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Center for Computational and Theoretical Biology

Ecosystem Modeling


Ecosystem Modeling Research

In the Ecosystem Modeling research group, we pursue the understanding of the processes underlying the origin, maintenance and spatiotemporal dynamics of biodiversity across scales, from local to global, and across levels of ecological organization, from individuals, over populations, species, communities, and metacommunities up to biomes. The working group applies a range of methods, including field work, data analyses and macroecology, but focuses on mechanistic simulation modeling.

The developed mechanistic models for virtual life can be used for theory testing, improving empirical sampling designs, understanding complex process interactions, and predicting biodiversity response to drivers and environmental change scenarios.


External collaborators

The EcoMods collaborate with:

Dr. Sonia Kéfi (CNRS, Montpellier, France)

Dr. Jan Engler (TU Dresden, Germany)

Dr. Viktoriia Radchuk  (Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany)

MSc. André Pinto da Silva (Uppsala University, Sweden)

Prof. Dr. Ana Paula de Moraes (Federal University of ABC, Brazil)

The BLIZ  consortium (one of the Bayklif  funded consortia)

The sELDIG  working group (started as sDiv-funded working group, still ongoing as a virtual group)

 


Publications

2022[ to top ]
  • Sarmento Cabral, J., Mendoza-Ponce, A., da Silva, A. P., Oberpriller, J., Mimet, A., Kieslinger, J., Berger, T., Blechschmidt, J., Brönner, M., Classen, A., Fallert, S., Hartig, F., Hof, C., Hoffmann, M., Knoke, T., Krause, A., Lewerentz, A., Pohle, P., Raeder, U., Rammig, A., Redlich, S., Rubanschi, S., Stetter, C., Weisser, W., Vedder, D., Verburg, P. H., & Zurell, D. The road to integrate climate change effects on land-use change in regional biodiversity models. Authorea, Preprint. https://doi.org/10.22541/au.164608831.19029067/v1
  • Kéfi, S., Saade, C., Berlow, E., Cabral, J. S. C., & Fronhofer, E. Scaling up our understanding of tipping points. Philosophical Transactions of the Royal Society B, 377, 20210386. https://doi.org/10.1098/rstb.2021.0386
  • Hietz, P., Wagner, K., Nunes Ramos, F., Cabral, J., Agudelo, C., Benavides, A. M., Cach-Pérez, M. J., Cardelús, C., Chilpa Galván, N., Costa, L., de Paula Oliveira, R., Einzmann, H., Farias, R., Guzmán Jacob, V., Kattge, J., Kessler, M., Kirby, C., Kreft, H., Kromer, T., Males, J., Monsalve Correa, S., Moreno-Chacón, M., Petter, G., Reyes-Garcia, C., Saldana, A., Schellenberger Costa, D., Taylor, A., Velázquez Rosas, N., Wanek, W., Woods, C., & Zotz, G. Putting vascular epiphytes on the traits map. Journal of Ecology, 110, 340-358. https://doi.org/https://doi.org/10.1111/1365-2745.13802
  • Lewerentz, A., Hoffmann, M., Hovestadt, T., Raeder, U., & Sarmento Cabral, J. Potential change in the future spatial distribution of submerged macrophyte species and species richness: the role of today’s lake type and strength of compounded environmental change. Preprint.
  • Vedder, D., Lens, L., Pellikka, P., Adhikari, H., Heiskanen, J., Engler, J., & Sarmento Cabral, J. Hybridisation may aid evolutionary rescue of an endangered east african passerine. Evolutionary Applications, 2022, early view. https://doi.org/10.1111/eva.13440
  • Figueiredo, L., Scherer, C., & Cabral, J. S. Computational notebooks to facilitate writing and improve reproducibility of (ecological) research. PLOS Computational Biology, accepted.
  • Moraes, A. P., Engel, T., Forni-Martins, E., Felix, L., & Cabral, J. Are chromosome number and genome size associated with habit and environmental niche variables? Insights from the Neotropical orchids. Annals of Botany, 130, 11-25. https://doi.org/https://doi.org/10.1093/aob/mcac021
2021[ to top ]
