References

Print version
Text Size: Change text to small (default) Change text to medium Change text to large
This is a repository for useful or seminal papers in spatial/temporal ecological modeling that are likely of use to marine mammalogists.  If you have a favorite paper that isn't listed here, please send it to Mark Baumgartner (mbaumgartner@whoi.edu), let us know which category it belongs in, and we'll post it here.


Review and general papers


Austin, M.P. 2002. Spatial prediction of species distribution: an interface between ecological theory and statistical modelling. Ecological Modelling 157:101-118.

Austin, M. 2007. Species distribution models and ecological theory: A critical assessment and some possible new approaches. Ecological Modelling 200:1–19.

Guisan A. and N.E. Zimmermann. 2000. Predictive habitat distribution models in ecology. Ecological Modelling 135:147–186.

Guisan, A. and W. Thuiller. 2005. Predicting species distribution: offering more than simple habitat models. Ecology Letters 8:993–1009.

Guisan, A., A. Lehmann, S. Ferrier, M. Austin, J. MC. C. Overton, R. Aspinall, and T. Hastie. 2006. Making better biogeographical predictions of species’ distributions. Journal of Applied Ecology 43:386–392.

Redfern, J.V., M.C. Ferguson, E.A. Becker, K.D. Hyrenbach, C. Good, J. Barlow, K. Kaschner, M.F. Baumgartner, K.A. Forney, L.T. Ballance, P. Fauchald, P. Halpin, T. Hamazaki, A.J. Pershing, S.S. Qian, A. Read, S.B. Reilly, L. Torres, and F. Werner.  2006.  Techniques for cetacean-habitat modeling: A review. Marine Ecology Progress Series 310:271-295.


Generalized linear and additive models

Guisan, A., T.C. Edwards, Jr., and T. Hastie. 2002. Generalized linear and generalized additive models in studies of species distributions: setting the scene. Ecological Modelling 157:89-100.

Pearce, J., and S. Ferrier. 2000. Evaluating the predictive performance of habitat models developed using logistic regression. Ecological Modelling 133:225–245.

Ecological Modelling, Volume 157, Issues 2-3, Pages 89-348 (30 November 2002)

Fisheries Research, Volume 70, Issues 2-3, Pages 137-428 (December 2004)

Ecological Modelling, Volume 199, Issue 2, Pages 129-216 (16 November 2006)


Presence-only techniques

Applications

Gregr, E.J. and A.W. Trites. 2001. Predictions of critical habitat for five whale species in the waters of coastal British Columbia. Canadian Journal of Fisheries and Aquatic Sciences 58:1265–1285.

Tittensor, D.P., A.R. Baco, P.E. Brewin, M.R. Clark, M. Consalvey, J. Hall-Spencer, A.A. Rowden, T. Schlacher, K.I. Stocks, and A.D. Rogers.  2009.  Predicting global habitat suitability for stony corals on seamounts. Journal of Biogeography 36:1111–1128.


Methods

Carpenter, G., A.N. Gillison, and J. Winter. 1993. DOMAIN: a flexible modelling procedure for mapping potential distributions of plants and animals. Biodiversity and Conservation 2:667-680.

Hengla, T., H. Sierdsema, A. Radović, and A. Dilod. Spatial prediction of species’ distributions from occurrence-only records: combining point pattern analysis, ENFA and regression-kriging.  Ecological Modelling. in press.  (see website)

Hirzel, A.H., J. Hausser, D. Chessel, and N. Perrin. 2002. Ecological-niche factor analysis: how to compute habitat-siutability maps without absence data? Ecology 83:2027–2036.

Kaschner, K., R. Watson, A.W. Trites, and D. Pauly. 2006. Mapping world-wide distributions of marine mammal species using a relative environmental suitability (RES) model. Marine Ecology Progress Series 316:285–310.

Phillips, S.J. , R.P. Anderson, and R.E. Schapire. 2006. Maximum entropy modeling of species geographic distributions. Ecological Modelling 190:231–259.

Phillips, S.J. and M. Dudik. 2008. Modeling of species distributions with Maxent: new extensions and a comprehensive evaluation. Ecography 31:161-175.


Dangers

Lozier, J.D., P. Aniello, and M.J. Hickerson. 2009. Predicting the distribution of Sasquatch in western North America: anything goes with ecological niche modelling. Journal of Biogeography 36:1623–1627.

Phillips, S.J., M. Dudik, J. Elith, C.H. Graham, A. Lehmann, J. Leathwick, and S. Ferrier. 2009. Sample selection bias and presence-only distribution models: implications for background and pseudo-absence data. Ecological Applications 19:181–197.


