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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    Altered Gut Microbial Fermentation and Colonization with Methanobrevibacter smithii in Renal Transplant Recipients
    Knobbe, Tim J. ; Douwes, Rianne M. ; Kremer, Daan ; Swarte, Casper J. ; Eisenga, Michele F. ; Gomes-Neto, António W. ; Londen, Marco van; Peters, Frans T.M. ; Blokzijl, Hans ; Nolte, Ilja M. ; Hendriks, Wouter H. ; Harmsen, Hermie J.M. ; Bakker, Stephan J.L. - \ 2020
    Journal of Clinical Medicine 9 (2020)2. - ISSN 2077-0383
    Renal transplant recipients (RTRs) often suffer from posttransplant diarrhea. The observed dysbiosis in RTR may influence the fermentation processes in the gut. In this study, we aimed to investigate whether fermentation differs between RTRs and healthy controls (HCs), by measuring breath H2 and CH4 concentrations. Additionally, we determined the fecal presence of the methanogen Methanobrevibacter smithii (M. smithii), which plays a main role in the process of methanogenesis. Data from the TransplantLines Biobank and Cohort Study (NCT03272841) was used. A total of 142 RTRs and 77 HCs were included. Breath H2 concentrations in RTRs were not significantly different from HCs. Breath CH4 concentrations in RTRs were significantly lower compared with HCs (median [interquartile range (IQR)] 7.5 [3.9–10.6] ppm vs. 16.0 [8.0–45.5] ppm, p < 0.001). M. smithii was less frequently present in the feces of RTRs compared to HCs (28.6% vs. 86.4% resp., p < 0.001). Our findings regarding the altered methanogenesis in the gut of RTRs show similarities with previous results in inflammatory bowel disease patients. These findings provide novel insight into the alterations of fermentation after renal transplantation, which may contribute to understanding the occurrence of posttransplant diarrhea. View Full-Text
    Urinary Excretion of N1-Methylnicotinamide and N1-Methyl-2-Pyridone-5-Carboxamide and Mortality in Kidney Transplant Recipients
    Deen, Carolien P.J. ; Veen, Anna van der; Gomes-Neto, António W. ; Geleijnse, Johanna M. ; Borgonjen van den Berg, Karin J. ; Heiner-Fokkema, M.R. ; Kema, Ido P. ; Bakker, Stephan J.L. - \ 2020
    Nutrients 12 (2020)7. - ISSN 2072-6643
    dietary intake - mortality - N1-methyl-2-pyridone-5-carboxamide - N1-methylnicotinamide - niacin status - renal transplantation - tryptophan - urinary excretion - vitamin B3

    It is unclear whether niacin nutritional status is a target for improvement of long-term outcome after renal transplantation. The 24-h urinary excretion of N1-methylnicotinamide (N1-MN), as a biomarker of niacin status, has previously been shown to be negatively associated with premature mortality in kidney transplant recipients (KTR). However, recent evidence implies higher enzymatic conversion of N1-MN to N1-methyl-2-pyridone-5-carboxamide (2Py) in KTR, therefore the need exists for interpretation of both N1-MN and 2Py excretion for niacin status assessment. We assessed niacin status by means of the 24-h urinary excretion of the sum of N1-MN and 2Py (N1-MN + 2Py), and its associations with risk of premature mortality in KTR. N1-MN + 2Py excretion was measured in a longitudinal cohort of 660 KTR with LS-MS/MS. Prospective associations of N1-MN + 2Py excretion were investigated with Cox regression analyses. Median N1-MN + 2Py excretion was 198.3 (155.9-269.4) µmol/day. During follow-up of 5.4 (4.7-6.1) years, 143 KTR died, of whom 40 due to an infectious disease. N1-MN + 2Py excretion was negatively associated with risk of all-cause mortality (HR 0.61; 95% CI 0.47-0.79; p < 0.001), and infectious mortality specifically (HR 0.47; 95% CI 0.29-0.75; p = 0.002), independent of potential confounders. Secondary analyses showed effect modification of hs-CRP on the negative prospective association of N1-MN + 2Py excretion, and sensitivity analyses showed negative and independent associations of N1-MN and 2Py excretion with risk of all-cause mortality separately. These findings add further evidence to niacin status as a target for nutritional strategies for improvement of long-term outcome in KTR.

    The global abundance of tree palms
    Muscarella, Robert ; Emilio, Thaise ; Phillips, Oliver L. ; Lewis, Simon L. ; Slik, Ferry ; Baker, William J. ; Couvreur, Thomas L.P. ; Eiserhardt, Wolf L. ; Svenning, Jens Christian ; Affum-Baffoe, Kofi ; Aiba, Shin Ichiro ; Almeida, Everton C. de; Almeida, Samuel S. de; Oliveira, Edmar Almeida de; Álvarez-Dávila, Esteban ; Alves, Luciana F. ; Alvez-Valles, Carlos Mariano ; Carvalho, Fabrício Alvim ; Guarin, Fernando Alzate ; Andrade, Ana ; Aragão, Luis E.O.C. ; Murakami, Alejandro Araujo ; Arroyo, Luzmila ; Ashton, Peter S. ; Corredor, Gerardo A.A. ; Baker, Timothy R. ; Camargo, Plinio Barbosa de; Barlow, Jos ; Bastin, Jean François ; Bengone, Natacha Nssi ; Berenguer, Erika ; Berry, Nicholas ; Blanc, Lilian ; Böhning-Gaese, Katrin ; Bonal, Damien ; Bongers, Frans ; Bradford, Matt ; Brambach, Fabian ; Brearley, Francis Q. ; Brewer, Steven W. ; Camargo, Jose L.C. ; Campbell, David G. ; Castilho, Carolina V. ; Castro, Wendeson ; Catchpole, Damien ; Cerón Martínez, Carlos E. ; Chen, Shengbin ; Chhang, Phourin ; Cho, Percival ; Chutipong, Wanlop ; Clark, Connie ; Collins, Murray ; Comiskey, James A. ; Medina, Massiel Nataly Corrales ; Costa, Flávia R.C. ; Culmsee, Heike ; David-Higuita, Heriberto ; Davidar, Priya ; Aguila-Pasquel, Jhon del; Derroire, Géraldine ; Fiore, Anthony Di; Do, Tran Van; Doucet, Jean Louis ; Dourdain, Aurélie ; Drake, Donald R. ; Ensslin, Andreas ; Erwin, Terry ; Ewango, Corneille E.N. ; Ewers, Robert M. ; Fauset, Sophie ; Feldpausch, Ted R. ; Ferreira, Joice ; Ferreira, Leandro Valle ; Fischer, Markus ; Franklin, Janet ; Fredriksson, Gabriella M. ; Gillespie, Thomas W. ; Gilpin, Martin ; Gonmadje, Christelle ; Gunatilleke, Arachchige Upali Nimal ; Hakeem, Khalid Rehman ; Hall, Jefferson S. ; Hamer, Keith C. ; Harris, David J. ; Harrison, Rhett D. ; Hector, Andrew ; Hemp, Andreas ; Herault, Bruno ; Pizango, Carlos Gabriel Hidalgo ; Honorio Coronado, Eurídice N. ; Hubau, Wannes ; Hussain, Mohammad Shah ; Ibrahim, Faridah Hanum ; Imai, Nobuo ; Joly, Carlos A. ; Joseph, Shijo ; Anitha, K. ; Kartawinata, Kuswata ; Kassi, Justin ; Killeen, Timothy J. ; Kitayama, Kanehiro ; Klitgård, Bente Bang ; Kooyman, Robert ; Labrière, Nicolas ; Larney, Eileen ; Laumonier, Yves ; Laurance, Susan G. ; Laurance, William F. ; Lawes, Michael J. ; Levesley, Aurora ; Lisingo, Janvier ; Lovejoy, Thomas ; Lovett, Jon C. ; Lu, Xinghui ; Lykke, Anne Mette ; Magnusson, William E. ; Mahayani, Ni Putu Diana ; Malhi, Yadvinder ; Mansor, Asyraf ; Peña, Jose Luis Marcelo ; Marimon-Junior, Ben H. ; Marshall, Andrew R. ; Melgaco, Karina ; Bautista, Casimiro Mendoza ; Mihindou, Vianet ; Millet, Jérôme ; Milliken, William ; Mohandass, D. ; Mendoza, Abel Lorenzo Monteagudo ; Mugerwa, Badru ; Nagamasu, Hidetoshi ; Nagy, Laszlo ; Seuaturien, Naret ; Nascimento, Marcelo T. ; Neill, David A. ; Neto, Luiz Menini ; Nilus, Rueben ; Vargas, Mario Percy Núñez ; Nurtjahya, Eddy ; Araújo, R.N.O. de; Onrizal, Onrizal ; Palacios, Walter A. ; Palacios-Ramos, Sonia ; Parren, Marc ; Paudel, Ekananda ; Morandi, Paulo S. ; Pennington, R.T. ; Pickavance, Georgia ; Pipoly, John J. ; Pitman, Nigel C.A. ; Poedjirahajoe, Erny ; Poorter, Lourens ; Poulsen, John R. ; Prasad, P.R.C. ; Prieto, Adriana ; Puyravaud, Jean Philippe ; Qie, Lan ; Quesada, Carlos A. ; Ramírez-Angulo, Hirma ; Razafimahaimodison, Jean Claude ; Reitsma, Jan Meindert ; Requena-Rojas, Edilson J. ; Correa, Zorayda Restrepo ; Rodriguez, Carlos Reynel ; Roopsind, Anand ; Rovero, Francesco ; Rozak, Andes ; Lleras, Agustín Rudas ; Rutishauser, Ervan ; Rutten, Gemma ; Punchi-Manage, Ruwan ; Salomão, Rafael P. ; Sam, Hoang Van; Sarker, Swapan Kumar ; Satdichanh, Manichanh ; Schietti, Juliana ; Schmitt, Christine B. ; Marimon, Beatriz Schwantes ; Senbeta, Feyera ; Nath Sharma, Lila ; Sheil, Douglas ; Sierra, Rodrigo ; Silva-Espejo, Javier E. ; Silveira, Marcos ; Sonké, Bonaventure ; Steininger, Marc K. ; Steinmetz, Robert ; Stévart, Tariq ; Sukumar, Raman ; Sultana, Aisha ; Sunderland, Terry C.H. ; Suresh, Hebbalalu Satyanarayana ; Tang, Jianwei ; Tanner, Edmund ; Steege, Hans ter; Terborgh, John W. ; Theilade, Ida ; Timberlake, Jonathan ; Torres-Lezama, Armando ; Umunay, Peter ; Uriarte, María ; Gamarra, Luis Valenzuela ; Bult, Martin van de; Hout, Peter van der; Martinez, Rodolfo Vasquez ; Vieira, Ima Célia Guimarães ; Vieira, Simone A. ; Vilanova, Emilio ; Cayo, Jeanneth Villalobos ; Wang, Ophelia ; Webb, Campbell O. ; Webb, Edward L. ; White, Lee ; Whitfeld, Timothy J.S. ; Wich, Serge ; Willcock, Simon ; Wiser, Susan K. ; Young, Kenneth R. ; Zakaria, Rahmad ; Zang, Runguo ; Zartman, Charles E. ; Zo-Bi, Irié Casimir ; Balslev, Henrik - \ 2020
    Global Ecology and Biogeography 29 (2020)9. - ISSN 1466-822X - p. 1495 - 1514.
    above-ground biomass - abundance patterns - Arecaceae - local abiotic conditions - Neotropics - pantropical biogeography - tropical rainforest - wood density

