Dr James Thomson - Researcher Profile

Biography

 Jim works in the School of Biological Sciences at Monash University as a Research Fellow

 

 Jim’s research areas of interest are:

Conservation Biology

Biodiversity assessment and prediction; landscape planning and optimal biodiversity management.
 

Ecological modelling and statistical analyses

Hierarchical Bayesian methods; spatio-temporal models; change-point models; multiple-response models; food-web models; landscape planning and optimization.
 

Freshwater ecology

Organisms-flow interactions; dispersal processes; predator-prey interactions; floodplain ecology; environmental flows; impacts and mitigation of climate change.
 

Landscape ecology

Connectivity and fragmentation impacts on dispersal and viability of birds, small mammals and aquatic species.
 

See also:

Australian Centre for Biodiversity Analysis, Policy and Management: www.biolsci.monash.edu.au/research/acb/index.html

 

Keywords

Conservation Biology, Ecological modelling and statistical analyses, Freshwater ecology, Landscape

Qualifications

GRADUATE DIPLOMA IN BIOSTATISTICS

Institution: Monash University

Year awarded: 2010

PHD

Institution: Monash University

Year awarded: 1999

Publications

Book Chapters

Vesk, P., Mac Nally, R., Thomson, J.R., Horrocks, G.F.B., 2008, Revegation and the significance of lags in tne provision of habitat resources for birds, in Landscape analysis and visualisation. Spatial models for Natural resource management and planning, eds C Pettit, W Cartwright, K Lovell, I Bishop, D Duncan, and D Pullar, Springer, Berlin, pp. 183-209.

Journal Articles

Yen, J.D.L., Thomson, J.R., Mac Nally, R.C., 2013, Is there an ecological basis for species abundance distributions?, Oecologia [P], vol 171, issue 2, Springer, Germany, pp. 517-525.

Cunningham, S.C., Metzeling, K., Mac Nally, R.C., Thomson, J.R., Cavagnaro, T., 2012, Changes in soil carbon of pastures after afforestation with mixed species: Sampling, heterogeneity and surrogates, Agriculture, Ecosystems and Environment [P], vol 158, Elsevier BV, Netherlands, pp. 58-65.

Hoogmoed, M., Cunningham, S.C., Thomson, J.R., Baker, P.J., Beringer, J., Cavagnaro, T., 2012, Does afforestation of pastures increase sequestration of soil carbon in Mediterranean climates?, Agriculture, Ecosystems and Environment [P], vol 159, Elsevier Science BV, Amsterdam Netherlands, pp. 176-183.

Horrocks, G.F.B., Cunningham, S.C., O'Dowd, D.J., Thomson, J.R., Mac Nally, R.C., 2012, Floodplain ants show a stronger response to an extensive flood than to variations in fallen-timber load, Austral Ecology [P], vol 37, issue 4, Wiley-Blackwell, New Jersey USA, pp. 518-528.

Horner, G.J., Cunningham, S.C., Thomson, J.R., Baker, P.J., Mac Nally, R.C., 2012, Forest structure, flooding and grazing predict understorey composition of floodplain forests in southeastern Australia, Forest Ecology and Management [P], vol 286, Elsevier Science, Amsterdam Netherlands, pp. 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 [P], vol 7, issue 2, Public Library of Science, United States, pp. 1-12.

Smith, M., Conte, P., Berns, A.E., Thomson, J.R., Cavagnaro, T., 2012, Spatial patterns of, and environmental controls on, soil properties at a riparian-paddock interface, Soil Biology and Biochemistry [P], vol 49, Pergamon-Elsevier Science, Oxford United Kingdom, pp. 38-45.

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 [P], vol 18, issue 5, Wiley-Blackwell, Malden USA, pp. 1582-1596.

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 [P], vol 47, American Geophysical Union, Washington USA, pp. 1-11.

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 [E], vol 56, issue 8, Wiley-Blackwell, Malden USA, pp. 1494-1508.

Fingerut, J., Hart, D., Thomson, J., 2011, Larval settlement in benthic environments: the effects of velocity and bed element geometry, Freshwater Biology [P], vol 56, issue 5, Wiley-Blackwell, USA, pp. 904-915.

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 [P], vol 94, issue 2, Royal Society of Western Australia, Perth Australia, pp. 171-182.

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 [P], vol 34, issue 6, Wiley-Blackwell, Malden USA, pp. 946-954.

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 [P], vol 62, issue 9, CSIRO Publishing, Collingwood Victoria, pp. 1043-1061.

Mac Nally, R., Thomson, J.R., 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 [P], vol 20, issue 5, Ecological Society of America, Washington DC USA, pp. 1417-1430.

Mac Nally, R., Vries, L.D., Thomson, J.R., 2010, Are replanted floodplain forests in southeastern Australia providing bird biodiversity benefits?, Restoration Ecology [P], vol 18, issue 1, Wiley-Blackwell Publishing Inc, Malden Massachusetts USA, pp. 85-94.

Thomson, J.R., 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 Appplications [P], vol 20, issue 5, Ecological Society of America, Washington DC USA, pp. 1431-1448.

