Dr Nicholas Clark
UQ Amplify Lecturer
School of Veterinary Science
+61 7 535 15104
Researcher biography
An ecologist by training – I hold a B.Sc. (Hons) in Marine Ecology from the University of North Carolina, Wilmington and a Ph.D. in Ecological Modelling from Griffith University. I am broadly interested in exploring new ways to (1) understand how natural communities are formed and (2) predict how they will change over time. As a DECRA fellow at UQ, my current research focuses on developing computational tools and adapting techniques from statistical forecasting to study how organisms and ecosystems respond to environmental change. This work can be applied to investigate natural dynamics for a range of ecological systems including wild birds, ectoparasites and microbes.
I am an active member of the R community and have written and/or maintain several popular R packages. For example, I'm a lead developer on the MRFcov package for multivariate conditional random fields analyses. I also wrote the mvgam R package for fitting dynamic Generalised Additive Models to analyse and forecast multivariate ecological time series, and I regularly provide training seminars and workshops to help researchers learn techniques in ecological data analysis.
I am currently seeking Honours and PhD candidates with interests and/or skills in data analysis, statistical programming and quantitative ecology to develop multivariate forecast tools and evaluate their abilities to predict how species occurrences, abundances and diversities respond to change.
Journal Articles
Karunarathna, K.A.N.K., Wells, Konstans and Clark, Nicholas J. (2024). Modelling nonlinear responses of a desert rodent species to environmental change with hierarchical dynamic generalized additive models. Ecological Modelling, 490 110648, 110648. doi: 10.1016/j.ecolmodel.2024.110648
Kennedy, U., Paterson, M. and Clark, N. (2023). Epidemiological insights into the burden of feline upper respiratory tract infections in Queensland RSPCA shelters. Australian Veterinary Journal, 102 (3), 87-95. doi: 10.1111/avj.13306
Owada, Kei, Abdullah, Swaid, Clark, Nicholas, Nguyen, Tu and Soares Magalhães, Ricardo J. (2023). Associations between canine hookworm infection and dog owners' awareness, perception, and behaviour: a cross‐sectional study in Brisbane, Queensland, 2019–2020. Zoonoses and Public Health, 70 (6), 498-510. doi: 10.1111/zph.13059
McGowan, Alexandra M., Seddon, Jennifer M., Lanyon, Janet M., Clark, Nicholas and Gibson, Justine S. (2023). Identification of antimicrobial resistance in faecal microbes from wild dugongs (Dugong dugon). Aquatic Mammals, 49 (4), 395-405. doi: 10.1578/am.49.4.2023.395
McGowan, Alexandra M., Lanyon, Janet M., Clark, Nicholas, Blair, David, Marsh, Helene, Wolanski, Eric and Seddon, Jennifer M. (2023). Cryptic marine barriers to gene flow in a vulnerable coastal species, the dugong (Dugong dugon). Marine Mammal Science, 39 (3), 918-939. doi: 10.1111/mms.13021
Norberg, Anna, Susi, Hanna, Sallinen, Suvi, Baran, Pezhman, Clark, Nicholas J. and Laine, Anna-Liisa (2023). Direct and indirect viral associations predict coexistence in wild plant virus communities. Current Biology, 33 (9), 1665-1676.e4. doi: 10.1016/j.cub.2023.03.022