    Aim: Palms are an iconic, diverse and often abundant component of tropical ecosystems that provide many ecosystem services. Being monocots, tree palms are evolutionarily, morphologically and physiologically distinct from other trees, and these differences have important consequences for ecosystem services (e.g., carbon sequestration and storage) and in terms of responses to climate change. We quantified global patterns of tree palm relative abundance to help improve understanding of tropical forests and reduce uncertainty about these ecosystems under climate change. Location: Tropical and subtropical moist forests. Time period: Current. Major taxa studied: Palms (Arecaceae). Methods: We assembled a pantropical dataset of 2,548 forest plots (covering 1,191 ha) and quantified tree palm (i.e., ≥10 cm diameter at breast height) abundance relative to co-occurring non-palm trees. We compared the relative abundance of tree palms across biogeographical realms and tested for associations with palaeoclimate stability, current climate, edaphic conditions and metrics of forest structure. Results: On average, the relative abundance of tree palms was more than five times larger between Neotropical locations and other biogeographical realms. Tree palms were absent in most locations outside the Neotropics but present in >80% of Neotropical locations. The relative abundance of tree palms was more strongly associated with local conditions (e.g., higher mean annual precipitation, lower soil fertility, shallower water table and lower plot mean wood density) than metrics of long-term climate stability. Life-form diversity also influenced the patterns; palm assemblages outside the Neotropics comprise many non-tree (e.g., climbing) palms. Finally, we show that tree palms can influence estimates of above-ground biomass, but the magnitude and direction of the effect require additional work. Conclusions: Tree palms are not only quintessentially tropical, but they are also overwhelmingly Neotropical. Future work to understand the contributions of tree palms to biomass estimates and carbon cycling will be particularly crucial in Neotropical forests.

    Sequence analysis of Ricinus communis small heat-shock protein (sHSP) subfamily and its role in abiotic stress responses
    Neto, Valdir G. ; Barbosa, Rhaissa R. ; Carosio, Maria G.A. ; Ferreira, Antônio G. ; Fernandez, Luzimar G. ; Castro, Renato D. de; Ligterink, Wilco ; Hilhorst, Henk ; Ribeiro, Paulo R. - \ 2020
    Industrial Crops and Products 152 (2020). - ISSN 0926-6690
    Abiotic stress - Oilseed crop - Regulatory mechanisms - Tolerance

    Small heat shock proteins (sHSPs) possess major roles in plant defense mechanisms towards abiotic stresses. sHSPs act as molecular chaperones providing the necessary tools to sustain cellular homeostasis under adverse conditions. sHSP genes display specific expression signatures, which depend on tissue-specificity, developmental stage and the nature of the abiotic stress. Despite the fact that Ricinus communis is an important oilseed crop with large socioeconomic impact on small family farmers in semi-arid regions worldwide, the characterization of RcsHSP genes and their possible contribution to plant survival under harsh environmental conditions has not been addressed. Hence, this study aimed at characterizing the R. communis sHSP subfamily, through phylogeny, gene structure, duplication, and expression profile analysis, as well as by characterizing Arabidopsis thaliana seeds overexpressing RcsHSP genes. We identified 41 RcsHSP genes with the α-crystallin domain and compatible molecular weight (<43 kDa). The RcsHSP subfamily showed different homology levels with sHSP genes from other plant species, suggesting the occurrence of specific gene expansion and loss. The RcsHSP subfamily was classified according to the cellular locations of the genes, which included cytosolic, chloroplastic, mitochondrial, and endoplasmic reticulum groups. Ten putative motifs were found among RcsHSP genes, but only motifs 4, 6 and 8 were sHSP protein domains. The RcsHSP subfamily showed 19 genes produced by tandem duplication events, which might have been crucial for RcsHSP diversification and acquisition of tolerance in R. communis. Gene expression analysis showed that the RcsHSP subfamily possesses different regulatory mechanisms in response to various abiotic stresses. Additionally, overexpression of RcsHSP genes in A. thaliana was followed by enhanced SOD activity and higher content of osmoprotectants, which ultimately led to enhanced seed germination under a variety of abiotic stresses. Our results may contribute to breeding programs aiming at developing high tolerant R. communis plants, providing economic and social support for farmers in semiarid areas worldwide.

    Mediterranean diet intervention alters the gut microbiome in older people reducing frailty and improving health status : The NU-AGE 1-year dietary intervention across five European countries
    Ghosh, Tarini Shankar ; Rampelli, Simone ; Jeffery, Ian B. ; Santoro, Aurelia ; Neto, Marta ; Capri, Miriam ; Giampieri, Enrico ; Jennings, Amy ; Candela, Marco ; Turroni, Silvia ; Zoetendal, Erwin G. ; Hermes, Gerben D.A. ; Elodie, Caumon ; Brugere, Corinne Malpuech ; Pujos-Guillot, Estelle ; Berendsen, Agnes M. ; Groot, Lisette C.P.G.M. De; Feskens, Edith J.M. ; Kaluza, Joanna ; Pietruszka, Barbara ; Bielak, Marta Jeruszka ; Comte, Blandine ; Maijo-Ferre, Monica ; Nicoletti, Claudio ; Vos, Willem M. de; Fairweather-Tait, Susan ; Cassidy, Aedin ; Brigidi, Patrizia ; Franceschi, Claudio ; O'Toole, Paul W. - \ 2020
    Gut 69 (2020)7. - ISSN 0017-5749
    ageing - diet - enteric bacterial microflora - inflammation - intestinal bacteria

    Objective: Ageing is accompanied by deterioration of multiple bodily functions and inflammation, which collectively contribute to frailty. We and others have shown that frailty co-varies with alterations in the gut microbiota in a manner accelerated by consumption of a restricted diversity diet. The Mediterranean diet (MedDiet) is associated with health. In the NU-AGE project, we investigated if a 1-year MedDiet intervention could alter the gut microbiota and reduce frailty. Design: We profiled the gut microbiota in 612 non-frail or pre-frail subjects across five European countries (UK, France, Netherlands, Italy and Poland) before and after the administration of a 12-month long MedDiet intervention tailored to elderly subjects (NU-AGE diet). Results: Adherence to the diet was associated with specific microbiome alterations. Taxa enriched by adherence to the diet were positively associated with several markers of lower frailty and improved cognitive function, and negatively associated with inflammatory markers including C-reactive protein and interleukin-17. Analysis of the inferred microbial metabolite profiles indicated that the diet-modulated microbiome change was associated with an increase in short/branch chained fatty acid production and lower production of secondary bile acids, p-cresols, ethanol and carbon dioxide. Microbiome ecosystem network analysis showed that the bacterial taxa that responded positively to the MedDiet intervention occupy keystone interaction positions, whereas frailty-associated taxa are peripheral in the networks. Conclusion: Collectively, our findings support the feasibility of improving the habitual diet to modulate the gut microbiota which in turn has the potential to promote healthier ageing.

    Mediterranean style diet and kidney function loss in kidney transplant recipients
    Gomes-Neto, António W. ; Osté, Maryse C.J. ; Sotomayor, Camilo G. ; Berg, Else van den; Geleijnse, Johanna Marianna ; Berger, Stefan P. ; Gans, Reinold O.B. ; Bakker, Stephan J.L. ; Navis, Gerjan J. - \ 2020
    Clinical Journal of the American Society of Nephrology 15 (2020)2. - ISSN 1555-9041 - p. 238 - 246.

