Jane Elith

Post-doctoral Research Fellow, Environmental Science

I'm appointed as a research fellow, funded by an ARC Future Fellowship. My research spans theoretical, methodological, and applied ecology, reflecting my broad interest in biodiversity and conservation and my attraction towards quantitative methods. 

In relation to methods, I have been exploring ecological applications of new methods developed in machine learning and statistics. My main interest has been in predicting distributions of species, communities and diversity, focussing on how best to use new methods, and providing introductory guides for the ecological community. Published results include papers and related tutorials for several regression-related methods, including generalised linear and additive models (GLMs and GAMs), multivariate adaptive regression splines (MARS), and boosted regression trees (BRT).  I am currently working on a guide to MaxEnt and contributing to books including one on machine learning methods for ecology. 

Most recently I have started working on problems associated with modelling non-equilibrial situations, exploring appropriate methods for predicting both the potential spread of invasive species and the likely responses of the biota to climate change. This has included research on linking mechanistic and correlative models with Michael Kearney (Zoology, University of Melbourne),  and participation as an invited member in various climate-change related initiatives (workshops in Perth and Townsville, and an ARC linkage grant with Wintle, Keith et al).

On the theoretical side, I am interested in how to robustly evaluate models and their predictions in ways that are appropriate for intended  applications, and how to deal with uncertainty and its impacts in conservation decision-making. 

Because I'm keen to ensure this work is relevant to real-world situations, I have also been involved in a range of conservation and resource management applications. These include modelling patterns of vegetation in NSW forests and species turnover in New Zealand rivers, providing advice to the Murray-Darling Basin Commission on the data infrastructure required for robust modelling in river ecosystems, and advising government departments on use of models for particular environmental and biosecurity issues. I am becoming increasingly involved in a range of applications related to climate change issues

Across these strands of work I've dealt with many types of data across a wide range of ecosystems, and at widely varying spatial scales: rare shrubs and floodplain vegetation in NSW, biological soil crusts in western Victoria , fish in Victorian rivers, cane toads in northern Australia; trees, shrubs, birds, reptiles and mammals  from 6 regions of the world; New Zealand marine and freshwater fish, and clownfish on coastal reefs in Papua New Guinea. I work with various students, including co-supervision of PhD students Cassia Read (the role of biological soil crusts in ecosystem function), Lucy Robinson (UQ; species distributions in marine systems) and Laura Shirley (the ecology and biogeography of eucalypts of the Grampians). 

Publications

Presentations & Collaborations

Photos

Elith Family contacts

Publications

Refereed Publications

• Yates, C., Elith, J., Latimer, A. le Maitre, D., Midgley, G., Schurr, F. and West, A. (2010 in press). Predicting the impacts of climate change on species distributions in the mega diverse Cape Floristic and Southwest Australian Floristic Regions - opportunities and limitations. Austral Ecology.

• Phillips, S. J. & Elith, J. (2010 in press) POC-plots: Calibrating species distribution models using presence-only data. Ecology.

• Leathwick, J., Snelder, T. H., Chadderton, L., Julian, K., Elith, J. & Ferrier, S. (2010 in press) Use of generalised dissimilarity modelling to improve the biological discrimination of river and stream classifications. Freshwater Biology.

• Yates, C., McNeill, A., Elith, J. &  Midgley, G. (2010) Assessing the impacts of climate change and land transformation on banksia in the south-west Australian floristic region. Diversity and Distributions 16, 187-201

• Elith, J. and Leathwick, J. (2009). Species distribution models: Ecological explanation and prediction across space and time. Annual Review of Ecology, Evolution and Systematics 40, 677-697 pdfs

• Elith, J. & Graham, C.G. (2009) Do they / how do they / WHY do they differ? - on finding reasons for differing performance of species distributions models. Ecography, 32, 66-77

• Van Wilgen, N., Wilson, J. R. U., Elith, J., Wintle, B. A. & Richardson, D. M. (in press) Alien invaders and reptile traders: What drives the live animal trade in south africa? Animal Conservation.

• Leathwick, J. R., Elith, J., Rowe, D. & Julian, K. (2009) Robust planning for restoring diadromous fish species in new zealand's lowland rivers and streams. New Zealand Journal of Marine & Freshwater Research, 43, 659-671.

