 scopus 로고    scopus 로고
    • Modern African ape populations as genetic and demographic models of the last common ancestor of humans, chimpanzees, and gorillas
    • Jensen-Seaman MI, Deinard AS, Kidd KK. 2001. Modern African ape populations as genetic and demographic models of the last common ancestor of humans, chimpanzees, and gorillas. J Hered 92: 475-480.
    • (2001) J Hered , vol.92 , pp. 475-480
    • Jensen-Seaman, M.I.1    Deinard, A.S.2    Kidd, K.K.3
  • 40
    • 47649104484 scopus 로고    scopus 로고
    • Horizontal gene transfer in eukaryotic evolution
    • Keeling PJ, Palmer JD. 2008. Horizontal gene transfer in eukaryotic evolution. Nat Rev Genet 9: 605-618.
    • (2008) Nat Rev Genet , vol.9 , pp. 605-618
    • Keeling, P.J.1    Palmer, J.D.2
  • 41
    • 15744388330 scopus 로고    scopus 로고
    • Evidence for widespread degradation of gene control regions in hominid genomes
    • DOI 10.1371/journal.pbio.0030042, e42
    • Keightley PD, Lercher MJ, Eyre-Walker A. 2005. Evidence for widespread degradation of gene control regions in hominid genomes. PLoS Biol 3: e42. doi: 10.1371/journal.pbio.0030042. (Pubitemid 40412647)
    • (2005) PLoS Biology , vol.3 , Issue.2 , pp. 282-288
    • Keightley, P.D.1    Lercher, M.J.2    Eyre-Walker, A.3
  • 42
    • 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. 2009. Accelerated genetic drift on chromosome X during the human dispersal out of Africa. Nat Genet 41: 66-70.
    • (2009) Nat Genet , vol.41 , pp. 66-70
    • Keinan, A.1    Mullikin, J.C.2    Patterson, N.3    Reich, D.4
  • 43
    • 0038349948 scopus 로고    scopus 로고
    • Sequencing and comparison of yeast species to identify genes and regulatory elements
    • DOI 10.1038/nature01644
    • Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES. 2003. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423: 241-254. (Pubitemid 40852689)
    • (2003) Nature , vol.423 , Issue.6937 , pp. 241-254
    • Kellis, M.1    Patterson, N.2    Endrizzi, M.3    Birren, B.4    Lander, E.S.5
  • 44
    • 0002556819 scopus 로고
    • On the genealogy of large populations
    • Kingman J. 1982a. On the genealogy of large populations. J Appl Probab 19A: 27-43.
    • (1982) J Appl Probab , vol.19 A , pp. 27-43
    • Kingman, J.1
  • 46
    • 33847302458 scopus 로고    scopus 로고
    • Inconsistency of phylogenetic estimates from concatenated data under coalescence
    • Kubatko LS, Degnan JH. 2007. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst Biol 56: 17-24.
    • (2007) Syst Biol , vol.56 , pp. 17-24
    • Kubatko, L.S.1    Degnan, J.H.2
  • 47
    • 0033756316 scopus 로고    scopus 로고
    • Maximum likelihood estimation of recombination rates from population data
    • Kuhner MK, Yamato J, Felsenstein J. 2000. Maximum likelihood estimation of recombination rates from population data. Genetics 156: 1393-1401. (Pubitemid 30826512)
    • (2000) Genetics , vol.156 , Issue.3 , pp. 1393-1401
    • Kuhner, M.K.1    Yamato, J.2    Felsenstein, J.3
  • 49
    • 37249036929 scopus 로고    scopus 로고
    • Genomewide spatial correspondence between nonsynonymous divergence and neutral polymorphism reveals extensive adaptation in Drosophila
    • DOI 10.1534/genetics.107.080226
    • Macpherson JM, Sella G, Davis JC, Petrov DA. 2007. Genomewide spatial correspondence between nonsynonymous divergence and neutral polymorphism reveals extensive adaptation in Drosophila. Genetics 177: 2083-2099. (Pubitemid 350276990)
    • (2007) Genetics , vol.177 , Issue.4 , pp. 2083-2099
    • Macpherson, J.M.1    Sella, G.2    Davis, J.C.3    Petrov, D.A.4
  • 50
    • 0016220238 scopus 로고
    • The hitch-hiking effect of a favourable gene
    • Maynard Smith J, Haigh J. 1974. The hitch-hiking effect of a favourable gene. Genet Res 23: 23-35.
