Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Wet and dry tropical forests show opposite successional pathways in wood density but converge over time
    Poorter, L. ; Rozendaal, Danaë ; Bongers, F. ; Almeida-Cortez, Jarcilene S. ; Almeyda Zambrano, Angélica María ; Álvarez, Francisco S. ; Andrade, José Luís ; Villa, Luis Felipe Arreola ; Balvanera, Patricia ; Becknell, Justin M. ; Bentos, Tony V. ; Bhaskar, Radika ; Boukili, Vanessa ; Brancalion, Pedro H.S. ; Broadbent, Eben N. ; César, Ricardo Gomes ; Chave, Jerome ; Chazdon, Robin L. ; Colletta, Gabriel Dalla ; Craven, Dylan ; Jong, Ben H.J. de; Denslow, Julie S. ; Dent, Daisy H. ; DeWalt, Saara J. ; García, Elisa Díaz ; Dupuy, Juan M. ; Durán, Sandra M. ; Espírito Santo, Mário Marcos ; Fandiño, María C. ; Fernandes, Geraldo Wilson ; Finegan, Bryan ; Moser, Vanessa Granda ; Hall, Jefferson S. ; Hernández-Stefanoni, José Luis ; Jakovac, A.C. ; Junqueira, André B. ; Kennard, Deborah ; Lebrija-Trejos, Edwin ; Letcher, Susan G. ; Lohbeck, M.W.M. ; Lopez, Omar R. ; Marín-Spiotta, Erika ; Martínez-Ramos, Miguel ; Martins, Sebastião Venâncio ; Massoca, Paulo E.S. ; Meave, Jorge A. ; Mesquita, Rita ; Mora, Francisco ; Souza Moreno, Vanessa De; Müller, Sandra C. ; Muñoz, Rodrigo ; Muscarella, Robert ; Oliveira Neto, Silvio Nolasco De; Nunes, Yule Roberta Ferreira ; Ochoa-Gaona, Susana ; Paz, Horacio ; Pena Claros, M. ; Piotto, Daniel ; Ruíz, Jorge ; Sanaphre-Villanueva, Lucía ; Sanchez-Azofeifa, Arturo ; Schwartz, Naomi B. ; Steininger, Marc K. ; Thomas, William Wayt ; Toledo, Marisol ; Uriarte, Maria ; Breugel, Michiel van; Wal, Hans van der - \ 2019
    Wageningen University & Research
    secondary succession - community assembly - community-weighted mean - wood density - Neotropics - tropical forest - Latin America
    We analyse how community wood density (WD) recovers during secondary tropical forest succession. In wet forests succession proceeds from low to high WD, in dry forests from high to low WD, resulting in convergence of community WD of dry and wet forests over time, as vegetation cover builds up.
    Wet and dry tropical forests show opposite successional pathways in wood density but converge over time
    Poorter, Lourens ; Rozendaal, Danaë M.A. ; Bongers, Frans ; Almeida-Cortez, Jarcilene S. de; Almeyda Zambrano, Angélica María ; Álvarez, Francisco S. ; Andrade, José Luís ; Villa, Luis Felipe Arreola ; Balvanera, Patricia ; Becknell, Justin M. ; Bentos, Tony V. ; Bhaskar, Radika ; Boukili, Vanessa ; Brancalion, Pedro H.S. ; Broadbent, Eben N. ; César, Ricardo G. ; Chave, Jerome ; Chazdon, Robin L. ; Colletta, Gabriel Dalla ; Craven, Dylan ; Jong, Ben H.J. de; Denslow, Julie S. ; Dent, Daisy H. ; DeWalt, Saara J. ; García, Elisa Díaz ; Dupuy, Juan Manuel ; Durán, Sandra M. ; Espírito Santo, Mário M. ; Fandiño, María C. ; Fernandes, Geraldo Wilson ; Finegan, Bryan ; Moser, Vanessa Granda ; Hall, Jefferson S. ; Hernández-Stefanoni, José Luis ; Jakovac, Catarina C. ; Junqueira, André B. ; Kennard, Deborah ; Lebrija-Trejos, Edwin ; Letcher, Susan G. ; Lohbeck, Madelon ; Lopez, Omar R. ; Marín-Spiotta, Erika ; Martínez-Ramos, Miguel ; Martins, Sebastião V. ; Massoca, Paulo E.S. ; Meave, Jorge A. ; Mesquita, Rita ; Mora, Francisco ; Souza Moreno, Vanessa de; Müller, Sandra C. ; Muñoz, Rodrigo ; Muscarella, Robert ; Oliveira Neto, Silvio Nolasco de; Nunes, Yule R.F. ; Ochoa-Gaona, Susana ; Paz, Horacio ; Peña-Claros, Marielos ; Piotto, Daniel ; Ruíz, Jorge ; Sanaphre-Villanueva, Lucía ; Sanchez-Azofeifa, Arturo ; Schwartz, Naomi B. ; Steininger, Marc K. ; Thomas, William Wayt ; Toledo, Marisol ; Uriarte, Maria ; Utrera, Luis P. ; Breugel, Michiel van; Sande, Masha T. van der; Wal, Hans van der; Veloso, Maria D.M. ; Vester, Hans F.M. ; Vieira, Ima C.G. ; Villa, Pedro Manuel ; Williamson, G.B. ; Wright, S.J. ; Zanini, Kátia J. ; Zimmerman, Jess K. ; Westoby, Mark - \ 2019
    Nature Ecology & Evolution 3 (2019). - ISSN 2397-334X - p. 928 - 934.

