Do human and JC virus genes show evidence of host-parasite codemography?

Infection, Genetics and Evolution

Volumn 1, Issue 1, 2001, Pages 3-12

  Wooding, Stephen ^a  

^a UNIVERSITY OF UTAH   (United States)

Author keywords

Host; JC virus; Parasite

Indexed keywords

JC VIRUS;

AFRICA; AMINO ACID SEQUENCE; ARTICLE; ASIA; EUROPE; GENETIC VARIABILITY; GENETICS; HOST PARASITE INTERACTION; HUMAN; JC VIRUS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; VIRUS INFECTION;

AFRICA; AMINO ACID SEQUENCE; ASIA; EUROPE; EVOLUTION, MOLECULAR; HOST-PARASITE RELATIONS; HUMANS; JC VIRUS; MOLECULAR SEQUENCE DATA; POLYOMAVIRUS INFECTIONS; TUMOR VIRUS INFECTIONS; VARIATION (GENETICS);

EID: 0001909391     PISSN: 15671348     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1567-1348(01)00002-8     Document Type: Article

References (42)

1. Alonso S., Armour J.A.L. A highly variable segment of human subterminal 16p reveals a history of population growth for modern humans outside Africa. Proc. Natl. Acad. Sci. U.S.A. 98:2001;864-869.
2. Anderson R.M., May R. Population biology of infectious diseases. Part I. Nature. 280:1979;361-367.
3. Ault G.S., Stoner G.L. Two major types of JC virus defined in progressive multifocal leukoencephalopathy brain by early and late coding region DNA sequences. J. Gen. Virol. 73:1992;2669-2678.
4. Berthier K., Langlais M., Auger P., Pontier D. Dynamics of a feline virus with two transmission modes within exponentially growing host populations. Proc. R. Soc. London Ser. B. 267:2000;2049-2056.
5. Boots M., Sasaki A. Small worlds and the evolution of virulence: infection occurs locally and at a distance. Proc. R. Soc. London Ser. B. 266:1999;1933-1938.
6. Cann R.L., Stoneking M., Wilson A.C. Mitochondrial DNA and human evolution. Nature. 325:1987;31-36.
7. Cavalli-Sforza, L.L., Menozzi, P., Piazza, A., 1994. The History and Geography of Human Genes. Princeton University Press, Princeton, NJ.
8. Chima S.C., Ryschkewitsch C.F., Fan K.J., Stoner G.L. Polyomavirus JC genotypes in an urban united states population reflect the history of African origin and genetic admixture in modern African Americans. Hum. Biol. 72:2000;837-850.
9. Ding Y., Wooding S., Harpending H., Chi H., Li H., Fu Y., Pang J., Yao Y., Yu J.X., Moyzis R., Zhang Y. Population structure and history in East Asia. Proc. Natl. Acad. Sci. U.S.A. 25:2000;14003-14006.
10. Eller E. Population substructure and isolation by distance in three continental regions. Am. J. Phys. Anthopol. 108:1999;147-159.
11. Guo J., Sugimoto C., Kitamura T., Ebihara H., Kato A., Guo Z., Liu J., Zheng S.P., Wang Y.L., Na Y.Q., Suzuki M., Taguchi F., Yogo Y. Four geographically distinct genotypes of JC virus are prevalent in China and Mongolia: implications for the racial composition of modern China. J. Gen. Virol. 79:1998;2499-2505.
12. Hamilton W.H. Haploid dynamical polymorphism in a host with matching parasites: effects of mutation/subdivision, linkage and patterns of selection. J. Heredity. 84:1993;328-338.
13. Harpending, H.C., Jenkins, T., 1973. Genetic distance among southern African populations. In: Crawford, M., Workman, P. (Eds.), Method and Theory in Anthropological Genetics. University of New Mexico Press, Albuquerque, pp. 177-199.
14. Harpending H.C., Rogers A.R. Genetic perspectives on human origins and differentiation. Ann. Rev. Genomics Hum. Gen. 1:2000;361-385.
15. Hatwell J.N., Sharp P.M. Evolution of human polyomavirus JC. J. Gen. Virol. 81:2000;1191-1200.
16. Horai S., Hayasaka K., Kondo R., Tsugane K., Takahata N. Recent African origin of modern humans revealed by complete sequences of hominoid mitochondrial DNAs. Proc. Natl. Acad. Sci. U.S.A. 92:1995;532-536.
17. Jakobsen I.B., Easteal S. A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences. BioInformatics. 12:1996;291-295.
18. Kato A., Kitamura T., Sugimoto C., Ogawa Y., Nakazato K., Nagashima K., Hall W.W., Kawabe K., Yogo Y. Lack of evidence for the transmission of JC polyomavirus between human populations. Arch. Virol. 142:1997;875-882.