  • Leidinger, L., Vedder, D., & Cabral, J. S. Temporal environmental variation imposes differential selection on both genomic and ecological traits. Oikos, 130, 1100-1115. https://doi.org/https://doi.org/10.1111/oik.08172
  • Vedder, D., Leidinger, L., & Sarmento Cabral, J. Propagule pressure and an invasion syndrome determine invasion success in a plant community model. Ecology and Evolution, 11, 17106-17116.
  • Engler, J. O., Lawrie, Y., Cabral, J. S., & Lens, L. Niche evolution reveals disparate signatures of speciation in the ‘great speciator‘ (White-eyes, Aves: genus Zosterops). Journal of Biogeography, 48, 1981-1993.
  • Petter, G., Kreft, H., Ong, Y., Zotz, G., & Sarmento, J. Modeling the long-term dynamics of tropical forests: from leaf traits to whole-tree growth patterns. Ecological Modelling, 460, 109735.
  • Hagen, O., Flück, B., Fopp, F., Cabral, J. S., Hartig, F., Pontarp, M., Rangel, T. F., & Pellissier, L. gen3sis: The GENeral Engine for Eco-Evolutionary SImulationS on the origins of biodiversity. Plos Biology, 19, e3001340. https://doi.org/https://doi.org/10.1371/journal.pbio.3001340
  • Figueiredo, L., Leidinger, L., Steffan-Dewenter, I., & Sarmento Cabral, J. Evolutionary rescue and community re-assembly contribute to the waiving of extinction debts. submitted.
  • Lewerentz, A., Hoffmann, M., & Cabral, J. S. Depth diversity gradients of macrophytes: shape, drivers and recent shifts. Ecology and Evolution, 11, 13830-13845.
  • Vedder, D., Ankenbrand, M., & Cabral, J. Dealing with software complexity in individual-based models. Methods in Ecology and Evolution, 12, 2324-2333. https://doi.org/https://doi.org/10.1111/2041-210X.13716
  • Wohlwend, M., Craven, D., Weigelt, P., Seebens, H., Kreft, H., Winter, M., Zurell, D., Cabral, J. S., Essl, F., van Kleunen, M., Pergl, J., Pysek, P., & Knight, T. Anthropogenic and environmental drivers shape diversity of non-native plants across the Pacific. Diversity and Distributions, 27, 1120-1133. https://doi.org/http://doi.org/10.1111/ddi.13260
  • Petter, G., Zotz, G., Kreft, H., & Cabral, J. S. Agent-based modeling of the effects of forest dynamics, selective logging, and fragment size on epiphyte communities. Ecology and Evolution, 11, 2937–2951. https://doi.org/10.1002/ece3.7255
  • Paligi, S. S., Link, R. M., Isaza, E., Bittencourt, P., Cabral, J. S., Jansen, S., Oliveira, R. S., Pereira, L., & Schuldt, B. Accuracy of the pneumatic method for estimating xylem vulnerability to embolism in temperate diffuse-porous tree species. BioRxiv. https://doi.org/https://doi.org/10.1101/2021.02.15.431295
2020[ to top ]
  • Matthews, T., Leidinger, L., & Cabral, J. The effect of species extinctions on island biogeographic patterns. Ecological Research, 35, 372-381. https://doi.org/https://doi.org/10.1111/1440-1703.12093
  • Koffel, T., Kremer, C. T., Bannar-Martin, K., Ernest, S. K. M., Eisenhauer, N., Roscher, C., Cabral, J. S., & Leibold, M. A. Modeling how community assembly alters the functioning of ecosystems. BioRxiv.
  • Bowler, D. E., Bjorkman, A., Dornelas, M., Myers-Smith, I., O’Connor, M., Navarro, L., Niamir, A., Supp, S., Waldock, C., Vellend, M., Blowes, S., Böhning-Gaese, K., Bruelheide, H., Elahi, R., Antão, L., Hines, J., Isbell, F., Jones, H., Magurran, A., Cabral, J., Winter, M., & Bates, A. Mapping human pressures on biodiversity across the planet uncovers anthropogenic threat complexes. People and Nature, 2, 380-394.
  • Wüest, R. O., Zimmermann, N. E., Zurell, D., Alexander, J., Fritz, S. A., Hof, C., Kreft, H., Normand, S., Sarmento Cabral, J., Szekely, E., Thuiller, W., Wikelski, M., & Karger, D. N. Macroecology in the age of big data – where to go from here?. Journal of Biogeography, 47, 1-12. https://doi.org/https://doi.org/10.1111/jbi.13633
