NASA Carbon Cycle & Ecosystems

Funded Research

Expanding Wallace Biodiversity Modeling Software to Support National Biodiversity Change Indicator Calculations for GEO BON Assessment and Reporting

Blair, Mary: American Museum of Natural History (Project Lead)

Project Funding: 2018 - 2021

NRA: 2016 NASA: Group on Earth Observations Work Programme

Funded by NASA

Abstract:
Effective policy responses to changes in biodiversity are only possible with adaptable analytic tools that leverage the influx of data from biodiversity observation systems. Such analytic tools must also be streamlined and readily mastered by researchers making scientific recommendations. In this project, we will create software to assess biodiversity change indicators by building on the recently developed software Wallace as a new GEO BON in a Box tool. Wallace is an R-based application with a graphical user interface that supports species distribution modeling (SDM) in a reproducible, flexible and extensible platform to facilitate a wide range of ecological analyses. These models characterize environmental suitability for species and can be used to estimate species’ geographic distributions —a GEO BON Essential Biodiversity Variable (EBV). Wallace harnesses biodiversity data from online databases or user input, assembles a variety of tools for building and evaluating models, and offers guidance for important conceptual and methodological issues. Critically, its modular nature facilitates the addition of new, cutting-edge innovations by other programmers, as we propose here. To expand Wallace as a new BON in a Box, we will develop two new R packages to be integrated as new modules for Wallace’s workflow to facilitate biodiversity change indicator calculations for GEO BON assessment and reporting, in collaboration with the Colombia BON as a model. The first package will use single species range maps in conjunction with remotely sensed (RS) products to estimate the species’ current range. It will harness RS products derived from NASA (and other) satellites, including percent forest cover, vegetation classes, and NDVI, which can be spatio-temporally matched with recent in situ observations of species’ occurrence to determine habitat tolerances (e.g., to land use change). The second package will allow calculation of key indicators including single-species biodiversity change indicators such as range size, extent of occurrence, percent suitable land cover, or projected trends under future scenarios at multiple spatial extents. Calculations will also include multi-species indicators, such as the EBV taxonomic diversity, and others not currently implemented through other BON in a Box tools, with a focus on ones most useful at regional scales. Module outputs from Wallace will be designed to feed directly into other BON in a Box tools, such as our international collaborator Instituto Humboldt’s BioModelos. BioModelos is a web application enabling expert validation of species range estimates in support of the Colombia BON. We will also develop training materials for Wallace targeting conservation practitioners that reflect best practices for using SDM for biodiversity change indicator calculations, resource management and biodiversity conservation decision-making. Our project results will address challenges to overcoming the gap between best modeling practices and biodiversity conservation decision-making and will facilitate responsible reporting on biodiversity by national BONs. Via focus on the development and enhancement of open-source, user-friendly software to contribute to BON in a Box, our proposal will advance broad application, exploration, visualization, and understanding of EBVs and generation of EBV data. Furthermore, developing a connection between Wallace and BioModelos, another BON in a Box tool, will be valuable for future interfacing with efforts at IUCN, BIEN (the Botanical Information and Ecology Network), and other similar projects that use SDM predictions as inputs. Finally, although we will focus development of our BON in a Box with the needs of the Colombia BON and with NASA Earth Science data, we will incorporate flexibility to address the needs of diverse users at multiple scales from national to global, and to work with remotely sensed data from any space agency in GEO.

Publications:

Anderson, R. P. 2022. Integrating habitat-masked range maps with quantifications of prevalence to estimate area of occupancy in IUCN assessments. Conservation Biology. 37(1). DOI: 10.1111/cobi.14019

Anderson, R. P., Araujo, M. B., Guisan, A., Lobo, J. M., Martinez-Meyer, E., Peterson, A. T., Soberon, J. M. 2020. Optimizing biodiversity informatics to improve information flow, data quality, and utility for science and society. Frontiers of Biogeography. 12(3). DOI: 10.21425/F5FBG47839

Burger, J. R., Anderson, R. P., Balk, M. A., Fristoe, T. S. 2019. A Constraint-based model of Dynamic Island Biogeography: environmental history and species traits predict hysteresis in populations and communities. Frontiers of Biogeography. 11(3). DOI: 10.21425/F5FBG44383

City University of New York Doctoral Programs in Psychology. SpringerReference. DOI: 10.1007/springerreference_224630

Galante, P. J., Chang Triguero, S., Paz, A., Aiello-Lammens, M., Gerstner, B. E., Johnson, B. A., Kass, J. M., Merow, C., Noguera-Urbano, E. A., Pinilla-Buitrago, G. E., Blair, M. E. 2022. changeRangeR: An R package for reproducible biodiversity change metrics from species distribution estimates. Conservation Science and Practice. 5(1). DOI: 10.1111/csp2.12863

