​

​2025-present

• de Gasper, A.L., Klipel, J., Bergamin, R.S., Vieira, S., Bordin, K., Silva, R.F.B., Müller, S.C., Alves, L.F., Carnaval, A.C., Nascimento, M.T., Marques, M.C., Lima, R.A.F., et al. 2026. Understanding the potential for climate adaptation of the Atlantic Forest hotspot requires a research collaboration network. Perspectives in Ecology and Conservation (in press).

• Daibes, L.F., Rogers, H.S., Gnonlonfoun, F.J., Zupo, T., Sühs, R.B., Vinha, D., Rother, D.C., Almeida Junior, P.A., de Avila, A.L., Barbosa, J.M., Begnini, R.M., (...), Lima, R.A.F., Silveira, L.F. and Pizo, M.A. 2026. Landscape features predict broad‐scale seed rain patterns across fragments of the Brazilian Atlantic Forest. Journal of Ecology 114(5): e70328.

• ​ter Steege, H., Ballarin, C.S., Pinto, C.E., Valadão-Mendes, L.B., Stevenson, P., Correa, D.F., Giannini, T.C., Gomes, V.H., McGlone, M. and Lima, R.A.F. 2026. Pollination and dispersal networks in the Amazonian tree flora. Communications Biology 9(1): 486.

• Kramer, J.M.F., Zwiener, V.P., Camana, M., Lima, R.A.F. and Müller, S.C., 2026. Effects of Deforestation and Fragmentation on Tree Beta Diversity and Endemism Across Landscapes in the Atlantic Forest Biodiversity Hotspot. Global Change Biology 32(4): e70855.

• Fischer, F.J., Chave, J., Zanne, A., Jucker, T., Fajardo, A., Fayolle, A., Lima, R.A.F., Vieilledent, G., Beeckman, et al. 2026. Beyond species means – the intraspecific contribution to global wood density variation. New Phytologist 249(6): 2630-2651.

 

2020-2025​

• Toledo, R.M., Pivello, V.R., Vangansbeke, P., Jakovac, C., Verheyen, K., Verdade, L.M. and Lima, R.A.F, 2025. Reassembly dynamics of tropical secondary succession: Evidence from Atlantic forests. Journal of Ecology 113(8): 2106-2119.

• Grittz, G.S., Lima, R.A.F., Kassner Filho, A., Vibrans, A.C. and Gasper, A.L. 2025. Assessing the extinction risk of tree species in the subtropical Atlantic Forest using multiple IUCN criteria. Oryx: 1–8. 

• Resende, B.O. et al. 2025. Collaborative research networks as a strategy to synthesize knowledge of Amazonian biodiversity. Proceedings of the Royal Society B: Biological Sciences, 292(2059): 20252069. 

• Simões, L.H. et al. 2025. Recovery of tree species functional composition in eucalypt plantations with natural regeneration differs among canopy strata. Forest Ecology and Management 594: 122952. 

• Brouwer, R. et al. 2025. Functional recovery of tropical forests: The role of restoration methods and environmental conditions. Biological Conservation 309: 111269.

• Dornelas, M. et al. 2025. BioTIME 2.0: Expanding and improving a database of biodiversity time series. Global Ecology and Biogeography, 34(5), p.e70003.

• International Tree Mortality Network 2025. Towards a global understanding of tree mortality. New Phytologist 245 (6): 2377-2392.

• Gorné, L.D., Aguirre-Gutiérrez, J., Souza, F.C., Swenson, N.G., Kraft, N.J.B., Schwantes Marimon, B., Baker, T.R., Lima, R.A.F., Vilanova, E., Álvarez-Dávila, E., et al. 2025. Use and misuse of trait imputation in ecology: the problem of using out‐of‐context imputed values. Ecography 2025(6): e07520.

• Almeida, C., Reid, J.L., Lima, R. A. F., Pinto, L. F. G., & Viani, R. A. G. 2025. High-diversity Atlantic Forest restoration plantings fail to represent local floras. Perspectives in Ecology and Conservation, 23(1), 6-11.

• Magalhães, D.V., Lima, R.A.F. and Massi, K.G. 2024. Is there variation in ten woody species reproductive phenology within the Atlantic Forest biodiversity hotspot? Botany Letters 171(4): 493-499.