Performance evaluation


Elith, J., C.H. Graham, R.P. Anderson, M. Dudik, S. Ferrier, A. Guisan, R.J. Hijmans, F. Huettmann, J.R. Leathwick, A. Lehmann, J. Li, L.G. Lohmann, B.A. Loiselle, G. Manion, C. Moritz, M. Nakamura, Y. Nakazawa, J. McC. Overton, A.T. Peterson, S.J. Phillips, K.S. Richardson, R. Scachetti-Pereira, R.E. Schapire, J. Soberon, S. Williams, M.S. Wisz, and N.E. Zimmermann. 2006. Novel methods improve prediction of species’ distributions from occurrence data. Ecography 29:129-151.

Farber, O. and R. Kadmon. 2003. Assessment of alternative approaches for bioclimatic modeling with special emphasis on the Mahalanobis distance. Ecological Modelling 160:115-130.

Gregr, E.J. and A.W. Trites. 2008. A novel presence-only validation technique for improved Steller sea lion Eumetopias jubatus critical habitat descriptions. Marine Ecology Progress Series 365:247–261.

Hirzel, A.H. , G. Le Lay, V. Helfer, C. Randin, and A. Guisan. 2006. Evaluating the ability of habitat suitability models to predict species presences. Ecological Modelling 199:142-152.


Movement analyses

Aarts, G., M. MacKenzie, B. McConnell, M. Fedak and J. Matthiopoulos. 2008. Estimating space-use and habitat preference from wildlife telemetry data. Ecography 31: 140-160.

Austin, D., W.D. Bowen, and J.I. McMillan. 2004. Intraspecific variation in movement patterns: modeling individual behaviour in a large marine predator. Oikos 105:15-30.

Bailey, H., B.R. Mate, D.M. Palacios, L. Irvine, S.J. Bograd, and D.P. Costa. 2009. Behavioural estimation of blue whale movements in the Northeast Pacific from state-space model analysis of satellite tracks. Endangered Species Research.

Bailey, H., G. Shillinger, D. Palacios, S. Bograd, J. Spotila, F. Paladino, and B. Block. 2008. Identifying and comparing phases of movement by leatherback turtles using state-space models. Journal of Experimental Marine Biology and Ecology 356:128-135.

Baumgartner, M.F. and B.R. Mate.  2005.  Summer and fall habitat of North Atlantic right whales (Eubalaena glacialis) inferred from satellite telemetry. Canadian Journal of Fisheries and Aquatic Sciences 62:527-543.

Breed, G.A., I.D. Jonsen, R.A. Myers, W.D. Bowen, and M.L. Leonard. 2009. Sex-specific, seasonal foraging tactics of adult grey seals (Halichoerus grypus) revealed by state-space analysis. Ecology 90:3209-3221.

Eckert, S.A., J.E. Moore, D.C. Dunn, R.S. van Buiten, K.L. Eckert, and P.N. Halpin. 2008. Modeling loggerhead turtle movement in the Mediterranean: importance of body size and oceanography. Ecological Applications 18:290-308.

Freitas, C., K.M. Kovacs, C. Lydersen, and R.A. Ims. 2008. A novel method for quantifying habitat selection and predicting habitat use. Journal of Applied Ecology 45:1213-1220.

Gurarie, E., R. Andrews, and K.L. Laidre. 2009. A novel method for identifying behavioral changes in animal movement data. Ecology Letters 12:395-408.

Johnson, D.S., J.M. London, M.A. Lea, and J.W. Durban. 2008. Continuous-time correlated random walk model for animal telemetry data. Ecology 89:1208-1215.

Jonsen, I.D., J.M. Fleming, and R.A. Myers. 2005. Robust state-space modeling of animal movement data. Ecology 86:2874-2880.

Jonsen, I.D., R.A. Myers, and M.C. James. 2007. Identifying leatherback turtle foraging behaviour from satellite-telemetry using a switching state-space model. Marine Ecology Progress Series 337:255-264.

Laidre K.L., M.P. Heide-Jørgensen, M.L. Lodgson, R.C. Hobbs, R. Dietz, and G.R. VanBlaricom. 2004. Fractal analysis of narwhal space use patterns. Zoology 107:3-11.

Laidre K.L., M.P. Heide-Jørgensen, M.L. Logdson, R.C. Hobbs, P. Heagerty, R. Dietz, O.A. Jørgensen, and M.A. Treble. 2004. Seasonal narwhal habitat associations in the high Arctic. Marine Biology 145:821-831.

Patterson, T.A., L. Thomas, C. Wilcox, O. Ovaskainen, and J. Matthiopoulos. 2008. State-space models of individual animal movement. Trends in Ecology and Evolution 23:87-94.

Schick, R.S., S.R. Loarie, F. Colchero, B.D. Best, A. Boustany, D.A. Conde, P.N. Halpin, L.N. Joppa, C.M. McClellan, and J.S. Clark. 2008. Understanding movement data and movement processes: current and emerging directions. Ecology Letters 11:1338–1350.

Tremblay, Y., S.A. Shaffer, S.L. Fowler, C.E. Kuhn, B.I. McDonald, M.J. Weise, C.A. Bost, H. Weimerskirch, D.E. Crocker, M.E. Goebel, and D.P. Costa. 2006. Interpolation of animal tracking data in a fluid environment. Journal of Experimental Biology 209:128-140.