19. Klein, R.G., 1999. The Human Career: Human Biological and Cultural Origins. University of Chicago Press, Chicago.
20. Kunitake T., Kitamura T., Guo J., Taguchi F., Kawabe K., Yogo Y. Parent-to-child transmission is relatively common in the spread of the human polyomavirus JC virus. J. Clin. Microbiol. 33:1995;1448-1451.
21. Li, W.H., 1997. Molecular Evolution. Sinauer Associates.
22. Marjoram P., Donnelly P. Pairwise comparisons of mitochondrial DNA sequences in subdivided populations and implications for early human evolution. Genetics. 136:1994;673-683.
23. May, R.M., 1991. The dynamics and genetics of host-parasite associations. In: Toft, C.A., Aeschlimann, A., Bolis, L. (Eds.), Parasite-Host Associations: Coexistence or Conflict? Oxford Science Publications, Oxford, pp. 102-128.
24. Nei, M., Kumar, S., 2000. Molecular Evolution and Phylogenetics. Oxford University Press, Oxford, UK.
25. Ochman H., Elwyn S., Moran N.A. Calibrating bacterial evolution. Proc. Natl. Acad. Sci. U.S.A. 96:1999;12638-12643.
26. Page R.D.M., Charleston M.A. Trees within trees: phylogeny and historical association. TREE. 13:1998;356-359.
27. Page, R.D.M., Holmes, E.C., 1998. Molecular Evolution: a Phylogenetic Approach. Blackwell Scientific Publications, London.
28. Poulin, R., 1998. Evolutionary Ecology of Parasites: from Individuals to Communities. Chapman & Hall, New York.
29. Rogers A.R. Genetic evidence for a Pleistocene population explosion. Evolution. 49:1995;608-615.
30. Rogers, A.R., 1997. Mismatch version 4.3. Computer program distributed by the author, Department of Anthropology, University of Utah.
31. Rogers A.R., Harpending H.C. Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. E. 9:1992;552-569.
32. Ryschkewitsch, C.F., Friedlaender, J.S., Mgone, C.S., D.V. Jobes, D., Agostini, H.T., Chima, S.C., Alpers, M.P., Koki, G., Yanagihara, R., Stoner, G.L., 2000. Human polyomavirus JC variants in Papua New Guinea and Guam reflect ancient population settlement and viral evolution. Microbes and Infection 2, pp. 987-996.
33. Stoneking, M., 1997. Recent African origin of human mitochondrial DNA: review of the evidence and current status of the hypothesis. In: Progress in Population Genetics and Evolution, pp. 1-14.
34. Sugimoto C., Kitamura T., Guo J., Al-Hadal M.N., Shchelkunov S.N., Otova B., Ondrejka P., Chollet J.Y., El-Safi S., Ettayebi M., Gresenguet G., Kocagoz T., Chaiyarasamee S., Thant K.Z., Moe K., Kobayashi N., Taguchi F., Yogo Y. Typing of urinary JC virus DNA offers a novel means of tracing human migrations. Proc. Natl. Acad. Sci. U.S.A. 94:1997;9191-9196.
35. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 123:1989;585-595.
36. Thompson, R., Pritchard, J.K., Shen, P., Oefner, P.J., Feldman, M.W., 2000. Recent common ancestry of human Y chromosomes: evidence form DNA sequence data. Proc. Natl. Acad. Sci. U.S.A. 7360-7365.
37. Wooding S., Rogers A. A Pleistocene population X-plosion? Hum. Biol. 72:2000;693-695.
38. Wooding S., Ward R. Phylogeography and Pleistocene evolution in the North American black bear. Mol. Biol. E. 14:1997;1096-1105.
39. Yang, Z., 2000. Phylogenetic Analysis by Maximum Likelihood (PAML), version 3.0c. Computer program distributed by the author, University College London, London, UK.
40. Yasunaga T., Miyata T. Evolutionary changes of nucleotide sequences of papova viruses BKV and SV40: they are possibly hybrids. J. Mol. Evol. 19:1982;72-92.
41. Zanotto P.M., Kallas E.G., de Souza R.F., Holmes E.C. Positive selection in the nef gene of HIV-1. Genetics. 153:1999;1077-1089.
42. Zhao Z., Jin L., Fu Y., Ramsay M., Jenkins T., Leskinen E., Pamilo P., Trexler M., Patthy L., Jorde L.B., Ramos-Onsins S., Yu N., Li W. Worldwide DNA sequence variation in a 10-kilobase noncoding region on human chromosome 22. Proc. Natl. Acad. Sci. U.S.A. 97:2000;11354-11358.