• Simões, L.H., Guillemot, J., Ronquim, C.C., Weidlich, E.W., Muys, B., Fuza, M.S., Lima, R.A.F. and Brancalion, P.H. 2024. Green deserts, but not always: A global synthesis of native woody species regeneration under tropical tree monocultures. Global Change Biology 30(4): e17269.

• Lima, R.A.F., Dauby, G., Gasper, A.L., Fernandez, E.P., Vibrans, A.C., Oliveira, A.A., Prado, P.I., Souza, V.C., Siqueira, M.F. and ter Steege, H., 2024. Comprehensive conservation assessments reveal high extinction risks across Atlantic Forest trees. Science 383(6679): 219-225.

• Almeida, C., Reid, J.L., Lima, R.A.F., Pinto, L.F.G. and Viani, R.A.G. 2024. Restoration plantings in the Atlantic Forest use a small, biased, and homogeneous set of tree species. Forest Ecology and Management 553: 121628.

• Sperandii, M.G., Bazzichetto, M., Mendieta‐Leiva, G., Schmidtlein, S., Bott, M., Lima, R.A.F., ... and Chytrý, M. 2024. Towards more reproducibility in vegetation research. Journal of Vegetation Science 35(1): e13224.

• Lima, V.P., Lima, R.A.F., Joner, F., D'Orangeville, L., Raes, N., Siddique, I. and ter Steege, H. 2023. Integrating climate change into agroforestry conservation: A case study on native plant species in the Brazilian Atlantic Forest. Journal of Applied Ecology 60(9): 1977-1994.

• Lima, R.B. de, Görgens, E.B., Silva, D.A.S. da, Oliveira, C.P. de, Batista, A.P.B., Caraciolo Ferreira, R.L., Costa, F.R., Lima, R.A.F. de et al. 2023. Giants of the Amazon: How does environmental variation drive the diversity patterns of large trees? Global Change Biology 29(17): 4861-4879.

• Pyles, M.V., Magnago, L.F., Maia, V.A., Pinho, B.X., Pitta, G., de Gasper, A.L., Vibrans, A.C., Santos, R.M., van den Berg E., Lima, R.A.F. 2022. Human impacts as the main driver of tropical forest carbon. Science Advances 8(24): eabl7968.

• Klipel, J., Bergamin, R.S., Esquivel‐Muelbert, A., Lima, R.A.F., Oliveira, A.A., Prado, P.I., Müller, S.C. 2022. Climatic distribution of tree species in the Atlantic Forest. Biotropica.

• Pinho, B.X., Trindade, D.P., Peres, C.A., Jamelli, D., Lima, R.A.F., Ribeiro, E.M., Melo, F.P., Leal, I.R., Tabarelli, M. 2022. Cross‐scale drivers of woody plant species commonness and rarity in the Brazilian drylands. Diversity and Distributions 28(7): 1497-511.

• Lima, R.A.F., Phillips, O.L., Duque, A. et al. 2022. Making forest data fair and open. Nature Ecology & Evolution 6: 656–658.

• Lima, V.P., de Lima, R.A.F., Joner, F. et al. 2022. Climate change threatens native potential agroforestry plant species in Brazil. Scientific reports 12 (1): 2267.

• Lima, R.A.F., Sánchez-Tapia, A., Mortara, S.R., Steege, H. and Siqueira, M.F. 2021. plantR: An R package and workflow for managing species records from biological collections. Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210X.13779

• Barreto, T.E., Ivanauskas, N.M., Lima, R.A.F., Toniato, M.T.Z., Souza, F.M. and Rodrigues, R.R. 2021. Canopy openness and soil conditions explain community structure and diversity in a tropical seasonal forest in south-eastern Brazil. Acta Botanica Brasilia 35 (4): 638-652.

• Marjakangas, E.‐L., Ovaskainen, O., Abrego, N., Grøtan, V., Oliveira, A.A., Prado, P.I., Lima, R.A.F. 2021. Co-occurrences of tropical trees in eastern South America: disentangling abiotic and biotic forces. Plant Ecology 222: 791–806.

