BIOE 149 Disease Ecology Syllabus

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

Office: Online!

Email: akilpatr@ucsc.edu

Phone: (831) 459-5070

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

 

TA: Christa Seidl

Email: cseidl@ucsc.edu

Office Hours: 

Th 3:30-5:30pm

 

TA: Matthew Montgomery

Email: mjmontgo@ucsc.edu

Office Hours: 

W 1:30-2:30pm

 

Lecture: M,W 3:25pm-5:00pm

Discussions:

M 5:15-6:20pm (two sections)

W 5:15-6:20pm

 

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 COVID-19, 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 highly encouraged.

Daily Assignments: There are short assignments on the reading for each day.

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.  

 

Wk

Day

Date

Topic

Readings

I       II      

1

Mon

Mar 30

What is disease ecology, and what is it good for?

1

2

 

1

Wed

Apr 1

Foundations of disease ecology: SIR models, R0, Frequency and density dependent transmission, Nth

4

5

 

2

Mon

Apr 6

SIR models continued

8

9

 

2

Wed

Apr 8

Directly transmitted human pathogens

10

 

 

3

Mon

Apr 13

Disease impacts on populations and ecosystems

11

12

 

3

Wed

Apr 15

Livestock, wildlife, zoonotic pathogens

16

17

 

4

Mon

Apr 20

Problem solving: Controlling influenza

19(16)

 

 

4

Wed

Apr 22

Disease control: Vaccination, Behavioral changes, culling

20

21

 

5

Mon

Apr 27

Midterm

 

 

 

5

Wed

Apr 29

Problem solving: Herpes dynamics

22

 

 

6

Mon

May 4

Problem solving: Evolution of virulence

23

 

 

6

Wed

May 6

Drug resistance

24

25

 

7

Mon

May 11

Vector borne disease ecology I.

30

31

 

7

Wed

May 13

Vector borne disease ecology II.

32

 

 

8

Mon

May 18

Seasonality, climate change and transmission dynamics

34

35

 

8

Wed

May 20

Co-infection

37

 

 

9

Mon

May 25

Holiday

 

 

 

9

Wed

May 27

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

38

39

 

10

Mon

Jun 1

Disease and conservation

 

 

 

10

Wed

Jun 3

Poster session

 

 

 

11

 

 

Take home final

 

 

 

 

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 Med2014; 371(16): 1481-95. PDF

10          Kucharski, A. J., and W. J. Edmunds. 2014. Case fatality rate for Ebola virus disease in west Africa. Lancet 384:1260-1260. 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
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          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
21          Metcalf, C. J. E., M. Ferrari, A. L. Graham, and B. T. Grenfell. 2015. Understanding Herd Immunity. Trends in Immunology 36:753-755. PDF

22          Problem Solving II Herpes dynamics

23         Myxoma virus evolution of virulence homework

  1. Levy SB, Marshall B. Antibacterial resistance worldwide: causes, challenges and responses. Nat Med2004; 10(12): S122-S9.PDF
  2. Read AF, Day T, Huijben S. The evolution of drug resistance and the curious orthodoxy of aggressive chemotherapy. Proc Natl Acad Sci U S A2011; 108: 10871-7. 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

  1. Mordecai EA, Paaijmans KP, Johnson LR, et al. Optimal temperature for malaria transmission is dramatically lower than previously predicted. Ecol Lett2013; 16(1): 22-30. PDF
  2.      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
  3.          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 America105 (45), 17436 (2008). PDF

37          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

  1. Parker IM, Saunders M, Bontrager M, et al. Phylogenetic structure and host abundance drive disease pressure in communities. Nature2015; 520(7548): 542-4 PDF
  2. Gilbert GS, Webb CO. Phylogenetic signal in plant pathogen-host range. Proc Natl Acad Sci U S A2007; 104(12): 4979-83.PDF
  3. 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
  4. McCallum H. Disease and the dynamics of extinction. Philos Trans R Soc B-Biol Sci2012; 367(1604): 2828-39. PDF