• Elith, J. & Leathwick, J. (2009). Conservation prioritisation using species distribution models. Chapter 6 in: Spatial conservation prioritization: quantitative methods and computational tools. ed. Moilanen, Wilson and Possingham. Oxford University Press.

• Phillips, S.J., Dudik, M., Elith, J., Graham, C., Lehmann, A., Leathwick, J., & Ferrier, S. (2009) Sample Selection Bias and Presence-Only Models Of Species Distributions: Implications for Selection of Background and Pseudo-absences Ecological Applications, 19, 181-197

• Read, C.F., Duncan, D.H., Vesk, P.A., & Elith, J. (2008) Biological soil crust distribution is related to patterns of fragmentation and landuse in a dryland agricultural landscape of southern Australia. Landscape Ecology23, 1093-1105

• Ward, G., Hastie, T., Barry, S.C., Elith, J., & Leathwick, J.R. (2009) Presence-only data and the EM algorithm. Biometrics 65, 554-563.

• Elith, J., Leathwick, J.R., & Hastie, T. (2008) A working guide to boosted regression trees. Journal of Animal Ecology, 77,  802-813.

• Leathwick, J.R., Elith, J., Chadderton, L., Rowe, D., & Hastie, T. (2008) Dispersal, disturbance, and the contrasting biogeographies of New Zealand's diadromous and non-diadromous fish species. Journal of Biogeography, 35, 1481-1497.

• Leathwick, J., Moilanen, A., Francis, M., Elith, J., Taylor, P., Julian, K., Hastie, T., & Duffy, C. (2008) Design and evaluation of large-scale marine protected areas. Conservation Letters, 1, 92-101.

• Graham, C.H., Elith, J., Hijmans, R., Guisan, A., Peterson, A.T., Loiselle, B.A., & NCEAS Modeling Group (2008) The influence of spatial errors in species occurrence data used in distribution models. Journal of Applied Ecology, 45, 239-247.

• Moilanen, A., Leathwick, J.R., & Elith, J. (2008) A method for spatial freshwater conservation prioritization. Freshwater Biology, 53, 577–592.

• Burgman, M., Elith, J., Gorrod, E., & Wintle, B. (2007). Tools for managing individual plant species in dynamic landscapes. In Managing and designing landscapes for conservation (eds D.B. Lindenmayer & R.J. Hobbs), pp. 330-342. Blackwell, Malden, Massachusetts.

• Elith, J. & Leathwick, J.R. (2007) Predicting species' distributions from museum and herbarium records using multiresponse models fitted with multivariate adaptive regression splines. Diversity and Distributions 13, 165-175

• Ferrier, S., G. Manion, J. Elith, and K. Richardson. (2007). Using generalised dissimilarity modelling to analyse and predict patterns of beta-diversity in regional biodiversity assessment. Diversity and Distributions 13, 252-264

• Guisan, A., C. H. Graham, J. Elith, F. Huettmann, and NCEAS Species Distribution Modelling Group. (2007). Sensitivity of predictive species distribution models to change in grain size: insights from a multi-models experiment across five continents. Diversity and Distributions 13, 332-340

• Leathwick, J.R., Elith, J., & Hastie, T. (2006) Comparative performance of generalized additive models and multivariate adaptive regression splines for statistical modelling of species distributions. Ecological Modelling 199, 188-196.

• Potts, J. & Elith, J. (2006) Comparing species' abundance models. Ecological Modelling 199, 153-163.

• Moilanen, A., Wintle, B., Elith, J., & Burgman, M. (2006) Uncertainty analysis for regional-scale reserve selection. Conservation Biology 20, 1688-1697.

• Moilanen, A., Runge, M.C., Elith, J., Tyre , D., Carmel , Y., Fegraus, E., Wintle, B., Burgman, M., & Ben-Haim, Y. (2006) Planning for robust reserve networks using uncertainty analysis. Ecological Modelling 199, 115-124.

• Leathwick, J.R., Elith, J., Francis, M.P., Hastie, T., & Taylor, P. (2006) Variation in demersal fish species richness in the oceans surrounding New Zealand : an analysis using boosted regression trees. Marine Ecology Progress Series 321, 267-281

• Elith, J., Graham, C.H., et al. (2006) Novel methods improve prediction of species' distributions from occurrence data. Ecography 29, 129-151

• Barry , S.C. & Elith, J. (2006) Error and uncertainty in habitat models. Journal of Applied Ecology 43, 413-423

• Burgman, M., Lindenmayer, D.B., & Elith, J. (2005) Managing landscapes for conservation under uncertainty. Ecology, 86, 2007-2017.