    Background and objectives Despite improvement of short-term graft survival over recent years, long-term graft survival after kidney transplantation has not improved. Studies in the general population suggest the Mediterranean diet benefits kidney function preservation. We investigated whether adherence to the Mediterranean diet is associated with kidney outcomes in kidney transplant recipients. Design, setting, participants, & measurements We included 632 adult kidney transplant recipients with a functioning graft for ≥1 year. Dietary intake was inquired using a 177-item validated food frequency questionnaire. Adherence to the Mediterranean diet was assessed using a nine-point Mediterranean Diet Score. Primary end point of the study was graft failure and secondary end points included kidney function decline (doubling of serum creatinine or graft failure) and graft loss (graft failure or death with a functioning graft). Cox regression analyses were used to prospectively study the associations of the Mediterranean Diet Score with study end points. Results During median follow-up of 5.4 (interquartile range, 4.9–6.0) years, 76 participants developed graft failure, 119 developed kidney function decline, and 181 developed graft loss. The Mediterranean Diet Score was inversely associated with all study end points (graft failure: hazard ratio [HR], 0.68; 95% confidence interval [95% CI], 0.50 to 0.91; kidney function decline: HR, 0.68; 95% CI, 0.55 to 0.85; and graft loss: HR, 0.74; 95% CI, 0.63 to 0.88 per two-point increase in Mediterranean Diet Score) independent of potential confounders. We identified 24-hour urinary protein excretion and time since transplantation to be an effect modifier, with stronger inverse associations between the Mediterranean Diet Score and kidney outcomes observed in participants with higher urinary protein excretion and participants transplanted more recently. Conclusions Adherence to the Mediterranean diet is associated with better kidney function outcomes in kidney transplant recipients.