    Tropical forests are converted at an alarming rate for agricultural use and pastureland, but also regrow naturally through secondary succession. For successful forest restoration, it is essential to understand the mechanisms of secondary succession. These mechanisms may vary across forest types, but analyses across broad spatial scales are lacking. Here, we analyse forest recovery using 1,403 plots that differ in age since agricultural abandonment from 50 sites across the Neotropics. We analyse changes in community composition using species-specific stem wood density (WD), which is a key trait for plant growth, survival and forest carbon storage. In wet forest, succession proceeds from low towards high community WD (acquisitive towards conservative trait values), in line with standard successional theory. However, in dry forest, succession proceeds from high towards low community WD (conservative towards acquisitive trait values), probably because high WD reflects drought tolerance in harsh early successional environments. Dry season intensity drives WD recovery by influencing the start and trajectory of succession, resulting in convergence of the community WD over time as vegetation cover builds up. These ecological insights can be used to improve species selection for reforestation. Reforestation species selected to establish a first protective canopy layer should, among other criteria, ideally have a similar WD to the early successional communities that dominate under the prevailing macroclimatic conditions.

    Biodiversity recovery of Neotropical secondary forests
    Rozendaal, Danaë M.A. ; Bongers, Frans ; Aide, T.M. ; Alvarez-Dávila, Esteban ; Ascarrunz, Nataly ; Balvanera, Patricia ; Becknell, Justin M. ; Bentos, Tony V. ; Brancalion, Pedro H.S. ; Cabral, George A.L. ; Calvo-Rodriguez, Sofia ; Chave, Jerome ; César, Ricardo G. ; Chazdon, Robin L. ; Condit, Richard ; Dallinga, Jorn S. ; Almeida-Cortez, Jarcilene S. De; Jong, Ben de; Oliveira, Alexandre De; Denslow, Julie S. ; Dent, Daisy H. ; Dewalt, Saara J. ; Dupuy, Juan Manuel ; Durán, Sandra M. ; Dutrieux, Loïc P. ; Espírito-Santo, Mario M. ; Fandino, María C. ; Fernandes, G.W. ; Finegan, Bryan ; García, Hernando ; Gonzalez, Noel ; Moser, Vanessa Granda ; Hall, Jefferson S. ; Hernández-Stefanoni, José Luis ; Hubbell, Stephen ; Jakovac, Catarina C. ; Hernández, Alma Johanna ; Junqueira, André B. ; Kennard, Deborah ; Larpin, Denis ; Letcher, Susan G. ; Licona, Juan-Carlos ; Lebrija-trejos, Edwin ; Marín-Spiotta, Erika ; Martínez-Ramos, Miguel ; Massoca, Paulo E.S. ; Meave, Jorge A. ; Mesquita, Rita C.G. ; Mora, Francisco ; Müller, Sandra C. ; Muñoz, Rodrigo ; Oliveira Neto, Silvio Nolasco De; Norden, Natalia ; Nunes, Yule R.F. ; Ochoa-Gaona, Susana ; Ortiz-Malavassi, Edgar ; Ostertag, Rebecca ; Peña-Caros, Marielos ; Pérez-García, Eduardo A. ; Piotto, Daniel ; Powers, Jennifer S. ; Aguilar-Cano, José ; Rodriguez-Buritica, Susana ; Rodríguez-Velázquez, Jorge ; Romero-Romero, Marco Antonio ; Ruíz, Jorge ; Sanchez-Azofeifa, Arturo ; Almeida, Arlete Silva De; Silver, Whendee L. ; Schwartz, Naomi B. ; Thomas, William Wayt ; Toledo, Marisol ; Uriarte, Maria ; Sá Sampaio, Everardo Valadares De; Breugel, Michiel van; Wal, Hans van der; Martins, Sebastião Venâncio ; Veloso, Maria D.M. ; Vester, Hans F.M. ; Vicentini, Alberto ; Vieira, Ima C.G. ; Villa, Pedro ; Williamson, G.B. ; Zanini, Kátia J. ; Zimmerman, Jess ; Poorter, Lourens - \ 2019
    Science Advances 5 (2019)3. - ISSN 2375-2548 - 10 p.
    Old-growth tropical forests harbor an immense diversity of tree species but are rapidly being cleared, while secondary forests that regrow on abandoned agricultural lands increase in extent. We assess how tree species richness and composition recover during secondary succession across gradients in environmental conditions and anthropogenic disturbance in an unprecedented multisite analysis for the Neotropics. Secondary forests recover remarkably fast in species richness but slowly in species composition. Secondary forests take a median time of five decades to recover the species richness of old-growth forest (80% recovery after 20 years) based on rarefaction analysis. Full recovery of species composition takes centuries (only 34% recovery after 20 years). A dual strategy that maintains both old-growth forests and species-rich secondary forests is therefore crucial for biodiversity conservation in human-modified tropical landscapes.
