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Phylogeography helps with investigating the building of human parasite communities

Published online by Cambridge University Press:  01 May 2012

SERGE MORAND
SERGE MORAND*
Affiliation:
Institut des Sciences de l'Evolution, UMR 5554 CNRS-IRD-UM2, CC65, Université de Montpellier 2, F-34095 Montpellier, France
*
Corresponding author: Serge Morand, serge.morand@univ-montp2.fr
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Summary

Phylogeography of parasites and microbes is a recent field. Phylogeographic studies have been performed mostly to test three major hypotheses that are not mutually exclusive on the origins and distributions of human parasites and microbes: (1) the “out of Africa” pattern where parasites are supposed to have followed the dispersal and expansion of modern humans in and out of Africa, (2) the “domestication” pattern where parasites were captured in the domestication centres and dispersed through them and (3) the “globalization” pattern, in relation to historical and more recent trade routes. With some exceptions, such studies of human protozoans, helminths and ectoparasites are quite limited. The conclusion emphasizes the need to acquire more phylogeographic data in non-Occidental countries, and particularly in Asia where all the animal domestications took place.

Keywords

Phylogeographyphylogenetics‘out of Africa’animal domesticationdomestication centresglobalizationhuman dispersal
Type
Research Article
Information
Parasitology , Volume 139 , Issue 14: Dynamics of parasite distributions: modern analytical approaches , December 2012 , pp. 1966 - 1974
Copyright
Copyright © Cambridge University Press 2012

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References

REFERENCES

Achtman, M. (2008). Evolution, population structure, and phylogeography of genetically monomorphic bacterial pathogens. Annual Review of Microbiology 62, 53–70.CrossRefGoogle ScholarPubMed
Achtman, M., Morelli, G., Zhu, P., Wirth, T., Diehl, I., Kusecek, B., Vogler, A. J., Wagner, D. M., Allender, C. J., Easterday, W. R., Chenal-Francisque, V., Worsham, P., Thomson, N. R., Parkhill, J., Lindler, L. E., Carniel, E. and Keim, P. (2004). Microevolution and history of the plague bacillus, Yersinia pestis. Proceedings of the National Academy of Sciences, USA 101, 17837–17842.CrossRefGoogle ScholarPubMed
Agostini, H. T., Yanagihara, R., Davis, V., Ryschkewitsch, C. F. and Stoner, G. L. (1997). Asian genotypes of JC virus in Native Americans and in a Pacific Island population: markers of viral evolution and human migration. Proceedings of the National Academy of Sciences, USA 94, 14542–14546.CrossRefGoogle Scholar
Ashford, R. W. and Crewe, W. (1998). The Parasites of Homo sapiens: An Annotated Checklist of the Protozoa, Helminths and Arthropods for which We are Home. Liverpool School of Tropical Medicine, Liverpool.Google Scholar
Avise, J. C. (2000). Phylogeography: The history and Formation of Species. Harvard University Press, London.CrossRefGoogle Scholar
Beaumont, M. A., Nielsen, R., Robert, C., Hey, J., Gaggiotti, O., Knowles, L., Estoup, A., Panchal, M., Corander, J., Hickerson, M., Sisson, S. A., Fagundes, N., Chikhi, L., Beerli, P., Vitalis, R., Cornuet, J. M., Huelsenbeck, J., Foll, M., Yang, Z. H., Rousset, F., Balding, D. and Excoffier, L. (2010). In defence of model-based inference in phylogeography. Reply. Molecular Ecology 19, 436–446.CrossRefGoogle ScholarPubMed