    NEOTROPICAL XENARTHRANS: a data set of occurrence of xenarthran species in the Neotropics
    Santos, Paloma Marques ; Bocchiglieri, Adriana ; Chiarello, Adriano Garcia ; Paglia, Adriano Pereira ; Moreira, Adryelle ; Souza, Agnis Cristiane de; Abba, Agustin Manuel ; Paviolo, Agustin ; Gatica, Ailin ; Medeiro, Akyllan Zoppi ; Costa, Alan Nilo ; Gallina, Alberto Gonzalez ; Yanosky, Alberto A. ; Jesus, Alejandro ; Bertassoni, Alessandra ; Rocha, Alessandro ; Bovo, Alex Augusto Abreu ; Bager, Alex ; Mol, Alexandra Cravino ; Martensen, Alexandre Camargo ; Faustino, Alexandre Casagrande ; Lopes, Alexandre Martins Costa ; Percequillo, Alexandre Reis ; Vogliotti, Alexandre ; Keuroghlian, Alexine ; Colina, María Alicia de la; Devlin, Allison L. ; García-Olaechea, Alvaro ; Sánchez, Amadeo ; Srbek-Araujo, Ana Carolina ; Ochoa, Ana Cecilia ; Oliveira, Ana Cristina Mendes ; Lacerda, Ana Cristyna Reis ; Campelo, Ana Kellen Nogueira ; Oliveira Paschoal, Ana Maria de; Costa, Ana Raíssa Cunha ; Meiga, Ana Yoko Ykeuti ; Jesus, Anamélia Souza ; Feijó, Anderson ; Hirsch, André ; Silva, André Luiz Ferreira da; Botelho, André Luis Moura ; Regolin, André Luis ; Lanna, André Monnerat ; Nunes, André Valle ; Kindel, Andreas ; Moraes, Andreia Magro ; Gatti, Andressa ; Noss, Andrew J. ; Nobre, Andrezza Bellotto ; Montanarin, Anelise ; Deffaci, Ângela Camila ; Albuquerque, Anna Carolina Figueiredo de; Oliveira, Anne Karoline de; Mangione, Antonio Marcelo ; Pontes, Antonio Rossano Mendes ; Bertoldi, Ariane Teixeira ; Calouro, Armando Muniz ; Desbiez, Arnaud L.J. ; Fernandes, Arthur ; Ferreguetti, Atilla Colombo ; Silva, Maria Augusta Andrade da; Zimbres, Barbara ; Luciano, Beatriz Fernandes Lima ; Thoisy, Benoit de; Niebuhr, Bernardo Brandão S. ; Papi, Bernardo ; Gómez-Valencia, Bibiana ; Santos, Bráulio A. ; Lima, Breno Campelo ; Oliveira, Bruna Gomes ; Santos, Bruna Silva ; Campos, Bruno Augusto Torres Parahyba ; Leles, Bruno ; Albuquerque França, Bruno Rodrigo de; Lim, Burton ; Oliveira, Caetano Troncoso ; Cantagallo, Camila ; Lara, Camila Clozato ; Lima, Camila Silveira ; Gestich, Carla Cristina ; Melo-Soares, Carla Danielle de; Peres, Carlos A. ; Kasper, Carlos Benhur ; Candia-Gallardo, Carlos ; Angelo, Carlos De; Fragoso, Carlos Eduardo ; Freitas, Carlos Henrique de; Salvador, Carlos Henrique ; Brocardo, Carlos R. ; Melo, Carolina Depolito ; Leuchtenberger, Caroline ; Braga, Caryne ; Sánchez-Lalinde, Catalina ; Bueno, Cecília ; Luna, Cecília Licarião ; Rojano, Cesar ; Hurtado, Cindy Meliza ; Santos, Cinthya Chiva dos; Tellaeche, Cintia ; Rosa, Clarissa ; Campos, Claudia Bueno de; Silva, Cláudia Regina ; Kanda, Claudia Zukeran ; Jenkins, Clinton N. ; McDonough, Colleen ; Trinca, Cristiano Trapé ; Cunha, Cristina Jaques da; Widmer, Cynthia Elisa ; Santos, Cyntia ; Buscariol, Daiane ; Carreira, Daiane Cristina ; Carvalho, Danianderson Rodrigues ; Silva Ferraz, Daniel da; Casali, Daniel ; Thornton, Daniel ; Vasconcellos, Daniela Rodrigues ; Barcelos, Daniele ; Brown, Danielle ; Ramos, Daniella Leal ; Moreira, Danielle Oliveira ; Yogui, Débora Regina ; Faria, Deborah ; Sana, Denis Alessio ; Mattia, Denise Lidoro de; Henz, Denison José ; Friedeberg, Diana B. ; Carvalho, Diana Letícia Kruger Pacheco ; Astúa, Diego ; Queirolo, Diego ; Varela, Diego M. ; Eaton, Donald P. ; Dias, Douglas Matos ; Rivadeneira, Edgar Federico ; Rocha, Ednaldo Cândido ; Abreu-Júnior, Edson Fiedler de; Carrano, Eduardo ; Santos, Eduardo Marques ; Setz, Eleonore Zulnara Freire ; Carvalho, Elildo Alves Ribeiro ; Almeida Chiquito, Elisandra de; Matos Cardoso, Elizandra de; Mendonça, Eloisa Neves ; Bastiani, Elvira D'; Vieira, Emerson M. ; Ramalho, Emiliano Esterci ; Guijosa-Guadarrama, Emiliano ; González, Enrique ; Maggiorini, Erica Vanessa ; Fischer, Erich ; Aguiar, Erick Francisco ; Castro, Érika Paula ; Peña-Cuéllar, Erika de la; Viveiros de Castro, Ernesto B. ; Brítez, Evelyn Beatriz ; Vanderhoeven, Ezequiel Andres ; Pedó, Ezequiel ; Rocha, Fabiana Lopes ; Girardi, Fabiane ; Oliveira Roque, Fabio de; Mazim, Fábio Dias ; Barros, Fabio Monteiro de; Martello, Felipe ; Fantacini, Felipe Moreli ; Pedrosa, Felipe ; Peters, Felipe Bortolotto ; Abra, Fernanda Delborgo ; Azevedo, Fernanda Cavalcanti de; Silva Santos, Fernanda da; Silva, Fernanda Guedes da; Teixeira, Fernanda Zimmermann ; Perini, Fernando Araujo ; Passos, Fernando C. ; Carvalho, Fernando ; Azevedo, Fernando Cesar Cascelli de; Pinho, Fernando Ferreira de; Gonçalves, Fernando ; Lima, Fernando ; Contreras-Moreno, Fernando M. ; Pedroni, Fernando ; Tortato, Fernando Rodrigo ; Santos, Filipe Pereira Rego ; Caruso, Flavia ; Tirelli, Flávia Pereira ; Miranda, Flávia Regina ; Rodrigues, Flávio Henrique Guimarães ; Ubaid, Flávio Kulaif ; Palmeira, Francesca Belem Lopes ; Silva, Franciane Almeida da; Grotta-Neto, Francisco ; Souza, Franco Leandro de; Costa, Francys Emanuelle ; Pérez-Garduza, Freddy ; Delsuc, Frédéric ; Lemos, Frederico ; Pinto, Fredy Ramirez ; Boaglio, Gabriel Ivan ; Massocato, Gabriel Fávero ; Preuss, Gabriel ; Hofmann, Gabriel Selbach ; Aguiar, Gabriel Lima ; Oliveira, Gabriela Schuck ; Duarte, Gabriela Teixeira ; Beca, Gabrielle ; Giné, Gastón Andrés Fernandez ; Batista, Graziele Oliveira ; Gil, Guillermo Eduardo ; Gonsioroski, Gustavo ; Secco, Helio ; Medeiros, Hugo Reis ; Coelho, Igor Pfeifer ; Franceschi, Ingridi Camboim ; Bernardi, Itiberê ; Torre, Antonio de la; Zocche, Jairo José ; Seibert, Jardel Brandão ; Faria Falcão, Jéssica Caroline de; Dias, Jéssica Helena Mangueira ; Nodari, Joana Zorzal ; Oliveira, João Alves ; Giovanelli, João Gabriel Ribeiro ; Favoretti, João Paulo Pandini ; Polisar, John ; Sponchiado, Jonas ; Cherem, Jorge José ; Ramírez, José Fernando Moreira ; Toledo, José Julio de; Duarte, José Maurício Barbanti ; Matos, Jose Roberto de; Arrabal, Juan Pablo ; Faria Oshima, Júlia Emi de; Ribeiro, Juliana Fernandes ; Bogoni, Juliano André ; Pacheco, Julio Javier Chacón ; Schuchmann, Karl L. ; Ferraz, Katia M.P.M.B. ; Santos Everton, Laís dos; Bailey, Larissa L. ; Gonçalves, Larissa Oliveira ; Cullen, Laury ; Andrade, Layla Reis de; Trevelin, Leonardo Carreira ; Bonjorne, Lilian ; Almeida Rodrigues, Livia de; Leuzinger, Lucas ; Perillo, Lucas Neves ; Araújo, Luciana Souza ; Hufnagel, Ludmila ; Ribeiro, Ludmilla Oliveira ; Bernardo, Luis Renato Rezende ; Oliveira-Santos, Luiz Gustavo Rodrigues ; Varzinczak, Luiz Henrique ; Borges, Luiz Henrique Medeiros ; Guimarães, Luiza Neves ; Möcklinghoff, Lydia ; Oliveira, Marcela Alvares ; Magioli, Marcelo ; Assis Jardim, Márcia Maria de; Oliveira, Márcio Leite de; Tortato, Marcos Adriano ; Dums, Marcos ; Iezzi, Maria Eugenia ; Pereira, Maria João Ramos ; Jorge, Maria Luísa ; Castro Morini, Maria Santina de; Landis, Mariana Bueno ; Xavier, Mariana Sampaio ; Barros, Marília A.S. ; Silva, Marina Lima da; Rivero, Marina ; Zanin, Marina ; Marques, Marinêz Isaac ; Alves, Mario Henrique ; Bitetti, Mario S. Di; Alvarez, Martín R. ; Graipel, Maurício Eduardo ; Godoi, Mauricio Neves ; Benedetti, Maximiliano Augusto ; Beltrão, Mayara Guimarães ; Monteiro, Miguel Coutinho Moretta ; Paula, Milton José de; Perilli, Miriam Lucia Lages ; Silva, Murillo Prado da; Villar, Nacho ; Albuquerque, Natasha Moraes De; Canassa, Nathália F. ; Filho, Newton Mota ; Rosa Oliveira, Nicole da; Pasqualotto, Nielson ; Cáceres, Nilton Carlos ; Attias, Nina ; Favarini, Marina Ochoa ; Ribeiro, Otávio Santi ; Gonçalves, Pablo Rodrigues ; Rocha, Patrício Adriano da; Condé, Paula Alves ; Akkawi, Paula ; Cruz, Paula ; Lira, Paula Koeler ; Ferreira, Paula Modenesi ; Arroyo-Gerala, Paulina ; Hartmann, Paulo Afonso ; Tarso Zuquim Antas, Paulo de; Marinho, Paulo Henrique ; Faria Peres, Pedro Henrique de; Peña-Mondragón, Juan Luis ; Lombardi, Pryscilla Moura ; Souza Laurindo, Rafael de; Alves, Rafael Souza Cruz ; Grangeiro, Raissa Danielle Praxedes ; Silva, Ramon Lima ; Beltrão-Mendes, Raone ; Bonikowski, Renata Twardowsky Ramalho ; Reppucci, Juan ; Arrais, Ricardo Corassa ; Sampaio, Ricardo ; Sartorello, Ricardo ; Bovendorp, Ricardo Siqueira ; McNab, Roan ; Hack, Robson Odeli Espíndola ; Magalhães, Rodolfo Assis ; Araújo, Rodrigo Costa ; Almeida Nobre, Rodrigo de; Pérez, Rodrigo Raúl León ; Massara, Rodrigo Lima ; Paula, Rogério Cunha de; Anleu, Rony García ; Marques, Rosane Vieira ; Dornas, Rubem ; Rolim, Samir Gonçalves ; Cavalcanti, Sandra M.C. ; Lima, Saulo Ramos ; Ballari, Sebastián A. ; Santamaría, Silvia Benito ; Silva, Sofia Marques ; Age, Stefani Gabrieli ; Godim, Tayana ; Sobral-Souza, Thadeu ; Maccarini, Thiago Bernardes ; Rodrigues, Thiago Ferreira ; Piovezan, Ubiratan ; Cunha Tavares, Valéria da; Quiroga, Verónica Andrea ; Krepschi, Victor Gasperotto ; Filho, Vilmar Picinatto ; Galvão Bastazini, Vinícius Augusto ; Oliveira Gasparotto, Vinicius Peron de; Orsini, Vinicius Santana ; Guedes Layme, Viviane Maria ; Hannibal, Wellington ; Dáttilo, Wesley ; Carvalho, William Douglas de; Loughry, William James ; Blanco, Yamil Edgardo Di; Núñez-Regueiro, Mauricio M. ; Giubbina, Marina Furlan ; Passamani, Marcelo ; Alagão Querido, Luciano Carramaschi de; Costa Toledo, Gustavo Alvez da; Ribeiro, Igor Kintopp ; Quintilham, Lucas ; Bustos, Soledad de; Maza, Javier de la; Lima Neto, Jorge Ferreira ; Kossel de Andrade Silva, Katyucha Von; Sartorello, Leonardo ; Rampim, Lilian Elaine ; Marás, Gustavo A. ; Camino, Micaela ; Freitas-Junior, Mozart ; Perovic, Pablo Gaston ; Paolino, Roberta Montanheiro ; Ferreira, Scarlat Dalva ; Towns, Valeria ; Esperandio, Isadora Beraldi ; Aximoff, Izar ; Beduschi, Júlia ; Guenther, Mariana ; Cassia Bianchi, Rita de; Keuroghlian-Eaton, Sean ; Mendes, Sérgio Lucena ; Fatima Cunha, Lerrane de; Cirignoli, Sebastián ; Ciocheti, Giordano ; Prado, Helena Alves do; Fernandes-Ferreira, Hugo ; Mendes de Sena, Liana Mara ; Yamane, Marcelo Hideki ; Brennand, Pamella G.G. ; Silva, Rayana Diniz da; Escobar, Santiago ; Endo, Whaldener ; Hurtado, Rafael Reyna ; Gontijo, Nila Rássia Costa ; Marsh, Laura K. ; Severo, Magnus Machado ; Pardo, Julia Martinez ; Costa, Sebastián Andrés ; Melo, Geruza Leal ; Santana, Gindomar Gomes ; Miranda Mourão, Guilherme de; Gaspari, Gustavo Gabirele ; Duarte, Herbert ; Cabral, Hugo ; Silva, Leonardo Henrique da; Mendonça, Luana ; Barbosa, Lucas Lobo ; Santos, Manuela Vieira dos; Moraes, Marcela Figuerêdo Duarte ; Gordo, Marcelo ; Versiani, Natalia Fraguas ; Cantero, Nicolás ; Pays, Olivier ; Guedes, Patrícia Gonçalves ; Colas-Rosas, Paul François ; Ribeiro, Paulo ; Renaud, Pierre Cyril ; Hoogesteijn, Rafael Jan ; Ayala, Rodrigo ; Cunha, Rogério Grassetto Teixeira da; Schaub, Roxane ; Laurito, Sabrina ; Betkowski, Samuel Eurich ; Cortez, Sara ; Silva, Shirley Seixas Pereira ; Oliveira, Tadeu Gomes de; Spironello, Wilson Roberto ; Gengler, Nicholas ; Hidalgo, Mircea Mihart ; Juárez, Rugieri ; Iglesias, Jesús A. ; Anacleto, Teresa Cristina ; Souza Fialho, Marcos de; Cavicchioli, Guilherme ; Beccato, Maria Angélica Barbosa ; Silva, Marcelo da; Neto, Omar Correia ; Lopes, Karine Galisteo Diemer ; Godoy, Leandro Perez ; Luiz, Micheli Ribeiro ; Rojas Bonzi, Viviana B. ; Ferreira, Guilherme Braga ; Oliveira, Marcelo Juliano Rabelo ; Hinojosa, Javier ; Oliveira, Luiz Flamarion Barbosa de; Nagy-Reis, Mariana Baldy ; Ramirez, Sixto Fernández ; Concone, Henrique Villas Boas ; Mourthe, Italo ; Martínez-Lanfranco, Juan A. ; Zanoni, Juliani Bruna ; Moreira, Tainah Cruz ; Guarderas, Zoila Vega ; Bazilio, Sérgio ; Cervini, Marcelo ; Pinheiro, Marcell Soares ; Morato, Ronaldo Gonçalves ; Peroni, Nivaldo ; Trigo, Tatiane Campos ; Machado, Ricardo Bomfim ; Gaspari, Fernando ; Koenemann, Joceleia G. ; Rudolf, Juan Carlos ; Benchimol, Maíra ; Vieira, Marcus Vinícius ; Retta, Lucía Martínez ; Santiago, Pablo Gerardo Fernández ; Ciccia, Paula Gonzalez ; Estrela, Pedro Cordeiro ; Carvalho, Santiago ; Esbérard, Carlos Eduardo Lustosa ; Cruz, Yaribeth Bravata de la; Castro-Prieto, Jessica ; Braga, Ricardo Miranda ; Cartes, Jose Luis ; Andrade-Núñez, María José ; Denkiewicz, Natalia Mariana ; Falconi, Nereyda ; Pezzuti, Juarez Carlos Brito ; Castillo Cordero, Hugo Fernando del; Sousa, Luziene Conceição de; Gaspari Júnior, Roque Lázaro de; Santos-Filho, Manoel ; Almeida, Josué Santos ; Thompson, Jeffrey J. ; Santos, Juliana Silveira dos; Pereira-Ribeiro, Juliane ; Burs, Kathrin ; Silva, Kena Ferrari Moreira da; Velilla, Marianela ; Silva, Marina Xavier da; Sancha, Noé U. de la; Pinheiro, Paula Fabiana ; Castilho, Pedro Volkmer de; Bercê, William ; Assis, Julia Camara ; Tonetti, Vinicius Rodrigues ; Alves-Eigenheer, Milene ; Chinem, Simonne ; Honda, Laura K. ; Godoy Bergallo, Helena de; Alberici, Vinicius ; Wallace, Robert ; Campos Krauer, Juan Manuel ; Ribeiro, Milton Cezar ; Galetti, Mauro - \ 2019
    Ecology 100 (2019)7. - ISSN 0012-9658
    biodiversity hotspot - cingulata - forest fragmentation - habitat loss - neotropical mammals - neotropical region - pilosa - xenarthra

