Jim Thomson

Jim joined the EAS group in early 2015 from the University of Canberra / Monash University where he held Research Fellow and Senior Research Fellowships over a period of more than a decade.  Prior to this Jim held a Post-doctoral Research Fellowships at the Patrick Center for Environmental Research in the Academy of Natural Sciences of Philadelphia, USA, and also at Macquarie University.

Jim’s primary expertise is in the disciplines of ecological statistics and modelling, freshwater and estuarine ecology, landscape ecology, and systematic conservation planning and optimization.  He also has a strong theoretical understanding and extensive practical experience using a wide range of modern statistical and modelling methods. These include: Machine learning predictive models; spatial optimization (Zonation) and decision theory; Hierarchical Bayes models; Generalized linear and mixed models; spatio-temporal models; meta-analysis; survival analysis; time-series / change-point models, missing data / observation error models, multiple-response models; and various non-parametric methods.

Jim’s highly developed skills in statistical computing and data management, particularly using R, are invaluable to the EAS research group, however he is also very competent with ArcGIS, WinBUGS, Stata, Python, MS Access and many other specialised programs.

Jim’s work along with other members of the EAS group focusses on the development of an innovative decision support system that will assist DELWP in the allocation of resources for conservation planning and management activities.


Publications  –  Jim has more than 70 peer-reviewed journal articles.

Thomson JR, Maron M, Catteral C et al. in press. Avifaunal disarray: quantifying models of the occurrence and ecological effects of a despotic bird species. Diversity and Distributions.

Yen J, Thomson J, Paganin D, Keith J & Mac Nally R. in press. Function regression in ecology and evolution: FREE. Methods in Ecology and Evolution.

Bond NR, Thomson JR, & Reich P. 2014. Incorporating climate change in conservation planning for freshwater fishes. Diversity and Distributions.

Fleishman E, Thomson JR, Kalies EL, Dickson BG, Dobkin DS, & Leu M. 2014. Projecting current and future location, quality, and connectivity of habitat for breeding birds in the Great Basin. Ecosphere, 5(7), art82.

Bennett JM, Nimmo DG, Clarke RH, Thomson JR, Cheers G, Horrocks GF, & Mac Nally R. 2014. Resistance and resilience: can the abrupt end of extreme drought reverse avifaunal collapse? Diversity and Distributions.

Bennett JM, Clarke RH, Thomson JR & Mac Nally R. 2014. Fragmentation, vegetation change and irruptive competitors affect recruitment of woodland birds. Ecography.

Bennett JM, Clarke RH, Thomson JR & Nally RM. 2014. Variation in abundance of nectarivorous birds: Does a competitive despot interfere with flower‐tracking? Journal of Animal Ecology.

Mac Nally R, Kutt AS, Eyre TJ, Perry JJ, Vanderduys EP, Mathieson M, & Thomson JR. 2014. The hegemony of the ‘despots’: the control of avifaunas over vast continental areas. Diversity and Distributions.

Yen JD, Paganin DM, Thomson JR & Mac Nally R. 2014. Thermodynamic extremization principles and their relevance to ecology. Austral Ecology.

Lada H, Thomson JR, Cunningham SC & Mac Nally R. 2014. Relating Demographic Characteristics of a Small Mammal to Remotely Sensed Forest‐Stand Condition. PloS one, (3), e91731.

Mac Nally R, Nerenberg S, Thomson JR, Lada H & Clarke RH. 2014. Do frogs bounce, and if so, by how much? Responses to the ‘Big Wet’following the ‘Big Dry’in south‐eastern Australia. Global Ecology and Biogeography, 23(2), 223‐234.

Kratina P, Mac Nally R, Kimmerer WJ, Thomson JR, & Winder M. 2014. Human‐induced biotic invasions and changes in plankton interaction networks. Journal of Applied Ecology.

Giling DP, Grace MR, Thomson JR, Mac Nally R, & Thompson RM. 2014. Effect of Native Vegetation Loss on Stream Ecosystem Processes: Dissolved Organic Matter Composition and Export in Agricultural Landscapes. Ecosystems 17(1), 82‐95.

Mac Nally R, Lada H, Cunningham SC, Thomson JR, Fleishman E.2014. Climate‐change driven deterioration of the condition of floodplain forest and the future for the avifauna. Global Ecology and Biogeography 23: 191‐202

Maron M., Grey MJ, Catterall CP, Major RE, Oliver DL, Clarke MF, & Thomson JR. 2013. Avifaunal disarray due to a single despotic species. Diversity and Distributions 19: 1468‐1479.