    • (1974) Genet Res , vol.23 , pp. 23-35
    • Maynard Smith, J.1    Haigh, J.2
  • 52
    • 0034714338 scopus 로고    scopus 로고
    • A primate genome project deserves high priority
    • McConkey EH, Varki A. 2000. A primate genome project deserves high priority. Science 289: 1295-1296. (Pubitemid 30656032)
    • (2000) Science , vol.289 , Issue.5483 , pp. 1295-1296
    • McConkey, E.H.1    Varki, A.2
  • 54
    • 67149096366 scopus 로고    scopus 로고
    • Widespread genomic signatures of natural selection in hominid evolution
    • doi: 10.1371/journal.pgen.1000471
    • McVicker G, Gordon D, Davis C, Green P. 2009. Widespread genomic signatures of natural selection in hominid evolution. PLoS Genet 5: e1000471. doi: 10.1371/journal.pgen.1000471.
    • (2009) PLoS Genet , vol.5
    • McVicker, G.1    Gordon, D.2    Davis, C.3    Green, P.4
  • 55
    • 0031840284 scopus 로고    scopus 로고
    • Phylogenetic relationships of the macaques (Cercopithecidae: Macaca), as revealed by high resolution restriction site mapping of mitochondrial ribosomal genes
    • Morales JC, Melnick DJ. 1998. Phylogenetic relationships of the macaques (Cercopithecidae: Macaca), as revealed by high resolution restriction site mapping of mitochondrial ribosomal genes. J Hum Evol 34: 1-23. (Pubitemid 28238798)
    • (1998) Journal of Human Evolution , vol.34 , Issue.1 , pp. 1-23
    • Morales, J.C.1    Melnick, D.J.2
  • 56
    • 1542563409 scopus 로고    scopus 로고
    • Initial sequencing and comparative analysis of the mouse genome
    • Mouse Genome Sequencing Consortium
    • Mouse Genome Sequencing Consortium. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
    • (2002) Nature , vol.420 , pp. 520-562
  • 58
    • 34147184456 scopus 로고    scopus 로고
    • Using genomic data to unravel the root of the placental mammal phylogeny
    • DOI 10.1101/gr.5918807
    • Murphy WJ, Pringle TH, Crider TA, Springer MS, Miller W. 2007. Using genomic data to unravel the root of the placental mammal phylogeny. Genome Res 17: 413-421. (Pubitemid 46556445)
    • (2007) Genome Research , vol.17 , Issue.4 , pp. 413-421
    • Murphy, W.J.1    Pringle, T.H.2    Crider, T.A.3    Springer, M.S.4    Miller, W.5
  • 60
    • 0001879933 scopus 로고
    • Molecular studies of evolution: A source of novel statistical problems
    • eds. S Gupta and J Yackel Academic Press, New York
    • Neyman J. 1971. Molecular studies of evolution: A source of novel statistical problems. In Statistical decision theory and related topics (eds. S Gupta and J Yackel), pp. 1-27. Academic Press, New York.