    Xenarthrans—anteaters, sloths, and armadillos—have essential functions for ecosystem maintenance, such as insect control and nutrient cycling, playing key roles as ecosystem engineers. Because of habitat loss and fragmentation, hunting pressure, and conflicts with domestic dogs, these species have been threatened locally, regionally, or even across their full distribution ranges. The Neotropics harbor 21 species of armadillos, 10 anteaters, and 6 sloths. Our data set includes the families Chlamyphoridae (13), Dasypodidae (7), Myrmecophagidae (3), Bradypodidae (4), and Megalonychidae (2). We have no occurrence data on Dasypus pilosus (Dasypodidae). Regarding Cyclopedidae, until recently, only one species was recognized, but new genetic studies have revealed that the group is represented by seven species. In this data paper, we compiled a total of 42,528 records of 31 species, represented by occurrence and quantitative data, totaling 24,847 unique georeferenced records. The geographic range is from the southern United States, Mexico, and Caribbean countries at the northern portion of the Neotropics, to the austral distribution in Argentina, Paraguay, Chile, and Uruguay. Regarding anteaters, Myrmecophaga tridactyla has the most records (n = 5,941), and Cyclopes sp. have the fewest (n = 240). The armadillo species with the most data is Dasypus novemcinctus (n = 11,588), and the fewest data are recorded for Calyptophractus retusus (n = 33). With regard to sloth species, Bradypus variegatus has the most records (n = 962), and Bradypus pygmaeus has the fewest (n = 12). Our main objective with Neotropical Xenarthrans is to make occurrence and quantitative data available to facilitate more ecological research, particularly if we integrate the xenarthran data with other data sets of Neotropical Series that will become available very soon (i.e., Neotropical Carnivores, Neotropical Invasive Mammals, and Neotropical Hunters and Dogs). Therefore, studies on trophic cascades, hunting pressure, habitat loss, fragmentation effects, species invasion, and climate change effects will be possible with the Neotropical Xenarthrans data set. Please cite this data paper when using its data in publications. We also request that researchers and teachers inform us of how they are using these data

    ATLANTIC BIRD TRAITS: a data set of bird morphological traits from the Atlantic forests of South America
    Rodrigues, Rodolpho Credo ; Hasui, Érica ; Assis, Julia Camara ; Pena, João Carlos Castro ; Muylaert, Renata L. ; Tonetti, Vinicius Rodrigues ; Martello, Felipe ; Regolin, André Luis ; Vernaschi Vieira da Costa, Thiago ; Pichorim, Mauro ; Carrano, Eduardo ; Lopes, Leonardo Esteves ; Vasconcelos, Marcelo Ferreira de; Fontana, Carla Suertegaray ; Roos, Andrei Langeloh ; Gonçalves, Fernando ; Banks-Leite, Cristina ; Cavarzere, Vagner ; Efe, Marcio Amorim ; Alves, Maria Alice S. ; Uezu, Alexandre ; Metzger, Jean Paul ; Tarso Zuquim de Antas, Paulo de; Paschoaletto Micchi de Barros Ferraz, Katia Maria de; Calsavara, Larissa Corsini ; Bispo, Arthur Angelo ; Araujo, Helder F.P. ; Duca, Charles ; Piratelli, Augusto João ; Naka, Luciano N. ; Dias, Rafael Antunes ; Gatto, Cassiano A.F.R. ; Villegas Vallejos, Marcelo Alejandro ; Reis Menezes, Gregório dos; Bugoni, Leandro ; Rajão, Henrique ; Zocche, Jairo José ; Willrich, Guilherme ; Silva, Elsimar Silveira da; Manica, Lilian Tonelli ; Camargo Guaraldo, André de; Althmann, Giulyana ; Serafini, Patricia Pereira ; Francisco, Mercival Roberto ; Lugarini, Camile ; Machado, Caio Graco ; Marques-Santos, Fernando ; Bobato, Rafaela ; Souza, Elivan Arantes de; Donatelli, Reginaldo José ; Ferreira, Carolina Demetrio ; Morante-Filho, José Carlos ; Paes-Macarrão, Natalia Dantas ; Macarrão, Arthur ; Lima, Marcos Robalinho ; Jacoboski, Lucilene Inês ; Candia-Gallardo, Carlos ; Alegre, Vanesa Bejarano ; Jahn, Alex E. ; Camargo Barbosa, Karlla Vanessa de; Cestari, Cesar ; Silva, José Nilton da; Silveira, Natalia Stefanini da; Vara Crestani, Ana Cristina ; Petronetto, Adeliane Peterle ; Abreu Bovo, Alex Augusto ; Viana, Anderson Durão ; Araujo, Andrea Cardoso ; Santos, Andressa Hartuiq dos; Araújo do Amaral, Andreza Clarinda ; Ferreira, Ariane ; Vieira-Filho, Arnaldo Honorato ; Ribeiro, Bianca Costa ; Missagia, Caio C.C. ; Bosenbecker, Camila ; Bronzato Medolago, Cesar Augusto ; Rodriguez Espínola, Cid Rodrigo ; Faxina, Claudenice ; Campodonio Nunes, Cristiane Estrela ; Prates, Cristine ; Apolinario da Luz, Daniela Tomasio ; Moreno, Daniele Janina ; Mariz, Daniele ; Faria, Deborah ; Meyer, Douglas ; Doná, Eder Afonso ; Alexandrino, Eduardo Roberto ; Fischer, Erich ; Girardi, Fabiane ; Giese, Felipe Borba ; Santos Shibuya, Felipe Leonardo ; Faria, Fernando Azevedo ; Bittencourt de Farias, Fernando ; Lima Favaro, Fernando de; Ferneda Freitas, Fernando José ; Chaves, Flávia G. ; Guedes Las-Casas, Flor Maria ; Rosa, Gabriel L.M. ; Massaccesi de laTorre, Gabriel ; Bochio, Gabriela Menezes ; Bonetti, Giselle Evelise ; Kohler, Glauco ; Toledo-Lima, Guilherme Santos ; Plucenio, Gustavo Piletti ; Menezes, Ícaro ; Denóbile Torres, Ingrid Maria ; Carvalho Provinciato, Ivan Celso ; Viana, Ivan Réus ; Roper, James Joseph ; Persegona, Jaqueline Evelyn ; Barcik, Jean Júnior ; Martins-Silva, Jimi ; Gava Just, João Paulo ; Tavares-Damasceno, João Paulo ; Almeida Ferreira, João Ricardo de; Rodrigues Rosoni, Jonas Rafael ; Teixeira Falcon, José Eduardo ; Schaedler, Laura Maria ; Mathias, Leonardo Brioschi ; Deconto, Leonardo Rafael ; Cruz Rodrigues, Licléia da; Meyer, Marcela Afonso P. ; Repenning, Márcio ; Melo, Marcos Antônio ; Santos de Carvalho, Maria Amélia ; Rodrigues, Marcos ; Conti Nunes, Maria Flavia ; Ogrzewalska, Maria Halina ; Lopes Gonçalves, Mariana ; Vecchi, Maurício B. ; Bettio, Maurício ; Matta Baptista, Michelle Noronha da; Arantes, Murilo Sérgio ; Ruiz, Nicolás Luciano ; Bisetto de Andrade, Paulo Guilherme ; Lima Ribeiro, Pedro Henrique ; Galetti Junior, Pedro Manoel ; Macario, Phoeve ; Oliveira Fratoni, Rafael de; Meurer, Rafael ; Saint-Clair, Rafael S. ; Romagna, Rafael Spilere ; Alves Lacerda, Raquel Caroline ; Serpa Cerboncini, Ricardo Augusto ; Lyra, Ricardo Brioschi ; Lau, Ricardo ; Rodrigues, Roberta Costa ; Faria, Rogério Rodrigues ; Laps, Rudi Ricardo ; Althoff, Sérgio Luiz ; Jesus, Shayana de; Namba, Sumiko ; Braga, Talita Vieira ; Molin, Tamara ; França Câmara, Thanyria P. ; Enedino, Thayz Rodrigues ; Wischhoff, Uschi ; Oliveira, Vanessa Cristina de; Leandro-Silva, Victor ; Araújo-Lima, Vitor ; Oliveira Lunardi, Vitor de; Gusmão, Reginaldo Farias de; Souza Correia, Jozélia Maria de; Gaspar, Lucas P. ; Batista Fonseca, Renata Cristina ; Fonseca Pires Neto, Paulo Affonso ; Medeiros Morato de Aquino, Ana Carla ; Camargo, Bruna Betagni de; Cezila, Beatriz Azevedo ; Costa, Leonardo Marques ; Paolino, Roberta Montanheiro ; Kanda, Claudia Zukeran ; Monteiro, Erison C.S. ; Oshima, Júlia Emi F. ; Alves-Eigenheer, Milene ; Pizo, Marco Aurelio ; Silveira, Luís F. ; Galetti, Mauro ; Ribeiro, Milton Cezar - \ 2019
    Ecology 100 (2019)6. - ISSN 0012-9658
    body size - functional diversity - individual variation - interspecific variation - phenotypic plasticity - phylogenetic diversity - rapid evolution - tropical forest

