​

​2025-present

• 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 (in press).

 

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.