Infectious organisms that cross species boundaries can cause severe impacts on human health, loss of livelihoods through disease in domesticated animals, and contribute to host population declines and the ongoing global biodiversity crisis.
My research focuses on the ecology and evolution of host-parasite interactions, and developing knowledge and tools to mitigate the impacts of parasites that infect multiple species. I am interested identifying the forces that shape both host and parasite biodiversity, how variation in host-specificity influences the ecology of infectious diseases, and generating methods to predict and track undocumented host-parasite interactions.
I tackle these questions using data-driven approaches from macroecology, computational statistics, text mining, and biodiversity genomics. Parallel to advancing theory, I work with interdisciplinary teams to synthesize global biodiversity data, explore fine-scale interactions among hosts and parasites, and apply novel computational approaches that inform both scales – from extracting ecological data from massive literature databases, to predicting missing links in ecological networks.
My research seeks to understand the broad scale ecology and evolution of host-parasite interactions. I am particularly interested in developing theory of how host-specificity influences disease ecology, and generating methods for predicton, monitoring, and synthesizing data on host-parasite interactions. I also love to do collaborative science, which has led me to work on a variety of topics, but my core research falls into three themes:
1) Macroecology of infectious diseases
Macroecology identifies patterns and processes at the broadest scales of organization. This involves analyses of comparative data across large spatial and temporal scales, and among all branches of the tree of life. Over the past decade, studies from diverse host-parasite systems show that cross-species parasite sharing is constrained by evolutionary relationships among hosts. Through the application of phylogenetic comparative methods and Bayesian statistics, I use evolutionary trees to evaluate macro-scale patterns of pathogen sharing across hosts, analyze biogeographic patterns of parasites, and predict undocumented host-parasite interactions.
2) Causes and consequences of host specificity
Most infectious organisms can infect multiple species. Some infections rarely result in death, whereas others are nearly always fatal. For multi-host parasites, the severeity of disease may be subject to multiple trade-offs, including the ecologies and evolutionary histories of their host species. Exploring these trade-offs is often limited by a lack of comparative data on infectious disease outcomes. Current global host-parasite databases are compiled via time-intensive manual searches of the primary literature, but as the volume of new papers expands exponentially, they can become rapidly outdated. In collaboration with Andrew Yates (University of Amsterdam), Liam Brierly (University of Liverpool), and Nicole Mideo (University of Toronto), I am exploring new approaches to address this using text mining and Natural Language Processing (NLP).
These approaches from computational linguistics can be used gather a range of crucial data on susceptible hosts, transmission modes, immune responses, and the contexts of natural infections. Collating measures of disease severity across multiple host-parasite combinations will allow the identification of eco-evolutionary processes driving the relationship between parasite host specificity and the outcome of cross-species infection.
3) Next generation tools for biodiversity monitoring
Approaches that allow us to predict undocumented host-parasite interactions can be used to identify potential reservoirs of high-consequence pathogens, efficiently expand existing global infectious disease databases, and prioritize disease surveillance. However, in many regions considered to have a high risk of harbouring future emerging diseases, even baseline surveys of biological diversity are lacking. I am working to asses the utility of environmental DNA for monitoring both hosts and potential pathogens. To pilot these methods, I study watering holes in the Kruger National Park, South Africa (collaboration with J. Davies, UBC, M. Hajibabaei, University of Guelph, M. van der Bank, University of Johannesburg, D. Govender, South African National Parks).
Throughought my career studies I was fortunate to be funded by fellowships, scholarships, and grants from the Natural Sciences and Engineering Research Council of Canada, the Vanier Canada Graduate Program, the University of Toronto, the Canadian Institutes of Health Research Systems Biology Training Program, the National Science Foundation, the Royal Bank of Canada, Borealis AI, the Queen Elizabeth II Diamond Jubilee Scholarship, and the Quebec Centre for Biodiversity Science
32. Farrell, M.J., Park, A.W., Cressler, C.E., Dallas, T., Huang, S., Mideo, N., Morales-Castilla, I., Davies, T. J., Stephens, P.R. (2021) The ghost of hosts past: impacts of host extinction on parasite specificity. Philosophical Transactions of the Royal Society B 376:20200351
31. Huang, S., Farrell, M.J., Stephens. P.R. (2021) Infectious disease macroecology: parasite diversity and dynamics across the globe. Philosophical Transactions of the Royal Society B 376:20200350
30. Carlson, C.J., Farrell, M.J., Grange, Z., Han, B.A., Mollentze, N., Phelan, A.L., Rasmussen, A.L., Albery, G.F., Bett, B., Brett-Major, D.M., Cohen, L.E., Dallas, T., Eskew, E.A., Fagre, A.C., Forbes, K.M., Gibb, R., Halabi, S., Hammer, C.C., Katz, R., Kindrachuk, J., Muylaert, R.L., Nutter, F.B., Ogola, J., Olival, K.J., Rourke, M., Ryan, S.J., Ross, N., Seifert, S.N., Sironen, T., Standley, C.J., Taylor, K., Venter, M., Webala, P.W. (2021) The future of zoonotic risk prediction. Philosophical Transactions of the Royal Society B 376:20200358
29. Morales-Castilla, I., Pappalardo, P., Farrell, M.J., Aguirre, A.A., Huang, S., Gehman, A.M., Dallas, T., Gravel, D., Carlson, C.C., Davies, T.J. (2021) Forecasting parasite sharing under climate change. Philosophical Transactions of the Royal Society B 376:20200360
28. Gibb, R., Albery, G.F., Becker, D.J., Brierley, L., Connor, R., Dallas, T.A., Eskew, E.A., Farrell, M.J., Rasmussen, A.L., Ryan, S.J., Sweeny, A., Carlson, C.J., Poisot,T., (2021) Data proliferation, reconciliation, and synthesis in viral ecology. BioScience biab080
27. Schmidt, J.P., Davies, T.J., Farrell, M.J. (2021), Opposing macroevolutionary and trait‐mediated patterns of threat and naturalisation in flowering plants. Ecology Letters 24: 1237-1250.