    Scientists have long been trying to understand why the Neotropical region holds the highest diversity of birds on Earth. Recently, there has been increased interest in morphological variation between and within species, and in how climate, topography, and anthropogenic pressures may explain and affect phenotypic variation. Because morphological data are not always available for many species at the local or regional scale, we are limited in our understanding of intra- and interspecies spatial morphological variation. Here, we present the ATLANTIC BIRD TRAITS, a data set that includes measurements of up to 44 morphological traits in 67,197 bird records from 2,790 populations distributed throughout the Atlantic forests of South America. This data set comprises information, compiled over two centuries (1820–2018), for 711 bird species, which represent 80% of all known bird diversity in the Atlantic Forest. Among the most commonly reported traits are sex (n = 65,717), age (n = 63,852), body mass (n = 58,768), flight molt presence (n = 44,941), molt presence (n = 44,847), body molt presence (n = 44,606), tail length (n = 43,005), reproductive stage (n = 42,588), bill length (n = 37,409), body length (n = 28,394), right wing length (n = 21,950), tarsus length (n = 20,342), and wing length (n = 18,071). The most frequently recorded species are Chiroxiphia caudata (n = 1,837), Turdus albicollis (n = 1,658), Trichothraupis melanops (n = 1,468), Turdus leucomelas (n = 1,436), and Basileuterus culicivorus (n = 1,384). The species recorded in the greatest number of sampling localities are Basileuterus culicivorus (n = 243), Trichothraupis melanops (n = 242), Chiroxiphia caudata (n = 210), Platyrinchus mystaceus (n = 208), and Turdus rufiventris (n = 191). ATLANTIC BIRD TRAITS (ABT) is the most comprehensive data set on measurements of bird morphological traits found in a biodiversity hotspot; it provides data for basic and applied research at multiple scales, from individual to community, and from the local to the macroecological perspectives. No copyright or proprietary restrictions are associated with the use of this data set. Please cite this data paper when the data are used in publications or teaching and educational activities.

    ATLANTIC EPIPHYTES: a data set of vascular and non-vascular epiphyte plants and lichens from the Atlantic Forest
    Ramos, Flavio Nunes ; Mortara, Sara Ribeiro ; Monalisa-Francisco, Nathalia ; Elias, João Pedro Costa ; Neto, Luiz Menini ; Freitas, Leandro ; Kersten, Rodrigo ; Amorim, André Márcio ; Matos, Fernando Bittencourt ; Nunes-Freitas, André Felippe ; Alcantara, Suzana ; Alexandre, Marcia Helena Nagahama ; Almeida-Scabbia, Renata Jimenez de; Almeida, Odair José Garcia de; Alves, Fernanda Eliane ; Oliveira Alves, Rogério Marcos de; Alvim, Francine Seehaber ; Andrade, Antônio Carlos Silva de; Andrade, Simone de; Aona, Lidyanne Yuriko Saleme ; Araujo, Andréa Cardoso ; Araújo, Kelianne Carolina Targino de; Ariati, Vanessa ; Assis, Julia Camara ; Azevedo, Cecília Oliveira de; Barbosa, Bruno Ferreira ; Barbosa, Daniel Elias Ferreira ; Reis Barbosa, Fernando dos; Barros, Fabio de; Basilio, Geicilaine Alves ; Bataghin, Fernando Antonio ; Bered, Fernanda ; Bianchi, Juliana Santos ; Blum, Christopher Thomas ; Boelter, Carlos Renato ; Bonnet, Annete ; Brancalion, Pedro Henrique Santin ; Breier, Tiago Bӧer ; Toledo Brion, Caio de; Buzatto, Cristiano Roberto ; Cabral, Andressa ; Cadorin, Tiago João ; Caglioni, Eder ; Canêz, Luciana ; Cardoso, Pedro Henrique ; Carvalho, Fábia Silva de; Carvalho, Renan Gonçalves ; Catharino, Eduardo Luis Martins ; Ceballos, Sergio Javier ; Cerezini, Monise Terra ; César, Ricardo Gomes ; Cestari, Cesar ; Chaves, Cleber Juliano Neves ; Citadini-Zanette, Vanilde ; Coelho, Luiz Francisco Mello ; Coffani-Nunes, João Vicente ; Colares, Renato ; Colletta, Gabriel Dalla ; Medeiros Corrêa, Nadjara de; Ferreira da Costa, Andrea ; Costa, Grênivel Mota da; Costa, Laís Mara Santana ; Costa, Natália Gabriela Souza ; Couto, Dayvid Rodrigues ; Cristofolini, Caroline ; Rodrigues da Cruz, Ana Carolina ; Neri, Leopoldo Angelo Del; Pasquo, Mercedes di; Santos Dias, Aline dos; Carmo Dutra Dias, Letícia do; Dislich, Ricardo ; Duarte, Marília Cristina ; Fabricante, Juliano Ricardo ; Farache, Fernando H.A. ; Gelli de Faria, Ana Paula ; Faxina, Claudenice ; Terrola Martins Ferreira, Mariana ; Fischer, Erich ; Fonseca, Carlos Roberto ; Fontoura, Talita ; Francisco, Talitha Mayumi ; Furtado, Samyra Gomes ; Galetti, Mauro ; Garbin, Mário Luís ; Gasper, André Luís de; Goetze, Márcia ; Gomes-da-Silva, Janaína ; Gonçalves, Mateus Felipe Araujo ; Gonzaga, Diego Rafael ; Granero e Silva, Ana Carolina ; Camargo Guaraldo, André de; Souza Gomes Guarino, Ernestino de; Votri Guislon, Aline ; Bitencourt Hudson, Luigy ; Jardim, Jomar Gomes ; Jungbluth, Patricia ; Santos Kaeser, Selma dos; Musauer Kessous, Igor ; Mossmann Koch, Natália ; Kuniyoshi, Yoshiko Saito ; Labiak, Paulo Henrique ; Lapate, Maria Esther ; Laurenti Santos, Ana Carolina ; Barbosa Leal, Roberta Luísa ; Leite, Felipe Silveira ; Leitman, Paula ; Liboni, Ana Paula ; Liebsch, Dieter ; Lingner, Débora Vanessa ; Lombardi, Julio Antonio ; Lucas, Eve ; Reis Luzzi, Jhonny dos; Mai, Patricia ; Mania, Luiz Felipe ; Mantovani, Waldir ; Maragni, Angelica Guidoni ; Marques, Marcia Cristina Mendes ; Marquez, Gonzalo ; Martins, Cristiane ; Nascimento Martins, Laura do; Luiz Sanglard Silva Martins, Pedro ; Fregolente Faracco Mazziero, Frederico ; Aguiar Melo, Camila de; Fiuza de Melo, Maria Margarida ; Mendes, Alex Fernando ; Mesacasa, Letícia ; Cerdeira Morellato, Leonor Patricia ; Souza Moreno, Vanessa de; Muller, Adelcio ; Silva Murakami, Mariana Moreira da; Cecconello, Edinete ; Nardy, Camila ; Nervo, Michelle Helena ; Neves, Beatriz ; Guimarães Cardoso Nogueira, Matheus ; Nonato, Fabiana Regina ; Oliveira-Filho, Ary Teixeira de; Oliveira, César Pedro Lopes de; Overbeck, Gerhard Ernst ; Marcusso, Gabriel Mendes ; Paciencia, Mateus Luís Barradas ; Padilha, Patricia ; Padilha, Peterson Teodoro ; Pereira, Ana Clara Alves ; Pereira, Luciana Carvalho ; Pereira, Rodrigo Augusto Santinelo ; Pincheira-Ulbrich, Jimmy ; Pires, José Salatiel Rodrigues ; Pizo, Marco Aurélio ; Pôrto, Kátia Cavalcanti ; Rattis, Ludmila ; Rodrigues de Mendonça Reis, Joice ; Gonçalves dos Reis, Simone ; Rocha-Pessôa, Thereza Christina da; Rocha, Carlos Frederico Duarte ; Rocha, Fernando Souza ; Rodrigues, Alba Regina Pereira ; Rodrigues, Ricardo Ribeiro ; Rogalski, Juliana Marcia ; Rosanelli, Roberta Luiza ; Rossado, Andrés ; Rossatto, Davi Rodrigo ; Rother, Débora Cristina ; Ruiz-Miranda, Carlos Ramon ; Saiter, Felipe Zamborlini ; Sampaio, Mauricio Bonesso ; Santana, Lucas Deziderio ; Silveira dos Santos, Juliana ; Sartorello, Ricardo ; Sazima, Marlies ; Schmitt, Juliane Luzía ; Schneider, Geniane ; Schroeder, Bruna Grosch ; Sevegnani, Lucia ; Júnior, Vasconcelos Oliveira Silva ; Silva, Fernando Rodrigues da; Silva, Maria Juliana da; Silva, Mércia Patrícia Pereira ; Silva, Rafaela Guimarães ; Silva, Sandro Menezes ; Singer, Rodrigo Bustos ; Siqueira, Geovane ; Soares, Luis Eduardo ; Sousa, Hildeberto Caldas de; Spielmann, Adriano ; Tonetti, Vinicius Rodrigues ; Toniato, Maria Teresa Zugliani ; Ulguim, Paulo Sérgio Bordoni ; Berg, Cássio van den; Berg, Eduardo van den; Varassin, Isabela Galarda ; Silva, Izabela Bitencourt Veloso da; Vibrans, Alexander Christian ; Waechter, Jorge Luiz ; Weissenberg, Erick Willy ; Windisch, Paulo Günter ; Wolowski, Marina ; Yañez, Agustina ; Yoshikawa, Vania Nobuko ; Zandoná, Luciano Ramos ; Zanella, Camila Martini ; Zanin, Elisabete Maria ; Zappi, Daniela Cristina ; Zipparro, Valesca Bononi ; Zorzanelli, João Paulo Fernandes ; Ribeiro, Milton Cezar - \ 2019
    Ecology 100 (2019)2. - ISSN 0012-9658
    abundance - Atlantic Forest - biodiversity data set - biodiversity hotspot - epiphyte - phorophyte - presence/absence - tropical forest