    • (1971) Statistical Decision Theory and Related Topics , pp. 1-27
    • Neyman, J.1
  • 61
    • 0034124688 scopus 로고    scopus 로고
    • Likelihood analysis of ongoing gene flow and historical association
    • Nielsen R, Slatkin M. 2000. Likelihood analysis of ongoing gene flow and historical association. Evolution 54: 44-50. (Pubitemid 30186267)
    • (2000) Evolution , vol.54 , Issue.1 , pp. 44-50
    • Nielsen, R.1    Slatkin, M.2
  • 62
    • 0034967295 scopus 로고    scopus 로고
    • Distinguishing migration from isolation: A Markov chain Monte Carlo approach
    • Nielsen R, Wakeley J. 2001. Distinguishing migration from isolation: A Markov chain Monte Carlo approach. Genetics 158: 885-896. (Pubitemid 32552323)
    • (2001) Genetics , vol.158 , Issue.2 , pp. 885-896
    • Nielsen, R.1    Wakeley, J.2
  • 63
    • 0031972161 scopus 로고    scopus 로고
    • Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
    • Nielsen R, Yang Z. 1998. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148: 929-936. (Pubitemid 28169008)
    • (1998) Genetics , vol.148 , Issue.3 , pp. 929-936
    • Nielsen, R.1    Yang, Z.2
  • 66
    • 0029962309 scopus 로고    scopus 로고
    • The effect of recombination on background selection
    • Nordborg M, Charlesworth B, Charlesworth D. 1996. The effect of recombination on background selection. Genet Res 67: 159-174.
    • (1996) Genet Res , vol.67 , pp. 159-174
    • Nordborg, M.1    Charlesworth, B.2    Charlesworth, D.3
  • 67
    • 13744253303 scopus 로고    scopus 로고
    • Inferring the mode of speciation from genomic data: A study of the great apes
    • DOI 10.1534/genetics.104.029231
    • Osada N, Wu CI. 2005. Inferring the mode of speciation from genomic data: A study of the great apes. Genetics 169: 259-264. (Pubitemid 40239168)
    • (2005) Genetics , vol.169 , Issue.1 , pp. 259-264
    • Osada, N.1    Wu, C.-I.2
  • 68
    • 0023822631 scopus 로고
    • Relationships between gene trees and species trees
    • Pamilo P, Nei M. 1988. Relationships between gene trees and species trees. Mol Biol Evol 5: 568-583.
    • (1988) Mol Biol Evol , vol.5 , pp. 568-583
    • Pamilo, P.1    Nei, M.2
  • 69
    • 33745591114 scopus 로고    scopus 로고
    • Genetic evidence for complex speciation of humans and chimpanzees
    • DOI 10.1038/nature04789, PII N04789
    • Patterson N, Richter DJ, Gnerre S, Lander ES, Reich D. 2006. Genetic evidence for complex speciation of humans and chimpanzees. Nature 441: 1103-1108. (Pubitemid 43990725)
    • (2006) Nature , vol.441 , Issue.7097 , pp. 1103-1108
    • Patterson, N.1    Richter, D.J.2    Gnerre, S.3    Lander, E.S.4    Reich, D.5
  • 71
    • 33750437728 scopus 로고    scopus 로고
    • Widespread discordance of gene trees with species tree in Drosophila: Evidence for incomplete lineage sorting
    • doi: 10.1371/journal.pgen.0020173
    • Pollard DA, Iyer VN, Moses AM, Eisen MB. 2006a. Widespread discordance of gene trees with species tree in Drosophila: Evidence for incomplete lineage sorting. PLoS Genet 2: e173. doi: 10.1371/journal.pgen.0020173.
    • (2006) PLoS Genet , vol.2
    • Pollard, D.A.1    Iyer, V.N.2    Moses, A.M.3    Eisen, M.B.4
  • 74
    • 0041817551 scopus 로고    scopus 로고
    • Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci
    • Rannala B, Yang Z. 2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164: 1645-1656. (Pubitemid 37102224)
    • (2003) Genetics , vol.164 , Issue.4 , pp. 1645-1656
    • Rannala, B.1    Yang, Z.2
  • 75
    • 1842684068 scopus 로고    scopus 로고
    • Genome sequence of the Brown Norway Rat yields insights into mammalian evolution
    • Rat Genome Sequencing Project Consortium
    • Rat Genome Sequencing Project Consortium. 2004. Genome sequence of the Brown Norway Rat yields insights into mammalian evolution. Nature 428: 493-521.