• Pinho, B.X., Tabarelli, M., ter Braak, C., Wright, S.J., ..., Lima, R.A.F., ..., & Melo, F.P.L. 2021. Functional biogeography of Neotropical moist forests: Trait–climate relationships and assembly patterns of tree communities. Global Ecology and Biogeography  30(7): 1430-1446.

• Zwiener, V.P., Lima, R.A.F., Sánchez-Tapia, A., Rocha, D.S.B., Marques, M.C.M. 2021. Tree diversity in the Brazilian Atlantic Forest: Biases and general patterns using different sources of information. Chapter 6 In: Marques M.C.M., Grelle C.E.V. (eds) The Atlantic Forest. Springer, Cham.

 

2015-2020

• Lima, R.A.F., Oliveira, A.A., Pitta, G.R., Gasper, A.L., Vibrans, A.C., Chave, J., ter Steege, H., Prado, P.I. 2020. The erosion of biodiversity and biomass in the Atlantic Forest biodiversity hotspot. Nature Communications 11: 6347.

• Lima, R.A.F., Souza, V.C., Siqueira, M.F., ter Steege, H. 2020. Defining endemism levels for biodiversity conservation: Tree species in the Atlantic Forest hotspot. Biological Conservation, 252, 108825.

• Lima, R.A.F., Condé, P. A., Banks-Leite, C., Campos, R. C., Hernández, M. I. M., Rodrigues, R. R., & Prado, P. I. (2020). Disentangling the effects of sampling scale and size on the shape of species abundance distributions. PLoS ONE 15 (9), e0238854.

• ter Steege, H., Prado, P.I., Lima, R.A.F., Pos, E., et al. 2020. Biased-corrected richness estimates for the Amazonian tree flora. Scientific Reports 10, 10130.

• Marjakangas, E.‐L., Abrego, N., Grøtan, V., Lima, R.A.F., et al. 2020. Fragmented tropical forests lose mutualistic plant–animal interactions. Diversity and Distributions 26(2): 154–168.

• Pansonato, M.P., Lima, R.A.F., Oliveira, A.A., Bertoncello, R., Martini, A.M.Z. 2019. Community structure and species composition of a periodically flooded Restinga forest in Caraguatatuba, São Paulo, Brazil. Biota Neotropica 19(1): e20170477.

• Marjakangas, E.-L., Genes, L., Pires, M.M., Fernandez, F.A.S., Lima, R.A.F., Oliveira, A.A., et al. 2018. Estimating interaction credit for trophic rewilding in tropical forests. Philosophical Transactions of the Royal Society B: Biological Sciences 373(1761): 20170435.

• Lima, R.A.F., Oliveira, A.A., Colletta, G.D., Flores, T.B., Coelho, R.L.G., Dias, P., et al. 2018. Can plant DNA barcoding be implemented in species-rich tropical regions? A perspective from São Paulo State, Brazil. Genetics and Molecular Biology 41(3): 661-670.

• Brancalion, P.H.S., Bello, C., Chazdon, R.L., Galetti, M. Jordano, P., Lima, R.A.F., Medina, A., Pizo, M.A., Reid, J.L. 2018. Maximizing biodiversity conservation and carbon stocking in restored tropical forests. Conservation Letters 11(4): e12454.

• Lima, R.A.F., Muller-Landau, H.C., Prado, P.I., Condit, R. 2016. How do size distributions relate to concurrently measured demographic rates? Evidence from over 150 tree species in Panama. Journal of Tropical Ecology 32: 179-192.

​

2010-2015

• Lima, R.A.F., Mori, D.P., Pitta, G., Melito, M.O., Bello, C., Magnago, L.F., Zwiener, V.P., Saraiva, D.D., Marques, M.C.M., Oliveira, A.A., Prado, P.I. 2015. How much do we know about the endangered Atlantic Forest? Reviewing nearly 70 years of information on tree community surveys. Biodiversity & Conservation 24: 2135-2148.

• Lima, R.A.F., Batista, J.L.F., Prado, P. I. 2015. Modeling tree diameter distributions in natural forests: An evaluation of 10 statistical models. Forest Science 61: 320-327.

