The landscape genetics of infectious disease emergence and spread

Molecular Ecology

Volumn 19, Issue 17, 2010, Pages 3515-3531

  Biek, Roman ^a   Real, Leslie A ^b,c  

^a UNIVERSITY OF GLASGOW   (United Kingdom)

^b EMORY UNIVERSITY   (United States)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

emerging infectious diseases; gene flow; heterogeneity; invasion; molecular epidemiology; parasite

Indexed keywords

ANIMAL; ARTICLE; ECOLOGY; GENE FLOW; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; HOST PARASITE INTERACTION; METHODOLOGY; MOLECULAR EPIDEMIOLOGY; PARASITOSIS; POPULATION GENETICS;

ANIMALS; ECOLOGY; GENE FLOW; GENETIC VARIATION; GENETICS, POPULATION; GEOGRAPHY; HOST-PARASITE INTERACTIONS; MOLECULAR EPIDEMIOLOGY; PARASITIC DISEASES;

EID: 77956071523     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2010.04679.x     Document Type: Article

References (105)

1. Anderson T (2009) Mapping the spread of malaria drug resistance. PLoS Medicine, 6, e1000054.
2. Anderson CD, Epperson BK, Fortin M-J et al. (2010) Considering spatial and temporal scale in landscape-genetic studies of gene flow. Molecular Ecology, 19, 3565 3575.
3. Anthony NM, Johnson-Bawe M, Jeffery K et al. (2007) The role of Pleistocene refugia and rivers in shaping gorilla genetic diversity in central Africa. Proceedings of the National Academy of Sciences, USA, 104, 20432 20436.
4. Archie EA, Luikart G, Ezenwa VO (2009) Infecting epidemiology with genetics: a new frontier in disease ecology. Trends in Ecology & Evolution, 24, 21 30.
5. Bahl J, Vijaykrishna D, Holmes EC, Smith GJ, Guan Y (2009) Gene flow and competitive exclusion of avian influenza A virus in natural reservoir hosts. Virology, 390, 289 297.
6. Balkenhol N, Gugerli F, Cushman SA et al. (2009) Identifying future research needs in landscape genetics: where to from here? Landscape Ecology, 24, 455 463.
7. Barrett LG, Thrall PH, Burdon JJ, Linde CC (2008) Life history determines genetic structure and evolutionary potential of host-parasite interactions. Trends in Ecology & Evolution, 23, 678 685.
8. Bataille A, Cunningham AA, Cedeno V et al. (2009) Evidence for regular ongoing introductions of mosquito disease vectors into the Galapagos Islands. Proceedings of the Royal Society B-Biological Sciences, 276, 3769 3775.
9. Berger PH, Zeyen RTJ, Groth JV (1987) Aphid retention of maize dwarf mosaic virus (potyvirus): epidemiological implications. Annals of Applied Biology, 111, 337 344.
10. Biek R, Drummond AJ, Poss M (2006) A virus reveals population structure and recent demographic history of its carnivore host. Science, 311, 538 541.
11. Biek R, Henderson JC, Waller LA, Rupprecht CE, Real LA (2007) A high-resolution genetic signature of demographic and spatial expansion in epizootic rabies virus. Proceedings of the National Academy of Sciences, USA, 104, 7993 7998.
12. Black WCt, Doty JB, Hughes MT, Beaty BJ, Calisher CH (2009) Temporal and geographic evidence for evolution of Sin Nombre virus using molecular analyses of viral RNA from Colorado, New Mexico and Montana. Virology Journal, 6, 102.
13. Blanchong JA, Samuel MD, Scribner KT et al. (2008) Landscape genetics and the spatial distribution of chronic wasting disease. Biology Letters, 4, 130 133.
14. Blouin MS, Yowell CA, Courtney CH, Dame JB (1995) Host movement and the genetic structure of populations of parasitic nematodes. Genetics, 141, 1007 1014.
15. Bourhy H, Kissi B, Audry L et al. (1999) Ecology and evolution of rabies virus in Europe. Journal of General Virology, 80, 2545 2557.
16. Bourhy H, Reynes JM, Dunham EJ et al. (2008) The origin and phylogeography of dog rabies virus. Journal of General Virology, 89, 2673 2681.
17. Bowden J, Gregory PH, Johnson CG (1971) Possible wind transport of coffee leaf rust across the Atlantic Ocean. Nature, 229, 500 501.