  • Shoemaker, L. G., Sullivan, L. L., Donohue, I., Cabral, J. S., Williams, R. J., Mayfield, M. M., Chase, J. M., Chu, C., Harpole, W. S., Huth, A., HilleRisLambers, J., James, A. R., Kraft, N. J., May, F., Muthukrishnan, R., Satterlee, S., Taubert, F., Wang, X., Wiegand, T., Yang, Q., & Abbott, K. C. Integrating the underlying structure of stochasticity into community ecology. Ecology, 101, e02922.
  • Karger, D. N., Wüest, R., König, C., Cabral, J., Weigelt, P., Zimmermann, N., & Linder, P. Disentangling the drivers of local species richness using probabilistic species pools. Journal of Biogeography, 47, 879-889. https://doi.org/https://doi.org/10.1111/jbi.13763
2019[ to top ]
  • Figueiredo, L., Krauß, J., Steffan-Dewenter, I., & Sarmento Cabral, J. Understanding extinction debts: spatio-temporal scales, mechanisms and a roadmap for future research. Ecography, 42, 1973-1990. https://doi.org/https://doi.org/10.1111/ecog.04740
  • Pontarp, M., Bunnefeld, L., Cabral, J. S., Etienne, R. S., Fritz, S. A., Gillespie, R., Graham, C. H., Hagen, O., Hartig, F., Huang, S., Jansson, R., Maliet, O., Münkemüller, T., Pellissier, L., Rangel, T. F., Storch, D., Wiegand, T., & Hurlbert, A. H. The latitudinal diversity gradient - novel understanding through mechanistic eco-evolutionary models. Trends in Ecology & Evolution, 34, 211-223. https://doi.org/https://doi.org/10.1016/j.tree.2018.11.009
  • Radchuk, V., De Laender, F., Sarmento Cabral, J., Boulangeat, I., Crawford, M., Bohn, F., De Raedt, J., Scherer, C., Svenning, J.-C., Thonicke, K., Schurr, F., Grimm, V., & Kramer-Schadt, S. The dimensionality of stability depends on disturbance type. Ecology Letters, 22, 674-684. https://doi.org/https://doi.org/10.1111/ele.13226
  • Chase, J., McGill, B., Thompson, P., Antao, L., Bates, A., Blowes, S., Dornelas, M., Gonzalez, A., Magurran, A., Supp, S., Winter, M., Bjorkman, A., Bruelheide, H., Byrnes, J., Cabral, J. S., Elahi, R., Gomez, C., Guzmán, H., Isbell, F., Myers-Smith, I., Jones, H., Hines, J., Vellend, M., Waldock, C., & O’Connor, M. Species richness change across spatial scales. Oikos. https://doi.org/10.1111/oik.05968
  • Cabral, J., Wiegand, K., & Kreft, H. Interactions between ecological, evolutionary, and environmental processes unveil complex dynamics of insular plant diversity. Journal of Biogeography, 46, 1582-1597. https://doi.org/10.1111/jbi.13606
  • Cabral, J., Whittaker, R., Wiegand, K., & Kreft, H. Assessing predicted isolation effects from the general dynamic model of island biogeography with an eco-evolutionary model for plants. Journal of Biogeography, 46, 1569-1581. https://doi.org/10.1111/jbi.13603
  • Etienne, R. S., Cabral, J. S., Hagen, O., Hartig, F., Hurlbert, A. H., Pellissier, L., Pontarp, M., & Storch, D. A minimal model for the latitudinal diversity gradient suggests a dominant role for ecological limits. The American Naturalist, 194, E122-E133. https://doi.org/doi.org/10.1086/705243
2018[ to top ]
  • Keil, P., Pereira, H., Cabral, J., Chase, J., May, F., Martins, I., & Winter, M. Spatial scaling of extinction rates: theory and data reveal non-linearity, and a major upscaling and downscaling challenge. Global Ecology and Biogeography, 27, 2-13. https://doi.org/10.1111/geb.12669
  • Bannar-Martin, K., Kremer, C., Ernest, M., Leibold, M., Auge, H., Chase, J., Declerck, S., Eisenhauer, N., Harpole, S., Hillebrand, H., Isbell, F., Koffel, T., Larsen, S., Narwani, A., Petermann, J., Roscher, C., Sarmento Cabral, J., & Supp, S. Integrating community assembly and biodiversity reveals new dimensions of ecosystem functions: the Community Assembly and the Functioning of Ecosystems (CAFE) approach. Ecology Letters, 21, 167–180.
2017[ to top ]
  • Borregaard, M. K., Amorim, I. R., Borges, P. A. V., Cabral, J. S., Fernández-Palacios, J. M., Field, R., Heaney, L. R., Kreft, H., Matthews, T. J., Olesen, J. M., Price, J., Rigal, F., Steinbauer, M. J., Triantis, K. A., Valente, L., Weigelt, P., & Whittaker, R. J. Oceanic island biogeography through the lens of the general dynamic model: assessment and prospect. Biological Reviews, 92, 830-853. https://doi.org/10.1111/brv.12256