    Epiphytes are hyper-diverse and one of the frequently undervalued life forms in plant surveys and biodiversity inventories. Epiphytes of the Atlantic Forest, one of the most endangered ecosystems in the world, have high endemism and radiated recently in the Pliocene. We aimed to (1) compile an extensive Atlantic Forest data set on vascular, non-vascular plants (including hemiepiphytes), and lichen epiphyte species occurrence and abundance; (2) describe the epiphyte distribution in the Atlantic Forest, in order to indicate future sampling efforts. Our work presents the first epiphyte data set with information on abundance and occurrence of epiphyte phorophyte species. All data compiled here come from three main sources provided by the authors: published sources (comprising peer-reviewed articles, books, and theses), unpublished data, and herbarium data. We compiled a data set composed of 2,095 species, from 89,270 holo/hemiepiphyte records, in the Atlantic Forest of Brazil, Argentina, Paraguay, and Uruguay, recorded from 1824 to early 2018. Most of the records were from qualitative data (occurrence only, 88%), well distributed throughout the Atlantic Forest. For quantitative records, the most common sampling method was individual trees (71%), followed by plot sampling (19%), and transect sampling (10%). Angiosperms (81%) were the most frequently registered group, and Bromeliaceae and Orchidaceae were the families with the greatest number of records (27,272 and 21,945, respectively). Ferns and Lycophytes presented fewer records than Angiosperms, and Polypodiaceae were the most recorded family, and more concentrated in the Southern and Southeastern regions. Data on non-vascular plants and lichens were scarce, with a few disjunct records concentrated in the Northeastern region of the Atlantic Forest. For all non-vascular plant records, Lejeuneaceae, a family of liverworts, was the most recorded family. We hope that our effort to organize scattered epiphyte data help advance the knowledge of epiphyte ecology, as well as our understanding of macroecological and biogeographical patterns in the Atlantic Forest. No copyright restrictions are associated with the data set. Please cite this Ecology Data Paper if the data are used in publication and teaching events.

    Plasma Malondialdehyde and Risk of New-Onset Diabetes after Transplantation in Renal Transplant Recipients: A Prospective Cohort Study
    Yepes-Calderón, Manuela ; Sotomayor, Camilo ; Gomes-Neto, António ; Gans, Rijk ; Berger, Stefan ; Rimbach, Gerald ; Esatbeyoglu, Tuba ; Rodrigo, Ramón ; Geleijnse, Johanna ; Navis, Gerjan ; Bakker, Stephan - \ 2019
    Journal of Clinical Medicine 8 (2019)4. - ISSN 2077-0383
    New-onset diabetes after transplantation (NODAT) is a frequent complication in renal transplant recipients (RTR). Although oxidative stress has been associated with diabetes mellitus, data regarding NODAT are limited. We aimed to prospectively investigate the long-term association between the oxidative stress biomarker malondialdehyde (measured by high-performance liquid chromatography) and NODAT in an extensively phenotyped cohort of non-diabetic RTR with a functioning graft ≥1 year. We included 516 RTR (51 ± 13 years-old, 57% male). Median plasma malondialdehyde (MDA) was 2.55 (IQR, 1.92–3.66) µmol/L. During a median follow-up of 5.3 (IQR, 4.6–6.0) years, 56 (11%) RTR developed NODAT. In Cox proportional-hazards regression analyses, MDA was inversely associated with NODAT, independent of immunosuppressive therapy, transplant-specific covariates, lifestyle, inflammation, and metabolism parameters (HR, 0.55; 95% CI, 0.36–0.83 per 1-SD increase; p < 0.01). Dietary antioxidants intake (e.g., vitamin E, α-lipoic acid, and linoleic acid) were effect-modifiers of the association between MDA and NODAT, with particularly strong inverse associations within the subgroup of RTR with relatively higher dietary antioxidants intake. In conclusion, plasma MDA concentration is inversely and independently associated with long-term risk of NODAT in RTR. Our findings support a potential underrecognized role of oxidative stress in post-transplantation glucose homeostasis.
    Urinary Excretion of N1-Methylnicotinamide, as a Biomarker of Niacin Status, and Mortality in Renal Transplant Recipients
    Deen, Carolien P.J. ; Veen, Anna Van Der; Faassen, Martijn Van; Minović, Isidor ; Gomes-Neto, António W. ; Geleijnse, Johanna M. ; Borgonjen-van Den Berg, Karin J. ; Kema, Ido P. ; Bakker, Stephan J.L. - \ 2019
    Journal of Clinical Medicine 8 (2019)11. - ISSN 2077-0383
    Renal transplant recipients (RTR) commonly suffer from vitamin B6 deficiency and its functional consequences add to an association with poor long-term outcome. It is unknown whether niacin status is affected in RTR and, if so, whether this affects clinical outcomes, as vitamin B6 is a cofactor in nicotinamide biosynthesis. We compared 24-h urinary excretion of N1-methylnicotinamide (N1-MN) as a biomarker of niacin status in RTR with that in healthy controls, in relation to dietary intake of tryptophan and niacin as well as vitamin B6 status, and investigated whether niacin status is associated with the risk of premature all-cause mortality in RTR. In a prospective cohort of 660 stable RTR with a median follow-up of 5.4 (4.7–6.1) years and 275 healthy kidney donors, 24-h urinary excretion of N1-MN was measured with liquid chromatography-tandem mass spectrometry LC-MS/MS. Dietary intake was assessed by food frequency questionnaires. Prospective associations of N1-MN excretion with mortality were investigated by Cox regression analyses. Median N1-MN excretion was 22.0 (15.8–31.8) μmol/day in RTR, compared to 41.1 (31.6–57.2) μmol/day in healthy kidney donors (p < 0.001). This difference was independent of dietary intake of tryptophan (1059 ± 271 and 1089 ± 308 mg/day; p = 0.19), niacin (17.9 ± 5.2 and 19.2 ± 6.2 mg/day; p < 0.001), plasma vitamin B6 (29.0 (17.5–49.5), and 42.0 (29.8–60.3) nmol/L; p < 0.001), respectively. N1-MN excretion was inversely associated with the risk of all-cause mortality in RTR (HR 0.57; 95% CI 0.45–0.71; p < 0.001), independent of potential confounders. RTR excrete less N1-MN in 24-h urine than healthy controls, and our data suggest that this difference cannot be attributed to lower dietary intake of tryptophan and niacin, nor vitamin B6 status. Importantly, lower 24-h urinary excretion of N1-MN is independently associated with a higher risk of premature all-cause mortality in RTR. View Full-Text
    Antioxidanten voor lammeren: trage kleurverandering voorkomt voedselverspilling
    Neto Leal, Leonel - \ 2019

    Promotie onderzoek Leonel Neto Leal

    The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery
    Santen, Jeffrey A. Van; Jacob, Grégoire ; Singh, Amrit Leen ; Aniebok, Victor ; Balunas, Marcy J. ; Bunsko, Derek ; Neto, Fausto Carnevale ; Castaño-Espriu, Laia ; Chang, Chen ; Clark, Trevor N. ; Cleary Little, Jessica L. ; Delgadillo, David A. ; Dorrestein, Pieter C. ; Duncan, Katherine R. ; Egan, Joseph M. ; Galey, Melissa M. ; Haeckl, Jake ; Hua, Alex ; Hughes, Alison H. ; Iskakova, Dasha ; Khadilkar, Aswad ; Lee, Jung Ho ; Lee, Sanghoon ; Legrow, Nicole ; Liu, Dennis Y. ; Macho, Jocelyn M. ; McCaughey, Catherine S. ; Medema, Marnix H. ; Neupane, Ram P. ; O'Donnell, Timothy J. ; Paula, Jasmine S. ; Sanchez, Laura M. ; Shaikh, Anam F. ; Soldatou, Sylvia ; Terlouw, Barbara R. ; Tran, Tuan Anh ; Valentine, Mercia ; Hooft, Justin J.J. Van Der; Vo, Duy A. ; Wang, Mingxun ; Wilson, Darryl ; Zink, Katherine E. ; Linington, Roger G. - \ 2019
    ACS Central Science 5 (2019)11. - ISSN 2374-7943 - p. 1824 - 1833.