Kennedy, Uttara, Paterson, Mandy and Clark, Nicholas (2023). Using a gradient boosted model for case ascertainment from free-text veterinary records. Preventive Veterinary Medicine, 212 105850, 1-8. doi: 10.1016/j.prevetmed.2023.105850
Mshelbwala, Philip P., J. Soares Magalhães, Ricardo, Weese, J. Scott, Ahmed, Nasir O., Rupprecht, Charles E. and Clark, Nicholas J. (2023). Modelling modifiable factors associated with the probability of human rabies deaths among self-reported victims of dog bites in Abuja, Nigeria. PLoS Neglected Tropical Diseases, 17 (2) e0011147, 1-20. doi: 10.1371/journal.pntd.0011147
Barshes, Neal R., Clark, Nicholas J., Bidare, Deeksha, Dudenhoeffer, J. H., Mindru, Cezarina and Rodriguez-Barradas, Maria C. (2022). Polymicrobial foot infection patterns are common and associated with treatment failure. Open Forum Infectious Diseases, 9 (10) ofac475, 1-6. doi: 10.1093/ofid/ofac475
Clark, Nicholas J. and Wells, Konstans (2022). Dynamic generalised additive models (
DGAMs
) for forecasting discrete ecological time series. Methods in Ecology and Evolution, 14 (3), 771-784. doi: 10.1111/2041-210x.13974
Proboste, Tatiana, Clark, Nicholas J., Tozer, Sarah, Wood, Caitlin, Lambert, Stephen B. and Soares Magalhães, Ricardo J. (2022). Profiling risk factors for household and community spatiotemporal clusters of Q fever notifications in Queensland between 2002 and 2017. Pathogens, 11 (8) 830, 1-12. doi: 10.3390/pathogens11080830
Powell‐Romero, Francisca, Fountain‐Jones, Nicholas M., Norberg, Anna and Clark, Nicholas J. (2022). Improving the predictability and interpretability of co‐occurrence modelling through feature‐based joint species distribution ensembles. Methods in Ecology and Evolution, 14 (1), 1-16. doi: 10.1111/2041-210x.13915
Mshelbwala, Philip P., Weese, J. Scott, Clark, Nicholas J., Tekki, Ishaya, Chakma, Shovon, Shamaki, David, Mamun, Abdullah A., Rupprecht, Charles E. and Soares Magalhães, Ricardo J. (2022). Spatiotemporal heterogeneity and determinants of canine rabies evidence at Local Government Area Level in Nigeria: implications for rabies prevention and control. One Health, 14 100378, 1-9. doi: 10.1016/j.onehlt.2022.100378
Hill, A.G., Boyd, S.P., Clark, N.J. and Proboste, T. (2022). Haemoprotozoa in wild short‐beaked echidnas (Tachyglossus aculeatus). Australian Veterinary Journal, 100 (3), 130-134. doi: 10.1111/avj.13132
Clark, Nicholas J., Proboste, Tatiana, Weerasinghe, Guyan and Soares Magalhães, Ricardo J. (2022). Near-term forecasting of companion animal tick paralysis incidence: an iterative ensemble model. PLoS Computational Biology, 18 (2) e1009874, e1009874. doi: 10.1371/journal.pcbi.1009874
Fecchio, Alan, Clark, Nicholas J., Bell, Jeffrey A., Skeen, Heather R., Lutz, Holly L., De La Torre, Gabriel M., Vaughan, Jefferson A., Tkach, Vasyl V., Schunck, Fabio, Ferreira, Francisco C., Braga, Érika M., Lugarini, Camile, Wamiti, Wanyoike, Dispoto, Janice H., Galen, Spencer C., Kirchgatter, Karin, Sagario, M. Cecilia, Cueto, Victor R., González‐Acuña, Daniel, Inumaru, Mizue, Sato, Yukita, Schumm, Yvonne R., Quillfeldt, Petra, Pellegrino, Irene, Dharmarajan, Guha, Gupta, Pooja, Robin, V. V., Ciloglu, Arif, Yildirim, Alparslan ... Kamath, Pauline (2021). Global drivers of avian haemosporidian infections vary across zoogeographical regions. Global Ecology and Biogeography, 30 (12) geb.13390, 2393-2406. doi: 10.1111/geb.13390
