BIOE 149 Disease Ecology Syllabus

Instructor: Dr. Marm Kilpatrick

Associate Professor, Ecology and Evolutionary Biology

Office: A332 EMS

Phone: (831) 459-5070


Office Hours: Tue 1-2pm  and by appt.


TA: Joseph Stewart


Office Hours: Thursdays 1:15-3:15 in EMS D450


Lecture: Cowell Clrm 131; Tu, Th 9:50am-11:25 am


W 4-5:05pm am N. Sci Annex 103

Th 3:20-4:25pm N. Sci Annex 102

Course Description: This is a class on problem solving and critical thinking.  We will focus on problems related to the ecological and evolutionary processes that drive the transmission of pathogens between hosts; the impact of disease on host populations; and what causes the emergence of an infectious disease. The course content includes a theoretical framework, hands-on experience with field techniques, and a discussion of wildlife and human diseases including Zika, Ebola, 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.

Quizzes: There will be a 5 minute quiz at the beginning of each lecture on the reading for that week.  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 for undergraduates.  4 things to get from each reading: 1) main question of paper, 2) type of study, 3) major finding, 4) major flaw(s).  Quizzes are written so that you can’t get answer from title/abstract, but it is obvious from reading paper.

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.

Poster Assignment with points 2017

Sample Posters

Grades: Quizzes 15%; Poster Project 15%; Midterm 25%; Discussion Activities: 15% Final: 30%.

Weekly Schedule. Everyone should read the paper in column I (before that class, except #1), grad students and undergrads looking for extra credit should read the paper in column II (columns I, II will be the material for the daily quizzes).  Papers in column III are either advanced readings, or additional readings for those especially interested in the topic. 




Wk Day Date Topic Readings

I       II       III

1 Tue Apr 4 What is disease ecology, and what is it good for? 1 2 3
1 Thu Apr 6 Foundations of disease ecology: SIR models, R0, Frequency and density dependent transmission, Nth 4 5 6, 7
2 Tue Apr 11 Directly transmitted human pathogens 8 9 10
2 Thu Apr 13 Disease impacts on populations and ecosystems 11 12 13
3 Tue Apr 18 Livestock, wildlife, zoonotic pathogens 14 15
3 Thu Apr 20 Plant pathogens 45 46 47
4 Tue Apr 25 Disease control: Vaccination, Behavioral changes, culling 16 17 18
4 Thu Apr 27 Building a model from data: Cholera 19,20
5 Tue May 2 Pathogen interactions via the immune system, and parasite caused changes in host behavior 21 22
5 Thu May 4 Evolution of virulence: hosts, pathogens, vectors 23 24 25-27
6 Tue May 9 Case study: White nose syndrome 48
6 Thu May 11 Midterm
7 Tue May 16 Vector borne disease ecology I. 30 31
7 Thu May 18 WNS-Follow-up 32
8 Tue May 23 Seasonality, climate change and transmission dynamics 34 36
8 Thu May 25 Evolution antibiotic resistance 37 39
9 Tue May 30 Multi-host pathogens, biodiversity and disease: the “dilution effect” 40 41 42
9 Thu Jun 1 The ecology of emerging infectious diseases 44
10 Tue Jun 6 Disease and conservation 49
10 Thu Jun 8 Poster session
11 Tu Jun 13 Final Exam 4-7pm




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          Harris, J. B., R. C. LaRocque, F. Qadri, E. T. Ryan, and S. B. Calderwood. 2012. Cholera. Lancet 379:2466-2476. PDF

20         Cholera Model Homework assignment

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

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         Quiz 8 follow up

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 Questions for Mordecai et al 2012 Ecol Lett

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 Proceedings of the National Academy of Sciences of the United States of America 105 (45), 17436 (2008). PDF

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

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.          Read AF, Lynch PA, Thomas MB. How to Make Evolution-Proof Insecticides for Malaria Control. PLoS Biol 2009; 7(4): e1000058. PDF

40.          Johnson PTJ, Preston DL, Hoverman JT, Richgels KLD. Biodiversity decreases disease through predictable changes in host community competence. Nature 2013; 494(7436): 230-3. PDF

41.          Logiudice K, Duerr STK, Newhouse MJ, Schmidt KA, Killilea ME, Ostfeld RS. Impact of host community composition on Lyme disease risk. Ecology 2008; 89(10): 2841-9. PDF

42.          Keesing F, Holt RD, Ostfeld RS. Effects of species diversity on disease risk. Ecol Lett 2006; 9(4): 485-98. 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 KE, Frick WF, Bried JT, Hicks AC, Kunz TH, Kilpatrick AM. Sociality, density-dependence and microclimates determine the persistence of populations suffering from a novel fungal disease, white-nose syndrome. Ecol Lett 2012; 15: 1050-7. PDF

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