Beheregaray, L. B. (2008). Twenty years of phylogeography: the state of the field and the challenges for the Southern Hemisphere. Molecular Ecology 17, 3754–3774.CrossRefGoogle ScholarPubMed
Bourhy, H., Reynes, J.-M., Dunham, E. J., Dacheux, L, Larrous, F., Thi Que Huong, V., Xu, G., Yan, J., Miranda, M. E. G. and Holmes, E. C. (2008). The origin and phylogeography of dog rabies virus. Journal of General Virology 89, 2673–2681.CrossRefGoogle ScholarPubMed
Cann, H. M., Toma, C., Cazes, L., Legrand, M-F., Morel, V., Piouffre, L., Bodmer, J., Bodmer, W. F., Bonne-Tamir, B., Cambon-Thomsen, A., Chen, Z., Chu, J., Carcassi, C., Contu, L., Du, R., Excoffier, L., Ferrara, G. B., Friedlaender, J. S., Groot, H., Gurwitz, D., Jenkins, T., Herrera, R. J., Huang, X., Kidd, J., Kidd, K. K., Langaney, A., Lin, A. A., Mehdi, S. Q., Parham, P., Piazza, A., Pistillo, M. P., Qian, Y., Shu, Q., Xu, J., Zhu, S., Weber, J. L., Greely, H. T., Feldman, M. W., Thomas, G., Dausset, J. and Cavalli-Sforza, L. L. (2002). A human genome diversity cell line panel. Science 296, 261–262.CrossRefGoogle ScholarPubMed
Caufield, P. W., Saxena, D., Fitch, D. and Li, Y. (2007). Population structure of plasmid-containing strains of Streptococcus mutans, a member of the human indigenous biota. Journal of Bacteriology 189, 1238–1243.CrossRefGoogle ScholarPubMed
Cavalli-Sforza, L. L., Menozzi, P. and Piazza, A. (1994). The History and Geography of Human Genes. Princeton, NJ, Princeton University Press.Google Scholar
Cleaveland, S., Laurenson, M. K. and Taylor, L. H. (2001). Diseases of humans and their domestic mammals: pathogen characteristics, host range and the risk of emergence. Philosophical Transaction of the Royal Society of London B 356, 991–999.CrossRefGoogle ScholarPubMed
Cockburn, T. (1967). The evolution of human Infectious diseases. In Infectious Diseases: Their Evolution and Eradication (ed. Cockburn, T.). Springfield IL: Charles C. Thomas. pp. 84–107.Google Scholar
Criscione, C. D. (2008). Parasite co-structure: broad and local scale approaches. Parasite 15, 439–443.CrossRefGoogle ScholarPubMed
Criscione, C. D., Anderson, J. D., Sudimack, D., Peng, W., Jha, B., Williams-Blangero, S. and Anderson, T. J. C. (2007). Disentangling hybridization and host colonization in parasitic roundworms of humans and pigs. Proceedings of the Royal Society of London B 274, 2669–2677.Google ScholarPubMed
Criscione, C. D., Poulin, R. and Blouin, M. S. (2005). Molecular ecology of parasites: elucidating ecological and microevolutionary processes. Molecular Ecology 14, 2247–2257.CrossRefGoogle ScholarPubMed
Davies, T. J. and Pedersen, A. B. (2008). Phylogeny and geography predict pathogen community similarity in wild primates and humans. Proceedings of the Royal Society of London B 275, 1695–701.Google ScholarPubMed
Diamond, J. (1997). Guns, Germs and Steel: The Fates of Human Societies. Norton, New York.Google Scholar
Dobson, A. P. and Carper, E. R. (1996). Infectious diseases and human population history. Bioscience 46, 115–126.CrossRefGoogle Scholar
Dominguez-Bello, M. G. and Blaser, M. J. (2011). The human microbiota as a marker for migrations of individuals and populations. Annual Reviews of Anthropology 40, 451–474.CrossRefGoogle Scholar
Driscoll, C. A., Menotti-Raymond, M., Roca, A. L., Hupe, K.Johnson, W. E.Geffen, E., Harley, E. H., Delibes, M., Pontier, D., Kitchener, A. C., Yamaguchi, N., O'Brien, S. J., Macdonald, D. W. (2007). The Near-Eastern origin of cat domestication. Science 317, 519–23.CrossRefGoogle ScholarPubMed
Fain, A. (1978). Epidemiological problems of scabies. International Journal of Dermatology 17, 20–30.CrossRefGoogle ScholarPubMed