26. LoScerbo, D.*, Farrell, M.J.*, Arrowsmith, J., Mlynarek, J., Lessard, J.P. (2020) Phylogenetically conserved host traits and local abiotic conditions jointly drive the geography of parasite intensity Functional Ecology 34: 2477– 2487 *Authors contributed equally
25. Elmasri, M., Farrell, M.J., Davies, T.J, Stephens, D.A. (2020), A Hierarchical Bayesian Model for Predicting Ecological Interactions Using Scaled Evolutionary Relationships. Annals of Applied Statistics 14(1), 221-240
24. Schmidt, J.P., Maher, S., Drake, J.M., Huang, T., Farrell, M.J., and Han, B.A. (2019), Ecological indicators of mammal exposure to Ebolavirus. Philosophical Transactions of the Royal Society B 374:20180337
23. Farrell, M.J. & Davies, T.J. (2019), Disease mortality in domesticated animals is predicted by host evolutionary relationships. Proceedings of the National Academy of Sciences 116 (16), 7911-7915
22. Farrell, M.J., Govender, D., Hajibabaei, M., Berrang-Ford, L., van der Bank, M., Davies, T.J. (2019), Bacterial diversity in the waterholes of the Kruger National Park: an eDNA metabarcoding approach. Genome 62 (3), 229-242
21. Dallas, T., Gehman, A.L., Aguirre, A.A., Budischak, S.A., Drake, J.M, Farrell, M.J., Ghai, R., Huang, S., Morales-Castilla, I. (2019), Contrasting latitudinal gradients of body size in helminth parasites and their hosts Global Ecology & Biogeography 28 (6), 804-813
20. Pearse, W.D, Morales-Castilla, I., James, L.S., Farrell, M.J., Boivin, F., Davies, T.J. (2018), Complexity is complicated and so too is comparing complexity metrics—a response to Mikula et al. Evolution 72 (12), 2836-2838
19. Dallas, T., Gehman A.L., Farrell, M.J. (2018), Variable bibliographic database access could limit reproducibility. BioScience 68 (8), 552-553
18. Park, A.W., Farrell, M.J., Schmidt, J.P., Huang, S., Dallas, T.A., Pappalardo, P., Drake, J.M., Stephens, P.R., Poulin, R., Nunn, C.L., Davies, T.J. (2018),Characterizing the phylogenetic specialism–generalism spectrum of mammal parasites. Proc. Roy. Soc. B 285:1874
17. Pearse, W.D, Morales-Castilla, I., James, L.S., Farrell, M.J., Boivin, F., Davies, T.J. (2018), Global macroevolution and macroecology of passerine song. Evolution (72) 4, 944-960
16. Perrault, N.*, Farrell, M.J.*, Davies, T.J. (2017), Tongues on the EDGE: language preservation priorities based on threat and lexical distinctiveness, Royal Society Open Science 4:171218 *Authors contributed equally
15. Stephens, P.R., Pappalardo, P., Huang, S., Byers, J.E., Farrell, M.J., Gehman, A., Ghai, R.R., Haas, S.E., Han, B.A., Park, A.W., Schmidt, J.P., Altizer, S., Ezenwa, V.O. and Nunn, C.L. (2017), Global Mammal Parasite Database version 2.0. Ecology 98: 1476-1476
14. Stephens, P.R., Altizer, S., Smith, K.F., Alonso Aguirre, A., Brown, J.H., Budischak, S.A., Byers, J.E., Dallas, T.A., Davies, T.J., Drake, J.M., Ezenwa, V.O., Farrell, M.J., Gittleman, J.L., Han, B.A., Huang, S., Hutchinson, R.A., Johnson, P., Nunn, C.L., Onstad, D., Park, A., Vazquez‐Prokopec, G.M., Schmidt, J.P. and Poulin, R. (2016), The macroecology of infectious diseases: a new perspective on global‐scale drivers of pathogen distributions and impacts. Ecology Letters 19: 1159-1171
13. Farrell, M.J., Stephens, P.R., Davies, T.J. (2016), Response to Strona & Fattorini: Are generalist parasites being lost from their hosts? Journal of Animal Ecology 85: 624-627