    • (2004) Nature , vol.428 , pp. 493-521
  • 77
    • 0036515730 scopus 로고    scopus 로고
    • The Probability of Topological Concordance of Gene Trees and Species Trees
    • DOI 10.1006/tpbi.2001.1568
    • Rosenberg NA. 2002. The probability of topological concordance of gene trees and species trees. Theor Popul Biol 61: 225-247. (Pubitemid 38042804)
    • (2002) Theoretical Population Biology , vol.61 , Issue.2 , pp. 225-247
    • Rosenberg, N.A.1
  • 78
    • 0016424695 scopus 로고
    • Minimal mutation trees of sequences
    • Sankoff D. 1975. Minimal mutation trees of sequences. SIAM J Appl Math 28: 35-42.
    • (1975) SIAM J Appl Math , vol.28 , pp. 35-42
    • Sankoff, D.1
  • 79
    • 4644325606 scopus 로고    scopus 로고
    • Ancestral population sizes and species divergence times in the primate lineage on the basis of intron and BAC end sequences
    • Satta Y, Hickerson M, Watanabe H, O'hUigin C, Klein J. 2004. Ancestral population sizes and species divergence times in the primate lineage on the basis of intron and BAC end sequences. J Mol Evol 59: 478-487.
    • (2004) J Mol Evol , vol.59 , pp. 478-487
    • Satta, Y.1    Hickerson, M.2    Watanabe, H.3    O'hUigin, C.4    Klein, J.5
  • 82
    • 15944363058 scopus 로고    scopus 로고
    • Constructing minimal ancestral recombination graphs
    • DOI 10.1089/cmb.2005.12.147
    • Song YS, Hein J. 2005. Constructing minimal ancestral recombination graphs. J Comput Biol 12: 147-169. (Pubitemid 40444585)
    • (2005) Journal of Computational Biology , vol.12 , Issue.2 , pp. 147-169
    • Song, Y.S.1    Hein, J.2
  • 85
    • 0022919117 scopus 로고
    • An attempt to estimate the effective size of the ancestral species common to two extant species from which homologous genes are sequenced
    • Takahata N. 1986. An attempt to estimate the effective size of the ancestral species common to two extant species from which homologous genes are sequenced. Genet Res 48: 187-190. (Pubitemid 17010161)
    • (1986) Genetical Research , vol.48 , Issue.3 , pp. 187-190
    • Takahata, N.1
  • 87
    • 0029415835 scopus 로고
    • Divergence time and population size in the lineage leading to modern humans
    • DOI 10.1006/tpbi.1995.1026
    • Takahata N, Satta Y, Klein J. 1995. Divergence time and population size in the lineage leading to modern humans. Theor Popul Biol 48: 198-221. (Pubitemid 26460272)
    • (1995) Theoretical Population Biology , vol.48 , Issue.2 , pp. 198-221
    • Takahata, N.1    Satta, Y.2    Klein, J.3
  • 89
    • 0030174857 scopus 로고    scopus 로고
    • Distinguishing migration from isolation using the variance of pairwise differences
    • DOI 10.1006/tpbi.1996.0018
    • Wakeley J. 1996. Distinguishing migration from isolation using the variance of pairwise differences. Theor Popul Biol 49: 369-386. (Pubitemid 26309937)
    • (1996) Theoretical Population Biology , vol.49 , Issue.3 , pp. 369-386
    • Wakeley, J.1
  • 90
    • 40749148589 scopus 로고    scopus 로고
    • Complex speciation of humans and chimpanzees
    • Wakeley J. 2008. Complex speciation of humans and chimpanzees. Nature 452: 3-4.
    • (2008) Nature , vol.452 , pp. 3-4
    • Wakeley, J.1
  • 92
    • 0031018637 scopus 로고    scopus 로고
    • Estimating ancestral population parameters
    • Wakeley J, Hey J. 1997. Estimating ancestral population parameters. Genetics 145: 847-855.
    • (1997) Genetics , vol.145 , pp. 847-855
    • Wakeley, J.1    Hey, J.2
  • 93
    • 0037277564 scopus 로고    scopus 로고
    • Estimating ancestral population sizes and divergence times
    • Wall JD. 2003. Estimating ancestral population sizes and divergence times. Genetics 163: 395-404.