Falush, D., Wirth, T., Linz, B., Pritchard, J. K., Stephens, M., Kidd, M., Blaser, M. J., Graham, D. Y., Vacher, S., Perez-Perez, G. I., Yamaoka, Y., Mégraud, F., Otto, K., Reichard, U., Katzowitsch, E., Wang, X., Achtman, M. and Suerbaum, S. (2003). Traces of human migrations in Helicobacter pylori populations. Science 299, 1582–1585.CrossRefGoogle ScholarPubMed
Gagneux, S. and Small, P. M. (2007). Global phylogeography of Mycobacterium tuberculosis and implications for tuberculosis product development. Lancet Infectious Diseases 7, 328–337.CrossRefGoogle ScholarPubMed
Gatewood Hoen, A., Margos, G., Bent, S. J., Diuk-Wasser, M. A., Barbour, A., Kurtenbach, K. and Fish, D. (2009). Phylogeography of Borrelia burgdorferi in the eastern United States reflects multiple independent Lyme disease emergence events. Proceedings of the National Academy of Sciences, USA 106, 15013–15018.CrossRefGoogle Scholar
Ghose, C., Perez-Perez, G. I., Dominguez-Bello, M. G., Pride, D. T., Bravi, C. M. and Blaser, M. J. (2002). East Asian genotypes of Helicobacter pylori strains in Amerindians provide evidence for its ancient human carriage. Proceedings of the National Academy of Sciences, USA 99, 15107–15111.CrossRefGoogle ScholarPubMed
Gray, R. D, Drummond, A. J and Greenhill, S. J. (2009). Language phylogenies reveal expansion pulses and pauses in Pacific settlements. Science 323, 479–483.CrossRefGoogle Scholar
Guernier, V., Hochberg, M. E. and Guégan, J.-F. (2004). Ecology drives the worldwide distribution of human diseases. PloS Biology 2, 740–745.CrossRefGoogle ScholarPubMed
Gupta, A. K. (2004). Origin of agriculture and domestication of plants and animals linked to early Holocene climate amelioration. Current Science 87, 54–59.Google Scholar
Gutierrez, M. C., Brisse, S., Brosch, R., Fabre, M., Omais, B. et al. (2005). Ancient origin and gene mosaicism of the progenitor of Mycobacterium tuberculosis. PLoS Pathogens 1, e5.CrossRefGoogle ScholarPubMed
Hammer, M. F., Karafet, T. M., Redd, A. J., Jarjanazi, H., Santachiara-Benerecetti, S., Soodyall, H. and Zegura, S. L. (2001). Hierarchical patterns of global human Y-chromosome diversity. Molecular Biology and Evolution 18, 1189–1203.CrossRefGoogle ScholarPubMed
Harper, K. N., Ocampo, P. S., Steiner, B. M., George, R. W., Silverman, M. S. et al. (2008). On the origin of the treponematoses: a phylogenetic approach. PLoS Neglected Tropical Diseases 2, e148.CrossRefGoogle ScholarPubMed
Hewitt, G. (2001). Speciation, hybrid zones and phylogeography - or seeing genes in space and time. Molecular Ecology 10, 537–49.CrossRefGoogle ScholarPubMed
Hoberg, E. P., Alkire, N. L., de Queiroz, A. and Jones, A. (2001). Out of Africa: origins of the Taenia tapeworms in humans. Proceedings of the Royal Society of London B 268, 781–787.CrossRefGoogle ScholarPubMed
Horwitz, L. K. and Smith, P. (2000). The contribution of animal domestication to the spread of zoonoses: a case study from the Southern Levant. Anthropozoologica 31, 77–84.Google Scholar
Holmes, E. C. (2004). The phylogeography of human viruses. Molecular Ecology 13, 745–756.CrossRefGoogle ScholarPubMed
Hugot, J. P., Demanche, C., Barriel, V., Dei-Cas, E. and Guillot, J. (2003). Phylogenetic systematics and evolution of the Pneumocystis parasite on primates. Systematic Biology 52, 735–744.CrossRefGoogle Scholar
Hugot, J.-P., Reinhard, K. J., Gardner, S. L. and Morand, S. (1999). Human enterobiasis in evolution: origin, specificity and transmission. Parasite 6, 201–208.CrossRefGoogle ScholarPubMed