Bennett JM, Cunningham SC, Connelly CA, Clarke RH, Thomson JR, Mac Nally R. 2013. The interaction between a drying climate and land use affects forest structure and above‐ground carbon storage. Global Ecology and Biogeography 22: 1238 – 1247.

Lada H, Thomson, JR, Cunningham SC, Mac Nally R. 2013. Rainfall in prior breeding seasons influences population size of a small marsupial. Austral Ecology 38: 581‐591

Bradshaw et al. 2013 Brave new green world ‐ Consequences of a carbon economy for the conservation of Australian biodiversity. Biological Conservation 161: 71‐90.

Gardner TA. et al. 2013. A social and ecological assessment of tropical land‐uses and multiple scales: the Sustainable Amazon Network. Philosophical Transactions of the Royal Society, B. 368(619).

Amos JN, Balasubramaniam S, Grootendorst L, Harrisson KA, Lill A, Mac Nally R, Pavlova A, Radford JQ, Takeuchi N, Thomson JR and Sunnucks P. 2013. Little evidence that condition, stress indicators, sex ratio, or homozygosity are related to landscape or habitat attributes in declining woodland birds. Journal of Avian Biology 44: 45‐54.

Yen J, Thomson J, Vesk P, Mac Nally R. 2013. Is there an ecological basis to species abundance distributions. Oecologia 171: 517‐525.

Thomson J, Bond N, Cunningham S, Metzeling L, Reich P, Thompson R, Mac Nally R. 2012. The influences of climatic variation and vegetation on stream biota: Lessons from the Big Dry in southeastern Australia, Global Change Biology 18: 1582‐1596.

Horner GJ, Cunningham SC, Thomson JR, Baker PJ, Mac Nally R. 2012. Forest structure, flooding and grazing predict understorey composition of floodplain forests in southeastern Australia. Forest Ecology and Management 286: 148‐158

Amos N, Bennett A, Mac Nally R, Newell G, Pavlova A, Radford J, Thomson J, White M, Sunnucks P. 2012. Predicting landscape‐genetic consequences of habitat loss, fragmentation and mobility for multiple species of woodland birds, PLoS ONE 7: 1‐12.

Cunningham SC, Metzeling K, Mac Nally RC, Thomson JR, Cavagnaro T. 2012. Changes in soil carbon of pastures after afforestation with mixed species: Sampling, heterogeneity and surrogates, Agriculture, Ecosystems and Environment 158: 58‐65.

Hoogmoed M, Cunningham SC, Thomson JR, Baker PJ, Beringer J, Cavagnaro T. 2012. Does afforestation of pastures increase sequestration of soil carbon in Mediterranean climates? Agriculture, Ecosystems and Environment 159: 176‐183.

Horrocks GFB, Cunningham SC, O’Dowd DJ, Thomson JR, Mac Nally RC. 2012. Floodplain ants show a stronger response to an extensive flood than to variations in fallen‐timber load, Austral Ecology 37: 518‐528.

Smith M, Conte P, Berns AE, Thomson JR, Cavagnaro T. 2012. Spatial patterns of, and environmental controls on, soil properties at a riparian‐paddock interface, Soil Biology and Biochemistry 49: 38‐45.

Bond N, Thomson J, Reich P. Stein J. 2011. Using species distribution models to infer potential climate change‐induced range shifts of freshwater fish in south‐eastern Australia, Marine and Freshwater Research 62:1043‐1061.

Clarke R, Carter M, Swann G, Thomson J. 2011. The status of breeding seabirds and herons at Ashmore Reef, off the Kimberley coast, Australia, Journal of the Royal Society of Western Australia 94: 171‐182.

Cunningham S, Thomson J, Mac Nally R, Read J, Baker P. 2011. Groundwater change forecasts widespread forest dieback across an extensive floodplain system, Freshwater Biology 56: 1494‐1508.

Fingerut J, Hart D, Thomson J. 2011. Larval settlement in benthic environments: the effects of velocity and bed element geometry, Freshwater Biology 56: 904‐915.

Mac Nally R, Cunningham S, Baker P, Horner G, Thomson J. 2011. Dynamics of Murray‐Darling floodplain forests under multiple stressors: The past, present and future of an Australian icon, Water Resources Research 47: 1‐11.

Yen J, Thomson J, Vesk P, Mac Nally R. 2011. To what are woodland birds responding?  Inference on relative importance of in‐site habitat variables using several ensemble habitat modelling techniques, Ecography 34: 946‐954.

