BIOE 149 Disease Ecology Syllabus

Instructor: Dr. Marm Kilpatrick

Assistant Professor, Ecology and Evolutionary Biology

Office: A332 EMS

Phone: (831) 459-5070

Email: akilpatr@ucsc.edu

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

 

TA: Tony Kovach

Email: tokovach@gmail.com

Office Hours: Tu 845-945 AM; Fr 1045-1145 AM  in Biomed 220

 

Lecture: Porter Acad 148; Tu, Th 10-11:45 am

Discussions:

Th 8:30-9:40 am Baskin Engineering 165

Fri 9:30-10:40 am Baskin Engineering 165

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.

 

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 ReadingsI       II       III

1

Tue

Mar 29

What is disease ecology, and what is it good for? 1 2 3

1

Thu

Mar 31

Foundations of disease ecology: SIR models, R0, Frequency and density dependent transmission, Nth 4 5 6, 7

2

Tue

Apr 5

Directly transmitted human pathogens 8 9 10

2

Tue

Apr 7

Disease impacts on populations and ecosystems 11 12 13

3

Thu

Apr 12

Livestock, wildlife, zoonotic pathogens 14 15

3

Thu

Apr 14

Disease control: Vaccination, Behavioral changes, culling 16 17 18

4

Tue

Apr 19

Building a model: Cholera 19,20  

4

Thu

Apr 21

Pathogen interactions via the immune system, and parasite caused changes in host behavior 21 22

5

Tue

Apr 26

Evolution of virulence: hosts, pathogens, vectors 23   24-27

5

Thu

Apr 28

Herd immunity 28  

6

Tue

May 3

Midterm

6

Thu

May 5

Vector borne disease ecology I. 30 31

7

Tue

May 10

Vector borne disease ecology II. 32 33

7

Thu

May 12

Seasonality, climate change and transmission dynamics 34 35 36

8

Tue

May 17

Evolution antibiotic resistance 37 38 39

8

Thu

May 19

Multi-host pathogens, biodiversity and disease: the “dilution effect” 40 41 42

9

Tue

May 24

The ecology of emerging infectious diseases 43 44

9

Thu

May 26

Plant pathogens 45 46 47

10

Tue

May 31

Disease and conservation 48 49

10

Thu

Jun 2

Poster session

11

Tu

Jun 7

Final Exam 8am

 

 

 

Readings

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          Druilhe, P., Tall, A., and Sokhna, C., Worms can worsen malaria: towards a new means to roll back malaria? Trends in Parasitology 21 (8), 359 (2005). 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          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 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

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