• Elith, J., Ferrier, S., Huettmann, F., & Leathwick, J.R. (2005) The evaluation strip: a new and robust method for plotting predicted responses from species distribution models. Ecological Modelling, 186, 280-289.

• Leathwick, J.R., Rowe, D., Richardson, J., Elith, J., & Hastie, T. (2005) Using multivariate adaptive regression splines to predict the distributions of New Zealand 's freshwater diadromous fish. Freshwater Biology, 50, 2034-2052.

• Wilson, K.A., Westphal, M.I., Possingham, H.P., & Elith, J. (2005) Sensitivity of conservation planning to uncertainty associated with predicted species distribution data. Biological Conservation,122, 99-112.

• Wintle, B.A., Elith, J., & Potts, J. (2005) Fauna habitat modelling and mapping in an urbanising environment; A case study in the Lower Hunter Central Coast region of NSW. Austral Ecology, 30, 719-738.

• Elith, J. & Burgman, M.A. (2003). Chapter 8: Habitat models for PVA. In Population Viability in Plants (eds C.A. Brigham & M.W. Schwartz). Springer-Verlag, New York.  Abstract

• Yamada, K., Elith, J., McMarthy, M.A., & Zerger, A. (2003) Eliciting and integrating expert knowledge for wildlife habitat modelling. Ecological Modelling,165, 251-264. Abstract

• Elith, J. & Burgman, M.A. (2002). Predictions and their validation: rare plants in the Central Highlands, Victoria, Australia. In Predicting Species  Occurrences:  Issues of Accuracy and Scale (eds J.M. Scott, P.J. Heglund, M.L. Morrison, M.G. Raphael, W.A. Wall & F.B. Samson), pp. 303-314. Island Press, Covelo, CA. Abstract

• Elith, J., Burgman, M.A., & Regan, H.M. (2002) Mapping epistemic uncertainties and vague concepts in predictions of species distribution. Ecological Modelling,157, 313-329. Abstract

• McCarthy, M.A. & Elith, J. (2002) Species mapping for conservation. Gap Analysis Bulletin, 11, 50-57

• Elith, J. (2000). Quantitative methods for modeling species habitat: comparative performance and an application to Australian plants. In Quantitative Methods in Conservation Biology (eds S. Ferson & M.A. Burgman), pp. 39-58. Springer, New York.

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Articles in progress

• Elith, J., Kearney, M. and Phillips, S. (in review) The art of modelling range-shifting species: how to skate on thin ice. 

• Chee, Y. & Elith, J. (in review) Predicting fish species distributions in freshwater ecosystems using a purpose-built GIS stream network and boosted regression trees. Ecography.

• Buston, P. and Elith, J. (in review). An analysis of the factors influencing lay and hatching for clownfish, with conservation implications. 

• Drake, J., Langford, W. and the NCEAS working group on Machine Learning Methods in Ecology (in prep). An introduction to Machine Learning methods for ecologists.

• Elith, J., Phillips, S. et al. (in prep) Modelling species distributions with MaxEnt: an ecological perspective. 

• Dormann, C. F., Bacher, S., Buchmann, C., Carl, G., Carré, G., Diekötter, T., Elith, J., García Marquéz, J., Gruber, B., Lafourcade, B., Leitão, P. J., Lautenbach, S., Münkemüller, T., McClean, C., Osborne, P., Reineking, B., Schröder, B., Skidmore, A. K. & Zurell, D. (in prep) Collinearity: A review of methods to deal with it and a simulation study evaluating their performance.

Contract and Technical Reports and Theses

• Elith, J. (2008). Species Distribution Modelling for Threatened Species Map Updates - Parts 1 and 2. Consultancy report for the Department of Environment, Water, Heritage and the Arts.

• Elith, J., Leonte, D., & Members of the working group (2008). New spatial analysis methods for improved hazard/risk identification: Report of ACERA working group 0603. The University of Melbourne; Australian Centre of Excellence for Risk Analysis. 

• Cribb, C., Barry, S., Elith, J. et al. (2008) Technical Advisory Group report to the cost-sharing and decision-making group for an Australian Biosecurity System for Primary Production and the Environment. 

