Publications

Page

Here’s a link to Meghan’s Google Scholar page (which may be more up-to-date than this one!)

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

If you would like to read any of these papers and cannot access them freely, please email Meghan (duffymeg at umich dot edu), who would be happy to send you a free pdf! 

2019

Emery, N., A. Hund, R. Burks, M.A. Duffy, C. Scoffoni, and A. Swei. 2019. Students as ecologists: Strategies for successful mentorship of undergraduate researchers. Ecology and Evolution, in press.

McLean, K.D.* and M.A. Duffy. 2019. Ecological context influences evolution in host-parasite interactions: insights from the Daphnia-parasite model system. Evolution in Action: Past, Present and Future, in press. (invited submission)

Sánchez, K.F.*, N. Huntley, M.A. Duffy, and M.D. Hunter. 2019. Toxins or medicines? Phytoplankton diets mediate host and parasite fitness in a freshwater system. Proceedings of the Royal Society, B, in press. https://doi.org/10.1098/rspb.2018.2231

Duffy, M.A.* and K.K. Hunsberger. 2019. Infectivity is influenced by parasite spore age and exposure to freezing: do shallow waters provide Daphnia a refuge from some parasites? Journal of Plankton Research, 41(1):12-16. doi: 10.1093/plankt/fby046

Clay, P.A., M.H. Cortez, M.A. Duffy, and V.H.W. Rudolf. 2019. Priority effects within coinfected hosts can drive unexpected population-scale patterns of parasite prevalence. Oikos, in press. doi: 10.1111/oik.05937

Wale, N.*, M.L. Turrill, and M.A. Duffy. 2019. A colorful killer: Daphnia infected with the bacterium Spirobacillus cienkowskii exhibit unexpected color variation. Ecology, 100(3):e02562. https://doi.org/10.1002/ecy.2562

Clay, P.A., K.L. Dhir, V.H.W. Rudolf, and M.A. Duffy. 2019. Within host priority effects systematically alter pathogen coexistence. American Naturalist, 193(2):187-199. https://doi.org/10.1086/701126

Duffy, M.A.*, C.E. Cáceres, and S.R. Hall. 2019. Healthy herds or predator spreaders? Insights from the plankton into how predators suppress and spread disease. Wildlife Disease Ecology: Linking theory to data and application (eds: Ken Wilson, Andy Fenton, and Dan Tompkins, Cambridge University Press)

2018

Bresciani, L., L.N. Lemos, N. Wale, J.Y. Lin, A.T. Strauss, M.A. Duffy, and J.L.M. Rodrigues. 2018. Draft genome sequence of “Candidatus Spirobacillus cienkowskii,” a pathogen of freshwater Daphnia species, reconstructed from hemolymph metagenomic reads. Microbiology Resource Announcements, 7(22):e01175-18.

Shocket, M.S., D. Vergara, A.J. Sickbert, J.M. Walsman, J.L. Hite, A.T. Strauss, M.A. Duffy, C.E. Cáceres, and S.R. Hall. 2018. Parasite rearing and infection temperatures jointly influence disease transmission and shape seasonality of epidemics. Ecology, 99(9):1975-1987.

Strauss, A.T., A.M. Bowling, M.A. Duffy, C.E. Cáceres, and S.R. Hall. 2018. Linking host traits, interactions with competitors and disease: Mechanistic foundations for disease dilution. Functional Ecology, 32(5):1271-1279. (recipient of the 2018 Haldane Prize for Early Career Research)

Shocket, M.S., A.T. Strauss, J.L. Hite, M. Šlijvar, D.J. Civitello, M.A. Duffy, C.E. Cáceres, and S.R. Hall. 2018. Temperature drives epidemics in a zooplankton-fungus disease system: A trait-driven approach points to transmission via host foraging. American Naturalist, 191(4): 435-451. (recipient of the 2018 American Naturalist Student Paper Award)

2017

Strauss, A.T., J.L. Hite, M.S. Shocket, M.A. Duffy, C.E. Cáceres, and S.R. Hall. 2017. Rapid evolution rescues hosts from competition and disease but – despite a dilution effect – increases the density of infected hosts. Proceedings of the Royal Society, B, 284:20171970.