• Lima, R.A.F., Rando, J.G., Barreto, K.D. 2015. Composição e diversidade no cerrado do leste de Mato Grosso do Sul, Brasil. Revista Árvore 39: 9-24.

• Bello, C., Galetti, M., Pizo, M.A., Magnago, L.F.S., Rocha, M.F., Lima, R.A.F., Peres, C.A., Ovaskainen, O., Jordano, P. 2015. Defaunation affects carbon storage in tropical forests. Science Advances 1: e1501105-e1501105.

• Oliveira, A.A., Vicentini, A., Chave, J., Castanho, C.D.T., Davies, S.J., Martini, A.M.Z., Lima, R.A.F., Ribeiro, R.R., Iribar, A., Souza, V.C. 2014. Habitat specialization and phylogenetic structure of tree species in a coastal Brazilian white-sand forest. J. Plant Ecology 7: 134-144.

• Lima, R.A.F., Prado, P.I., Martini, A.M.Z., Fonseca, L.J., Gandolfi, S., Rodrigues, R.R. 2013. Improving methods in gap ecology: Revisiting size and shape distributions using a model selection approach. Journal of Vegetation Science 24: 484-495.

• Brocardo, C.R., Zipparro, V.B., Lima, R.A.F., Guevara, R., Galetti, M. 2013. No changes in seedling recruitment when terrestrial mammals are excluded in a partially defaunated Atlantic rainforest. Biological Conservation 163: 107-114.

• Lima, R.A.F., Rother, D.C., Muler, A.E., Lepsch, I.F., Rodrigues, R.R. 2012. Bamboo overabundance alters forest structure and dynamics in the Atlantic Forest hotspot. Biological Conservation 147: 32-39.

• Lima, R.A.F., Souza, V.C., Dittrich, V.A.O., Salino, A. 2012. Composition, diversity and geographical distribution of vascular plants of an Atlantic rain forest, southeastern Brazil. Biota Neotropica 12: 241-249.

• Lima, R.A.F., Oliveira, A.A., Martini, A.M.Z., Sampaio, D., Souza, V.C., Rodrigues, R.R. 2011. Structure, diversity, and spatial patterns in a permanent plot of high Restinga forest in Southeastern Brazil. Acta Botanica Brasilica, 25: 633–645.

• Lima, R.A.F., Dittrich, V.A.O.; Souza, V.C., Salino, A., Breier, T.B., Aguiar, O.T. 2011. Vascular flora of the Carlos Botelho State Park, São Paulo, Brazil. Biota Neotropica 11: 173-214.

​

Before 2010

• Lima, R.A.F., Gandolfi, S. 2009. Structure of the herb stratum under different light regimes in the Lower Montane Atlantic Rain Forest. Brazilian Journal of Biology 69(1): 631–637.

• Rodrigues, R.R., Lima, R.A.F., Gandolfi, S., Nave, A.G. 2009. On the restoration of high diversity forests: 30 years of experience in the Brazilian Atlantic Forest. Biological Conservation 142(6): 1242–1251.

• Lima, R.A.F., Moura, L.C. 2008. Gap disturbance regime and composition in the Atlantic Montane Rain Forest: the influence of topography. Plant Ecology 197: 239–253.

• Martini, A.M.Z., Lima, R.A.F., Franco, G.A.D.C., Rodrigues, R.R. 2008. The need for full inventories of tree modes of disturbance to improve forest dynamics comprehension: an example from a semideciduous forest in Brazil. Forest Ecology and Management 255(5–6): 1479–1488.

• Lima, R.A.F., Martini, A.M.Z., Gandolfi, S., Rodrigues, R.R. 2008. Repeated disturbances and their influences on canopy disturbance regime in a tropical semi-deciduous forest. Journal of Tropical Ecology 24: 1–9.

• Lima, R.A.F., Moura, L.C. 2006. Canopy gap colonization in the Atlantic Montane Rain Forest. Brazilian Archives of Biology and Technology 49(6): 953–965.

• Lima, R.A.F. 2005. Canopy gap structure and regeneration in tropical rain forests. Revista Brasileira de Botânica 28(4): 651–670.

• Lima, R.A.F. 2005. Gap size measurement: the proposal of a new field method. Forest Ecology and Management 214: 413–419.