    Legume abundance along successional and rainfall gradients in Neotropical forests
    Gei, Maga ; Rozendaal, Danaë M.A. ; Poorter, Lourens ; Bongers, Frans ; Sprent, Janet I. ; Garner, Mira D. ; Aide, T.M. ; Andrade, José Luis ; Balvanera, Patricia ; Becknell, Justin M. ; Brancalion, Pedro H.S. ; Cabral, George A.L. ; César, Ricardo Gomes ; Chazdon, Robin L. ; Cole, Rebecca J. ; Colletta, Gabriel Dalla ; Jong, Ben De; Denslow, Julie S. ; Dent, Daisy H. ; Dewalt, Saara J. ; Dupuy, Juan Manuel ; Durán, Sandra M. ; Espírito Santo, Mário Marcos Do; Fernandes, G.W. ; Nunes, Yule Roberta Ferreira ; Finegan, Bryan ; Moser, Vanessa Granda ; Hall, Jefferson S. ; Hernández-Stefanoni, José Luis ; Junqueira, André B. ; Kennard, Deborah ; Lebrija-Trejos, Edwin ; Letcher, Susan G. ; Lohbeck, Madelon ; Marín-Spiotta, Erika ; Martínez-Ramos, Miguel ; Meave, Jorge A. ; Menge, Duncan N.L. ; Mora, Francisco ; Muñoz, Rodrigo ; Muscarella, Robert ; Ochoa-Gaona, Susana ; Orihuela-Belmonte, Edith ; Ostertag, Rebecca ; Peña-Claros, Marielos ; Pérez-García, Eduardo A. ; Piotto, Daniel ; Reich, Peter B. ; Reyes-García, Casandra ; Rodríguez-Velázquez, Jorge ; Romero-Pérez, I.E. ; Sanaphre-Villanueva, Lucía ; Sanchez-Azofeifa, Arturo ; Schwartz, Naomi B. ; Almeida, Arlete Silva De; Almeida-Cortez, Jarcilene S. ; Silver, Whendee ; Souza Moreno, Vanessa De; Sullivan, Benjamin W. ; Swenson, Nathan G. ; Uriarte, Maria ; Breugel, Michiel Van; Wal, Hans Van Der; Veloso, Maria Das Dores Magalhães ; Vester, Hans F.M. ; Vieira, Ima Célia Guimarães ; Zimmerman, Jess K. ; Powers, Jennifer S. - \ 2018
    Nature Ecology & Evolution 2 (2018)7. - ISSN 2397-334X - p. 1104 - 1111.
    The nutrient demands of regrowing tropical forests are partly satisfied by nitrogen-fixing legume trees, but our understanding of the abundance of those species is biased towards wet tropical regions. Here we show how the abundance of Leguminosae is affected by both recovery from disturbance and large-scale rainfall gradients through a synthesis of forest inventory plots from a network of 42 Neotropical forest chronosequences. During the first three decades of natural forest regeneration, legume basal area is twice as high in dry compared with wet secondary forests. The tremendous ecological success of legumes in recently disturbed, water-limited forests is likely to be related to both their reduced leaflet size and ability to fix N2, which together enhance legume drought tolerance and water-use efficiency. Earth system models should incorporate these large-scale successional and climatic patterns of legume dominance to provide more accurate estimates of the maximum potential for natural nitrogen fixation across tropical forests.
    Phylogenetic classification of the world's tropical forests
    Slik, J.W.F. ; Franklin, Janet ; Arroyo-Rodríguez, Víctor ; Field, Richard ; Aguilar, Salomon ; Aguirre, Nikolay ; Ahumada, Jorge ; Aiba, Shin Ichiro ; Alves, Luciana F. ; Anitha, K. ; Avella, Andres ; Mora, Francisco ; Aymard, Gerardo A.C. ; Báez, Selene ; Balvanera, Patricia ; Bastian, Meredith L. ; Bastin, Jean François ; Bellingham, Peter J. ; Berg, Eduardo Van Den; Conceição Bispo, Polyanna Da; Boeckx, Pascal ; Boehning-Gaese, Katrin ; Bongers, Frans ; Boyle, Brad ; Brambach, Fabian ; Brearley, Francis Q. ; Brown, Sandra ; Chai, Shauna Lee ; Chazdon, Robin L. ; Chen, Shengbin ; Chhang, Phourin ; Chuyong, George ; Ewango, Corneille ; Coronado, Indiana M. ; Cristóbal-Azkarate, Jurgi ; Culmsee, Heike ; Damas, Kipiro ; Dattaraja, H.S. ; Davidar, Priya ; DeWalt, Saara J. ; Din, Hazimah ; Drake, Donald R. ; Duque, Alvaro ; Durigan, Giselda ; Eichhorn, Karl ; Eler, Eduardo Schmidt ; Enoki, Tsutomu ; Ensslin, Andreas ; Fandohan, Adandé Belarmain ; Farwig, Nina ; Feeley, Kenneth J. ; Fischer, Markus ; Forshed, Olle ; Garcia, Queila Souza ; Garkoti, Satish Chandra ; Gillespie, Thomas W. ; Gillet, Jean Francois ; Gonmadje, Christelle ; Granzow-De La Cerda, Iñigo ; Griffith, Daniel M. ; Grogan, James ; Hakeem, Khalid Rehman ; Harris, David J. ; Harrison, Rhett D. ; Hector, Andy ; Hemp, Andreas ; Homeier, Jürgen ; Hussain, M.S. ; Ibarra-Manríquez, Guillermo ; Hanum, I.F. ; Imai, Nobuo ; Jansen, Patrick A. ; Joly, Carlos Alfredo ; Joseph, Shijo ; Kartawinata, Kuswata ; Kearsley, Elizabeth ; Kelly, Daniel L. ; Kessler, Michael ; Killeen, Timothy J. ; Kooyman, Robert M. ; Laumonier, Yves ; Laurance, Susan G. ; Laurance, William F. ; Lawes, Michael J. ; Letcher, Susan G. ; Lindsell, Jeremy ; Lovett, Jon ; Lozada, Jose ; Lu, Xinghui ; Lykke, Anne Mette ; Mahmud, Khairil Bin; Mahayani, Ni Putu Diana ; Mansor, Asyraf ; Marshall, Andrew R. ; Martin, Emanuel H. ; Matos, Darley Calderado Leal ; Meave, Jorge A. ; Melo, Felipe P.L. ; Mendoza, Zhofre Huberto Aguirre ; Metali, Faizah ; Medjibe, Vincent P. ; Metzger, Jean Paul ; Metzker, Thiago ; Mohandass, D. ; Munguía-Rosas, Miguel A. ; Muñoz, Rodrigo ; Nurtjahy, Eddy ; Oliveira, Eddie Lenza De; Onrizal, ; Parolin, Pia ; Parren, Marc ; Parthasarathy, N. ; Paudel, Ekananda ; Perez, Rolando ; Pérez-García, Eduardo A. ; Pommer, Ulf ; Poorter, Lourens ; Qi, Lan ; Piedade, Maria Teresa F. ; Pinto, José Roberto Rodrigues ; Poulsen, Axel Dalberg ; Poulsen, John R. ; Powers, Jennifer S. ; Prasad, Rama Chandra ; Puyravaud, Jean Philippe ; Rangel, Orlando ; Reitsma, Jan ; Rocha, Diogo S.B. ; Rolim, Samir ; Rovero, Francesco ; Rozak, Andes ; Ruokolainen, Kalle ; Rutishauser, Ervan ; Rutten, Gemma ; Mohd Said, Mohd Nizam ; Saiter, Felipe Z. ; Saner, Philippe ; Santos, Braulio ; Santos, João Roberto Dos; Sarker, Swapan Kumar ; Schmitt, Christine B. ; Schoengart, Jochen ; Schulze, Mark ; Sheil, Douglas ; Sist, Plinio ; Souza, Alexandre F. ; Spironello, Wilson Roberto ; Sposito, Tereza ; Steinmetz, Robert ; Stevart, Tariq ; Suganuma, Marcio Seiji ; Sukri, Rahayu ; Sultana, Aisha ; Sukumar, Raman ; Sunderland, Terry ; Supriyadi, S. ; Suresh, H.S. ; Suzuki, Eizi ; Tabarelli, Marcelo ; Tang, Jianwei ; Tanner, Ed V.J. ; Targhetta, Natalia ; Theilade, Ida ; Thomas, Duncan ; Timberlake, Jonathan ; Morisson Valeriano, Márcio De; Valkenburg, Johan Van; Do, Tran Van; Sam, Hoang Van; Vandermeer, John H. ; Verbeeck, Hans ; Vetaas, Ole Reidar ; Adekunle, Victor ; Vieira, Simone A. ; Webb, Campbell O. ; Webb, Edward L. ; Whitfeld, Timothy ; Wich, Serge ; Williams, John ; Wiser, Susan ; Wittmann, Florian ; Yang, Xiaobo ; Yao, C.Y.A. ; Yap, Sandra L. ; Zahawi, Rakan A. ; Zakaria, Rahmad ; Zang, Runguo - \ 2018
    Proceedings of the National Academy of Sciences of the United States of America 115 (2018)8. - ISSN 0027-8424 - p. 1837 - 1842.
    Biogeographic legacies - Forest classification - Forest functional similarity - Phylogenetic community distance - Tropical forests

    Knowledge about the biogeographic affinities of the world's tropical forests helps to better understand regional differences in forest structure, diversity, composition, and dynamics. Such understanding will enable anticipation of region-specific responses to global environmental change. Modern phylogenies, in combination with broad coverage of species inventory data, now allow for global biogeographic analyses that take species evolutionary distance into account. Here we present a classification of the world's tropical forests based on their phylogenetic similarity. We identify five principal floristic regions and their floristic relationships: (i) Indo-Pacific, (ii) Subtropical, (iii) African, (iv) American, and (v) Dry forests. Our results do not support the traditional neo- versus paleotropical forest division but instead separate the combined American and African forests from their Indo-Pacific counterparts. We also find indications for the existence of a global dry forest region, with representatives in America, Africa, Madagascar, and India. Additionally, a northern-hemisphere Subtropical forest region was identified with representatives in Asia and America, providing support for a link between Asian and American northernhemisphere forests.

