Patterns of genetic variation in populations of infectious agents

BMC Evolutionary Biology

Volumn 7, Issue , 2007, Pages

  Gordo, Isabel ^a   Campos, Paulo R A ^b  

^a INSTITUTO GULBENKIAN DE CIÊNCIA   (Portugal)

^b UNIVERSIDADE FEDERAL RURAL DE PERNAMBUCO   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; DISEASE TRANSMISSION; GENETIC VARIABILITY; MATHEMATICAL MODEL; METAPOPULATION; MUTATION RATE; NONHUMAN; POPULATION SIZE; RNA VIRUS; ANIMAL; ANTIGENIC VARIATION; BIOLOGICAL MODEL; GENE FREQUENCY; GENETIC SELECTION; GENETICS; HOST PARASITE INTERACTION; HUMAN; INFECTION; MICROBIOLOGY; POPULATION GENETICS; VIROLOGY;

ANIMALS; ANTIGENIC VARIATION; GENE FREQUENCY; GENETICS, POPULATION; HOST-PARASITE RELATIONS; HUMANS; INFECTION; MODELS, GENETIC; SELECTION (GENETICS); VARIATION (GENETICS);

EID: 34547925652     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-7-116     Document Type: Article

References (51)

1. A principal target of human immunity to malaria identified by molecular population genetics and immunological analyses. D Connway D Cavanagh K Tanabe C Roper Z Mikes N Sakihama K Bojang A Oduola P Kremsner D Arnot B Greenwood J McBride, Nature Medicine 2000 6 689 692 10.1038/76272 10835687
2. Traces of human migrations in Helicobacter pylori populations. D Falush T Wirth B Linz J Pritchard M Stephens M Kidd M Blaser D Graham S Vacher G Perez-Perez Y Yamaoka F Megraud K Otto U Reichard E Katzowitsch X Wang M Achtman S Suerbaum, Science 2003 299 1582 1585 10.1126/science.1080857 12624269
3. Pathogen population genetics, evolutionary potential, and durable resistance. B McDonald C Linde, Annu Rev Phytopathol 2002 40 349 379 10.1146/annurev.phyto.40.120501.101443 12147764
4. The interface between epidemiology and population genetics. S Paterson M Viney, Parasitology Today 2000 16 528 532 10.1016/S0169-4758(00)01776-2 11121850
5. Unifying the epidemiological and evolutionary dynamics of pathogens. B Grenfell O Pybus J Gog J Wood J Daly J Mumford E Holmes, Science 2004 303 327 331 10.1126/science.1090727 14726583
6. Germs, genomes and genealogies. D Wilson D Falush G McVean, Trends in Ecology and Evolution 2005 420 1 39 45 10.1016/j.tree.2004.10.009
7. Epidemiology meets evolutionary ecology. A Galvani, Trends in Ecology and Evolution 2003 18 132 139 10.1016/S0169-5347(02)00050-2
8. Methods to detect selection in populations with applications to the human. M Kreitman, Annu Rev Genomics Hum Genet 2000 1 539 559 10.1146/annurev.genom.1.1.539 11701640
9. Adjusting the focus on human variation. M Przeworski R Hudson A Di Rienzo, Trends in Genetics 2000 16 296 302 10.1016/S0168-9525(00)02030-8 10858659
10. R Levins, Evolution in changing environments Princeton, NJ: Princeton University Press 1968
11. Some demographic and genetic consequences of environmental heterogeneity for biological control. R Levins, Bull Entomol Soc Am 1969 15 237 240
12. Metapopulation Dynamics. I Hansky, Nature 1998 396 41 49 10.1038/23876
13. Neutral genetics diversity in a metapopulation with recurrent local extinction and recolonization. J Pannell B Charlesworth, Evolution 1999 53 664 676 10.2307/2640708
14. Effects of metapopulation processes on measures of genetic diversity. J Pannell B Charlesworth, Phil Trans R Soc Lond B 2000 355 1851 1864 10.1098/rstb.2000.0740
15. F Rousset, Genetic Structure and Selection in Subdivided Populations Princeton, NJ: Princeton University Press 2004
16. The effects of genetic and geographic structure on neutral variation. B Charlesworth D Charlesworth N Barton, Annu Rev Ecol Evol Syst 2003 23 99 125 10.1146/annurev.ecolsys.34.011802.132359
17. ST not equal 1/(4Nm + 1). M Whitlock D McCauley, Heredity 1999 82 117 125 10.1038/sj.hdy.6884960 10098262
18. How viruses apread among computers and people. A Lloyd R May, Science 2001 292 1316 1317 10.1126/science.1061076 11360990
19. On the evolution of random graphs. P Erdös A Rényi, Inst Hung Acad Sci 1960 5 17 61
20. The structure and function of complex networks. M Newman, SIAM 2003 45 167 256 10.1137/S003614450342480
21. Statistical mechanics of complex networks. R Albert AL Barabási, Rev Mod Phys 2002 74 47 97 10.1103/RevModPhys.74.47
22. Diameter of the world-wide web. R Albert H Jeong AL Barabási, Nature 1999 401 130 131 10.1038/43601