Gavrutenko, M., Gerstner, B. E., Kass, J. M., Goodman, S. M., Anderson, R. P. 2021. Temporal matching of occurrence localities and forest cover data helps improve range estimates and predict climate change vulnerabilities. Global Ecology and Conservation. 27, e01569. DOI: 10.1016/j.gecco.2021.e01569

Gutirrez-Molina, M., Caminero Rodrguez, A., Martnez Garca, C., Arpa Gutirrez, J., Morales Bastos, C., Amer, G. 1994. Small arterial granular degeneration in familial Binswanger's syndrome. Acta Neuropathologica. 87(1), 98-105. DOI: 10.1007/bf00386260

Kass, J. M., Meenan, S. I., Tinoco, N., Burneo, S. F., Anderson, R. P. 2020. Improving area of occupancy estimates for parapatric species using distribution models and support vector machines. Ecological Applications. 31(1). DOI: 10.1002/eap.2228

Kass, J. M., Meenan, S. I., Tinoco, N., Burneo, S. F., Anderson, R. P. 2021. Improving Area of Occupancy Estimates for Parapatric Species Using Distribution Models and Support Vector Machines. The Bulletin of the Ecological Society of America. 102(1). DOI: 10.1002/bes2.1813

Kass, J. M., Muscarella, R., Galante, P. J., Bohl, C. L., Pinilla-Buitrago, G. E., Boria, R. A., Soley-Guardia, M., Anderson, R. P. 2021. ENMeval 2.0: Redesigned for customizable and reproducible modeling of species' niches and distributions. Methods in Ecology and Evolution. 12(9), 1602-1608. DOI: 10.1111/2041-210X.13628

Kass, J. M., Pinilla-Buitrago, G. E., Paz, A., Johnson, B. A., Grisales-Betancur, V., Meenan, S. I., Attali, D., Broennimann, O., Galante, P. J., Maitner, B. S., Owens, H. L., Varela, S., Aiello-Lammens, M. E., Merow, C., Blair, M. E., Anderson, R. P. 2023. wallace 2: a shiny app for modeling species niches and distributions redesigned to facilitate expansion via module contributions. Ecography. 2023(3). DOI: 10.1111/ecog.06547

Kass, J., Pinilla-Buitrago, G., Paz, A., Johnson, B., Grisales-Betancur, V., Meenan, S., Attali, D., Broennimann, O., Galante, P., Maitner, B., Owens, H., Varela, S., Aiello-Lammens, M., Merow, C., Blair, M., Anderson, R. 2022. Author response for "<i>wallace</i> 2: a shiny app for modeling species niches and distributions redesigned to facilitate expansion via module contributions" DOI: 10.1111/ecog.06547/v2/response1

Merow, C., Boyle, B., Enquist, B. J., Feng, X., Kass, J. M., Maitner, B. S., McGill, B., Owens, H., Park, D. S., Paz, A., Pinilla-Buitrago, G. E., Urban, M. C., Varela, S., Wilson, A. M. 2023. Better incentives are needed to reward academic software development. Nature Ecology & Evolution. 7(5), 626-627. DOI: 10.1038/s41559-023-02008-w

Merow, C., Galante, P. J., Kass, J. M., Aiello-Lammens, M. E., Babich Morrow, C., Gerstner, B. E., Grisales Betancur, V., Moore, A. C., Noguera-Urbano, E. A., Pinilla-Buitrago, G. E., Velasquez-Tibata, J., Anderson, R. P., Blair, M. E. 2022. Operationalizing expert knowledge in species' range estimates using diverse data types. Frontiers of Biogeography. 14(2). DOI: 10.21425/F5FBG53589

Peterson, A. T., Aiello-Lammens, M., Amatulli, G., Anderson, R., Cobos, M., Diniz-Filho, J. A., Escobar, L., Feng, X., Franklin, J., Gadelha, L., Georges, D., Gueguen, M., Gueta, T., Ingenloff, K., Jarvie, S., Jimenez, L., Karger, D., Kass, J., Kearney, M., Loyola, R., Machado-Stredel, F., Martinez-Meyer, E., Merow, C., Mondelli, M. L., Mortara, S., Muscarella, R., Myers, C., Naimi, B., Noesgaard, D., Ondo, I., Osorio-Olvera, L., Owens, H., Pearson, R., Pinilla-Buitrago, G., Sanchez-Tapia, A., Saupe, E., Thuiller, W., Varela, S., Warren, D., Wieczorek, J., Yates, K., Zhu, G., Zuquim, G., Zurell, D. 2022. ENM2020: A Free Online Course and Set of Resources on Modeling Species' Niches and Distributions. Biodiversity Informatics. 17. DOI: 10.17161/bi.v17i.15016

More details may be found in the following project profile(s):

NASA Biological Diversity & Ecological Conservation (BDEC) Project Profile

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