Saunders, Manu E., M.A. Duffy, S.B. Heard, M. Kosmala, S.R. Leather, T. McGlynn, J. Ollerton, and A.E. Parachnowitsch. 2017. Bringing ecology blogs into the scientific fold: quantifying reach and impact of science-community blogs. Royal Society Open Science, 4:170957.

Duffy, M.A. 2017. Last and corresponding authorship practices in ecology. Ecology and Evolution, 7:8876-8887. doi: 10.1002/ece3.3435

Hite, J.L., R.M. Penczykowski, M.S. Shocket, K. Griebel, A.T. Strauss, M.A. Duffy, C.E. Cáceres, and S.R. Hall. 2017. Allocation, not male resistance, increases male frequency during epidemics: A case study in facultatively sexual hosts. Ecology, 98(11): 2773-2783.

Auld, S.K.J.R., C.L. Searle, and M.A. Duffy. 2017. Parasite transmission in a natural multihost-multiparasite community. Philosophical Transactions of the Royal Society, B, 372:20160097.

Rogalski, M.A., C.D. Gowler, C.L. Shaw, R.A. Hufbauer, and M.A. Duffy. 2017. Human drivers of ecological and evolutionary dynamics in emerging and disappearing infectious disease systems. Philosophical Transactions of the Royal Society, B, 372:20160043.

2016

Strauss, A.T., M.S. Shocket, D.J. Civitello, J.L. Hite, R.M. Penczykowski, M.A. Duffy, C.E. Cáceres, and S.R. Hall. 2016. Habitat, predators, and hosts regulate disease in Daphnia through direct and indirect pathways. Ecological Monographs, 86:393-411.

Searle, C.L., M.H. Cortez, K.K. Hunsberger, D.C. Grippi, I.A. Oleksy, C.L. Shaw, S.B. de la Serna, C.L. Lash, K.L. Dhir, and M.A. Duffy. 2016. Population density, not host competence, drives patterns of disease in an invaded community. American Naturalist, 188(5):554-566.

Searle, C.L., C.L. Shaw, K.K. Hunsberger, M. Prado, and M.A. Duffy. 2016. Salinization decreases population densities of the freshwater crustacean, Daphnia dentifera. Hydrobiologia, 770:165-172.

Hite, J.L., R.M. Penczykowski, M.S. Shocket, A.T. Strauss, P.A. Orlando, M.A. Duffy, C.E. Cáceres, and S.R. Hall. 2016. Parasites destabilize host populations by shifting stage-structured interactions. Ecology, 97:439-449.

2015

Duffy, M.A., T.Y. James, and A. Longworth. 2015. Ecology, virulence, and phylogeny of Blastulidium paedophthorum, a widespread brood parasite of Daphnia spp. Applied and Environmental Microbiology, 81(16):5486-5496.                       (cover article)

Searle, C.L., J. Housley Ochs, C.E. Cáceres, S. Chiang, N.M. Gerardo, S.R. Hall, and M.A. Duffy. 2015. Plasticity, not genetic variation, drives infection success of a fungal parasite. Parasitology, 142:839-848.

Civitello, D.J., A.N. Smith, R.M. Penczykowski, M.S. Shocket, M.A. Duffy, and S.R. Hall. 2015. Resources, key traits, and the size of fungal epidemics in Daphnia populations. Journal of Animal Ecology, 84:1010-1017.

2014

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

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.

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)

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

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.

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.

2013

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)

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.

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.

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.

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.

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.

2012

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

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.

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.

2011

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.

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.)

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.

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.

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

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.

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

2010

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.

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.

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.

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

2009

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

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

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.

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

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.

2008

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.

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

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.)

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.

2007

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

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.

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

2006

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.

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.

2005

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.

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.

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.

2004

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.

2000

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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