• Leathwick, J., Julian, K., Elith, J., Chadderton, L., Ferrier, S., & Snelder, T.H. (2008). A biologically optimised environmental classification of New Zealand's rivers and streams: reanalysis using human impact variables. NIWA Client Report HAM 2008-027. National Institute of Water and Atmospheric Research Ltd.

• Leathwick, J., Julian, K., Elith, J., & Rowe, D. (2008). Predicting the distribution of freshwater fish species for all New Zealand's rivers and streams. NIWA Client Report HAM2008-005. National Institute of Water and Atmospheric Research Ltd.

• Leathwick, J., Julian, K., Chadderton, L., Ferrier, S., & Elith, J. (2007). Selection of fresh waters of national importance. NIWA Client Report HAM2006-044. National Institute of Water and Atmospheric Research Ltd.

• Cant, B., Elith, J., Leathwick, J., Chee, Y., Taranto, J., Case, M., & Pritchard, J. (2007). Spatial Management Model of Murray-Darling Fish Populations; Report to the Murray-Darling Basin Commission, Native Fish Management Strategy.  Project MD740. Arthur Rylah Institute.

• Morrongiello, J., Elith, J., & Crook, D. (2007). Understanding The Impacts Of Drought On Native Fish Populations In Victorian Rivers. Department of Sustainability and Environment, Melbourne, Australia.
  

• Elith, J. (2006). Vegetation modelling for the Hunter Central Coast;  Hunter and Central Coast Regional Environmental Management Strategy, Newcastle, NSW.

• Elith, J. (2006). Evaluation of the Contribution of API Mapping  and Satellite Image Classification  to Vegetation Mapping in the Hunter Central Rivers Catchment Management Authority. Consultancy report to Environment Division, Hunter Councils.

• Elith, J. & Bidwell, S. (2004). Identification and assessment of nationally threatened woodlands - Description of ecological communities: Arid eucalypt woodlands. Consultancy RFT 22/2002 for Environment Australia.

• Wintle, B.A., Elith, J., Yamada, K., & Burgman, M. (2004). LHCCREMS Fauna Survey and Mapping Project. Lower Hunter Central Coast Regional Environmental Management Strategy.

• Elith J. 2002. Predicting the distribution of plants. PhD thesis. School of Botany, The University of Melbourne.

• Elith J., Burgman M.A. and Minchin P. 1998. Improved protection strategies for rare plants. Report to Environment Australia, Project FN-NP22. 150 pp.

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Presentations and Collaborations

I have presented work at some local and international conferences and workshops including these:

• Ecological Society of Australia - Annual conferences
  
• Advances in GLM/GAM Modeling: workshops in Riederalp, Switzerland (2001, 2004, 2008). A photo of the venue is on my photo page.
• Conference on Computational Sustainability at Cornell Uni, Ithaca, NY
  
• Workshop on species modelling in Germany 2006, organised by Thomas Gottschalk
• Workshop on species modelling in Spain, 2005, organised by Javier Bustamante
• Workshop on habitat modelling in Finland, 2004, organised by Atte Moilanen
• Predicting species' occurrences: Issues of scale and accuracy - conference in Utah, USA

• an NCEAS working group focusing on modelling presence-only datafrom herbaria and museums led by Town Peterson and Craig Moritz, prompted much shared work, and particularly with Catherine Graham, Simon Ferrier and Steven Phillips. Steven and I have a few active projects
  
• the Swiss workshops (above) led to work with John Leathwick and Trevor Hastie, Simon Barry, and Antoine Guisan.  If you want to contact John Leathwick about any of the papers we've co-authored, his email address is: j.leathwick@niwa.co.nz
• the German workshop has created ongoing links with Boris Schroeder and Carsten Dormann
• our lab works with Atte Moilanen (Helsinki, Finland) and sometimes I have the pleasure of joining with him on spatial prioritization projects; also with David Keith from DECC NSW
• I've been involved in an NCEAS working group looking at the use of machine learning methods in ecology - led by John Drake and Bill Langford. And about to start a new one, on predictor variables for modelling, led by Brian McGill.
• I'm starting work on climate change/invasive species problems, which brings connections to Mike Kearney, Brendan Wintle, David Keith, Colin Yates, Barry Brook and Stephen Williams.
  
• and last but not least I share an office with Terry Walshe who is the deputy director of ACERA and a great roommate.