Germs, genomes and genealogies

Trends in Ecology and Evolution

Volumn 20, Issue 1, 2005, Pages 39-45

  Wilson, Daniel J ^a   Falush, Daniel ^a   McVean, Gilean ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EPIDEMIOLOGY; GENETIC VARIATION; PATHOGEN; PHYLOGENETICS;

ANIMALIA;

EID: 11444265823     PISSN: 01695347     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tree.2004.10.009     Document Type: Review

References (79)

1. P. Lemey Tracing the origin and history of the HIV-2 epidemic Proc. Natl. Acad. Sci. U. S. A. 100 2003 6588 6592
2. P. Lemey The molecular population genetics of HIV-1 Group O Genetics 167 2004 1059 1068
3. K.E. Robbins U.S. Human immunodeficiency virus type 1 epidemic: date of origin, population history, and characterization of early strains J. Virol. 77 2003 6359 6366
4. O.G. Pybus The epidemiology and iatrogenic transmission of hepatitis C virus in Egypt: a Bayesian coalescent approach Mol. Biol. Evol. 20 2003 381 387
5. S.M. Rich Malaria's Eve: evidence of a recent population bottleneck throughout the world populations of Plasmodium falciparum Proc. Natl. Acad. Sci. U. S. A. 95 1998 4425 4430
6. A.J. Drummond Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data Genetics 161 2002 1307 1320
7. A. Drummond Inference of viral evolutionary rates from molecular sequences Adv. Parasitol. 54 2003 331 358
8. D. Falush Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies Genetics 164 2003 1567 1587
9. D. Falush Traces of human migrations in Helicobacter pylori populations Science 299 2003 1582 1585
10. I. Carbone Recombination and migration of Cryphonectria hypovirus 1 as inferred from gene genealogies and the coalescent Genetics 166 2004 1611 1629
11. A. Rambaut The causes and consequences of HIV evolution Nat. Rev. Genet. 5 2004 52 61
12. D. Shriner Influence of random genetic drift on human immunodeficiency virus type 1 env evolution during chronic infection Genetics 166 2004 1155 1164
13. T. De Oliveira Mapping sites of positive selection and amino acid diversification in the HIV genome: an alternative approach to vaccine design? Genetics 167 2004 1047 1058
14. M. Choisy Comparative study of adaptive molecular evolution in different human immunodeficiency virus groups and subtypes J. Virol. 78 2004 1962 1970
15. J. Baum Evidence for diversifying selection on erythrocyte-binding antigens of Plasmodium falciparum and P. vivax Genetics 163 2003 1327 1336
16. Y. Haraguchi, and A. Sasaki Evolutionary pattern of intra-host pathogen antigenic drift: effect of cross-reactivity in immune response Philos. Trans. R. Soc. Lond. Ser. B 352 1997 11 20
17. S. Gupta Chaos, persistence, and evolution of strain structure in antigenically diverse infectious agents Science 280 1998 912 915
18. K.A. Lythgoe Effects of acquired immunity and mating strategy on the genetic structure of parasite populations Am. Nat. 159 2002 519 529
19. S.D. Polley Allele frequency-based analyses robustly map sequence sites under balancing selection in a malaria vaccine candidate antigen Genetics 165 2003 555 561
20. K.A. Jolley Carried meningococci in the Czech Republic: a diverse recombining population J. Clin. Microbiol. 38 2000 4492 4498
21. M.C. Maiden Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms Proc. Natl. Acad. Sci. U. S. A. 95 1998 3140 3145
22. N. Ferguson The effect of antibody-dependent enhancement on the transmission dynamics and persistence of multiple-strain pathogens Proc. Natl. Acad. Sci. U. S. A. 96 1999 790 794
23. T.J. Anderson Mapping drug resistance genes in Plasmodium falciparum by genome-wide association Curr. Drug Targets Infect. Disord. 4 2004 65 78
24. M. Anisimova Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites Genetics 164 2003 1229 1236
25. D. Shriner Potential impact of recombination on sitewise approaches for detecting positive natural selection Genet. Res. 81 2003 115 121
26. M.H. Schierup, and J. Hein Consequences of recombination on traditional phylogenetic analysis Genetics 156 2000 879 891
27. D.L. Suarez Recombination resulting in virulence shift in avian influenza outbreak, Chile Emerg. Infect. Dis. 10 2004 693 699
28. K. Strimmer A novel exploratory method for visual recombination detection Genome Biol. 4 2003 R33
29. M.A. Suchard Oh brother, where art thou? A Bayes factor test for recombination with uncertain heritage Syst. Biol. 51 2002 715 728
30. D. Husmeier, and G. McGuire Detecting recombination in 4-taxa DNA sequence alignments with Bayesian hidden Markov models and Markov chain Monte Carlo Mol. Biol. Evol. 20 2003 315 337
31. P. Awadalla The evolutionary genomics of pathogen recombination Nat. Rev. Genet. 4 2003 50 60
32. D. Posada Recombination in evolutionary genomics Annu. Rev. Genet. 36 2002 75 97
33. S.R. Myers, and R.C. Griffiths Bounds on the minimum number of recombination events in a sample history Genetics 163 2003 375 394
34. M.P. Stumpf, and G.A. McVean Estimating recombination rates from population-genetic data Nat. Rev. Genet. 4 2003 959 968
35. G. McVean A coalescent-based method for detecting and estimating recombination from gene sequences Genetics 160 2002 1231 1241
36. M.K. Kuhner Maximum likelihood estimation of recombination rates from population data Genetics 156 2000 1393 1401
