Powerpoints and reading material
This page will be populated during the course, as I update or write lectures.
(last year's lectures here, but will be updated)
Lecture 1: Host genetic diversity: MHC variation
Lecture 1 powerpoint pdf
Bernatchez L, Landry C (2003) MHC studies in nonmodel vertebrates: what have we learned about natural selection in 15 years? Journal of Evolutionary Biology, 16, 363–377. DOI: 10.1046/j.1420-9101.2003.00531.x
Piertney SB, Oliver MK (2006) The evolutionary ecology of the major histocompatibility complex. Heredity, 96, 7–21. doi:10.1038/sj.hdy.6800724
Trowsdale J (2011) The MHC, disease and selection. Immunology Letters, 137, 1–8. doi:10.1016/j.imlet.2011.01.002
Lecture 2: Host genetic diversity: genome-wide approaches
Lecture 2 powerpoint pdf
Genetics of human susceptibility to infectious disease. Cooke and Hill (2001) Nature Reviews Genetics 2, 967-977 doi:10.1038/35103577
Chapman, S. J., & Hill, A. V. S. (2012). Human genetic susceptibility to infectious disease. Nature Reviews Genetics, 13, 175–188. doi: 10.1038/nrg3114
http://www.malariagen.net/
Lecture 3: Virus evolution: HIV contact networks
Lecture 3 powerpoint pdf
de Oliveira, T., Pybus, O. G., Rambaut, A., Salemi, M., Cassol, S., Ciccozzi, M., et al. (2006). Molecular Epidemiology: HIV-1 and HCV sequences from Libyan outbreak. Nature, 444, 836–837. doi:10.1038/444836a
Holmes, E. C., Zhang, L. Q., Robertson, P., Cleland, A., Harvey, E., Simmonds, P., & Leigh Brown, A. J. (1995). The molecular epidemiology of human immunodeficiency virus Type 1 in Edinburgh. The Journal of Infectious Diseases, 171, 45–53. doi: 10.1093/infdis/171.1.45
Rambaut, A., Posada, D., Crandall, K. A., & Holmes, E. C. (2004). The causes and consequences of HIV evolution. Nat Rev Genet, 5, 52–61. doi: 10.1038/nrg1246
Ross, H. A., & Rodrigo, A. G. (2002). Immune-mediated positive selection drives human immunodeficiency virus type 1 molecular variation and predicts disease duration. Journal of Virology, 76, 11715–11720. doi: 10.1128/JVI.76.22.11715-11720.200
Sharp, P. M., & Hahn, B. H. (2008). Aids - Prehistory of HIV-1. Nature, 455, 605–606. doi:10.1038/455605a
Lecture 4: Virus evolution: SARS
Lecture 4 powerpoint pdf
Anderson, R. M., Fraser, C., Ghani, A. C., Donnelly, C. A., Riley, S., Ferguson, N. M., et al. (2004). Epidemiology, transmission dynamics and control of SARS: the 2002-2003 epidemic. Philos Trans R Soc Lond B Biol Sci, 359(1447), 1091–1105. doi:10.1098/rstb.2004.1490
Guan, Y., Zheng, B. J., He, Y. Q., Liu, X. L., Zhuang, Z. X., Cheung, C. L., et al. (2003). Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China. Science (New York, N.Y.), 302(5643), 276–278. doi: 10.1126/science.1087139
Li, W., Shi, Z., Yu, M., Ren, W., Smith, C., Epstein, J. H., et al. (2005). Bats are natural reservoirs of SARS-like coronaviruses. Science (New York, N.Y.), 310(5748), 676–679. doi: 10.1126/science.1118391
The Chinese SARS Molecular Epidemiology Consortium. (2004). Molecular Evolution of the SARS Coronavirus During the Course of the SARS Epidemic in China. Science (New York, N.Y.), 303(5664), 1666–1669. doi:10.1126/science.1092002
Zhao, G. P. (2007). SARS molecular epidemiology: a Chinese fairy tale of controlling an emerging zoonotic disease in the genomics era. Philos Trans R Soc Lond B Biol Sci, 362(1482), 1063–1081. doi:10.1098/rstb.2007.2034