23. The web of human sexual contact. F Liljeros C Edling L Amaral H Stanley Y Aberg, Nature 2001 401 907 908 10.1038/35082140
24. S Camazine JL Deneubourg N Franks J Sneyd G Theraulaz E Bonabeau, Self-Organizations in Biological Systems Princeton, NJ: Princeton University Press 2001
25. Social insect networks. J Fewell, Science 2003 301 1867 1870 10.1126/science.1088945 14512616
26. Epidemic spreading in scale-free networks. R Pastor-Satorras A Vespignani, Phys Rev Lett 2001 86 3200 3204 10.1103/PhysRevLett.86.3200 11290142
27. Velocity and Hierarchical Spread of Epidemic Outbreaks in Scale-Free Networks. M Barthélemy A Barrat R Pastor-Satorras A Vespignani, Phys Rev Lett 2004 92 17 178701 10.1103/PhysRevLett.92.178701 15169200
28. Networks and epidemic models. M Keeling K Eames, J R Soc Interface 2005 22 2 295 307 10.1098/rsif.2005.0051
29. Network structure and the biology of populations. R May, Trends in ecology and Evolution 2006 21 394 399 10.1016/j.tree.2006.03.013
30. Muller's ratchet in random graphs and scale-free networks. P Campos J Combadao F Dionisio I Gordo, Phys Rev E 2006 74 4 Pt 1 042901 10.1103/PhysRevE.74.042901
31. Biological and biomedical implications of the co-evolution of pathogens and their hosts. M Woolhouse J Webster E Domingo B Charlesworth B Levin, Nature Genetics 2002 32 569 77 10.1038/ng1202-569 12457190
32. Species interactions and the evolution of sex. S Otto S Nuismer, Science 2004 304 1018 20 10.1126/science.1094072 15143283
33. Host-parasite interactions and the evolution of ploidy. S Nuismer S Otto, Proc Natl Acad Sci USA 2004 101 11036 9 15252199 10.1073/pnas.0403151101
34. Host-parasite interactions and the evolution of gene expression. S Nuismer S Otto, PLoS Biol 2005 3 1283 8 10.1371/journal.pbio.0030203
35. Multilocus genetics and the coevolution of quantitative traits. M Kopp S Gavrilets, Evolution 2006 60 1321 36 16929650
36. The transmission dynamics of human immunodeficiency virus (HIV). R May R Anderson, Philos Trans R Soc London B 1988 321 565 607 10.1098/rstb.1988.0108
37. Gene flow and genetic drift in a species subject to frequent local extinction. M Slatkin, Theor Popul Biol 1997 12 253 262 10.1016/0040-5809(77) 90045-4
38. The effective size of a subdivided population. M Whitlock N Barton, Genetics 1997 146 427 441 9136031
39. M Kimura, The neutral theory of molecular evolution Princeton, NJ: Princeton University Press 1983
40. Influence of random genetic drift on human immunodeficiency virus type 1 env evolution during chronic infection. D Shriner, Genetics 2004 166 1155 1164 15082537 10.1534/genetics.166.3.1155
41. Allele frequency based analyses robustly identify sites under balancing selection in a malaria vaccine candidate antigen. S Polley W Chokejindachai D Conway, Genetics 2003 165 555 561 14573469
42. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. F Tajima, Genetics 1989 123 585 595 2513255
43. Gene genealogies in a metapopulation. J Wakeley N Aliacar, Genetics 2001 159 893 905 11606561
44. Coalescence in a metapopulation with recurrent local extinction and recolonization. J Pannell, Evolution 2003 57 949 961 12836814
45. The distribution of rates of spontaneous mutation over viruses, prokaryotes, and eukaryotes. J Drake, Ann N Y Acad Sci 1999 870 100 107 10.1111/j.1749-6632.1999.tb08870.x 10415476
46. Measures of divergence between populations and the effect of forces that reduce variability. B Charlesworth, Mol Biol Evol 1998 15 538 43 9580982
47. Patterns of intra and interhost nonsynonymous variation reveal strong purifying selection in dengue virus. E Holmes, J Virol 2003 77 11296 8 14512579 10.1128/JVI.77.20.11296-11298.2003
48. Evolution of intrahost HIV-1 genetic diversity during chronic infection. D Shriner Y Liu D Nickle J Mullins, Evolution 2006 60 6 1165 1176 16892967
49. The signature of positive selection on standing genetic variation. M Przeworski G Coop W JD, Evolution 2005 59 2312-232355-561 16396172
50. Soft sweeps: molecular population genetics of adaptation from standing genetic variation. J Hermisson P Pennings, Genetics 2005 169 2335 2352 15716498 10.1534/genetics.104.036947
51. Unifying the spatial population dynamics and molecular evolution of epidemic rabies virus. L Real J Henderson R Biek J Snaman T Jack J Childs E Stahl L Waller R Tinline S Nadin-Davis, Proc Natl Acad Sci USA 2005 102 12107 12111 16103358 10.1073/pnas.0500057102