    Data from: Environmental gradients and the evolution of successional habitat specialization: a test case with 14 Neotropical forest sites
    Letcher, Susan G. ; Lasky, Jesse R. ; Chazdon, Robin L. ; Norden, Natalia ; Wright, S.J. ; Meave, Jorge A. ; Pérez-García, Eduardo A. ; Muñoz, Rodrigo ; Romero-Pérez, Eunice ; Andrade, Ana ; Balvanera, Patricia ; Bongers, Frans ; Lohbeck, Madelon - \ 2016
    State University of New York (SUNY)
    Determinants of plant community diversity and structure - Life History Evolution - Precipitation gradient - Tropical wet forest - Tropical dry forest - Functional traits - phylogeny - Pioneer species
    1. Successional gradients are ubiquitous in nature, yet few studies have systematically examined the evolutionary origins of taxa that specialize at different successional stages. Here we quantify successional habitat specialization in Neotropical forest trees and evaluate its evolutionary lability along a precipitation gradient. Theoretically, successional habitat specialization should be more evolutionarily conserved in wet forests than in dry forests due to more extreme microenvironmental differentiation between early and late successional stages in wet forest. 2. We applied a robust multinomial classification model to samples of primary and secondary forest trees from 14 Neotropical lowland forest sites spanning a precipitation gradient from 788 to 4000 mm annual rainfall, identifying species that are old growth specialists and secondary forest specialists in each site. We constructed phylogenies for the classified taxa at each site and for the entire set of classified taxa, and tested whether successional habitat specialization is phylogenetically conserved. We further investigated differences in the functional traits of species specializing in secondary vs. old-growth forest along the precipitation gradient, expecting different trait associations with secondary forest specialists in wet vs. dry forests since water availability is more limiting in dry forests and light availability more limiting in wet forests. 3. Successional habitat specialization is non-randomly distributed in the angiosperm phylogeny, with a tendency towards phylogenetic conservatism overall and a trend toward stronger conservatism in wet forests than in dry forests. However, the specialists come from all the major branches of the angiosperm phylogeny, and very few functional traits showed any consistent relationships with successional habitat specialization in either wet or dry forests. 4. Synthesis: The niche conservatism evident in the habitat specialization of Neotropical trees suggests a role for radiation into different successional habitats in the evolution of species-rich genera, though the diversity of functional traits that lead to success in different successional habitats complicates analyses at the community scale. Examining the distribution of particular lineages with respect to successional gradients may provide more insight into the role of successional habitat specialization in the evolution of species-rich taxa.
    Environmental gradients and the evolution of successional habitat specialization : A test case with 14 Neotropical forest sites
    Letcher, Susan G. ; Lasky, Jesse R. ; Chazdon, Robin L. ; Norden, Natalia ; Wright, S.J. ; Meave, Jorge A. ; Pérez-García, Eduardo A. ; Muñoz, Rodrigo ; Romero-Pérez, Eunice ; Andrade, Ana ; Balvanera, Patricia ; Bongers, Frans ; Lohbeck, Madelon - \ 2015
    Journal of Ecology 103 (2015)5. - ISSN 0022-0477 - p. 1276 - 1290.
    Determinants of plant community diversity and structure - Functional traits - Life-history evolution - Phylogeny - Pioneer species - Precipitation gradient - Tropical dry forest - Tropical wet forest

    Successional gradients are ubiquitous in nature, yet few studies have systematically examined the evolutionary origins of taxa that specialize at different successional stages. Here we quantify successional habitat specialization in Neotropical forest trees and evaluate its evolutionary lability along a precipitation gradient. Theoretically, successional habitat specialization should be more evolutionarily conserved in wet forests than in dry forests due to more extreme microenvironmental differentiation between early and late-successional stages in wet forest. We applied a robust multinomial classification model to samples of primary and secondary forest trees from 14 Neotropical lowland forest sites spanning a precipitation gradient from 788 to 4000 mm annual rainfall, identifying species that are old-growth specialists and secondary forest specialists in each site. We constructed phylogenies for the classified taxa at each site and for the entire set of classified taxa and tested whether successional habitat specialization is phylogenetically conserved. We further investigated differences in the functional traits of species specializing in secondary vs. old-growth forest along the precipitation gradient, expecting different trait associations with secondary forest specialists in wet vs. dry forests since water availability is more limiting in dry forests and light availability more limiting in wet forests. Successional habitat specialization is non-randomly distributed in the angiosperm phylogeny, with a tendency towards phylogenetic conservatism overall and a trend towards stronger conservatism in wet forests than in dry forests. However, the specialists come from all the major branches of the angiosperm phylogeny, and very few functional traits showed any consistent relationships with successional habitat specialization in either wet or dry forests. Synthesis. The niche conservatism evident in the habitat specialization of Neotropical trees suggests a role for radiation into different successional habitats in the evolution of species-rich genera, though the diversity of functional traits that lead to success in different successional habitats complicates analyses at the community scale. Examining the distribution of particular lineages with respect to successional gradients may provide more insight into the role of successional habitat specialization in the evolution of species-rich taxa.

    Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
    Schoch, C.L. ; Robbertse, B. ; Robert, V. ; Vu, D. ; Cardinali, G. ; Irinyi, L. ; Meyer, W. ; Nilsson, R.H. ; Hughes, K. ; Miller, A.N. ; Kirk, P.M. ; Abarenkov, K. ; Aime, M.C. ; Ariyawansa, H.A. ; Bidartondo, M. ; Boekhout, T. ; Buyck, B. ; Cai, Q. ; Chen, J. ; Crespo, A. ; Crous, P.W. ; Damm, U. ; Beer, Z.W. de; Dentinger, B.T.M. ; Divakar, P.K. ; Duenas, M. ; Feau, N. ; Fliegerova, K. ; Garcia, M.A. ; Ge, Z.W. ; Griffith, G.W. ; Groenewald, J.Z. ; Groenewald, M. ; Grube, M. ; Gryzenhout, M. ; Gueidan, C. ; Guo, L. ; Hambleton, S. ; Hamelin, R. ; Hansen, K. ; Hofstetter, V. ; Hong, S.B. ; Houbraken, J. ; Hyde, K.D. ; Inderbitzin, P. ; Johnston, P.A. ; Karunarathna, S.C. ; Koljalg, U. ; Kovacs, G.M. ; Kraichak, E. ; Krizsan, K. ; Kurtzman, C.P. ; Larsson, K.H. ; Leavitt, S. ; Letcher, P.M. ; Liimatainen, K. ; Liu, J.K. ; Lodge, D.J. ; Luangsa-ard, J.J. ; Lumbsch, H.T. ; Maharachchikumbura, S.S.N. ; Manamgoda, D. ; Martin, M.P. ; Minnis, A.M. ; Moncalvo, J.M. ; Mule, G. ; Nakasone, K.K. ; Niskanen, T. ; Olariaga, I. ; Papp, T. ; Petkovits, T. ; Pino-Bodas, R. ; Powell, M.J. ; Raja, H.A. ; Redecker, D. ; Sarmiento-Ramirez, J.M. ; Seifert, K.A. ; Shrestha, B. ; Stenroos, S. ; Stielow, B. ; Suh, S.O. ; Tanaka, K. ; Tedersoo, L. ; Telleria, M.T. ; Udayanga, D. ; Untereiner, W.A. ; Dieguez Uribeondo, J. ; Subbarao, K.V. ; Vagvolgyi, C. ; Visagie, C. ; Voigt, K. ; Walker, D.M. ; Weir, B.S. ; Weiss, M. ; Wijayawardene, N.N. ; Wingfield, M.J. ; Xu, J.P. ; Yang, Z.L. ; Zhang, N. ; Zhuang, W.Y. ; Federhen, S. - \ 2014
    Database : the Journal of Biological Databases and Curation 2014 (2014). - ISSN 1758-0463 - 21 p.
    internal transcribed spacer - arbuscular mycorrhizal fungi - ribosomal dna - interspecific hybridization - sequence analyses - species complex - identification - evolution - barcode - life
    DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
    Phylogenetic community structure during succession: evidence from three Neotropical forest sites
    Letcher, S.G. ; Chazdon, R.L. ; Andrade, A. ; Bongers, F. ; Breugel, M. van; Finegan, B. ; Laurance, S.G. ; Mesquita, R. ; Martinez-Ramos, M. ; Williamson, G.B. - \ 2012
    Perspectives in plant ecology, evolution and systematics 14 (2012)2. - ISSN 1433-8319 - p. 79 - 87.
    dependent seedling mortality - bornean rain-forest - tropical forest - tree community - density - diversity - ecology - growth - size - disturbances
    The phylogenetic structure of communities can reveal forces shaping community assembly, but the vast majority of work on phylogenetic community structure has been conducted in mature ecosystems. Here, we present an analysis of the phylogenetic structure of three Neotropical rain forest communities undergoing succession. In each site, the net relatedness of the community is initially high and consistently declines during succession. This pattern is evident both when comparing plots of different age classes and when comparing stem size classes within each plot: the oldest plots and the youngest stem cohorts, representing the most advanced stages of succession, have the lowest relatedness. Our results suggest that succession leaves a distinct signature in the phylogenetic structure of communities, which may reflect an increasing role of biotic interactions in community assembly during succession. We discuss theoretical explanations for the decline in community phylogenetic relatedness during succession, and suggest directions for future study.
    Rates of change in tree communities of secondary Neotropical forests following major disturbances
    Chazdon, R.L. ; Letcher, S.G. ; Breugel, M. van; Martínez-Ramos, M. ; Bongers, F.J.J.M. ; Finegan, B. - \ 2007
    Philosophical Transactions of the Royal Society B. Biological sciences 362 (2007)1478. - ISSN 0962-8436 - p. 273 - 289.
    tropical dry-forest - upper rio negro - rain-forest - puerto-rico - costa-rica - deciduous forest - species composition - central amazonia - land-use - hurricane disturbance
    Rates of change in tree communities following major disturbances are determined by a complex set of interactions between local site factors, landscape history and structure, regional species pools and species life histories. Our analysis focuses on vegetation change following abandonment of agricultural fields or pastures, as this is the most extensive form of major disturbance in Neotropical forests. We consider five tree community attributes: stem density, basal area, species density, species richness and species composition. We describe two case studies, in northeastern Costa Rica and Chiapas, Mexico, where both chronosequence and annual tree dynamics studies are being applied. These case studies show that the rates of change in tree communities often deviate from chronosequence trends. With respect to tree species composition, sites of different ages differ more than a single site followed over time through the same age range. Dynamic changes in basal area within stands, on the other hand, generally followed chronosequence trends. Basal area accumulation was more linked with tree growth rates than with net changes in tree density due to recruitment and mortality. Stem turnover rates were poor predictors of species turnover rates, particularly at longer time-intervals. Effects of the surrounding landscape on tree community dynamics within individual plots are poorly understood, but are likely to be important determinants of species accumulation rates and relative abundance patterns.
