BIOE 149 Disease Ecology Syllabus

Instructor: Dr. Marm Kilpatrick, Associate Professor, Ecology and Evolutionary Biology

Office: CBB 252

Phone: (831) 459-5070


Office Hours: Th 12pm-1pm and by appt.

TA: Carla Sette


Office Hours: CBB 158, M 2-3pm, W 2-3pm

Lecture: CBB 110 M,W 3:25pm-5:00pm


M 5:15-6:20pm CBB 110

W 5:15-6:20pm CBB 110

Course Description: This is a class on problem solving and critical thinking focusing on problems related to the ecological and evolutionary processes that drive the transmission of pathogens between hosts and the impact of disease on host populations. The course content includes a theoretical framework, hands-on experience with field techniques, and a discussion of wildlife and human diseases including Ebola, Zika, influenza (swine flu, bird flu), malaria, West Nile virus, Lyme disease, HIV, Chikungunya, tuberculosis, chytridiomycosis, and many others.

Course Readings: There is no book.  See schedule of readings below.

Attendance: Attendance at lectures and discussion is mandatory and attendance will be taken.  Course readings complement the lectures but only represent 25% of the material discussed in a given week, so if you miss a lecture you need to find a fellow student who will share their notes.

Daily Assignments: There are short quizzes on the reading for each day. There will be questions on the two papers in columns I and II (see below), with questions on papers in column II providing extra credit.

Poster Assignment with points 2019

Sample posters

Grades: Daily assignments 15%; Poster Project 15%; Midterm 25%; Discussion Activities: 15% Final take home exam: 30%.

Weekly Schedule. Everyone should read the papers in column I; the papers in column II are for extra credit.  Papers in column III are additional readings for those especially interested in the topic.

Wk Day Date Topic Readings




I       II       III

1 Mon Apr 1 What is disease ecology, and what is it good for? 1 2 3
1 Wed Apr 3 Foundations of disease ecology: SIR models, R0, Frequency and density dependent transmission, Nth 4   6, 7
2 Mon Apr 8 Directly transmitted human pathogens 8 9 10
2 Wed Apr 10 Disease impacts on populations and ecosystems 11 12 13
3 Mon Apr 15 Livestock, wildlife, zoonotic pathogens 14    
3 Wed Apr 17 Disease control: Vaccination, Behavioral changes, culling 16 17 18
4 Mon Apr 22 Problem solving: Controlling influenza 16,19    
4 Wed Apr 24 Problem solving: Herpes dynamics 20 22  
5 Mon Apr 29 Mid-term      
5 Wed May 1 Problem solving: Evolution of virulence 23 24 25-27
6 Mon May 6 Problem solving: Herpes dynamics, again! 20    
6 Wed May 8 Vector borne disease ecology I. 32    
7 Mon May 13 Vector borne disease ecology II. 31    
7 Wed May 15 Seasonality, climate change and transmission dynamics 34 35 36
8 Mon May 20 Antibiotic resistance 37 38 39
8 Wed May 22 Ingrid Parker guest lecture! 45 46 47
9 Mon May 27 Holiday      
9 Wed May 29 Co-infection 21 22  
10 Mon Jun 3 Disease and conservation      
10 Wed Jun 5 Poster session      
11     Take home final      


1           Kilpatrick, A. M. and Altizer, S., Disease Ecology. Nature Education Knowledge 1 (11), 13 (2010). Link to Article

2           Smith, K. F., Dobson, A. P., McKenzie, F. E., Real, L. A., Smith, D. L., and Wilson, M. L., Ecological theory to enhance infectious disease control and public health policy Frontiers in Ecology and the Environment 3 (1), 29 (2005). PDF

3           Plowright, R. K., Sokolow, S. H., Gorman, M. E., Daszak, P., and Foley, J. E., Causal inference in disease ecology: investigating ecological drivers of disease emergence Frontiers in Ecology and the Environment 6 (8), 420 (2008). PDF

4           Anderson, R. M. and May, R. M., A framework for discussing the population biology of infectious diseases in Infectious diseases of humans. Dynamics and control. (Oxford University Press, London, 1991), pp. 13. PDF

5           Lloyd-Smith, J. O., Cross, P. C., Briggs, C. J., Daugherty, M., Getz, W. M., Latto, J., Sanchez, M. S., Smith, A. B., and Swei, A., Should we expect population thresholds for wildlife disease?Trends in Ecology & Evolution 20 (9), 511 (2005).PDF

6           Anderson, R. M. and May, R. M., Population biology of infectious diseases I Nature 280 (5721), 361 (1979). PDF