Fountain‐Jones, Nicholas M., Kozakiewicz, Christopher P., Forester, Brenna R., Landguth, Erin L., Carver, Scott, Charleston, Michael, Gagne, Roderick B., Greenwell, Brandon, Kraberger, Simona, Trumbo, Daryl R., Mayer, Michael, Clark, Nicholas J. and Machado, Gustavo (2021). MrIML: Multi‐response interpretable machine learning to model genomic landscapes. Molecular Ecology Resources, 21 (8) 1755-0998.13495, 2766-2781. doi: 10.1111/1755-0998.13495
Hill, A. G., Clark, N. J. and Tokonami, F. (2021). Tick paralysis in Australian birds caused by Ixodes holocyclus. Australian Veterinary Journal, 99 (12) avj.13119, 1-7. doi: 10.1111/avj.13119
Nguyen, Tu, Clark, Nicholas, Jones, Malcolm K., Herndon, Aaron, Mallyon, John, Soares Magalhaes, Ricardo J. and Abdullah, Swaid (2021). Perceptions of dog owners towards canine gastrointestinal parasitism and associated human health risk in Southeast Queensland. One Health, 12 100226, 100226. doi: 10.1016/j.onehlt.2021.100226
Abeykoon, A. M. Hasanthi, Clark, Nicholas Joshua, Soares Magalhaes, Ricardo Jorge, Vincent, Gemma Anne, Stevenson, Mark Anthony, Firestone, Simon Matthew and Wiethoelter, Anke Katrin (2021). Coxiella burnetii in the environment: a systematic review and critical appraisal of sampling methods. Zoonoses and Public Health, 68 (3), 165-181. doi: 10.1111/zph.12791
Clark, Nicholas J., Drovetski, Sergei V. and Voelker, Gary (2020). Robust geographical determinants of infection prevalence and a contrasting latitudinal diversity gradient for haemosporidian parasites in Western Palearctic birds. Molecular Ecology, 29 (16) mec.15545, 3131-3143. doi: 10.1111/mec.15545
Mone, N.K., Clark, N.J., Kyaw‐Tanner, M., Turni, C., Barnes, T.S., Parke, C.R., Alawneh, JA, Blackall, P.J. and Meers, J. (2020). Genetic analysis of porcine circovirus type 2 (PCV2) in Queensland, Australia. Australian Veterinary Journal, 98 (8) avj.12952, 388-395. doi: 10.1111/avj.12952
Clark, Nicholas J., Tozer, Sarah, Wood, Caitlin, Firestone, Simon M., Stevenson, Mark, Caraguel, Charles, Chaber, Anne‐Lise, Heller, Jane and Soares Magalhães, Ricardo J. (2020). Unravelling animal exposure profiles of human Q fever cases in Queensland, Australia, using natural language processing. Transboundary and Emerging Diseases, 67 (5) tbed.13565, 2133-2145. doi: 10.1111/tbed.13565
Clark, Nicholas J., Owada, Kei, Ruberanziza, Eugene, Ortu, Giuseppina, Umulisa, Irenee, Bayisenge, Ursin, Mbonigaba, Jean Bosco, Mucaca, Jean Bosco, Lancaster, Warren, Fenwick, Alan, Soares Magalhães, Ricardo J. and Mbituyumuremyi, Aimable (2020). Parasite associations predict infection risk: incorporating co-infections in predictive models for neglected tropical diseases. Parasites and Vectors, 13 (1) 138, 138. doi: 10.1186/s13071-020-04016-2
Clark, Nicholas J., Kerry, James T. and Fraser, Ceridwen I. (2020). Rapid winter warming could disrupt coastal marine fish community structure. Nature Climate Change, 10 (9), 862-867. doi: 10.1038/s41558-020-0838-5