    Reconstructing the early evolution of the fungi using a six gene phylogeny
    James, T.Y. ; Kauff, F. ; Schoch, C.L. ; Matheny, P.B. ; Hofstetter, V. ; Cox, C.J. ; Celio, G. ; Gueidan, C. ; Fraker, E. ; Miadlikowska, J. ; Lumbsch, H.T. ; Rauhut, A. ; Reeb, V. ; Arnold, A.E. ; Amtoft, A. ; Stajich, J.E. ; Hosaka, K. ; Sung, G.H. ; Johnson, D. ; O'Rourke, B. ; Binder, M. ; Curtis, J.M. ; Slot, J.C. ; Wang, Z. ; Wilson, A.W. ; Schüßler, A. ; Longcore, J.E. ; O'Donnell, K. ; Mozley-Standridge, S. ; Porter, D. ; Letcher, P.M. ; Powell, M.J. ; Taylor, J.W. ; White, M.M. ; Griffith, G.W. ; Davies, D.R. ; Sugiyama, J. ; Rossman, A.Y. ; Rogers, J.D. ; Pfister, D.H. ; Hewitt, D. ; Hansen, K. ; Hambleton, S. ; Shoemaker, R.A. ; Kohlmeyer, J. ; Volkmann-Kohlmeyer, B. ; Spotts, R.A. ; Serdani, M. ; Crous, P.W. ; Hughes, K.W. ; Matsuura, K. ; Langer, E. ; Langer, G. ; Untereiner, W.A. ; Lücking, R. ; Büdel, B. ; Geiser, D.M. ; Aptroot, A. ; Diederich, P. ; Schmitt, I. ; Schultz, M. ; Yahr, R. ; Hibbett, D.S. ; Lutzoni, F. ; McLaughlin, D.J. ; Spatafora, J.W. ; Vilgalys, R. - \ 2006
    Nature 443 (2006)7113. - ISSN 0028-0836 - p. 818 - 822.
    arbuscular mycorrhizal fungi - molecular phylogeny - maximum-likelihood - land plants - tree - microsporidia - sequences - animals - chytridiomycota - glomeromycota
    The ancestors of fungi are believed to be simple aquatic forms with flagellated spores, similar to members of the extant phylum Chytridiomycota (chytrids). Current classifications assume that chytrids form an early-diverging clade within the kingdom Fungi and imply a single loss of the spore flagellum, leading to the diversification of terrestrial fungi. Here we develop phylogenetic hypotheses for Fungi using data from six gene regions and nearly 200 species. Our results indicate that there may have been at least four independent losses of the flagellum in the kingdom Fungi. These losses of swimming spores coincided with the evolution of new mechanisms of spore dispersal, such as aerial dispersal in mycelial groups and polar tube eversion in the microsporidia (unicellular forms that lack mitochondria). The enigmatic microsporidia seem to be derived from an endoparasitic chytrid ancestor similar to Rozella allomycis, on the earliest diverging branch of the fungal phylogenetic tree
    Indications for the involvement of a CYP3A-like iso-enzyme in the metabolism of chlorobornane (Toxaphene®) congeners in seals from inhibition studies with liver microsomes
    Hezik, C.M. van; Letcher, R.J. ; Geus, H.J. de; Wester, P.G. ; Goksoyr, A. ; Lewis, W.E. ; Boon, J.P. - \ 2001
    Aquatic Toxicology 51 (2001)3. - ISSN 0166-445X - p. 319 - 333.
    In vitro estrogenicity of polybrominated diphenyl ethers, hydroxylated PBDEs, and polybrominated bisphenol A compounds
    Meerts, I.A.T.M. ; Letcher, R.J. ; Hoving, S. ; Marsh, G. ; Bergman, A. ; Lemmen, J.G. ; Burg, B. van der; Brouwer, A. - \ 2001
    Environmental Health Perspectives 109 (2001). - ISSN 0091-6765 - p. 399 - 407.