7           May, R. M. and Anderson, R. M., Population Biology of Infectious-Diseases II Nature 280 (5722), 455 (1979).PDF

8           Woolhouse, M. E. J., Dye, C., Etard, J. F., Smith, T., Charlwood, J. D., Garnett, G. P., Hagan, P., Hii, J. L. K., Ndhlovu, P. D., Quinnell, R. J., Watts, C. H., Chandiwana, S. K., and Anderson, R. M., Heterogeneities in the transmission of infectious agents: Implications for the design of control programs Proceedings of the National Academy of  Sciences 94 (1), 338 (1997).PDF

9.         Aylward B, Barboza P, Bawo L, et al. Ebola Virus Disease in West Africa – The First 9 Months of the Epidemic and Forward Projections. N Engl J Med 2014; 371(16): 1481-95. PDF

10          Ferguson, N. M., Cummings, D. A. T., Fraser, C., Cajka, J. C., Cooley, P. C., and Burke, D. S., Strategies for mitigating an influenza pandemic Nature 442 (7101), 448 (2006). PDF

11          Hudson, P. J., Dobson, A. P., and Newborn, D., Prevention of population cycles by parasite removal Science 282 (5397), 2256 (1998).PDF

12          Holdo, R. M., Sinclair, A. R. E., Dobson, A. P., Metzger, K. L., Bolker, B. M., Ritchie, M. E., and Holt, R. D., A Disease-Mediated Trophic Cascade in the Serengeti and its Implications for Ecosystem C Plos Biology 7 (9), e1000210 (2009).PDF

13          LaDeau, S. L., Kilpatrick, A. M., and Marra, P. P., West Nile virus emergence and large-scale declines of North American bird populations Nature 447 (7145), 710 (2007). PDF

14          Hochachka WM, Dhondt AA. Density-dependent decline of host abundance resulting from a new infectious disease. Proc Natl Acad Sci U S A 2000; 97(10): 5303-6. PDF

15          Dobson, A. and Meagher, M., The population dynamics of brucellosis in the Yellowstone National Park Ecology 77 (4), 1026 (1996). PDF

16          Fraser, C., Riley, S., Anderson, R. M., and Ferguson, N. M., Factors that make an infectious disease outbreak controllable Proceedings of the National Academy of Sciences of the United States of America 101 (16), 6146 (2004). PDF

17          Donnelly, C. A., Woodroffe, R., Cox, D. R., Bourne, J., Gettinby, G., Le Fevre, A. M., McInerney, J. P., and Morrison, W. I., Impact of localized badger culling on tuberculosis incidence in British cattle Nature 426 (6968), 834 (2003). PDF

18          Galvani, A. P., Reluga, T. C., and Chapman, G. B., Long-standing influenza vaccination policy is in accord with individual self-interest but not with the utilitarian optimum Proceedings of the National Academy of Sciences of the United States of America 104 (13), 5692 (2007). PDF

19          Problem solving I Controlling influenza

20          Problem Solving II Herpes dynamics

21          Graham, A. L., Ecological rules governing helminth-microparasite coinfection Proceedings of the National Academy of Sciences of the United States of America 105 (2), 566 (2008). PDF

22          Mina, M. J., C. J. E. Metcalf, R. L. de Swart, A. Osterhaus, and B. T. Grenfell. 2015. Long-term measles-induced immunomodulation increases overall childhood infectious disease mortality. Science 348:694-699. PDF

23         Myxoma virus evolution of virulence homework

24          Grenfell, B. T., Pybus, O. G., Gog, J. R., Wood, J. L. N., Daly, J. M., Mumford, J. A., and Holmes, E. C., Unifying the epidemiological and evolutionary dynamics of pathogens Science 303(5656), 327 (2004). PDF

25          Woolhouse, M. E. J., Webster, J. P., Domingo, E., Charlesworth, B., and Levin, B. R., Biological and biomedical implications of the co-evolution of pathogens and their hosts Nature Genetics32 (4), 569 (2002). PDF

26          Mackinnon, M. J., Gandon, S., and Read, A. F., Virulence evolution in response to vaccination: The case of malaria Vaccine 26, C42 (2008). PDF

27          Ewald, P. W., Evolution of infectious disease. (Oxford University Press, Oxford, 1994).

28          Metcalf, C. J. E., M. Ferrari, A. L. Graham, and B. T. Grenfell. 2015. Understanding Herd Immunity. Trends in Immunology 36:753-755. PDF

29.      Langwig KE, Frick WF, Reynolds R, et al. Host and pathogen ecology drive the seasonal dynamics of a fungal disease, white-nose syndrome. Proceedings of the Royal Society B: Biological Sciences 2015; 282: 20142335. PDF