  • Cabral, J. S., Valente, L., & Hartig, F. Mechanistic models in macroecology and biogeography: state-of-art and prospects. Ecography, 40(267-280), Article 267-280.
  • Moraes, A., de Mesquita Filho, J., Koehler, S., Cabral, J., Lopes Gomes, S., Viccini, L., Barros, F., Felix, L., Guerra, M., & Forni-Martins, E. Karyotype diversity and genome size variation in Neotropical Maxillariinae orchids. Plant Biology, 19, 298-308.
  • Cabral, J., Wiegand, K., & Kreft, H. Interactions between ecological, evolutionary, and environmental processes unveil complex dynamics of island biodiversity. BioRxiv, 099978, Article 099978. https://doi.org/https://doi.org/10.1101/099978
  • Kalinkat, G., Cabral, J., Darwall, W., Ficetola, F., Fisher, J., Giling, D., Gosselin, M.-P., Grossart, H.-P., Jähnig, S., Jeschke, J., Knopf, K., Larsen, S., Onandia, G., Pätzig, M., Saul, W.-C., Singer, G., & Jarić, I. Flagship umbrella species needed for conservation of overlooked biodiversity. Conservation Biology, 31, 481-485.
  • Cabral, J., Whittaker, R., Wiegand, K., & Kreft, H. Effects of time and isolation on plant diversity: testing island biogeography theory with an eco-evolutionary model. BioRxiv, 100289, Article 100289. https://doi.org/https://doi.org/10.1101/100289
  • Leidinger, L., & Cabral, J. S. Biodiversity dynamics on islands: explicitly accounting for causality in mechanistic models. Diversity, 9(3), Article 3. https://doi.org/10.3390/d9030030
2016[ to top ]
  • Weigelt, P., Steinbauer, M. J., Cabral, J. S., & Kreft, H. Late Quaternary climate change shapes island biodiversity. Nature, 532(7597), 99-102. http://dx.doi.org/10.1038/nature17443
  • Petter, G., Wagner, K., Wanek, W., Sánchez Delgado, E., Zotz, G., Cabral, J., & Kreft, H. Functional leaf traits of vascular epiphytes: vertical trends within the forest, intra- and interspecific trait variability, and taxonomic signals. Functional Ecology, 30, 188-198.
  • Karger, D., Cord, A., Kessler, M., Kreft, H., Kühn, I., Pompe, S., Sandel, B., Sarmento Cabral, J., Smith, A., Svenning, J.-C., Tuomisto, H., Weigelt, P., & Wesche, K. Delineating probabilistic species pools in ecology and biogeography. Global Ecology and Biogeography, 25, 489-501.
  • Zurell, D., Thuiller, W., Pagel, J., Cabral, J. S., Münkemüller, T., Gravel, D., Dullinger, S., Normand, S., Schiffers, K. H., Moore, K. A., & Zimmermann, N. E. Benchmarking novel approaches for modelling species range dynamics. Global Change Biology, 22(8), 2651-2664. https://doi.org/10.1111/gcb.13251
2015[ to top ]
  • de Oliveira, I., Moraes, A., de Almeida, E., de Assis, F., Cabral, J., de Barros, F., & Felix, L. Chromosomal evolution in Pleurothallidinae (Orchidaceae: Epidendroideae) with emphasis on the genus Acianthera: chromosome numbers and heterochromatin. Botanical Journal of the Linnean Society, 178, 102-120.
  • Cabral, J., Petter, G., Mendieta-Leiva, G., Wagner, K., Zotz, G., & Kreft, H. Branchfall as a demographic filter for epiphyte communities: Lessons from a forest floor-based sampling. PloS One, 10, e0128019.
2014[ to top ]
  • Cabral, J. S., Weigelt, P., Kissling, W. D., & Kreft, H. Biogeographic, climatic and spatial drivers differentially affect α-, β- and γ-diversities on oceanic archipelagos. Proceedings of the Royal Society of London B: Biological Sciences, 281(1784), Article 1784. http://rspb.royalsocietypublishing.org/content/281/1784/20133246.short
2013[ to top ]
  • Schymanski, S., Dormann, C., Cabral, J., Chuine, I., Graham, C., Hartig, F., Kearney, M., Morin, X., Römermann, C., Schröder, B., & Singer, A. Process, correlation and parameter fitting in species distribution models: a response to Kriticos et al. 2012. Journal of Biogeography, 40, 611-613.