Katinas, L., Posadas, L. and Crisci, J. G. (2003). Historical Biogeography: An Introduction. Harvard University Press, Cambridge, USA.Google Scholar
Kapur, V., Whittam, T. S. and Musser, J. M. (1994). Is Mycobacterium tuberculosis 15,000 years old? Journal of Infectious Diseases 170, 1348–1349.CrossRefGoogle Scholar
Kasuga, T., Taylor, J. W. and White, T. J. (1999). Phylogenetic relationships of varieties and geographical groups of the human pathogenic fungus Histoplasma capsulatum Darling. Journal of Clinical Microbiology 37, 653–663.CrossRefGoogle ScholarPubMed
Keim, P. S. and Wagner, D. M. (2009). Humans, evolutionary and ecologic forces shaped the phylogeography of recently emerged diseases. Nature Reviews Microbiology 7, 813–821.CrossRefGoogle ScholarPubMed
Knowles, L. L. (2009). Statistical phylogeography. Annual Review of Ecology, Evolution and Systematics 40, 593–612.CrossRefGoogle Scholar
Kremer, K., van Soolingen, D., Frothingham, R., Haas, W. H., Hermans, P. W. M., Martín, C., Palittapongarnpim, P., Plikaytis, B. B., Riley, L. W., Yakrus, M. A., Musser, J. M., and van Embden, J. D. A. (1999). Comparison of methods based on different molecular epidemiological markers for typing of Mycobacterium tuberculosis complex strains: interlaboratory study of discriminatory power and reproducibility. Journal of Clinical Microbiology 37: 2607–2618.CrossRefGoogle ScholarPubMed
Larson, G., Albarella, U., Dobney, K., Rowley-Conwy, P., Schibler, J., Tresset, A., Vigne, J. D., Edwards, C. J., Schlumbaum, A.,Dinu, A., Balacsescu, A.,Dolman, G., Tagliacozzo, A., Manaseryan, N., Miracle, P., Van Wijngaarden-Bakker, L., Masseti, M., Bradley, D. G. and Cooper, A. (2007). Ancient DNA, pig domestication, and the spread of the Neolithic into Europe. Proceedings of the National Academy of Sciences, USA 104, 15276–15281.CrossRefGoogle ScholarPubMed
Larson, G., Dobney, K., Albarella, U., Fang, M., Matisoo-Smith, E., Robins, J., Lowden, S., Finlayson, H., Brand, T., Willerslev, E., Rowley- Conwy, P., Andersson, L. and Cooper, A. (2005). Worldwide phylogeography of wild boar reveals multiple centers of pig domestication. Science 307, 1618–1621.CrossRefGoogle ScholarPubMed
Lemey, P., Rambaut, A., Drummond, A. and Suchard, M. A. (2009). Bayesian phylogeography finds its roots. PLoS Computation Biology 5, e1000520.CrossRefGoogle ScholarPubMed
Li, Y., Carroll, D. S., Gardner, S. N., Walsh, M. C, Vitalis, E. A., and Damon, I. K. (2007). On the origin of smallpox: Correlating variola phylogenics with historical smallpox records. Proceedings of the National Academy of Sciences, USA 104, 15787–15792.CrossRefGoogle ScholarPubMed
Linz, B., Balloux, F., Moodley, Y., Manica, A., Liu, H., Roumagnac, P., Falush, D., Stamer, C., Prugnolle, F, van der Merwe, S. W., Yamaoka, Y., Graham, D. Y., Perez-Trallero, E., Wadstrom, T., Suerbaum, S. and Achtman, M. (2007). An African origin for the intimate association between humans and Helicobacter pylori. Nature 445, 915–918.CrossRefGoogle ScholarPubMed
Lockwood, J. L., Hoopes, M. F. and Marchetti, M. P. (2007). Invasion Ecology. Blackwell, Malden, UK.Google Scholar
Loureiro, C. L., Alonso, R., Pacheco, B. A., Uzcategui, M. G., Villegas, L., León, G., De Saéz, A., Liprandi, F., López, J. L. and Pujol, F. H. (2002). High prevalence of GB virus C/hepatitis G virus genotype 3 among autochthonous Venezuelan populations. Journal of Medical Virology 68, 357–362.CrossRefGoogle ScholarPubMed
Manso-Silvan, L., Dupuy, V., Chu, Y. and Thiaucourt, F. (2011). Multi-locus sequence analysis of Mycoplasma capricolum subsp. capripneumoniae for the molecular epidemiology of contagious caprine pleuropneumonia. Veterinary Research, 42, 86.CrossRefGoogle ScholarPubMed