Spring, D., Baum, J., Mac Nally, R., MacKenzie, M., Sanchez-Azofeifa, A., Thomson, J.R., 2010, Building a regionally connected reserve network in a changing and uncertain world, Conservation Biology [P], vol 24, issue 3, Wiley-Blackwell Publishing Inc, Malden Massachusetts USA, pp. 691-700.

Sam Lake, P., Thomson, J.R., Lada, H., Mac Nally, R., Reid, D., Stanaway, J., Taylor, A.C., 2010, Diversity and distribution of macroinvertebrates in lentic habitats in massively altered landscapes in south-eastern Australia, Diversity and Distributions [E], vol 16, issue 5, Wiley-Blackwell Publishing Inc, Malden Massachusetts USA, pp. 713-724.

Cunningham, S.C., Thomson, J.R., Read, J., Baker, P.J., Mac Nally, R., 2010, Does stand structure influence susceptibility of eucalypt floodplain forests to dieback?, Austral Ecology [P], vol 35, issue 3, Wiley-Blackwell Publishing Inc, Malden Massachusetts USA, pp. 348-356.

Schmidt, D.F., Spring, D.A., Mac Nally, R., Thomson, J.R., Brook, B., Cacho, O.J., McKenzie, M., 2010, Finding needles (or ants) in haystacks: predicting locations of invasive organisms to inform eradication and containment, Ecological Appplications [P], vol 20, issue 5, Ecological Society of America, Washington DC USA, pp. 1217-1227.

Horner, G.J., Baker, P.J., Mac Nally, R., Cunningham, S.C., Thomson, J.R., Hamilton, F., 2010, Forest structure, habitat and carbon benefits from thinning floodplain forests: Managing early stand density makes a difference, Forest Ecology and Management [P], vol 259, issue 3, Elsevier, Netherlands, pp. 286-293.

Bond, N.R., McMaster, D., Reich, P., Thomson, J.R., Lake, P.S., 2010, Modelling the impacts of flow regulation on fish distributions in naturally intermittent lowland streams: an approach for predicting restoration responses, Freshwater Biology [E], vol 55, issue 9, Wiley-Blackwell Publishing Inc, Malden Massachusetts USA, pp. 1997-2010.

Cant, B., Mac Nally, R., Thomson, J.R., Beardall, J., 2010, Relative effects of local and landscape factors on wetland algal biomass over a salinity gradient, Aquatic Sciences [P], vol 72, issue 2, Birkhausar Verlag AG, Basel Switzerland, pp. 191-202.

Camilleri, S.M., Thomson, J.R., Mac Nally, R., 2010, The interaction between land use and catchment physiognomy: understanding avifaunal patterns of the Murray-Darling Basin, Australia, Journal Of Biogeography [P], vol 37, issue 2, Wiley-Blackwell Publishing Inc, Malden Massachusetts USA, pp. 293-304.

Cunningham, S.C., Mac Nally, R., Read, J., Baker, P.J., White, M., Thomson, J.R., Griffioen, P., 2009, A robust technique for mapping vegetation condition across a major river system, Ecosystems [P], vol 12, issue 2, Springer, New York USA, pp. 207-219.

Mac Nally, R., Bennett, A.F., Thomson, J.R., Radford, J.Q., Unmack, G., Horrocks, G.F.B., Vesk, P., 2009, Collapse of an avifauna: climate change appears to exacerbate habitat loss and degradation, Diversity And Distributions [P], vol 15, issue 4, Wiley-Blackwell, UK, pp. 720-730.

Mac Nally, R., Horrocks, G.F.B., Lada, H., Lake, P.S., Thomson, J.R., Taylor, A.C., 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 [P], vol 18, issue 5, Blackwell Publishing, UK, pp. 575-585.

Horner, G.J., Baker, P.J., Mac Nally, R., Cunningham, S.C., Thomson, J.R., Hamilton, F., 2009, Mortality of developing floodplain forests subjected to a drying climate and water extraction, Global Change Biology [E], vol 15, Wiley-Blackwell, UK, pp. 2176-2186.

Loo, S.E., Mac Nally, R., O'Dowd, D.J., Thomson, J.R., Lake, P.S., 2009, Multiple scale analysis of factors influencing the distribution of an invasive aquatic grass, Biological Invasions [P], vol 11, issue 8, Springer, Netherlands, pp. 1903-1912.

Selwood, K., Mac Nally, R., Thomson, J.R., 2009, Native bird breeding in a chronosequence of revegetated sites, Oecologia [P], vol 159, issue 2, Springer, Netherlands, pp. 435-446.

Thomson, J.R., Moilanen, A.J., Vesk, P., Bennett, A.F., Mac Nally, R., 2009, Where and when to revegetate: a quantitative method for scheduling landscape reconstruction, Ecological Appplications [P], vol 19, issue 4, Ecological Society of America, USA, pp. 817-828.

Lada, H., Thomson, J., Mac Nally, R., Taylor, A.C., 2008, Impacts of massive landscape change on a carnivorous marsupial in south-eastern Australia: Inferences from landscape genetics analysis, Journal of Applied Ecology, vol 45, British Ecological Society, UK, pp. 1732-1741.