http://www.sciencemag.org/content/339/6125/1266.full
Lecture 5: Coevolution
Lecture 5 powerpoint pdf
Barrick, J. E., & Lenski, R. E. (2013). Genome dynamics during experimental evolution. Nature Reviews Genetics, 14(12), 827–839. doi:10.1038/nrg3564
Buckling, A., & Rainey, P. B. (2002). Antagonistic coevolution between a bacterium and a bacteriophage, 269(1494), 931. doi:10.1098/rspb.2001.1945
Obbard, D. J., Jiggins, F. M., Halligan, D. L., & Little, T. J. (2006). Natural selection drives extremely rapid evolution in antiviral RNAi genes. Current Biology : CB, 16(6), 580–585. doi:10.1016/j.cub.2006.01.065
Obbard, D. J., Welch, J. J., Kim, K. W., & Jiggins, F. M. (2009). Quantifying Adaptive Evolution in the Drosophila Immune System. PLoS Genetics, 5(10), e1000698. doi:10.1371/Journal.Pgen.1000698
Paterson, S., Vogwill, T., Buckling, A., Benmayor, R., Spiers, A. J., Thomson, N. R., et al. (2010). Antagonistic coevolution accelerates molecular evolution. Nature, 464(7286), 275–278. doi:10.1038/nature08798
Lecture 6: Honeybee collapse
Lecture 6 powerpoint pdf
Cox-Foster, D. L., Conlan, S., Holmes, E. C., Palacios, G., Evans, J. D., Moran, N. A., et al. (2007). A Metagenomic Survey of Microbes in Honey Bee Colony Collapse Disorder. Science (New York, N.Y.), 318(5848), 283–287. doi:10.1126/science.1146498
Martin, S. J., Highfield, A. C., Brettell, L., Villalobos, E. M., Budge, G. E., Powell, M., et al. (2012). Global Honey Bee Viral Landscape Altered by a Parasitic Mite. Science (New York, N.Y.), 336(6086), 1304–1306. doi:10.1126/science.1220941
Moret, Y., & Schmid-Hemple, P. (2000). Survival for immunity: the price of immune system activation for bumblebee workers. Science (New York, N.Y.), 290, 1166–1168. DOI: 10.1126/science.290.5494.1166
Nazzi, F., Brown, S. P., Annoscia, D., Del Piccolo, F., Di Prisco, G., Varricchio, P., et al. (2012). Synergistic Parasite-Pathogen Interactions Mediated by Host Immunity Can Drive the Collapse of Honeybee Colonies. PLoS Pathog, 8(6), e1002735. doi:10.1371/journal.ppat.1002735
Ratnieks, F. L. W., & Carreck, N. L. (2010). Clarity on Honey Bee Collapse? Science 327:152-153 DOI: 10.1126/science.1185563
vanEngelsdorp, D., Evans, J. D., Saegerman, C., Mullin, C., Haubruge, E., Nguyen, B. K., et al. (2009). Colony Collapse Disorder: A Descriptive Study. PloS One, 4(8), e6481. doi:10.1371/journal.pone.0006481
Lecture 7: Evolution of virulence
Lecture 7 powerpoint pdf (in progress)
Barclay, V. C., Sim, D., Chan, B. H. K., Nell, L. A., Rabaa, M. A., Bell, A. S., et al.(2012). The Evolutionary Consequences of Blood-Stage Vaccination on the Rodent Malaria Plasmodium chabaudi. PLoS Biol, 10(7), e1001368. doi:10.1371/journal.pbio.1001368
Boots, M., & Mealor, M. (2007). Local Interactions Select for Lower Pathogen Infectivity. Science (New York, N.Y.), 315(5816), 1284–1286. doi:10.1126/science.1137126
Boots, M., & Sasaki, A. (1999). “Small worlds” and the evolution of virulence: infection occurs locally and at a distance. Proceedings of the Royal Society, Series B, 266(1432), 1933–1938.
Gandon, S., MacKinnon, M. J., Nee, S., & Read, A. F. (2001). Imperfect vaccines and the evolution of pathogen virulence. Nature, 414, 751–756.
Watts, D. J., & Strogatz, S. H. (1998). Collective dynamics of “small-world” networks. Nature, 393, 440–442.