  • Sarmento Cabral, J., Jeltsch, F., Thuiller, W., Higgins, S., Midgley, G. F., Rebelo, A. G., Rouget, M., & Schurr, F. M. Impacts of past habitat loss and future climate change on the range dynamics of South African Proteaceae. Diversity and Distributions, 19(4), 363-376. https://doi.org/10.1111/ddi.12011
2012[ to top ]
  • Cabral, J. S., & Kreft, H. Linking ecological niche, community ecology and biogeography: insights from a mechanistic niche model. Journal of Biogeography, 39(12), 2212-2224. https://doi.org/10.1111/jbi.12010
  • Schurr, F. M., Pagel, J., Cabral, J. S., Groeneveld, J., Bykova, O., O’Hara, R. B., Hartig, F., Kissling, W. D., Linder, H. P., Midgley, G. F., Schröder, B., Singer, A., & Zimmermann, N. E. How to understand species’ niches and range dynamics: a demographic research agenda for biogeography. Journal of Biogeography, 39(12), 2146-2162. https://doi.org/10.1111/j.1365-2699.2012.02737.x
  • Dormann, C. F., Schymanski, S. J., Cabral, J., Chuine, I., Graham, C., Hartig, F., Kearney, M., Morin, X., Römermann, C., Schröder, B., & Singer, A. Correlation and process in species distribution models: bridging a dichotomy. Journal of Biogeography, 39(12), 2119-2131. https://doi.org/10.1111/j.1365-2699.2011.02659.x
2011[ to top ]
  • Cabral, J. S., Bond, W. J., Midgley, G. F., Rebelo, A. G., Thuiller, W., & Schurr, F. M. Effects of Harvesting Flowers from Shrubs on the Persistence and Abundance of Wild Shrub Populations at Multiple Spatial Extents. Conservation Biology, 25(1), 73-84. https://doi.org/10.1111/j.1523-1739.2010.01628.x
2010[ to top ]
  • Zurell, D., Berger, U., Cabral, J. S., Jeltsch, F., Meynard, C. N., Münkemüller, T., Nehrbass, N., Pagel, J., Reineking, B., Schröder, B., & Grimm, V. The virtual ecologist approach: simulating data and observers. Oikos, 119(4), 622-635. https://doi.org/10.1111/j.1600-0706.2009.18284.x
  • Krug, C., Brandl, R., Boonzaier, C., Cabral, J., Esler, K., Grant, P., Heelemann, S., Horn, A., Keil, M., Kongor, R., Meyer, J., Nottebrock, H., Poschlod, P., Reisch, C., Rösner, S., Samways, M. J., Schurr, F., & Vrdoljak, S. Keeping the Cape Lowland archipelago afloat: Vol Biodiversity in southern Africa. Volume 3: Implications for landuse and management (bll 151-179). Klaus Hess Publishers, Göttingen & Windhoek.
  • Cabral, J. S., & Schurr, F. M. Estimating demographic models for the range dynamics of plant species. Global Ecology and Biogeography, 19(1), 85-97. https://doi.org/10.1111/j.1466-8238.2009.00492.x
2008[ to top ]
  • Koehler, S., Cabral, J., Whiten, W., Williams, N., Singer, R., Neubig, K., Guerra, M., Souza, A., & Amaral, M. Molecular phylogeny of the neotropical genus Christensonella (Orchidaceae, Maxillariinae): species delimitations and insights into chromosome evolution. Annals of Botany, 102(491-507), Article 491-507.
2006[ to top ]
  • Cabral, J. S., Felix, L. P., & Guerra, M. {Heterochromatin diversity and its co-localization with 5S and 45S rDNA sites in chromosomes of four Maxillaria species (Orchidaceae)}. {Genetics and Molecular Biology}, 29, 659-664. http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572006000400015&nrm=iso
  • Siqueira-Filho, J., Santos, A., Leme, E., & Cabral, J. Atlantic forest fragments in Pernambuco and Alagoas and theirs bromeliads: distribution, composition, richness and conservation: Vol Fragments of the Atlantic Forest of Northeast Brazil: Biodiversity, Conservation and the Bromeliads (bll 101-131). Andrea Jakobsson Estúdio, Rio de Janeiro.
2003[ to top ]
  • Cabral, J., de Vasconcelos, S., Rodrigues, M., Pontual, R., & Mascarenhas, L. Dieta de coruja murucututu (Pulsatrix perspicillata perspicillata Lathan, 1790) no Campus de UFRPE, Recife, PE. VI Congresso De Ecologia Do Brasil, Volume III, 273-274.