May, J. M. (1958). The Ecology of Human Disease. M.D. Publications, New York, USA.Google Scholar
McNeil, W. H. (1976). Plagues and People. Anchor Press, New York, USA.Google Scholar
Megens, H. J., Crooijmans, R. P. M. A., San Cristobal, M., Hui, X., Li, N. and Groenen, M. A. M. (2008). Biodiversity of pig breeds from China and Europe estimated from pooled DNA samples: differences in microsatellite variation between two areas of domestication. Genetics Selection Evolution 40, 103–128.Google ScholarPubMed
Miura, T., Fukunaga, T., Igarashi, T., Yamashita, M., Ido, E., Funahashi, S., Ishida, T., Washio, K., Ueda, S. and Hashimoto, K. (1994). Phylogenetic subtypes of human T-lymphotropic virus type I and their relations to the anthropological background. Proceedings of the National Academy of Sciences, USA 91, 1124–1127.CrossRefGoogle Scholar
Monot, M., Honore, N., Garnier, T., Araoz, R., Coppee, J. Y., Lacroix, C., Sow, S., Spencer, J. S., Truman, R. W., Williams, D. L., Gelber, R., Virmond, M., Flageul, B., Cho, S. N., Ji, B., Paniz-Mondolfi, A., Convit, J., Young, S., Fine, P. E., Rasolofo, V., Brennan, P. J. and Cole, S. T. (2005). On the origin of leprosy. Science 308, 1040–1042.CrossRefGoogle ScholarPubMed
Monot, M., Honoré, N., Garnier, T., Zidane, N., Sherafi, D., Paniz-Mondolfi, A.,Matsuoka, M., Taylor, G. M., Donoghue, H. D., Bouwman, A., Mays, S., Watson, C., Lockwood, D., Khamesipour, A., Dowlati, Y., Jianping, S., Rea, T. H., Vera-Cabrera, L., Stefani, M. M., Banu, S., Macdonald, M., Sapkota, B. R., Spencer, J. S., Thomas, J., Harshman, K., Singh, P., Busso, P., Gattiker, A., Rougemont, J., Brennan, P. J. and Cole, S. T. (2009). Comparative genomic and phylogeographic analysis of Mycobacterium leprae. Nature Genetics 41, 1282–1289.CrossRefGoogle ScholarPubMed
Morand, S. and Krasnov, B. R. (2010). The Biogeography of Host-Parasite Interactions. Oxford University Press, Oxford, UK.Google Scholar
Muerhoff, A. S., Leary, T. P., Sathar, M. A., Dawson, G. J. and Desai, S. M. (2005). African origin of GB virus C determined by phylogenetic analysis of a complete genotype 5 genome from South Africa. Journal of General Virology 86, 1729– 1735.CrossRefGoogle ScholarPubMed
Musser, J. M., Kroll, J. S., Granoff, D. M., Richard Moxon, E., Brodeur, B. R., Campos, J., Dabernat, H., Frederiksen, W., Hamel, J., Hammond, G., Høiby, E. A., Jonsdottir, K. E., Kabeer, M., Kallings, I., Khan, W. N., Kilian, M., Knowles, K., Koornhof, H. J., Law, B., Li, K. I., Montgomery, J., Pattison, P. E., Piffaretti, J.-C., Takala, A. K., Len Thong, M., Wall, R. A., Ward, J. I. and Selander, R. K. (1990). Global genetic structure and molecular epidemiology of encapsulated Haemophilus influenzae. Reviews of Infectious Diseases 12, 75–111.CrossRefGoogle ScholarPubMed
Naderi, S., Rezaei, H. R., Pompanon, F., Blum, M. G. B., Negrini, R., Naghash, H. R., Balkız, Ö, Mashkour, M., Gaggiotti, O. E., Ajmone-Marsan, P., Kence, A., Vigne, J. D. and Taberlet, P. (2008). The goat domestication process inferred from large-scale mitochondrial DNA analysis of wild and domestic individuals. Proceedings of the National Academic Sciences, USA 105, 17659–17664.CrossRefGoogle ScholarPubMed
Nieberding, C., Jousselin, E. and Desdevises, Y. (2010). The use of co-phylogeographic patterns to predict the nature of host– parasite interactions, and vice versa. In The Biogeography of Host-Parasite Interactions (eds. Morand, S. and Krasnov, B. R.), pp. 59–69, Oxford University Press, UK.Google Scholar