    Polybrominated diphenyl ethers (PBDEs) are used in large quantities as additive flame retardants in plastics and textile materials. PBDEs are persistent compounds and have been detected in wildlife and in human adipose tissue and plasma samples. In this study, we investigated the (anti)estrogenic potencies of several PBDE congeners, three hydroxylated PBDEs (HO-PBDEs), and differently brominated bisphenol A compounds in three different cell line assays based on estrogen receptor (ER)-dependent luciferase reporter gene expression. In human T47D breast cancer cells stably transfected with an estrogen-responsive luciferase reporter gene construct (pEREtata-Luc), 11 PBDEs showed estrogenic potencies, with concentrations leading to 50␒nduction (EC50) varying from 2.5 to 7.3 μM. The luciferase induction of the most potent HO-PBDE [2-bromo-4-(2,4,6-tribromophenoxy)phenol] exceeded that of estradiol (E2), though at concentrations 50,000 times higher. As expected, brominated bisphenol A compounds with the lowest degree of bromination showed highest estrogenic potencies (EC50 values of 0.5 μM for 3-monobromobisphenol A). In an ERα-specific, stably transfected human embryonic kidney cell line (293-ERα-Luc), the HO-PBDE 4-(2,4,6-tribromophenoxy)phenol was a highly potent estrogen with an EC50 < 0.1 μM and a maximum 35- to 40-fold induction, which was similar to E2. In an analogous ERβ-specific 293-ERβs-Luc cell line, the agonistic potency of the 4-(2,4,6-tribromophenoxy)phenol was much lower (maximum 50␒nduction compared to E2), but EC50 values were comparable. These results indicate that several pure PBDE congeners, but especially HO-PBDEs and brominated bisphenol A-analogs, are agonists of both ERα and ERβ receptors, thus stimulating ER-mediated luciferase induction in vitro. These data also suggest that in vivo metabolism of PBDEs may produce more potent pseudoestrogens.
    Identification of 4-hydroxyheptachlorostyrene in polar bear plasma and its binding affinity to transthyretin : a metabolite of octachlorostyrene?
    Standau, C.D. ; Meerts, I.A.T.M. ; Letcher, R.J. ; McAlees, A.J. ; Chittim, B. ; Brouwer, A. ; Norstrom, R.J. - \ 2000
    Environmental Science and Technology 34 (2000)18. - ISSN 0013-936X - p. 3871 - 3877.
    A new compound, 4-hydroxyheptachlorostyrene (4-OH-HpCS), was identified as a major component in the chlorinated phenolic compound fraction of polar bear plasma. The structure was hypothesized to be 4-OH-HpCS based on mass spectral interpretation, the assumption that it was a metabolite of octachlorostyrene, and the similarity of the structure to hydroxylated polychlorinated biphenyls (OH-PCBs) identified in plasma. High-resolution, electron impact (EI) ionization mass spectrometry of the methylated compound indicated a molecular formula of C9H3OCl7 and major fragment ions of [M - 15] , [M - 35] , and [M - 43] , which was a mass spectral pattern identical to a synthesized and methylated 4-OH-HpCS standard. The identity was further confirmed by matching gas chromatography (GC) retention times on three different GC columns of differing polarity. Levels of 4-OH-HpCS ranged from 2.89 to 22.9 ng/g wet weight in polar bear plasma (N = 30) and constituted between 3.8 and 24.8␘f the total quantified level of chlorinated phenolic compounds. The mean ratio of 4-OH-HpCS to CB153 concentrations in polar bear plasma samples was 0.712 (± 0.580 SD), which suggests selective retention of the 4-OH-HpCS in plasma. The presumed mechanism of retention involves 4-OH-HpCS binding to transthyretin (TTR). The presence of TTR was confirmed for the first time in polar bear plasma by binding of 125I-thyroxine (T4), the natural ligand of TTR, to separated plasma proteins. The binding affinity of 4-OH-HpCS to human TTR was tested and found to be 1.1 relative to T4. This suggests that 4-OH-HpCS has the potential to disrupt T4 and retinol transport, by analogy to OH-PCBs with similar structure. Metabolism of octachlorostyrene (OCS) is the most likely source of 4-OH-HpCS. OCS was shown to be present at low concentrations in polar bear tissues as well as in plasma of ringed seal, the principal prey species of polar bears. The ratio of 4-OH-HpCS to OCS and 4-OH-HpCS to CB153 concentrations were 150- and 44-fold higher in polar bear plasma than in ringed seal plasma. This study indicates that the phenolic metabolites of relatively minor contaminants possess the capacity to bind to circulating proteins, and their significance as potential endocrine-disrupting agents may be underestimated.
    In vitro thyroidogenic estrogenic and dioxin-like activity of polybrominated diphenyl ethers (PBDEs)
    Meerts, I.A.T.M. ; Letcher, R. ; Hoving, S. ; Leeuwen-Bol, I. van; Luijks, E.A.C. ; Bergman, A. ; Brouwer, A. - \ 2000
    In: SETAC Congres 2000. - [S.l..] : [s.n.], 2000 - p. np 03:A1 - np 03:A1.
    In vitro estrogenic potency of polybrominated diphenyl ethers
    Hoving, S. ; Meerts, I.A.T.M. ; Letcher, E. ; Bergman, A. ; Burg, B. van der; Brouwer, A. - \ 2000
    The Toxicologist 54 (2000)1. - ISSN 0731-9193 - p. 238 - 238.
    Anti-oestrogenic effects of four toxaphene congeners and the technical mixture in stably transfected human T47D.Luc breast cancer cells
    Drenth, H.J. ; Letcher, R.J. ; Legler, J. ; Oehme, M. ; Brouwer, A. ; Berg, M. van den - \ 2000
    Organohalogen Compounds 49 (2000). - ISSN 1026-4892 - p. 367 - 370.
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