18. Brown JK, Hovmoller MS (2002) Aerial dispersal of pathogens on the global and continental scales and its impact on plant disease. Science, 297, 537 541.
19. Bruyndonckx N, Henry I, Christe P, Kerth G (2009) Spatio-temporal population genetic structure of the parasitic mite Spinturnix bechsteini is shaped by its own demography and the social system of its bat host. Molecular Ecology, 18, 3581 3592.
20. Campbell CL, Madden LV (1990) Introduction to Plant Disease Epidemiology. John Wiley & Sons, New York.
21. Cleaveland S, Laurenson MK, Taylor LH (2001) Diseases of humans and their domestic mammals: pathogen characteristics, host range and the risk of emergence. Philosophical Transactions of the Royal Society of London Series B-Biological Sciences, 356, 991 999.
22. Clements AC, Pfeiffer DU (2009) Emerging viral zoonoses: frameworks for spatial and spatiotemporal risk assessment and resource planning. Veterinary Journal, 182, 21 30.
23. Cottam EM, Thebaud G, Wadsworth J et al. (2008) Integrating genetic and epidemiological data to determine transmission pathways of foot-and-mouth disease virus. Proceedings of the Royal Society B-Biological Sciences, 275, 887 895.
24. Criscione CD, Blouin MS (2004) Life cycles shape parasite evolution: comparative population genetics of salmon trematodes. Evolution, 58, 198 202.
25. Criscione CD, Poulin R, Blouin MS (2005) Molecular ecology of parasites: elucidating ecological and microevolutionary processes. Molecular Ecology, 14, 2247 2257.
26. Cross PC, Lloyd-Smith JO, Johnson PLF, Getz WM (2005) Duelling timescales of host movement and disease recovery determine invasion of disease in structured populations. Ecology Letters, 8, 587 595.
27. CSMEC (2004) Molecular evolution of the SARS coronavirus during the course of the SARS epidemic in China. Science, 303, 1666 1669.
28. Cullingham CI, Kyle CJ, Pond BA, Rees EE, White BN (2009) Differential permeability of rivers to raccoon gene flow corresponds to rabies incidence in Ontario, Canada. Molecular Ecology, 18, 43 53.
29. Cushman SA, Landguth EL (2010) Spurious correlations and inference in landscape genetics. Molecular Ecology, 19, 3592 3602.
30. Cushman SA, McKelvey KS, Hayden J, Schwartz MK (2006) Gene flow in complex landscapes: testing multiple hypotheses with causal modeling. American Naturalist, 168, 486 499.
31. Dragoo JW, Lackey JA, Moore KE et al. (2006) Phylogeography of the deer mouse (Peromyscus maniculatus) provides a predictive framework for research on hantaviruses. Journal of General Virology, 87, 1997 2003.
32. Dugan VG, Chen R, Spiro DJ et al. (2008) The evolutionary genetics and emergence of avian influenza viruses in wild birds. PLoS Pathogens, 4, e1000076.
33. Dybdahl MF, Storfer A (2003) Parasite local adaptation: Red Queen versus Suicide King. Trends in Ecology & Evolution, 18, 523 530.
34. Eggert LS, Terwilliger LA, Woodworth BL et al. (2008) Genetic structure along an elevational gradient in Hawaiian honeycreepers reveals contrasting evolutionary responses to avian malaria. BMC Evolutionary Biology, 8, 315.
35. Epperson BK, McRae BH, Scribner K et al. (2010) Utility of computer simulations in landscape genetics. Molecular Ecology, 19, 3549 3564.
36. Excoffier L, Ray N (2008) Surfing during population expansions promotes genetic revolutions and structuration. Trends in Ecology & Evolution, 23, 347 351.
37. Frantz AC, Cellina S, Krier A, Schley L, Burke T (2009) Using spatial Bayesian methods to determine the genetic structure of a continuously distributed population: clusters or isolation by distance? Journal of Applied Ecology, 46, 493 505.