Fecchio, Alan, Bell, Jeffrey A., Bosholn, Mariane, Vaughan, Jefferson A., Tkach, Vasyl V., Lutz, Holly L., Cueto, Victor R., Gorosito, Cristian A., González‐Acuña, Daniel, Stromlund, Chad, Kvasager, Danielle, Comiche, Kiba J. M., Kirchgatter, Karin, Pinho, João B., Berv, Jacob, Anciães, Marina, Fontana, Carla S., Zyskowski, Kristof, Sampaio, Sidnei, Dispoto, Janice H., Galen, Spencer C., Weckstein, Jason D. and Clark, Nicholas J. (2019). An inverse latitudinal gradient in infection probability and phylogenetic diversity for Leucocytozoon blood parasites in New World birds. Journal of Animal Ecology, 89 (2) 1365-2656.13117, 423-435. doi: 10.1111/1365-2656.13117
Clark, Nicholas J., Umulisa, Irenee, Ruberanziza, Eugene, Owada, Kei, Colley, Daniel G., Ortu, Giuseppina, Campbell, Carl H., Ruzindana, Emmanuel, Lancaster, Warren, Mbonigaba, Jean Bosco, Mbituyumuremyi, Aimable, Fenwick, Alan, Soares Magalhaes, Ricardo J. and Turate, Innocent (2019). Mapping Schistosoma mansoni endemicity in Rwanda: a critical assessment of geographical disparities arising from circulating cathodic antigen versus Kato-Katz diagnostics. PLoS Neglected Tropical Diseases, 13 (9) e0007723, e0007723. doi: 10.1371/journal.pntd.0007723
Peel, Alison J., Wells, Konstans, Giles, John, Boyd, Victoria, Burroughs, Amy, Edson, Daniel, Crameri, Gary, Baker, Michelle L., Field, Hume, Wang, Lin-Fa, McCallum, Hamish, Plowright, Raina K. and Clark, Nicholas (2019). Synchronous shedding of multiple bat paramyxoviruses coincides with peak periods of Hendra virus spillover. Emerging Microbes and Infections, 8 (1), 1314-1323. doi: 10.1080/22221751.2019.1661217
Proboste, Tatiana, Corvalan, Paloma, Clark, Nicholas, Beyer, Hawthorne L., Goldizen, Anne W. and Seddon, Jennifer M. (2019). Commensal bacterial sharing does not predict host social associations in kangaroos. Journal of Animal Ecology, 88 (11) 1365-2656.13064, 1696-1707. doi: 10.1111/1365-2656.13064
Ruberanziza, Eugene, Owada, Kei, Clark, Nicholas J., Umulisa, Irenee, Ortu, Giuseppina, Lancaster, Warren, Munyaneza, Tharcisse, Mbituyumuremyi, Aimable, Bayisenge, Ursin, Fenwick, Alan and Soares Magalhães, Ricardo J. (2019). Mapping soil-transmitted helminth parasite infection in Rwanda: estimating endemicity and identifying at-risk populations. Tropical Medicine and Infectious Disease, 4 (2) 93, 93. doi: 10.3390/tropicalmed4020093
Lawrence, Andrea L., Webb, Cameron E., Clark, Nicholas J., Halajian, Ali, Mihalca, Andrei D., Miret, Jorge, D'Amico, Gianluca, Brown, Graeme, Kumsa, Bersissa, Modrý, David and Šlapeta, Jan (2019). Out-of-Africa, human-mediated dispersal of the common cat flea, Ctenocephalides felis: the hitchhiker’s guide to world domination. International Journal for Parasitology, 49 (5), 321-336. doi: 10.1016/j.ijpara.2019.01.001
Wells, Konstans and Clark, Nicholas J. (2019). Host specificity in variable environments. Trends in Parasitology, 35 (6), 452-465. doi: 10.1016/j.pt.2019.04.001
Fecchio, Alan, Wells, Konstans, Bell, Jeffrey A., Tkach, Vasyl V., Lutz, Holly L., Weckstein, Jason D., Clegg, Sonya M. and Clark, Nicholas J. (2019). Climate variation influences host specificity in avian malaria parasites. Ecology Letters, 22 (3), 547-557. doi: 10.1111/ele.13215
Fountain-Jones, Nicholas M., Clark, Nicholas J., Kinsley, Amy C., Carstensen, Michelle, Forester, James, Johnson, Timothy J., Miller, Elizabeth A., Moore, Seth, Wolf, Tiffany M. and Craft, Meggan E. (2019). Microbial associations and spatial proximity predict North American moose (Alces alces) gastrointestinal community composition. Journal of Animal Ecology, 89 (3) 1365-2656.13154, 1-12. doi: 10.1111/1365-2656.13154