Thomson JR, Kimmerer W, Brown L, Newman K, Mac Nally, R, Bennett W, Feyrer F, Fleishmann E. 2010. Bayesian change point analysis of abundance trends for pelagic fishes in the upper San Francisco Estuary, Ecological Applications 20: 1431‐1448.

Mac Nally R, Thomson JR, Kimmerer W, Feyrer F, Newman K, Sih A., Bennett W, Brown L, Fleishmann E, Culberson S, Castillo G. 2010, Analysis of pelagic species decline in the upper San Francisco Estuary using multivariate autoregressive modeling (MAR), Ecological Appplications 20, issue 5, Ecological Society of America, Washington DC USA, pp. 1417‐1430.

Lake PS, Thomson JR, Lada H, Mac Nally R, Reid D, Stanaway J, Taylor AC. 2010. Diversity and distribution of macroinvertebrates in lentic habitats in massively altered landscapes in south‐eastern Australia, Diversity and Distributions 16: 713‐724.

Bond NR, McMaster D, Reich P, Thomson JR, Lake PS. 2010. Modelling the impacts of flow regulation on fish distributions in naturally intermittent lowland streams: an approach for predicting restoration responses, Freshwater Biology 55: 1997‐2010.

Camilleri SM, Thomson JR, Mac Nally R. 2010. The interaction between land use and catchment physiognomy: understanding avifaunal patterns of the Murray‐Darling Basin, Australia, Journal Of Biogeography 37: 293‐304.

Cant B, Mac Nally R, Thomson JR, Beardall J. 2010. Relative effects of local and landscape factors on wetland algal biomass over a salinity gradient, Aquatic Sciences 72:191‐202.

Cunningham SC, Thomson JR, Read J, Baker PJ, Mac Nally R. 2010. Does stand structure influence susceptibility of eucalypt floodplain forests to dieback? Austral Ecology 35: 348‐356.

Horner GJ, Baker PJ, Mac Nally R, Cunningham SC, Thomson JR, Hamilton F. 2010. Forest structure, habitat and carbon benefits from thinning floodplain forests: Managing early stand density makes a difference, Forest Ecology and Management 259: 286‐293.

Mac Nally R, Vries LD, Thomson JR. 2010. Are replanted floodplain forests in southeastern Australia providing bird biodiversity benefits?, Restoration Ecology 18: 85‐94.

Schmidt DF, Spring DA, Mac Nally R, Thomson JR, Brook B, Cacho OJ, McKenzie M. 2010. Finding needles (or ants) in haystacks: predicting locations of invasive organisms to inform eradication and containment, Ecological Appplications 20: 1217‐1227.

Spring D, Baum J, Mac Nally R, MacKenzie M, Sanchez‐Azofeifa A, Thomson JR 2010. Building a regionally connected reserve network in a changing and uncertain world.  Conservation Biology 24: 691‐700.

Cunningham SC, Mac Nally R, Read J, Baker PJ, White M, Thomson JR, Griffioen P. 2009.  A robust technique for mapping vegetation condition across a major river system. Ecosystems 12: 207‐219.

Thomson JR, Moilanen AJ, Vesk P, Bennett AF, Mac Nally R. 2009. Where and when to revegetate: a quantitative method for scheduling landscape reconstruction, Ecological Appplications 19: 817‐828.

Horner GJ, Baker PJ, Mac Nally R, Cunningham SC, Thomson JR, Hamilton F. 2009. Mortality of developing floodplain forests subjected to a drying climate and water extraction, Global Change Biology 15: 2176‐2186.

Loo SE, Mac Nally R, O’Dowd DJ, Thomson JR, Lake PS. 2009. Multiple scale analysis of factors influencing the distribution of an invasive aquatic grass, Biological Invasions 11: 1903‐1912.

Mac Nally R, Bennett AF, Thomson JR, Radford JQ, Unmack G, Horrocks GFB, Vesk P. 2009. Collapse of an avifauna: climate change appears to exacerbate habitat loss and degradation, Diversity And Distributions 15: 720‐730.

Mac Nally R, Horrocks GFB, Lada H, Lake PS, Thomson JR, Taylor AC. 2009. Distribution of anuran amphibians in massively altered landscapes in south‐eastern Australia: effects of climate change in an aridifying region, Global Ecology and Biogeography 18: 575‐585.

Selwood, K, Mac Nally R, Thomson, JR 2009. Native bird breeding in a chronosequence of revegetated sites, Oecologia 159: 435‐446.