37. R. Bowden High recombination rate in herpes simplex virus type 1 natural populations suggests significant co-infection Infect. Genet. Evol. 4 2004 115 123
38. X. Su A genetic map and recombination parameters of the human malaria parasite Plasmodium falciparum Science 286 1999 1351 1353
39. D.N. Levy Dynamics of HIV-1 recombination in its natural target cells Proc. Natl. Acad. Sci. U. S. A. 101 2004 4204 4209
40. J. Zhuang Human immunodeficiency virus type 1 recombination: rate, fidelity, and putative hot spots J. Virol. 76 2002 11273 11282
41. T.J. Anderson Microsatellite markers reveal a spectrum of population structures in the malaria parasite Plasmodium falciparum Mol. Biol. Evol. 17 2000 1467 1482
42. D.A. Steinhauer, and J.J. Skehel Genetics of influenza viruses Annu. Rev. Genet. 36 2002 305 332
43. K.S. Li Genesis of a highly pathogenic and potentially pandemic H5N1 influenza virus in eastern Asia Nature 430 2004 209 213
44. P. Zhu Fit genotypes and escape variants of subgroup III Neisseria meningitidis during three pandemics of epidemic meningitis Proc. Natl. Acad. Sci. U. S. A. 98 2001 5234 5239
45. B. Linz Frequent interspecific genetic exchange between commensal Neisseriae and Neisseria meningitidis Mol. Microbiol. 36 2000 1049 1058
46. B.T. Grenfell Unifying the epidemiological and evolutionary dynamics of pathogens Science 303 2004 327 332
47. I. Sheridan High-resolution phylogenetic analysis of hepatitis C virus adaptation and its relationship to disease progression J. Virol. 78 2004 3447 3454
48. R. Nielsen, and J.P. Huelsenbeck Detecting positively selected amino acid sites using posterior predictive P-values Pac. Symp. Biocomput. 2002 2002 76 588
49. A.J. Leslie HIV evolution: CTL escape mutation and reversion after transmission Nat. Med. 10 2004 282 289
50. R. Nielsen, and Z. Yang Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene Genetics 148 1998 929 936
51. W. Yang Widespread adaptive evolution in the human immunodeficiency virus type 1 genome J. Mol. Evol. 57 2003 212 221
52. B. Korber Timing the ancestor of the HIV-1 pandemic strains Science 288 2000 1789 1796
53. Y. Suzuki, and T. Gojobori A method for detecting positive selection at single amino acid sites Mol. Biol. Evol. 16 1999 1315 1328
54. D.J. Smith Mapping the antigenic and genetic evolution of influenza virus Science 305 2004 371 376
55. N.M. Ferguson Ecological and immunological determinants of influenza evolution Nature 422 2003 428 433
56. J.F. Kingman The coalescent Stochast. Process. Appl. 13 1982 235 248
57. R.R. Hudson Properties of a neutral allele model with intragenic recombination Theor. Popul. Biol. 23 1983 183 201
58. M. Nordborg Coalescent theory D.J. Balding Handbook of Statistical Genetics 2nd edn 2003 John Wiley & Sons 602 635
59. M. Przeworski Estimating the time since the fixation of a beneficial allele Genetics 164 2003 1667 1676
60. F. Tajima Statistical method for testing the neutral mutation hypothesis by DNA polymorphism Genetics 123 1989 585 595
61. Y.X. Fu, and W.H. Li Statistical tests of neutrality of mutations Genetics 133 1993 693 709
62. J.C. Fay, and C.I. Wu Hitchhiking under positive Darwinian selection Genetics 155 2000 1405 1413
63. J.H. McDonald, and M. Kreitman Adaptive protein evolution at the Adh locus in Drosophila Nature 351 1991 652 654
64. R.R. Hudson A test of neutral molecular evolution based on nucleotide data Genetics 116 1987 153 159
65. M. Kreitman Methods to detect selection in populations with applications to the human Annu. Rev. Genomics Hum. Genet. 1 2000 539 559
66. R. Nielsen Statistical tests of selective neutrality in the age of genomics Heredity 86 2001 641 647
67. G. Coop, and R.C. Griffiths Ancestral inference on gene trees under selection Theor. Popul. Biol. 66 2004 219 232
68. J. Maynard Smith How clonal are bacteria? Proc. Natl. Acad. Sci. U. S. A. 90 1993 4384 4388
69. M.A. Beaumont Approximate Bayesian computation in population genetics Genetics 162 2002 2025 2035
70. N. Li, and M. Stephens Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data Genetics 165 2003 2213 2233
71. A.E. Hirsh Stable association between strains of Mycobacterium tuberculosis and their human host populations Proc. Natl. Acad. Sci. U. S. A. 101 2004 4871 4876
72. J. Maynard Smith, and J. Haigh The hitch-hiking effect of a favourable gene Genet. Res. 23 1974 23 35
73. J.M. Braverman The hitchhiking effect on the site frequency spectrum of DNA polymorphisms Genetics 140 1995 783 796
74. M. Przeworski The signature of positive selection at randomly chosen loci Genetics 160 2002 1179 1189
75. S. Williamson Adaptation in the env gene of HIV-1 and evolutionary theories of disease progression Mol. Biol. Evol. 20 2003 1318 1325
76. H.A. Ross, and A.G. Rodrigo Immune-mediated positive selection drives human immunodeficiency virus type 1 molecular variation and predicts disease duration J. Virol. 76 2002 11715 11720
77. N.T.J. Bailey The Mathematical Theory of Infectious Diseases and its Applications 1975 Charles Griffin and Company
78. J. Wakeley, and N. Aliacar Gene genealogies in a metapopulation Genetics 159 2001 893 905
79. J.R. Pannell Coalescence in a metapopulation with recurrent local extinction and recolonization Evolution 57 2003 949 961