30          Wonham, M. J., de-Camino-Beck, T., and Lewis, M. A., An epidemiological model for West Nile virus: invasion analysis and control applications Proceedings of the Royal Society of London Series B-Biological Sciences 271 (1538), 501 (2004). PDF

31.          Sachs, J. and Malaney, P., The economic and social burden of malaria Nature 415 (6872), 680 (2002). PDF

32          Ostfeld, R. S., Canham, C. D., Oggenfuss, K., Winchcombe, R. J., and Keesing, F., Climate, deer, rodents, and acorns as determinants of variation in Lyme-disease risk Plos Biology 4 (6), 1058 (2006). PDF

33.       Alonso PL, Brown G, Arevalo-Herrera M, et al. A Research Agenda to Underpin Malaria Eradication. PLoS Med 2011; 8(1) e1000400.PDF

34.       Mordecai EA, Paaijmans KP, Johnson LR, et al. Optimal temperature for malaria transmission is dramatically lower than previously predicted. Ecol Lett 2013; 16(1): 22-30. PDF

35.      Gething, P. W., D. L. Smith, A. P. Patil, A. J. Tatem, R. W. Snow, and S. I. Hay. 2010. Climate change and the global malaria recession. Nature 465:342-346. PDF

36.          Rohr, J. R., Raffel, T. R., Romansic, J. M., McCallum, H., and Hudson, P. J., Evaluating the links between climate, disease spread, and amphibian declines. PNAS 105 (45), 17436 (2008). PDF

37.          Holmes, A. H., L. S. P. Moore, A. Sundsfjord, M. Steinbakk, S. Regmi, A. Karkey, P. J. Guerin, and L. J. V. Piddock. 2016. Understanding the mechanisms and drivers of antimicrobial resistance. Lancet 387:176-187. PDF

38.          Read AF, Day T, Huijben S. The evolution of drug resistance and the curious orthodoxy of aggressive chemotherapy. Proc Natl Acad Sci U S A 2011; 108: 10871-7. PDF

39.          Levy SB, Marshall B. Antibacterial resistance worldwide: causes, challenges and responses. Nat Med 2004; 10(12): S122-S9.PDF

40.          Keesing, F., R. D. Holt, and R. S. Ostfeld. 2006. Effects of species diversity on disease risk. Ecology Letters 9:485-498. PDF

41.         Kilpatrick, A. M., D. J. Salkeld, G. Titcomb, and M. B. Hahn. 2017. Conservation of biodiversity as a strategy for improving human health and well-being. Philosophical Transactions of the Royal Society B-Biological Sciences 372:20160131. PDF

42. Civitello, D. J., J. Cohen, H. Fatima, N. T. Halstead, J. Liriano, T. A. McMahon, C. N. Ortega, E. L. Sauer, T. Sehgal, S. Young, and J. R. Rohr. 2015. Biodiversity inhibits parasites: Broad evidence for the dilution effect. PNAS 112:8667-8671. PDF

43.          Wolfe ND, Dunavan CP, Diamond J. Origins of major human infectious diseases. Nature 2007; 447(7142): 279-83. PDF

44.          Faria NR, Rambaut A, Suchard MA, et al. The early spread and epidemic ignition of HIV-1 in human populations. Science 2014; 346(6205): 56-61. PDF

45.       Parker IM, Saunders M, Bontrager M, et al. Phylogenetic structure and host abundance drive disease pressure in communities. Nature 2015; 520(7548): 542-4 PDF

46.          Gilbert GS, Webb CO. Phylogenetic signal in plant pathogen-host range. Proc Natl Acad Sci U S A 2007; 104(12): 4979-83.PDF

47.          Parker IM, Gilbert GS. The evolutionary ecology of novel plant-pathogen interactions. Annu Rev Ecol Evol Syst 2004; 35: 675-700.PDF

48.          Langwig, K. E., J. Voyles, M. Q. Wilber, W. F. Frick, K. A. Murray, B. M. Bolker, J. P. Collins, T. L. Cheng, M. C. Fisher, J. R. Hoyt, D. L. Lindner, H. I. McCallum, R. Puschendorf, E. B. Rosenblum, M. Toothman, C. K. R. Willis, C. J. Briggs, and A. M. Kilpatrick. 2015. Context dependent conservation responses to emerging wildlife diseases. Frontiers in Ecology and the Environment 13:195–202. PDF

49.          McCallum H. Disease and the dynamics of extinction. Philos Trans R Soc B-Biol Sci 2012; 367(1604): 2828-39. PDF