Ecology and evolution of infectious disease (fall 2023)

Last updated: 30 Nov 2023 12:19

This web page is under construction: some material may still be left over from the previous offering of the course

Course meetings

12:30-1:20 Mon/Thurs, 1:30-2:20 Tues (all Toronto time), location on Mosaic
Masking is encouraged but not required
Please ask me if you need to participate remotely or access lecture recordings

Misc info

Textbook: Claude Combes, The Art of Being A Parasite; available from the bookstore, also on the Internet Archive (info on IA borrowing)
Platforms: Avenue to Learn, course web page, forums (TBD) (see below)
Full course bibliography

Where to find stuff

schedule, readings, notes, course outline, etc.: here
dropbox for assignments, marks: Avenue
discussion questions: Piazza (sign up here)
Perusall: join the course with BOLKER-FJ6XP
SpringerLink

Communication

instructor: Ben Bolker
- Questions are best asked in the appropriate channel on Piazza (publicly or privately)
- if necessary, e-mail to bolker@mcmaster.ca with “BIO 4AE3” in the subject line; include your MacID in your message if not e-mailing from your McMaster e-mail account
- office hours: 1:30-2:30 Monday, 11:30-12:30 Thursday, HH 314
teaching assistant: TBA
- weekly office hours, TBA
- please contact via Piazza (privately if necessary)
- will answer as soon as possible, but will be more readily available during normal working hours (9 AM to 5 PM Toronto time)
- responses are not guaranteed within 24 hours of an assignment deadline; please plan ahead!

Schedule

(subject to revision!)

start date	topic	reading/viewing	notes	assignments
05-Sep	introduction & concepts; epidemic models and epidemic dynamics	Combes (2005) ch. 1-2	intro; intro docx; intro pdf; definitions; definitions docx; definitions pdf; class scribbles	register for Piazza (and eventually Perusall); send me a private message with your name, something memorable about you, and (if you’re willing) a photo
11-Sep	intro continued, epidemic dynamics	Vredenburg et al. (2010)	epi1; epi1 docx; epi1 pdf; Monday scribbles; Wednesday scribbles; Thursday scribbles	Read & comment on Combes on Perusall (by Friday afternoon)
18-Sep	parasites and host demography; extinction & conservation		vredenburg; vredenburg docx; vredenburg pdf; hostpop1; hostpop1 docx; hostpop1 pdf; Monday scribbles; Wednesday scribbles; Thursday scribbles	Read and comment on Vredenburg et al. (2010) (by Weds 5 PM) on Perusall; 22 Sep: mini-essay 1 due
25-Sep	parasites and host communities		Monday scribbles; parahostcomm; parahostcomm docx; parahostcomm pdf; Friday scribbles
02-Oct	within-host dynamics of parasites	Stewart Merrill, Rapti, and Cáceres (2021)	Monday scribbles; Wednesday scribbles	Read and comment on Stewart Merrill, Rapti, and Cáceres (2021) (by Weds Oct 4 at 5 PM) on Perusall
09-Oct	midterm recess
16-Oct	host-parasite coevolution	Decaestecker et al. (2007)	Red Queen; RQ docx; RQ pdf; Monday scribbles	16 Oct: term paper topic/references due. Read and comment on Decaestecker et al. (2007) (by Sunday Oct 22 at 5 PM) on Perusall
19-Oct	midterm test 1 (in class)	example midterm from 2009
23-Oct	Evolution of virulence		virulence evolution; virul-evol docx; virul-evol pdf; Tuesday scribbles; Thursday scribbles
30-Oct	Evolution of host resistance and tolerance	Schneider and Ayres (2008)	host resistance and tolerance; host_resist_tol docx; host_resist_tol pdf; Monday scribbles	2 Nov (6 PM); Perusall for Schneider and Ayres; 3 Nov: mini-essay 2 (see assignments)
06-Nov	Evolution of antimicrobial resistance and immune escape		parasite resistance; para_resist docx; para_resist pdf; coalescent theory; Monday scribbles; Tuesday scribbles; Thursday scribbles
13-Nov	(continued)		host manipulation; host_manip docx; host_manip pdf	Monday no class; Tuesday guest lecture, Dr. Hendrik Poinar; 17 Nov: term paper draft due
20-Nov	Parasite manipulation of host behaviour			24 Nov: group project due
27-Nov	Parasite-mediated sexual selection; Ecosystems and emerging disease?		sexsel notes; sexsel docx; sexsel pdf; emerg notes; emerg docx; emerg pdf	27 Nov: Mini-essay 3; 29 Nov, peer reviews of term paper drafts
4-Dec				midterm test 2 (in class)
14-Dec				final drafts of term papers due

References

Combes, Claude. 2005. The Art of Being a Parasite. Chicago, IL: University of Chicago Press. https://archive.org/details/artofbeingparasi0000comb.

Decaestecker, Ellen, Sabrina Gaba, Joost A. M. Raeymaekers, Robby Stoks, Liesbeth Van Kerckhoven, Dieter Ebert, and Luc De Meester. 2007. “Host–Parasite ‘Red Queen’ Dynamics Archived in Pond Sediment.” Nature 450 (7171): 870–73. https://doi.org/10.1038/nature06291.

Schneider, David S., and Janelle S. Ayres. 2008. “Two Ways to Survive Infection: What Resistance and Tolerance Can Teach Us about Treating Infectious Diseases.” Nature Reviews Immunology 8 (11): 889–95. https://doi.org/10.1038/nri2432.

Stewart Merrill, Tara E., Zoi Rapti, and Carla E. Cáceres. 2021. “Host Controls of Within-Host Disease Dynamics: Insight from an Invertebrate System.” The American Naturalist 198 (3): 317–32. https://doi.org/10.1086/715355.

Vredenburg, Vance T., Roland A. Knapp, Tate S. Tunstall, and Cheryl J. Briggs. 2010. “Dynamics of an Emerging Disease Drive Large-Scale Amphibian Population Extinctions.” Proceedings of the National Academy of Sciences 107 (21): 9689–94. https://doi.org/10.1073/pnas.0914111107.