Lab Reading List

[This page is still a work in progress]

The lab reading list provides a starting point for new Weecologists to become familiar with the types of questions, projects, and perspectives of the lab. Every topic contains an overview paper (i.e. if there’s only one paper you read on a topic, read that one) and several “deep-dive” papers. Every new member to the lab should read all the overview papers for all the topics and the deep-dive papers for the projects relevant to them (especially if they are funded off a grant working in that area).

If you are off campus, you may need to use the VPN into the UF network to access papers (if you need to install the VPN).

Computer Vision

• Overview paper: Weinstein, B.G. 2017 A computer vision for animal ecology. Journal of Animal Ecology 87:533-545
• Everglades computer vision workflow: White, E.P., L. Garner, B.G. Weinstein, H. Senyondo, A. Ortega, A. Steinkraus, G.M. Yenni, P. Frederick, S.K.M. Ernest. 2024. Near real-time monitoring of wading birds using uncrewed aircraft systems and computer vision. Remote Sensing in Ecology and Conservation
• Mapping trees at scale: Weinstein, B.G., S. Marconi, A. Zare, S.A. Bohlman, A.Singh, S.J. Graves, L. Magee, D.J. Johnson, S. Record, V.E. Rubio, N.G. Swenson, P. Townsend, T.T. Veblen, R.A. Andrus, E.P. White. 2024. Individual tree crown maps for the National Ecological Observatory Network. PLOS Biology 22:e3002700
• Bird detection: Weinstein, B.G., L. Garner, V.R. Saccomanno, A. Steinkraus, A. Ortega, K. Brush, G.M. Yenni, A.E. McKellar, R. Converse, C.D. Lippitt, A. Wegmann, N.D. Holmes, A.J. Edney, T. Hart, M.J. Jessopp, R.H. Clarke, D. Marchowski, H. Senyondo, R. Dotson, E.P. White, P. Frederick, S.K.M. Ernest. 2022. A general deep learning model for bird detection in high‐resolution airborne imagery. Ecological Applications: e2694
• DeepForest: Weinstein, B.G., S. Marconi, M. Aubry-Kientz, G. Vincent, H. Senyondo, E.P. White. 2020. DeepForest: A Python package for RGB deep learning tree crown delineation. Methods in Ecology and Evolution 11:1743–1751

Ecological Forecasting

• Overview paper: Dietze, M. C., A. Fox, L. M. Beck-Johnson, J. L. Betancourt, M. B. Hooten, C. S. Jarnevich, T. H. Keitt, M. A. Kenney, C. M. Laney, L. G. Larsen, H. W. Loescher, C. K. Lunch, B. C. Pijanowski, J. T. Randerson, E. K. Read, A. T. Tredennick, R. Vargas, K. C. Weathers, and E. P. White. 2018. Iterative near-term ecological forecasting: Needs, opportunities, and challenges. Proceedings of the National Academy of Sciences:201710231
• Automated forecasting workflow for Portal: White, E.P., G.M. Yenni, S.D. Taylor, E.M. Christensen, E.K. Bledsoe, J.L. Simonis, S.K.M. Ernest. 2019. Developing an automated iterative near-term forecasting system for an ecological study. Methods in Ecology and Evolution 10:332–344
• Forecasting in different biotic conditions: Dumandan, P.K.T., J.L. Simonis, G.M Yenni, S.K.M. Ernest, and E.P. White. 2024. Transferability of ecological forecasting models to novel biotic conditions in a long‐term experimental study. Ecology: 105:e4406
• DGAM forecasting models: Clark, N.J., S.K.M Ernest, H. Senyondo, J. Simonis, E.P. White, G.M. Yenni, K.A.N.K. Karunarathna. 2023. Beyond single-species models: leveraging multispecies forecasts to navigate the dynamics of ecological predictability. EcoEvoRxiv
• Everglades forecasting by USGS: D’Acunto, L.E., Pearlstine, L., Haider, S.M., Hackett, C.E., Shinde, D. and Romañach, S.S., 2023. The Everglades vulnerability analysis: Linking ecological models to support ecosystem restoration. Frontiers in Ecology and Evolution, 11, p.1111551.

Portal Project

• Overview paper: Brown, J. H. 1998. The desert granivory experiments at Portal. Pages 71–95 in W. J. Resetarits and J. Bernardo, editors. Experimental Ecology. Oxford University Press, New York (book available in Morgan’s office)
• Desert Natural History: Brown, J. H., O. J. Reichman, and D. W. Davidson. 1979. Granivory in Desert Ecosystems. Annual Review of Ecology and Systematics 10:201–227
• Rodent community change: Ernest, S. K. M., J. H. Brown, K. M. Thibault, E. P. White, and J. R. Goheen. 2008. Zero Sum, the Niche, and Metacommunities: Long-Term Dynamics of Community Assembly. American Naturalist 172:E257–E269
• Rodent impact on plants: Valone, T. J., and M. R. Schutzenhofer. 2007. Reduced rodent biodiversity destabilizes plant populations. Ecology 88:26–31
• Data Management Workflow: Yenni, G. M., E. M. Christensen, E. K. Bledsoe, S. R. Supp, R. M. Diaz, E. P. White, and S. K. M. Ernest. 2019. Developing a modern data workflow for regularly updated data. PLOS Biology 17:e3000125