E-mail me at duffymeg at for pre-prints

Notes on Authorship:

For papers from my laboratory, I have chosen to use the first & last author emphasis
Duffy Lab graduate students/postdocs/technicians are indicated in italics
Duffy Lab undergrads are indicated by underlining
* indicates Duffy or Duffy Lab member corresponding author


45) Duffy, M.A. 2014. It helps to be well-connected. (Invited Perspective, not peer-reviewed) Science, 344:1229-1230.

44) Lively, C.M., J.C. de Roode, M.A. Duffy, A.L. Graham, and B. Koskella. 2014. Interesting open questions in disease ecology and evolution. American Naturalist, 18:S1-S8.

43) Auld, S.K.J.R., S.R. Hall, J.H. Ochs, M. Sebastian, and M.A. Duffy. 2014. Predators and patterns of within-host growth can mediate both among-host competition and the evolution of transmission potential of parasites. American Naturalist, 184:S77-S90. (Supplement)

42) Penczykowski, R.M., B.C.P. Lemanski, R.D. Sieg, S.R. Hall, J.H. Ochs, J. Kubanek, and M.A. Duffy*. When bad food is good: Poor resource quality lowers transmission potential by changing foraging behavior. Functional Ecology, 28: 1245-1255.

41) Cáceres, C.E., A.J. Tessier, M.A. Duffy, and S.R. Hall. 2014. Disease in freshwater zooplankton: what have we learned and where are we going? J. Plankton Res. 0(0): 1–8.

40) Penczykowski, R.M.*, S.R. Hall, D.J. Civitello, and M.A. Duffy*. 2014. Habitat structure and ecological drivers of disease. Limnology and Oceanography, 59(2), 340–348.


39) Searle, C.L.*, J.R. Mendelson III, L.E. Green, and M.A. Duffy*. 2013. Daphnia predation on the amphibian chytrid fungus and its impacts on disease risk in tadpoles. Ecology and Evolution, 3(12):4129-4138.  (cover article)

38) Bertram, C.R., M. Pinkowski, S.R. Hall, M.A. Duffy, and C.E. Cáceres. 2013. Trait-mediated indirect effects, predators, and disease: test of a size-based model. Oecologia, 173:1023–1032.

37) Auld, S.K.J.R., R.M. Penczykowski, J.H. Ochs, D.C. Grippi, S.R. Hall, and M.A. Duffy*. 2013. Variation in costs of parasite resistance among natural host populations. Journal of Evolutionary Biology, 26(11):2479-2486.

36) Civitello, D.J., S. Pearsall, M.A. Duffy, and S.R. Hall. 2013. Parasite consumption and host interference can inhibit disease spread in dense populations. Ecology Letters, 16(5):626-634.

35) Civitello, D.J., R.M. Penczykowski, J.L. Hite, M.A. Duffy*, and S.R. Hall. 2013. Potassium stimulates fungal epidemics in a freshwater invertebrate. Ecology, 94:380–388.

34) Auld, S.K.J.R.*, S.R. Hall, and M.A. Duffy*. 2012. Epidemiology of a Daphnia-multiparasite system and its implications for the Red Queen. PLoS ONE, 7(6): e39564.


33) Duffy, M.A.*, J. Housley Ochs, R.M. Penczykowski, D.J. Civitello, C.A. Klausmeier, and S.R. Hall. Ecological context influences epidemic size and parasite-mediated selection. Science, 335:1636-1638. / cover image

32) Hall, S.R., C.R. Becker, M.A. Duffy, and C.E. Cáceres. 2012. A power-efficiency tradeoff in resource use alters epidemiological relationships. Ecology, 93:645-656.

31) Overholt, E.P., S.R. Hall, C.E. Williamson, C.E. Meikle, M.A. Duffy, and C.E. Cáceres. 2012. Solar radiation decreases parasitism in Daphnia. Ecology Letters, 15:47-54.


30) Prior, N.H., C.N. Washington, J.M. Housley, S.R. Hall, M.A. Duffy, and C.E. Cáceres. 2011. Maternal effects and epidemiological traits in a planktonic host-parasite system. Evolutionary Ecology Research, 13:401-413.

29) Duffy, M.A.*, J.M. Housley, R.M. Penczykowski, C.E. Cáceres, S.R. Hall. 2011. Unhealthy herds: indirect effects of predators enhance two drivers of disease spread. Functional Ecology, 25(5):945-953. (This article was the focus of a Spotlight by Welch & Harwood, pages 943-944.)

28) Thomas, S.H., C. Bertram, K. van Rensburg, C.E. Cáceres, and M.A. Duffy*. 2011. Spatiotemporal dynamics of free-living stages of a bacterial parasite of zooplankton. Aquatic Microbial Ecology, 63(3):265-272.

27) Hall, S.R., C.R. Becker, M.A. Duffy, C.E. Cáceres. 2011. Epidemic size determines population-level effects of parasites. Oecologia, 166:833-842.

26) Kestrup, Å.M.*, S.H. Thomas*, K. van Rensburg, A. Ricciardi, and M.A. Duffy*. 2011. Differential infection of exotic and native freshwater amphipods by a parasitic water mold in the St. Lawrence River. Biological Invasions, 13(3):769-779.
*these authors contributed equally

25) Thomas, S.H., J.M. Housley, A.N. Reynolds, R.M. Penczykowski, K.H. Kenline, N. Hardegree, S. Schmidt, and M.A. Duffy*. 2011. The ecology and phylogeny of oomycete infections in Asplanchna rotifers. Freshwater Biology, 56:384-394.

24) R.M. Penczykowski, S.E. Forde and M.A. Duffy*.2011. Rapid evolution as a possible constraint on emerging infectious diseases. Freshwater Biology, 56:689-704.