Wells, Konstans, Gibson, David I. and Clark, Nicholas J. (2018). Global patterns in helminth host specificity: phylogenetic and functional diversity of regional host species pools matter. Ecography, 42 (3), 416-427. doi: 10.1111/ecog.03886
Wells, Konstans, Gibson, David I., Clark, Nicholas J., Ribas, Alexis, Morand, Serge and McCallum, Hamish I. (2018). Global spread of helminth parasites at the human-domestic animal-wildlife interface. Global Change Biology, 24 (7), 3254-3265. doi: 10.1111/gcb.14064
Clark, Nicholas J. (2018). Phylogenetic uniqueness, not latitude, explains the diversity of avian blood parasite communities worldwide. Global Ecology and Biogeography, 27 (6), 744-755. doi: 10.1111/geb.12741
Clark, Nicholas J., Wells, Konstans and Lindberg, Oscar (2018). Unravelling changing interspecific interactions across environmental gradients using Markov random fields. Ecology, 99 (6), 1277-1283. doi: 10.1002/ecy.2221
Clark, Nicholas J. and Soares Magalhães, Ricardo J. (2018). Airborne geographical dispersal of Q fever from livestock holdings to human communities: a systematic review and critical appraisal of evidence. BMC Infectious Diseases, 18 (1) 218, 218. doi: 10.1186/s12879-018-3135-4
Clark, Nicholas J., Seddon, Jennifer M., Šlapeta, Jan and Wells, Konstans (2018). Parasite spread at the domestic animal - wildlife interface: anthropogenic habitat use, phylogeny and body mass drive risk of cat and dog flea (Ctenocephalides spp.) infestation in wild mammals. Parasites & Vectors, 11 (1) 8, 1-11. doi: 10.1186/s13071-017-2564-z
Clark, Nicholas J, Seddon, Jennifer M, Kyaw-Tanner, Myat, Al-Alawneh, John, Harper, Gavin, McDonagh, Phillip and Meers, Joanne (2017). Emergence of canine parvovirus subtype 2b (CPV-2b) infections in Australian dogs. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 58, 50-55. doi: 10.1016/j.meegid.2017.12.013
Clark, Nicholas J., Clegg, Sonya M., Sam, Katerina, Goulding, William, Koane, Bonny and Wells, Konstans (2017). Climate, host phylogeny and the connectivity of host communities govern regional parasite assembly. Diversity and Distributions, 24 (1), 13-23. doi: 10.1111/ddi.12661
Clark, Nicholas J. and Clegg, Sonya M. (2017). Integrating phylogenetic and ecological distances reveals new insights into parasite host specificity. Molecular Ecology, 26 (11), 3074-3086. doi: 10.1111/mec.14101
McKee, J., Clark, N., Shapter, F. and Simmons, G. (2017). A new look at the origins of gibbon ape leukemia virus. Virus Genes, 53 (2), 165-172. doi: 10.1007/s11262-017-1436-0
Clark, Nicholas J., Wells, Konstans, Dimitrov, Dimitar and Clegg, Sonya M. (2016). Co-infections and environmental conditions drive the distributions of blood parasites in wild birds. Journal of Animal Ecology, 85 (6), 1461-1470. doi: 10.1111/1365-2656.12578
Aharon-Rotman, Yaara, Buchanan, Katherine L., Clark, Nicholas J., Klaassen, Marcel and Buttemer, William A. (2016). Why fly the extra mile? Using stress biomarkers to assess wintering habitat quality in migratory shorebirds. Oecologia, 182 (2), 385-395. doi: 10.1007/s00442-016-3679-1
Clark, Nicholas J., Clegg, Sonya M. and Klaassen, Marcel (2016). Migration strategy and pathogen risk: non-breeding distribution drives malaria prevalence in migratory waders. Oikos, 125 (9), 1358-1368. doi: 10.1111/oik.03220