Lada H., Thomson, J, Mac Nally R, Taylor AC. 2008. Impacts of massive landscape change on a carnivorous marsupial in south‐eastern Australia: Inferences from landscape genetics analysis, Journal of Applied Ecology 45: 1732‐1741.

Mac Nally R, Fleishman E, Thomson JR, Dobkin DS. 2008. Use of guilds for modelling avian responses to vegetation in the Intermountain West (USA), Global Ecology and Biogeography 17: 758‐769.

Mac Nally R, Molyneux G, Thomson JR, Lake PS, Read J. 2008. Variation in widths of riparian‐zone vegetation of higher‐elevation streams and implications for conservation management, Plant Ecology 198: 89‐100.

Vesk P, Nolan RH, Thomson JR, Dorrough, J, Mac Nally R. 2008. Time lags in provision of habitat resources through revegetation, Biological Conservation 141: 174‐186.

Thomson, J., R. Mac Nally, E. Fleishman, and G. Horrocks. 2007. Predicting bird species distributions in reconstructed landscapes. Conservation Biology 21: 752‐766.

Lada H., J.R. Thomson, R. Mac Nally, G. Horrocks and A. Taylor. 2007 .Evaluating simultaneous impacts of three anthropogenic effects on a floodplain‐dwelling marsupial Antechinus flavipes. Biological Conservation 134: 527‐536.

Thomson J.R., E. Fleishman, R. Mac Nally, and D.S. Dobkin. 2007. Comparison of predictor sets for species richness and the number of rare species of butterflies and birds. Journal of Biogeography 34: 90‐101. 60.

Thomson J.R., E. Fleishman, R. Mac Nally, and D.S. Dobkin. 2005. Influence of the temporal resolution of data on the success of indicator species models of species richness across multiple taxonomic groups. Biological Conservation 124: 503‐518.

Fleishman, E., J.R. Thomson, R. Mac Nally, D.D. Murphy and J.P. Fay. 2005. Using indicator species to predict species richness of multiple taxonomic groups. Conservation Biology 19:1125‐1137.

Thomson J.R., D.D. Hart, D.F. Charles, T.L. Nightengale and D.M. Winter. 2005. The effects of a small dam removal on downstream macroinvertebrate and algal assemblages in a Pennsylvania stream. Journal of the North American Benthological Society 24: 192‐207

Fleishman E., R. Mac Nally and J.R. Thomson. 2004. Challenges and opportunities for conserving faunal biodiversity in arid ecosystems. Annals of Arid Zone 43: 427‐444.

Thomson J.R., B.D. Clark, J.T. Fingerut and D.D. Hart. 2004. Local modification of benthic flow environments by suspension‐feeding stream insects. Oecologia 140: 533‐542.

Thomson J.R., M.P. Taylor and G.J. Brierley. 2004. Are River Styles ecologically meaningful? A test of the ecological relevance of a geomorphological river characterization scheme. Marine and Freshwater Ecosystems 14: 25‐48

Thomson J.R. 2002. The effects of hydrological disturbance on the densities of macroinvertebrate predators and their prey in coastal stream. Freshwater Biology 47: 1333‐1351.

Thomson J.R., P.S. Lake and B.J. Downes. 2002. The effect of hydrological disturbance on the impact of a benthic invertebrate predator. Ecology 83: 628‐642.

Bushaw‐Newton K., D.D. Hart, T.E. Johnson, J.E. Pizzuto, J. Egan, M. Keeley, J. Lawrence, J.R. Thomson, J.T. Ashley, R.J. Horwitz, D. Charles, C. Gatenby, D.A. Kreeger, T. Nightengale, R.L. Thomas and D.J. Velinsky. 2002. An integrative approach towards understanding dam removal: The Manatawny Creek study. Journal American Water Resources Association. 38:1581‐1599

Thomson J.R., M.P. Taylor, K. Fryirs and G.J. Brierley. 2001. A geomorphic framework for river characterization and habitat assessment. Aquatic Conservation: Marine and Freshwater Ecosystems 11: 373 ‐ 389.

Taylor M.P., J.R. Thomson, K. Fryirs and G.J. Brierley. 2000. Habitat mapping using the River Styles methodology. Ecological Management and Restoration 1: 223‐226.

Book Chapters

Vesk, P., R. Mac Nally, G. Horrocks, and J. Thomson. 2008. Revegetation and the significance of lags in the provision of habitat resources for birds. In C. Pettit, W. Cartwright, K. Lowell, I. Bishop, D. Duncan, and D. Pullar, editors. Landscape analysis and visualisation. spatial models for natural resource management and planning. Springer‐Verlag, Berlin/Heidelberg.