23) Hall, S.R., C.R. Becker, M.A. Duffy, and C.E. Cáceres. 2010. Variation in resource acquisition and use among hosts can create key epidemiological tradeoffs. American Naturalist, 176:557-565.

22) Duffy, M.A.*, C.E. Cáceres, S.R. Hall, A.J. Tessier and A.R. Ives. 2010. Temporal, spatial and between-host comparisons of patterns of parasitism in lake zooplankton. Ecology, 91(11):3322-3331.

21) Hall, S.R., R. Smyth, C.R. Becker, M.A. Duffy, C.M. Knight, S. MacIntyre, A.J. Tessier, and C.E. Cáceres. 2010. Why are some lakes sicker? Disease ecology, habitat structure and the plankton. BioScience, 60(5):363-375.

20) Duffy, M.A.* 2010. Ecological consequences of intraspecific variation in lake Daphnia. Freshwater Biology, 55: 995-1004.


19) Duffy, M.A.* and S.E. Forde. 2009. Ecological feedbacks and the evolution of resistance. Journal of Animal Ecology,78:1106-1112.

18) Duffy, M.A.*, S.R. Hall, C.E. Cáceres and A.R. Ives. 2009. Rapid evolution, seasonality, and the termination of parasite epidemics. Ecology, 90(6):1441-1448. Appendix Link to supplemental files

17) Duffy, M.A.* 2009. Staying alive: the post-consumption fate of parasite spores and its implications for disease dynamics. Limnology and Oceanography, 54(3):770-773.

16) Hall, S.R., C.M. Knight, C.R. Becker, M.A. Duffy, A.J. Tessier and C.E. Cáceres. 2009. Quality matters: resource quality for hosts and the timing of epidemics. Ecology Letters, 12(2):118-128. appendix

15) Hall, S.R., C.R. Becker, J.L. Simonis, M.A. Duffy, A.J. Tessier, and C.E. Cáceres. 2009. Friendly competition: evidence for a dilution effect in a planktonic host-parasite system. Ecology, 90(3):791-801.


14) Duffy, M.A.*, C.E. Brassil, S.R. Hall, A.J. Tessier, C.E. Cáceres, and J.K. Conner. 2008. Parasite-mediated disruptive selection in a natural Daphnia population. BMC Evolutionary Biology, 8:80.

13) Cáceres, C.E., A.J. Tessier, A. Andreou, M.A. Duffy. 2008. Stoichiometric relationships in vernal pond plankton communities. Freshwater Biology 53:1291–1302.

12) Duffy, M.A.* and S.R. Hall. 2008. Selective predation and rapid evolution can jointly dampen effects of virulent parasites on Daphnia populations. American Naturalist, 171(4): 499-510. / appendices  / profile of this work (This paper received the Mercer Award from the Ecological Society of America.)

11) Rodrigues, J.L.M., M.A. Duffy, A.J. Tessier, D. Ebert, L. Mouton and T.M. Schmidt. 2008. Phylogenetic characterization and prevalence of Spirobacillus cienkowskii: a red-pigmented, spiral-shaped bacterial pathogen of freshwater Daphnia species. Applied and Environmental Microbiology, 74(5):1575-1582.


10) Duffy, M.A.* 2007. Selective predation, parasitism, and trophic cascades in a bluegill-Daphnia-parasite system. Oecologia 153(2):453-460. / Code for MAR model (requires Matlab; if doesn’t download properly, right click on link and save file to computer) Data that goes along with code

9) Hall, S.R., L. Sivars-Becker, C. Becker, M.A. Duffy, A.J. Tessier and C.E. Cáceres. 2007. Eating yourself sick: transmission of disease as a function of foraging ecology. Ecology Letters 10(3):207-218.

8) Duffy, M.A.* and L. Sivars-Becker. 2007. Rapid evolution and ecological host-parasite dynamics. Ecology Letters 10(1):44-53. code for evolutionary epidemiological model (requires Mathematica; if file doesn’t download properly, right click and save it to your computer)
*reviewed by Faculty of 1000


7) Hall, S.R., A.J. Tessier, M.A. Duffy, M. Huebner and C.E. Cáceres. 2006. Warmer does not have to mean sicker: Temperature and predators can jointly drive timing of epidemics. Ecology 87(7):1684-1695.

6) Cáceres, C.E., S.R. Hall, M.A. Duffy, A.J. Tessier, C. Helmle and S. MacIntyre. 2006. Physical structure of lakes constrains epidemics in Daphnia populations. Ecology 87(6):1438-1444.


5) Hall, S.R., M.A. Duffy, A.J. Tessier and C.E. Cáceres. 2005. Spatial heterogeneity of daphniid parasitism in lakes. Oecologia 143(4):635-644.

4) Duffy, M.A.*, S.R. Hall, A.J. Tessier and M. Huebner. 2005. Selective predators and their parasitized prey: Are epidemics in zooplankton under top-down control? Limnology and Oceanography 50:412-420.

3) Hall, S.R., M.A. Duffy and C.E. Cáceres. 2005. Selective predation and productivity jointly drive complex behavior in host-parasite systems. American Naturalist 165:70-81.


2) Duffy, M. A.*, A.J. Tessier and M.A. Kosnik. 2004. Testing the ecological relevance of Daphnia species designations. Freshwater Biology 49(1):55-64.


1) Duffy, M.A.*, L.J. Perry, C.M. Kearns, L.J. Weider, and N.G. Hairston, Jr. 2000. Paleogenetic evidence for a past invasion of Onondaga Lake, New York, by exotic Daphnia curvirostris using mtDNA from dormant eggs. Limnology and Oceanography 45(6):1409-1414.

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