38. Gagneux P, Gonder MK, Goldberg TL, Morin PA (2001) Gene flow in wild chimpanzee populations: what genetic data tell us about chimpanzee movement over space and time. Philosophical Transactions of the Royal Society of London Series B-Biological Sciences, 356, 889 897.
39. Geraldes A, Ferrand N, Nachman MW (2006) Contrasting patterns of introgression at X-linked loci across the hybrid zone between subspecies of the European rabbit (Oryctolagus cuniculus). Genetics, 173, 919 933.
40. Gilbert M, Xiao X, Pfeiffer DU et al. (2008) Mapping H5N1 highly pathogenic avian influenza risk in Southeast Asia. Proceedings of the National Academy of Sciences, USA, 105, 4769 4774.
41. Girard JM, Wagner DM, Vogler AJ et al. (2004) Differential plague-transmission dynamics determine Yersinia pestis population genetic structure on local, regional, and global scales. Proceedings of the National Academy of Sciences, USA, 101, 8408 8413.
42. Giraud T (2004) Patterns of within population dispersal and mating of the fungus Microbotryum violaceum parasitising the plant Silene latifolia. Heredity, 93, 559 565.
43. Glass GE, Shields T, Cai B, Yates TL, Parmenter R (2007) Persistently highest risk areas for hantavirus pulmonary syndrome: potential sites for refugia. Ecological Applications, 17, 129 139.
44. Gloster J, Burgin L, Witham C, Athanassiadou M, Mellor PS (2008) Bluetongue in the United Kingdom and northern Europe in 2007 and key issues for 2008. Veterinary Record, 162, 298 302.
45. Goka K, Yokoyama J, Une Y et al. (2009) Amphibian chytridiomycosis in Japan: distribution, haplotypes and possible route of entry into Japan. Molecular Ecology, 18, 4757 4774.
46. Grenfell BT, Bjornstad ON, Kappey J (2001) Travelling waves and spatial hierarchies in measles epidemics. Nature, 414, 716 723.
47. Harris SR, Feil EJ, Holden MT et al. (2010) Evolution of MRSA during hospital transmission and intercontinental spread. Science, 327, 469 474.
48. Holmes EC (2003) Molecular clocks and the puzzle of RNA virus origins. Journal of Virology, 77, 3893 3897.
49. Holmes EC (2004) The phylogeography of human viruses. Molecular Ecology, 13, 745 756.
50. James TY, Litvintseva AP, Vilgalys R et al. (2009) Rapid global expansion of the fungal disease chytridiomycosis into declining and healthy amphibian populations. PLoS Pathogens, 5, e1000458.
51. Jancovich JK, Davidson EW, Parameswaran N et al. (2005) Evidence for emergence of an amphibian iridoviral disease because of human-enhanced spread. Molecular Ecology, 14, 213 224.
52. Jones KE, Patel NG, Levy MA et al. (2008) Global trends in emerging infectious diseases. Nature, 451, 990 993.
53. Keele BF, Van Heuverswyn F, Li Y et al. (2006) Chimpanzee reservoirs of pandemic and nonpandemic HIV-1. Science, 313, 523 526.
54. Keeney DB, King TM, Rowe DL, Poulin R (2009) Contrasting mtDNA diversity and population structure in a direct-developing marine gastropod and its trematode parasites. Molecular Ecology, 18, 4591 4603.
55. Keim PS, Wagner DM (2009) Humans and evolutionary and ecological forces shaped the phylogeography of recently emerged diseases. Nature Reviews Microbiology, 7, 813 821.
56. Kidd DM, Ritchie MG (2006) Phylogeographic information systems: putting the geography into phylogeography. Journal of Biogeography, 33, 1851 1865.
57. Kilpatrick AM, Chmura AA, Gibbons DW et al. (2006) Predicting the global spread of H5N1 avian influenza. Proceedings of the National Academy of Sciences, USA, 103, 19368 19373.
58. Kingman JFC (1982) On the genealogy of large populations. Journal of Applied Probability, 19A, 27 43.
59. Lahm SA, Kombila M, Swanepoel R, Barnes RF (2007) Morbidity and mortality of wild animals in relation to outbreaks of Ebola haemorrhagic fever in Gabon, 1994-2003. Transactions of the Royal Society of Tropical Medicine and Hygiene, 101, 64 78.