Nieberding, C. M., Durette-Desset, M.-C., Vanderpoorten, A., Casanovas, J. C., Ribas, A., Deffontaine, V., Feliu, C., Morand, S., Libois, R. and Michaux, J. R. (2008). Geography and host biogeography matter for understanding the phylogeography of a parasite Molecular Phylogenetics and Evolution 47, 538–554.CrossRefGoogle ScholarPubMed
Nieberding, C. M., Morand, S., Libois, R. and Michaux, J. R. (2004). A parasite reveals cryptic phylogeographic history of its host. Proceedings of the Royal Society of London B 271, 2559–2568.CrossRefGoogle ScholarPubMed
Nieberding, C. M. and Olivieri, I. (2007). Parasites: proxies for host genealogy and ecology? Trends in Ecology and Evolution 22, 156–165.CrossRefGoogle ScholarPubMed
Perrin, P., Herbreteau, V., Hugot, J.-P. and Morand, S. (2010). Biogeography, humans and their parasites. In The Biogeography of Host-Parasite Interactions (eds. Morand, S. and Krasnov, B. R.), pp. 41–57, Oxford University Press, UK.Google Scholar
Rasmussen, M., Guo, X., Wang, Y., Lohmueller, K. E., Rasmussen, S., Albrechtsen, A., Skotte, L., Lindgreen, S., Metspalu, M., Jombart, T., Kivisild, T., Zhai, W., Eriksson, A., Manica, A., Orlando, L., De La Vega, F. M., Tridico, S., Metspalu, E., Nielsen, K., Ávila-Arcos, M. C., Moreno-Mayar, J. V., Muller, C., Dortch, J., Gilbert, M. T., Lund, O., Wesolowska, A., Karmin, M., Weinert, L. A., Wang, B., Li, J., Tai, S., Xiao, F., Hanihara, T., van Driem, G., Jha, A. R., Ricaut, F. X., de Knijff, P., Migliano, A. B., Gallego Romero, I., Kristiansen, K., Lambert, D. M., Brunak, S., Forster, P., Brinkmann, B., Nehlich, O., Bunce, M., Richards, M., Gupta, R., Bustamante, C. D., Krogh, A., Foley, R. A., Lahr, M. M., Balloux, F., Sicheritz-Pontén, T., Villems, R., Nielsen, R., Wang, J. and Willerslev, E. (2011). An Aboriginal Australian genome reveals separate human dispersals into Asia. Science 334, 94–98.CrossRefGoogle ScholarPubMed
Reed, D. L., Light, J. E., Allen, J. M. and Kirchman, J. J. (2007). Pair of lice lost or parasites regained: the evolutionary history of anthropoid primate lice. BMC Biology 5, 7.CrossRefGoogle ScholarPubMed
Roumagnac, P., Weill, F.-X., Dolecek, C., Baker, S., Brisse, S., Chinh, N. T., Le, T. A., Acosta, C. J., Farrar, J., Dougan, G. and Achtman, M. (2006). Evolutionary history of Salmonella typhi. Science 314, 1301–1304.CrossRefGoogle ScholarPubMed
Rosenthal, B. M., LaRosa, G., Zarlenga, D., Dunams, D., Chunyu, Y., Mingyuan, L. and Pozio, E. (2008). Human dispersal of Trichinella spiralis in domesticated pigs. Infection, Genetics and Evolution 8, 799–805.CrossRefGoogle ScholarPubMed
Savolainen, P., Zhang, Y.-P., Luo, J., Lundeberg, J. and Leitner, T. (2002). Genetic evidence for an East Asian origin of domestic dogs. Science 298, 1610–1613.CrossRefGoogle ScholarPubMed
Schurr, T. and Sherry, S. T. (2004). Mitochondrial DNA and Y chromosome diversity and the peopling of the Americas: evolutionary and demographic evidence. American Journal of Human Biology 16, 420–439.CrossRefGoogle ScholarPubMed
Shackelton, L. A, Rambaut, A., Pybus, O. G. and Holmes, E. C. (2006). JC virus evolution and its association with human populations. Journal of Virology 80, 9928–9933.CrossRefGoogle ScholarPubMed
Smith, N. H., Hewinson, R. G., Kremer, K., Brosch, R. and Gordon, S. V. (2009). Myths and misconceptions: the origin and evolution of Mycobacterium tuberculosis. Nature Reviews Microbiology 7, 537–544.CrossRefGoogle ScholarPubMed