Goulding, W., Adlard, R. D., Clegg, S. M. and Clark, N. J. (2016). Molecular and morphological description of Haemoproteus (Parahaemoproteus) bukaka (species nova), a haemosporidian associated with the strictly Australo-Papuan host subfamily Cracticinae. Parasitology Research, 115 (9), 3387-3400. doi: 10.1007/s00436-016-5099-x
Clark, Nicholas J., Olsson-Pons, Sophie, Ishtiaq, Farah and Clegg, Sonya M. (2015). Specialist enemies, generalist weapons and the potential spread of exotic pathogens: malaria parasites in a highly invasive bird. International Journal for Parasitology, 45 (14), 891-899. doi: 10.1016/j.ijpara.2015.08.008
Olsson-Pons, Sophie, Clark, Nicholas J., Ishtiaq, Farah and Clegg, Sonya M. (2015). Differences in host species relationships and biogeographic influences produce contrasting patterns of prevalence, community composition and genetic structure in two genera of avian malaria parasites in southern Melanesia. Journal of Animal Ecology, 84 (4), 985-998. doi: 10.1111/1365-2656.12354
Clark, Nicholas J., Adlard, Robert D. and Clegg, Sonya M. (2015). Molecular and morphological characterization of Haemoproteus (Parahaemoproteus) ptilotis, a parasite infecting Australian honeyeaters (Meliphagidae), with remarks on prevalence and potential cryptic speciation. Parasitology Research, 114 (5), 1921-1928. doi: 10.1007/s00436-015-4380-8
Clark, Nicholas J. and Clegg, Sonya M. (2015). The influence of vagrant hosts and weather patterns on the colonization and persistence of blood parasites in an island bird. Journal of Biogeography, 42 (4), 641-651. doi: 10.1111/jbi.12454
Clark, Nicholas J., Adlard, Robert D. and Clegg, Sonya M. (2014). First evidence of avian malaria in capricorn silvereyes (zosterops lateralis chlorocephalus) on heron island. Sunbird, 44 (1), 1-11.
Clark, Nicholas J., Clegg, Sonya M. and Lima, Marcos R. (2014). A review of global diversity in avian haemosporidians (Plasmodium and Haemoproteus: Haemosporida): new insights from molecular data. International Journal for Parasitology, 44 (5), 329-338. doi: 10.1016/j.ijpara.2014.01.004
Clark, Nicholas J. and Russ, Garry R. (2012). Ontogenetic shifts in the habitat associations of butterflyfishes (F. Chaetodontidae). Environmental Biology of Fishes, 94 (4), 579-590. doi: 10.1007/s10641-011-9964-2
Conference Papers
Chakma, Shovon, Mshelbwala, Philip P., Samad, Mohammed Abdus, Karim, Md Rezaul, Giasuddin, Mohammad, Akwar, Holy, Hasan, Zakiul, Nasrin, Tanzinah, Brum, Eric, Osmani, Muzaffar G., Islam, S.K. Shaheenur, Ibrahim, Nelima, McKenzie, Joanna, Clark, Nicholas J., Islam, Zahir, Sly, Peter and Soares Magalhães, Ricardo J. (2021). Role of live poultry movement on environmental contamination patterns of avian influenza A viruses circulating in live bird markets,
Dhaka, Bangladesh. 7th One Health Aotearoa Symposium, Wellington, New Zealand, 7-8 December 2021.
Mshelbwala, Philip P., Weese, J. Scott, Tekki, Ishaya, Chakma, Shovon, Shamaki, David, Mamun, Abdullah A., Clark, Nicholas J., Rupprecht, Charles E. and Soares Magalhães, Ricardo J. (2021). Spatial patterns of canine rabies evidence at the local government area level in Nigeria: association with socioeconomic and ecological
determinants. 7th One Heath Aotearoa Symposium, Wellington, New Zealand, 6-7 December 2021.