60. Lemey P, Rambaut A, Drummond AJ, Suchard MA (2009) Bayesian phylogeography finds its roots. PLoS Computational Biology, 5, e1000520.
61. Lemey P, Rambaut A, Welch JJ, Suchard MA (2010) Phylogeography takes a relaxed random walk in continuous space and time. Molecular Biology and Evolution, in press.
62. Leroy EM, Kumulungui B, Pourrut X et al. (2005) Fruit bats as reservoirs of Ebola virus. Nature, 438, 575 576.
63. Lewis F, Hughes GJ, Rambaut A, Pozniak A, Leigh Brown AJ (2008) Episodic sexual transmission of HIV revealed by molecular phylodynamics. PLoS Medicine, 5, e50.
64. Makarova NV, Kaverin NV, Krauss S, Senne D, Webster RG (1999) Transmission of Eurasian avian H2 influenza virus to shorebirds in North America. Journal of General Virology, 80, 3167 3171.
65. Manel S, Schwartz MK, Luikart G, Taberlet P (2003) Landscape genetics: combining landscape ecology and population genetics. Trends in Ecology & Evolution, 18, 189 197.
66. Manel S, Joost J, Epperson BK et al. (2010) Perspectives on the use of landscape genetics to detect genetic adaptive variation in the field. Molecular Ecology, 19, 3760 3772.
67. McRae BH (2006) Isolation by resistance. Evolution, 60, 1551 1561.
68. Muller A, Freitas J, Silva E et al. (2009) Evolution of rabbit haemorrhagic disease virus (RHDV) in the European rabbit (Oryctolagus cuniculus) from the Iberian Peninsula. Veterinary Microbiology, 135, 368 373.
69. Nadin-Davis SA, Casey GA, Wandeler AI (1994) A molecular epidemiological study of rabies virus in central Ontario and western Quebec. Journal of General Virology, 75, 2575 2583.
70. Nadler SA (1995) Microevolution and the genetic structure of parasite populations. Journal of Parasitology, 81, 395 403.
71. Nelson MI, Simonsen L, Viboud C, Miller MA, Holmes EC (2009) The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. Virology, 388, 270 278.
72. Nieberding CM, Olivieri I (2007) Parasites: proxies for host genealogy and ecology? Trends in Ecology & Evolution, 22, 156 165.
73. Ostfeld RS, Glass GE, Keesing F (2005) Spatial epidemiology: an emerging (or re-emerging) discipline. Trends in Ecology & Evolution, 20, 328 336.
74. Pearce RJ, Pota H, Evehe MS et al. (2009) Multiple origins and regional dispersal of resistant dhps in African Plasmodium falciparum malaria. PLoS Medicine, 6, e1000055.
75. Peterson AT (2006) Ecologic niche modeling and spatial patterns of disease transmission. Emerging Infectious Diseases, 12, 1822 1826.
76. Pomeroy LW, Bjornstad ON, Holmes EC (2008) The evolutionary and epidemiological dynamics of the paramyxoviridae. Journal of Molecular Evolution, 66, 98 106.
77. Purdy LH, Krupa SV, Dean JL (1985) Introduction of sugar cane rust into the Americas and its spread in Florida. Plant Diseases, 69, 469 474.
78. Pybus OG, Rambaut A (2009) Evolutionary analysis of the dynamics of viral infectious disease. Nature Reviews Genetics, 10, 540 550.
79. Rambaut A, Pybus OG, Nelson MI et al. (2008) The genomic and epidemiological dynamics of human influenza A virus. Nature, 453, 615 619.
80. Ramsden C, Melo FL, Figueiredo LM, Holmes EC, Zanotto PM (2008) High rates of molecular evolution in hantaviruses. Molecular Biology and Evolution, 25, 1488 1492.
81. Real LA, Biek R (2007) Spatial dynamics and genetics of infectious diseases on heterogeneous landscapes. Journal of the Royal Society Interface, 4, 935 948.
82. Real LA, Henderson JC, Biek R et al. (2005) Unifying the spatial population dynamics and molecular evolution of epidemic rabies virus. Proceedings of the National Academy of Sciences, USA, 102, 12107 12111.
83. Root JJ, Black WCt, Calisher CH et al. (2003) Analyses of gene flow among populations of deer mice (Peromyscus mani-culatus) at sites near hantavirus pulmonary syndrome case-patient residences. Journal of Wildlife Diseases, 39, 287 298.