    Despite rapid evolution in the area of microbial natural products chemistry, there is currently no open access database containing all microbially produced natural product structures. Lack of availability of these data is preventing the implementation of new technologies in natural products science. Specifically, development of new computational strategies for compound characterization and identification are being hampered by the lack of a comprehensive database of known compounds against which to compare experimental data. The creation of an open access, community-maintained database of microbial natural product structures would enable the development of new technologies in natural products discovery and improve the interoperability of existing natural products data resources. However, these data are spread unevenly throughout the historical scientific literature, including both journal articles and international patents. These documents have no standard format, are often not digitized as machine readable text, and are not publicly available. Further, none of these documents have associated structure files (e.g., MOL, InChI, or SMILES), instead containing images of structures. This makes extraction and formatting of relevant natural products data a formidable challenge. Using a combination of manual curation and automated data mining approaches we have created a database of microbial natural products (The Natural Products Atlas, www.npatlas.org) that includes 24 594 compounds and contains referenced data for structure, compound names, source organisms, isolation references, total syntheses, and instances of structural reassignment. This database is accompanied by an interactive web portal that permits searching by structure, substructure, and physical properties. The Web site also provides mechanisms for visualizing natural products chemical space and dashboards for displaying author and discovery timeline data. These interactive tools offer a powerful knowledge base for natural products discovery with a central interface for structure and property-based searching and presents new viewpoints on structural diversity in natural products. The Natural Products Atlas has been developed under FAIR principles (Findable, Accessible, Interoperable, and Reusable) and is integrated with other emerging natural product databases, including the Minimum Information About a Biosynthetic Gene Cluster (MIBiG) repository, and the Global Natural Products Social Molecular Networking (GNPS) platform. It is designed as a community-supported resource to provide a central repository for known natural product structures from microorganisms and is the first comprehensive, open access resource of this type. It is expected that the Natural Products Atlas will enable the development of new natural products discovery modalities and accelerate the process of structural characterization for complex natural products libraries.

    Circummed pine forest database: An electronic archive for mediterranean and submediterranean pine forest vegetation data
    Bonari, Gianmaria ; Knollová, Ilona ; Vlčková, Pavla ; Xystrakis, Fotios ; Çoban, Süleyman ; Sağlam, Coşkun ; Didukh, Yakiv P. ; Hennekens, Stephan M. ; Acosta, Alicia T.R. ; Angiolini, Claudia ; Bergmeier, Erwin ; Bertacchi, Andrea ; Costa, José C. ; Fanfarillo, Emanuele ; Gigante, Daniela ; Guarino, Riccardo ; Landi, Marco ; Neto, Carlos S. ; Pesaresi, Simone ; Rosati, Leonardo ; Selvi, Federico ; Sotiriou, Alexandros ; Stinca, Adriano ; Turcato, Claudia ; Tzonev, Rossen ; Viciani, Daniele ; Chytrý, Milan - \ 2019
    Phytocoenologia 49 (2019)3. - ISSN 0340-269X - p. 311 - 318.
    CircumMed Pine Forest Database - European Vegetation Archive (EVA) - Forest vegetation - Mediterranean Basin - Phytosociology - Pine forest - Pinus - Relevé - Turboveg - Vegetation plot

    Large thematic databases of vegetation plots are increasingly needed for vegetation studies and biodiversity research. In this paper, we present the CircumMed Pine Forest Database (GIVD ID: EU-00-026), which in November 2018, comprised records from 6317 pine-dominated vegetation plots (relevés) and associated vegetation types from 20 countries of the Mediterranean Basin, Near East and Crimea. These vegetation plots were collected through a detailed literature search for plots not previously included in the European Vegetation Archive (EVA), in order to fill geographic gaps in data coverage. The database comprises Mediterranean (including Oromediterranean) pine-forest vegetation plots from both published and unpublished sources. All vegetation plots are georeferenced, although coordinates vary in accuracy. The database is accessible through EVA or from its Custodian. We anticipate the CircumMed Pine Forest Database will be a valuable resource for various types of broad-scale studies in the fields of vegetation classification, plant invasion ecology, macroecology and biological conservation.

    Urinary Taurine Excretion and Risk of Late Graft Failure in Renal Transplant Recipients
    Post, Adrian ; Said, Yusof ; Gomes-Neto, Antonio W. ; Krogt, Jennifer van der; Blaauw, Pim de; Berger, Stefan P. ; Geleijnse, Johanna M. ; Borgonjen, Karin ; Berg, Else van den; Goor, Harry van; Rimbach, Gerald ; Kema, Ido P. ; Tsikas, Dimitrios ; Heiner-Fokkema, Rebecca ; Bakker, Stephan J.L. - \ 2019
    Nutrients 11 (2019)9. - ISSN 2072-6643
    graft survival - renal transplant recipients - taurine - taurine excretion

    Taurine is a sulfur containing nutrient that has been shown to protect against oxidative stress, which has been implicated in the pathophysiology leading to late graft failure after renal transplantation. We prospectively investigated whether high urinary taurine excretion, reflecting high taurine intake, is associated with low risk for development of late graft failure in renal transplant recipients (RTR). Urinary taurine excretion was measured in a longitudinal cohort of 678 stable RTR. Prospective associations were assessed using Cox regression analyses. Graft failure was defined as the start of dialysis or re-transplantation. In RTR (58% male, 53 ± 13 years old, estimated glomerular filtration rate (eGFR) 45 ± 19 mL/min/1.73 m2), urinary taurine excretion (533 (210-946) µmol/24 h) was significantly associated with serum free sulfhydryl groups (β = 0.126; P = 0.001). During median follow-up for 5.3 (4.5-6.0) years, 83 (12%) patients developed graft failure. In Cox regression analyses, urinary taurine excretion was inversely associated with graft failure (hazard ratio: 0.74 (0.67-0.82); P < 0.001). This association remained significant independent of potential confounders. High urinary taurine excretion is associated with low risk of late graft failure in RTR. Therefore, increasing taurine intake may potentially support graft survival in RTR. Further studies are warranted to determine the underlying mechanisms and the potential of taurine supplementation.

    Fruit and vegetable intake and risk of post trans plantation diabetes in renal transplant recipients
    Gomes-Neto, António W. ; Osté, Maryse C.J. ; Sotomayor, Camilo G. ; Berg, Else V.D. ; Geleijnse, Johanna M. ; Gans, Reinold O.B. ; Bakker, Stephan J.L. ; Navis, Gerjan J. - \ 2019
    Diabetes Care 42 (2019)9. - ISSN 0149-5992 - p. 1645 - 1652.

    OBJECTIVE Posttransplantation diabetes mellitus (PTDM) contributes to risk for cardiovascular morbidity and mortality in renal transplant recipients (RTRs). In the general population, consumption of a diet containing few fruits and vegetables predisposes to type 2 diabetes. The role of diet as a potential modifiable risk factor for PTDM has not been explored. Our focus was to investigate the prospective associations of fruit and vegetable intake with risk of PTDM in stable RTRs. RESEARCH DESIGN AND METHODS We included 472 adult RTRs who had a functioning graft ≥1 year. Fruit and vegetable intake was assessed by using a 177-item food frequency questionnaire. PTDM was defined according the American Diabetes Association's diagnostic criteria for diabetes. RESULTS During 5.2 years of follow-up, 52 RTRs (11%) developed PTDM. Fruit intake was not associated with PTDM (hazard ratio [HR] 0.90 [95% CI 0.79-1.03] per 2log g/day; P = 0.13), whereas vegetable intake was inversely associated with PTDM (HR 0.77 [95% CI 0.63-0.94] per 2log g/day; P = 0.009). Mediation analyses revealed that 650% of the association between vegetable intake and PTDM was mediated by variations in key components of the metabolic syndrome (i.e., HDL cholesterol, triglycerides, and waist circumference) as determined by the National Cholesterol Education Program's Adult Treatment Panel III Expert Panel. CONCLUSIONS In this study vegetable intake, but not fruit intake, was associated with lower risk of PTDM in RTRs, likely largely through beneficial effects on key components of the metabolic syndrome. These findings further support accumulating evidence that supports a recommendation of higher vegetable intake by RTRs.

    Development and evaluation of a genome-wide Coffee 8.5K SNP array and its application for high-density genetic mapping and for investigating the origin of Coffea arabica L.
    Merot-L'anthoene, Virginie ; Tournebize, Rémi ; Darracq, Olivier ; Rattina, Vimel ; Lepelley, Maud ; Bellanger, Laurence ; Tranchant-Dubreuil, Christine ; Coulée, Manon ; Pégard, Marie ; Metairon, Sylviane ; Fournier, Coralie ; Stoffelen, Piet ; Janssens, Steven B. ; Kiwuka, Catherine ; Musoli, Pascal ; Sumirat, Ucu ; Legnaté, Hyacinthe ; Kambale, Jean Léon ; Ferreira da Costa Neto, João ; Revel, Clara ; Kochko, Alexandre de; Descombes, Patrick ; Crouzillat, Dominique ; Poncet, Valérie - \ 2019
    Plant Biotechnology Journal 17 (2019)7. - ISSN 1467-7644 - p. 1418 - 1430.
    C. canephora - C. eugenioides - Coffea arabica origin - genetic map - single-nucleotide polymorphism - SNP array

    Coffee species such as Coffea canephora P. (Robusta) and C. arabica L. (Arabica) are important cash crops in tropical regions around the world. C. arabica is an allotetraploid (2n = 4x = 44) originating from a hybridization event of the two diploid species C. canephora and C. eugenioides (2n = 2x = 22). Interestingly, these progenitor species harbour a greater level of genetic variability and are an important source of genes to broaden the narrow Arabica genetic base. Here, we describe the development, evaluation and use of a single-nucleotide polymorphism (SNP) array for coffee trees. A total of 8580 unique and informative SNPs were selected from C. canephora and C. arabica sequencing data, with 40% of the SNP located in annotated genes. In particular, this array contains 227 markers associated to 149 genes and traits of agronomic importance. Among these, 7065 SNPs (~82.3%) were scorable and evenly distributed over the genome with a mean distance of 54.4 Kb between markers. With this array, we improved the Robusta high-density genetic map by adding 1307 SNP markers, whereas 945 SNPs were found segregating in the Arabica mapping progeny. A panel of C. canephora accessions was successfully discriminated and over 70% of the SNP markers were transferable across the three species. Furthermore, the canephora-derived subgenome of C. arabica was shown to be more closely related to C. canephora accessions from northern Uganda than to other current populations. These validated SNP markers and high-density genetic maps will be useful to molecular genetics and for innovative approaches in coffee breeding.

    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.
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