Sugimoto, C., Hasegawa, M., Kato, A., Zheng, H. Y., Ebihara, H., Taguchi, F., Kitamura, T. and Yogo, Y. (2002). Evolution of human polyomavirus JC: Implications for the population history of humans. Journal of Molecular Evolution 54, 285–297.CrossRefGoogle ScholarPubMed
Switzer, W. M., Salemi, M., Shanmugam, V., Gao, F., Cong, M., Kuiken, C., Bhullar, V., Beer, B. E., Vallet, D., Gautier-Hion, A., Tooze, Z., Villinger, F., Holmes, E. C. and Heneine, W. (2005). Ancient co-speciation of simian foamy viruses and primates. Nature 434, 376–380.CrossRefGoogle ScholarPubMed
Taylor, L. H., Latham, S. M. and Woolhouse, M. E. J. (2001). Risk factors for human disease emergences. Philosophical Transaction of the Royal Society of London B 356, 983–989.CrossRefGoogle Scholar
Templeton, A. R. (2010). Coalescent-based, maximum likelihood inference in phylogeography. Molecular Ecology 19, 431–446.CrossRefGoogle ScholarPubMed
Troell, K., Engström, A., Morrison, D. A., Mattsson, J. G. and Höglund, J. (2006). Global patterns reveal strong population structure in Haemonchus contortus, a nematode parasite of domesticated ruminants. International Journal for Parasitology 36, 1305–1316.CrossRefGoogle ScholarPubMed
Van Ert, M. N., Easterday, W. R., Huynh, L. Y., Okinaka, R. T., Hugh-Jones, M. E., Ravel, J., Zanecki, S. R., Pearson, T., Simonson, T. S., U'Ren, J. M., Kachur, S. M., Leadem-Dougherty, R. R., Rhoton, S. D., Zinser, G., Farlow, J.Coker, P. R.Smith, K. L., Wang, B., Kenefic, L. J., Fraser-Liggett, C. M., Wagner, D. M. and Paul Keim, P. (2007). Global genetic population structure of Bacillus anthracis. PLoS ONE 2, e461.CrossRefGoogle ScholarPubMed
Weiss, R. A. (2001). The Leeuwenhoek Lecture 2001. Animal Origins of Human Infectious Disease Philosophical Transactions: Biological Sciences 356, 957–977.Google ScholarPubMed
Wirth, T., Meyer, A. and Achtman, M. (2005). Deciphering host migrations and origins by means of their microbes. Molecular Ecology 14, 3289–3306.CrossRefGoogle ScholarPubMed
Wirth, T., Wang, X., Linz, B., Novick, R. P., Lum, J. K., Blaser, M., Morelli, G., Falush, D. and Achtman, M. (2004). Distinguishing human ethnic groups by means of sequences from Helicobacter pylori: lessons from Ladakh. Proceedings of the National Academy of Sciences, USA 101, 4746–4751.CrossRefGoogle ScholarPubMed
Wolfe, N. D., Panosian Dunavan, C. and Diamond, J. (2007). Origins of major human infectious diseases. Nature 447, 279–283.CrossRefGoogle ScholarPubMed
Wooding, S. (2001). Do human and JC virus genes show evidence of host–parasite codemography? Infection, Genetics and Evolution 1, 3–12.CrossRefGoogle ScholarPubMed
Woolhouse, M. E. J. and Gowtage-Sequeria, S. (2005). Host range and emerging and reemerging pathogens. Emerging Infectious Diseases 11, 1842–1847.CrossRefGoogle ScholarPubMed
Zhang, W., Qi, W., Albert, T. J., Motiwala, A. S., Alland, D., Hyytia-Trees, E. K., Ribot, E. M., Fields, P. I., Whittam, T. S. and Swaminathan, B. (2006). Probing genomic diversity and evolution of Escherichia coli O157 by single-nucleotide polymorphisms. Genome Research 16, 757–767.CrossRefGoogle ScholarPubMed
Zheng, H.-Y., Sugimoto, C., Hasegawa, M., Kobayashi, N., Kanayama, A., Rodas, A., Mejia, S. M., Nakamichi, S. J., Guo, J., Kitamura, T. and Yogo, Y. (2003). Phylogenetic relationships among JC virus strains in Japanese/Koreans and native Americans speaking Amerind or Na-Dene. Journal of Molecular Evolution 56, 18–27.CrossRefGoogle ScholarPubMed
Zhou, C., Li, M., Yuan, K., Hu, N. and Peng, W. (2011). Phylogeography of Ascaris lumbricoides and A. suum from China. Parasitology Research 109, 329–338.CrossRefGoogle Scholar