Tremblay, Y., A.J. Roberts, and D.P. Costa. 2007. Fractal landscape method: an alternative approach to measuring area-restricted searching behavior. Journal of Experimental Biology 210:935-945.

Tremblay, Y., P.W. Robinson, and D.P. Costa. 2009. A parsimonious approach to modeling animal movement data.  PLoS ONE 4:e4711. doi:4710.1371/journal.pone.0004711.

Weng, K.C., D.G. Foley, J.E. Ganong, C. Perle, G.L. Shillinger, and B.A. Block. 2008. Migration of an upper trophic level predator, the salmon shark Lamna ditropis, between distant ecoregions. Marine Ecology Progress Series 372:253-264.

Whitehead, H., A. Coakes, N. Jaquet, and S. Lusseau. 2008. Movements of sperm whales in the tropical Pacific. Marine Ecology Progress Series 361:291-300.


Autocorrelation and pseudoreplication

Carl, G. and I. Kühn. 2007. Analyzing spatial autocorrelation in species distributions using Gaussian and logit models. Ecological Modelling 207:159–170.

Dormann, C.F. 2007. Effects of incorporating spatial autocorrelation into the analysis of species distribution data. Global Ecology and Biogeography 16:129–138.

Dormann, C. F., J.M. McPherson, M.B. Araújo, R. Bivand, J. Bolliger, G. Carl, R.G. Davies, A. Hirzel, W. Jetz, W.D. Kissling, I. Kühn, R. Ohlemüller, P.R. Peres-Neto, B. Reineking, B. Schröder, F.M. Schurr, and R. Wilson. 2007. Methods to account for spatial autocorrelation in the analysis of species distributional data: a review. Ecography 30:609-628.

Betts, M.G., L.M. Ganio, M.M.P. Huso, N.A. Som, F. Huettmann, J. Bowman, and B.A. Wintle. 2009. Comment on ‘‘Methods to account for spatial autocorrelation in the analysis of species distributional data: a review’’ Ecography 32:374-378.

Dormann, C.F. 2009. Response to comment on “Methods to account for spatial autocorrelation in the analysis of species distributional data: a review” Ecography 32: 379-381.

Millar, R.B. and M.J. Anderson. 2004. Remedies for pseudoreplication. Fisheries Research 70:397–407.

Segurado, P., M.B. Araújo, and W.E. Kunin. 2006. Consequences of spatial autocorrelation for niche-based models. Journal of Applied Ecology 43:433–444.


Model evaluation

Boyce, M.S., P.R. Vernier, S.E. Nielsen, and F.K.A. Schmiegelow. 2002. Evaluating resource selection functions. Ecological Modelling 157:281-300.

Lobo, J.M., A. Jiménez-Valverde, and R. Real. 2008. AUC: a misleading measure of the performance of predictive distribution models. Global Ecology and Biogeography 17:145–151.

Peterson, A.T., M. Papes, and J. Soberón. 2008. Rethinking receiver operating characteristic analysis applications in ecological niche modeling. Ecological Modelling 213:63–72.

Rykiel, E.J., Jr. 1996. Testing ecological models: the meaning of validation. Ecological Modelling 90:229-244.


Model comparisons

MacLeod, C.D., L. Mandleberg, C. Schweder, S.M. Bannon, and G.J. Pierce. 2008. A comparison of approaches for modelling the occurrence of marine animals. Hydrobiologia 612:21–32.

Praca, E., A. Gannier, K. Das, and S. Laran. 2009. Modelling the habitat suitability of cetaceans: Example of the sperm whale in the northwestern Mediterranean Sea. Deep-Sea Research I 56:648–657.


Some exciting and useful controversy in marine mammal habitat modeling!

Hamazaki, T. 2002. Spatiotemporal prediction models of cetacean habitats in the mid-western North Atlantic Ocean (from Cape Hatteras, North Carolina, U.S.A. to Nova Scotia, Canada). Marine Mammal Science 18:920-939.

Gregr, E.J. 2004. Modeling species-habitat relationships in the marine environment: a comment on Hamazaki (2002). Marine Mammal Science 20:353-355.

Hamazaki, T. 2004. Modeling species-habitat relationship in the marine environment: a response to Gregr (2004). Marine Mammal Science 20:356-358.


Scale and resolution

Guisan, A., C.H. Graham, J. Elith, F. Huettmann and the NCEAS Species Distribution Modelling Group. 2007. Sensitivity of predictive species distribution models to change in grain size. Diversity and Distributions 13:332–340.


Other

Dormann, C.F. 2007. Promising the future? Global change projections of species distributions. Basic and Applied Ecology 8:387-397.



 

WHOI logo

Last updated January 25, 2010
© Woods Hole Oceanographic Institution. All rights reserved