    • (2003) Genetics , vol.163 , pp. 395-404
    • Wall, J.D.1
  • 94
    • 0034913468 scopus 로고    scopus 로고
    • Perfect phylogenetic networks with recombination
    • Wang L, Zhang K, Zhang L. 2001. Perfect phylogenetic networks with recombination. J Comput Biol 8: 69-78.
    • (2001) J Comput Biol , vol.8 , pp. 69-78
    • Wang, L.1    Zhang, K.2    Zhang, L.3
  • 95
    • 56049110263 scopus 로고    scopus 로고
    • Sequencing and comparative analysis of a conserved syntenic segment in the Solanaceae
    • Wang Y, Diehl A, Wu F, Vrebalov J, Giovannoni J, Siepel A, Tanksley SD. 2008. Sequencing and comparative analysis of a conserved syntenic segment in the Solanaceae. Genetics 180: 391-408.
    • (2008) Genetics , vol.180 , pp. 391-408
    • Wang, Y.1    Diehl, A.2    Wu, F.3    Vrebalov, J.4    Giovannoni, J.5    Siepel, A.6    Tanksley, S.D.7
  • 96
    • 0035339920 scopus 로고    scopus 로고
    • Molecular phylogenetics: State-of-the-art methods for looking into the past
    • DOI 10.1016/S0168-9525(01)02272-7, PII S0168952501022727
    • Whelan S, Liò P, Goldman N. 2001. Molecular phylogenetics: State-of-the-art methods for looking into the past. Trends Genet 17: 262-272. (Pubitemid 32378749)
    • (2001) Trends in Genetics , vol.17 , Issue.5 , pp. 262-272
    • Whelan, S.1    Lio, P.2    Goldman, N.3
  • 98
    • 0033150745 scopus 로고    scopus 로고
    • Recombination as a point process along sequences
    • DOI 10.1006/tpbi.1998.1403
    • Wiuf C, Hein J. 1999. Recombination as a point process along sequences. Theor Popul Biol 55: 248-259. (Pubitemid 29384456)
    • (1999) Theoretical Population Biology , vol.55 , Issue.3 , pp. 248-259
    • Wiuf, C.1    Hein, J.2
  • 99
    • 0026031181 scopus 로고
    • Inferences of species phylogeny in relation to segregation of ancient polymorphisms
    • Wu CI. 1991. Inferences of species phylogeny in relation to segregation of ancient polymorphisms. Genetics 127: 429-435.
    • (1991) Genetics , vol.127 , pp. 429-435
    • Wu, C.I.1
  • 100
    • 0742271150 scopus 로고    scopus 로고
    • Genes and speciation
    • Wu CI, Ting CT. 2004. Genes and speciation. Nat Rev Genet 5: 114-122.
    • (2004) Nat Rev Genet , vol.5 , pp. 114-122
    • Wu, C.I.1    Ting, C.T.2
  • 101
    • 0028064845 scopus 로고
    • Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
    • Yang Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. J Mol Evol 39: 306-314. (Pubitemid 24283346)
    • (1994) Journal of Molecular Evolution , vol.39 , Issue.3 , pp. 306-314
    • Yang, Z.1
  • 102
    • 0030741747 scopus 로고    scopus 로고
    • On the estimation of ancestral population sizes of modern humans
    • DOI 10.1017/S001667239700270X
    • Yang Z. 1997. On the estimation of ancestral population sizes of modern humans. Genet Res 69: 111-116. (Pubitemid 27356694)
    • (1997) Genetical Research , vol.69 , Issue.2 , pp. 111-116
    • Yang, Z.1
  • 103
    • 0036961518 scopus 로고    scopus 로고
    • Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci
    • Yang Z. 2002. Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci. Genetics 162: 1811-1823. (Pubitemid 36114665)
    • (2002) Genetics , vol.162 , Issue.4 , pp. 1811-1823
    • Yang, Z.1


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