84. Rupprecht CE, Smith JS (1994) Raccoon rabies: the re-emergence of an epizootic in a densely populated area. Seminars in Virology, 5, 155 164.
85. Russell CA, Jones TC, Barr IG et al. (2008) The global circulation of seasonal influenza A (H3N2) viruses. Science, 320, 340 346.
86. SanmartÌn I, Mark Pvd, Ronquist F (2008) Inferring dispersal: a Bayesian approach to phylogeny-based island biogeography, with special reference to the Canary Islands. Journal of Biogeography, 35, 428 449.
87. Sellers RF, Maarouf AR (1991) Possible introduction of epizootic hemorrhagic disease of deer virus (serotype 2) and bluetongue virus (serotype 11) into British Columbia in 1987 and 1988 by infected Culicoides carried on the wind. Canadian Journal of Veterinary Research, 55, 367 370.
88. Smith GJ, Vijaykrishna D, Bahl J et al. (2009) Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature, 459, 1122 1125.
89. Smith NH, Gordon SV, de la Rua-Domenech R, Clifton-Hadley RS, Hewinson RG (2006) Bottlenecks and broomsticks: the molecular evolution of Mycobacterium bovis. Nature Reviews Microbiology, 4, 670 681.
90. Sobesky R, Feray C, Rimlinger F et al. (2007) Distinct hepatitis C virus core and F protein quasispecies in tumoral and nontumoral hepatocytes isolated via microdissection. Hepatology, 46, 1704 1712.
91. Storfer A, Murphy MA, Evans JS et al. (2007) Putting the 'landscape' in landscape genetics. Heredity, 98, 128 142.
92. Takehisa J, Kraus MH, Ayouba A et al. (2009) Origin and biology of simian immunodeficiency virus in wild-living western gorillas. Journal of Virology, 83, 1635 1648.
93. Telfer PT, Souquiere S, Clifford SL et al. (2003) Molecular evidence for deep phylogenetic divergence in Mandrillus sphinx. Molecular Ecology, 12, 2019 2024.
94. Tsujimoto H, Cooper RW, Kodama T et al. (1988) Isolation and characterization of simian immunodeficiency virus from mandrills in Africa and its relationship to other human and simian immunodeficiency viruses. Journal of Virology, 62, 4044 4050.
95. Van Heuverswyn F, Li Y, Bailes E et al. (2007) Genetic diversity and phylogeographic clustering of SIVcpzPtt in wild chimpanzees in Cameroon. Virology, 368, 155 171.
96. Wallace RG, Hodac H, Lathrop RH, Fitch WM (2007) A statistical phylogeography of influenza A H5N1. Proceedings of the National Academy of Sciences, USA, 104, 4473 4478.
97. Waller LA, Gotway CA (2004) Applied Spatial Statistics for Public Health Data. Wiley, New York.
98. Walsh PD, Biek R, Real LA (2005) Wave-like spread of Ebola Zaire. PLoS Biology, 3, e371.
99. Whiteman NK, Parker PG (2005) Using parasites to infer population history: a new rationale for parasite conservation. Animal Conservation, 8, 175 181.
100. Wimberly MC, Baer AD, Yabsley MJ (2008) Enhanced spatial models for predicting the geographic distributions of tick-borne pathogens. International Journal of Health Geographics, 7, 15.
101. Winker K, McCracken KG, Gibson DD et al. (2007) Movements of birds and avian influenza from Asia into Alaska. Emerging Infectious Diseases, 13, 547 552.
102. Wong JK, Ignacio CC, Torriani F et al. (1997) In vivo compartmentalization of human immunodeficiency virus: evidence from the examination of pol sequences from autopsy tissues. Journal of Virology, 71, 2059 2071.
103. Woolhouse ME (2002) Population biology of emerging and re-emerging pathogens. Trends in Microbiology, 10, S3 S7.
104. Wylie JL, Cabral T, Jolly AM (2005) Identification of networks of sexually transmitted infection: a molecular, geographic, and social network analysis. Journal of Infectious Diseases, 191, 899 906.
105. Xia Y, Bjornstad ON, Grenfell BT (2004) Measles metapopulation dynamics: a gravity model for epidemiological coupling and dynamics. American Naturalist, 164, 267 281.