12. Farrell, M.J., Stephens, P.R., Berrang-Ford, L., Gittleman, J.L., Davies, T.J. (2015), The path to host extinction can lead to loss of generalist parasites. Journal of Animal Ecology 84: 978–984
11. Farrell, M.J., Berrang-Ford, L., Davies, T.J. (2013), The study of parasite sharing for surveillance of zoonotic disease. Environmental Research Letters 8 (1) 015036
10. Reid, A.J., Farrell, M.J., Luke, M.N. and Chapman, L.J. (2013), Implications of hypoxia tolerance for wetland refugia use in Lake Nabugabo, Uganda. Ecology of Freshwater Fish, 22 (3) 421-429
9. Farrell, M.J., Elmasri, M., Stephens, D.A., Davies, T.J. (2021), Predicting missing links in global host-parasite networks (in review at Journal of Animal Ecology), bioRxiv preprint: 10.1101/2020.02.25.965046
8. Farrell, M.J., Govender, D., Hajibabaei, M, van der Bank, M, Davies, T.J. Stephens, D.A., Davies, T.J. (2020), Environemental DNA for tracking waterhole visitation in savanna ecosystems, bioRxiv preprint doi: 10.1101/2020.11.03.367417
7. Poisot, T., Ouellet, M., Mollentze, N., Farrell, M.J., Becker, D.J., Albery, G.F., Gibb, R..J., Carlson, C.J. Imputing the mammalian virome with linear filtering and singular value decomposition. arXiv preprint: https://arxiv.org/abs/2105.14973
6. Fagre, A. C., Cohen, L., Eskew, E. A., Farrell, M.J., Glennon, E., Joseph, M. B., … Albery, G. (2021, April 12). Spillback in the Anthropocene: the risk of human-to-wildlife pathogen transmission for conservation and public health. EcoEvoRxiv preprint:10.32942/osf.io/sx6p8
5. Stephens, P.R., Farrell, M.J., Davies, T.J., Gittleman, J.L, Meiri, S., Roll, U., Wiens, J.J. (2020) Global diversity patterns are explained by diversification rates at ancient, not shallow, timescales.
4. Becker, D., Albery, G.F., Sjodin, A.R., Poisot, T., Dallas, T,. Eskew, E.A., Farrell, M.J., Guth, S., Han, B.A., Simmons, N.B., Stock, M., Teeling, E.C., Carlson, C.J. (2020) Optimizing predictive models to prioritize viral discovery in zoonotic reservoirs, bioRxiv preprint: 10.1101/2020.05.22.111344
3. Albery, G.F., Becker, D.J., Brierley, L., Brook, C.E., Christofferson, R.C., Cohen, L.E., Dallas, T.A., Eskew, E.A., Fagre, A., Farrell, M.J., Glennon, E., Guth, S., Joseph, M.B., Mollentze, N., Neely, B.A., Poisot, T., Rasmussen, A.L., Ryan, S.J., Sjodin, A.R., Seifert, S., Sorrell, E.M, Carlson, C.J., (2020) Modeling cross-species viral transmission and predicting zoonotic potential
2. Strydom, T., Bouskila, S., Banville, F., Barros, C., Caron, D., Farrell, M.J., Fortin, M.J., Hemming, V., Mercier, B., Pollock, L., Runghen, R., Dalla Riva, G.V., Poisot, T. (2021) Food web reconstruction through phylogenetic transfer of low-rank network representation. EcoEvoRxiv preprint: https://ecoevorxiv.org/y7sdz/
1. Carlson, C.J., Gibb, R.J., Albery, G.F., Brierley, L., Connor, R.P., Dallas, T.A., Eskew, E.A., Fagre, A.C., Farrell, M.J., Frank, H.K., Muylaert, R.L., Poisot, T., Rasmussen, A.L., Ryan, S.J., Seifert, S.N. (2021) The Global Virome in One Network (VIRION): an atlas of vertebrate-virus associations. bioRxiv preprint: https://doi.org/10.1101/2021.08.06.455442
Maxwell J. Farrell
Department of Ecology & Evolutionary Biology
University of Toronto
25 Willcocks St.
Toronto, ON M5S 3B2
maxwellfarrell _ at _ gmail.com
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