Vesk, P., Nolan, R.H., Thomson, J.R., Dorrough, J., Mac Nally, R., 2008, Time lags in provision of habitat resources through revegetation, Biological Conservation, vol 141, Elsevier, Netherlands, pp. 174-186.

Mac Nally, R., Fleishman, E., Thomson, J.R., Dobkin, D.S., 2008, Use of guilds for modelling avian responses to vegetation in the Intermountain West (USA), Global Ecology and Biogeography, vol 17, issue 6, Blackwell, UK, pp. 758-769.

Mac Nally, R., Molyneux, G., Thomson, J.R., Lake, P.S., Read, J., 2008, Variation in widths of riparian-zone vegetation of higher-elevation streams and implications for conservation management, Plant Ecology, vol 198, issue 1, Springer, Netherlands, pp. 89-100.

Thomson, J.R., Fleishman, E., Mac Nally, R., Dobkin, D.S., 2007, Comparison of predictor sets for species richness and the number of rare species of butterflies and birds, Journal of Biogeography, vol 34, issue 1, Blackwell Publishing, Oxford England, pp. 90-101.

Lada, H., Thomson, J.R., Horrocks, G.F.B., Taylor, A.C., Mac Nally, R., 2007, Evaluating simultaneous impacts of three anthropogenic effects on a floodplain-dwelling marsupial Antechinus flavipes, Biological Conservation, vol 134, issue 4, Elsevier Science Ltd, Oxford England, pp. 527-536.

Thomson, J.R., Mac Nally, R., Fleishman, E., Horrocks, G.F.B., 2007, Predicting bird species distributions in reconstructed landscapes, Conservation Biology, vol 21, issue 3, Blackwell Publishing Inc, USA, pp. 752-766.

Thomson, J.R., Hart, D., Charles, D.F., Nightengale, T.L., Winter, D.M., 2005, Effects of removal of a small dam on downstream macroinvertebrate and algal assemblages in a Pennsylvania stream, Journal of the North American Benthological Society [P], vol 24, issue 1, North American Benthological Society, Lawrence USA, pp. 192-207.

Thomson, J.R., Fleishman, E., Mac Nally, R., Dobkin, D.S., 2005, Influence of the temporal resolution of data on the success of indicator species models of species richness across multiple taxonomic groups, Biological Conservation, vol 124, issue 4, Elsevier Sci Ltd, Oxford England, pp. 503-518.

Fleishman, E., Thomson, J.R., Mac Nally, R., Murphy, D.D., Fay, J.P., 2005, Using indicator species to predict species richness of multiple taxonomic groups, Conservation Biology, vol 19, issue 4, Blackwell Science Inc, Malden MA, pp. 1125-1137.

Fleishman, E., Mac Nally, R., Thomson, J.R., 2004, Challenges and opportunities for conserving faunal biodiversity in arid ecosystems, Annals of Arid Zone, vol 43, Arid Zone Research Assoc. India, Jodhpur India, pp. 427-444.

Thomson, J.R., Taylor, M.P., Brierley, G.J., 2003, Are River Styles ecologically meaningful? A test of the ecological significance of a geomorphic characterization scheme., Aquatic Conservation-Marine And Freshwater Ecosystems [P], vol 14, issue 1, John Wiley & Sons, Ltd, W Sussex, England, pp. 25-48.

Cooper, S., Bennett, W., Andrade, J., Reubinoff, B.E., Thomson, J., Pera, M., 2002, Biochemical properties of a keratan sulphate/chondroitin sulphate proteoglycan expressed in primate pluripotent stem cells, Journal of Anatomy, vol 200, issue 3, Blackwell Science Ltd, UK, pp. 259-265.

Thomson, J.R., Lake, P.S., Downes, B.J., 2002, The effect of hydrological disturbance on the impact of a benthic invertebrate predator, Ecology, vol 83, issue 3, Ecological Society of America, Washington DC, pp. 628-642.

Thomson, J.R., 2002, The effects of hydrological disturbance on the densities of macroinvertebrate predators and their prey in a coastal stream, Freshwater Biology, vol 47, issue 8, Blackwell Science Ltd, Oxford UK, pp. 1333-1351.

Other

Cunningham, S.C., Mac Nally, R., White, M., Read, J., Thomson, J.R., Griffioen, P., 2007, Mapping the Current Condition of River red gum (Eucalyptus camaldulensis Dehnh.) Stands Along the Victorian Murray River Floodplain, Monash University, Clayton Campus Victoria, pp. 1-59.

Thomson, J., 1999, Effects of disturbance on the impact of invertebrate predators in stream benthic communities.

Thomson, J., 1997, Predator impacts in variable flow environments (Abstract, p.135), Australian Society for Limnology 36th Congress, Albury Wodonga, 27-29 September 1997.

Postgraduate Research Supervisions

Current Supervision

Program of Study:

(DOCTORATE BY RESEARCH).

Thesis Title:

Thermodynamic ecology: theoretical and empirical approaches.

Supervisors:

Macnally, R (Main), Paganin, D (Associate), Thomson, J (Associate).