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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Local temperature and ecological similarity drive distributional dynamics of tropical mammals worldwide
Beaudrot, Lydia ; Acevedo, Miguel A. ; Lessard, Jean Philippe ; Zvoleff, Alex ; Jansen, Patrick A. ; Sheil, Douglas ; Rovero, Francesco ; O’Brien, Timothy ; Larney, Eileen ; Fletcher, Christine ; Andelman, Sandy ; Ahumada, Jorge - \ 2019
Global Ecology and Biogeography 28 (2019)7. - ISSN 1466-822X - p. 976 - 991.
coexistence - dynamic occupancy modelling - imperfect detection - occupancy–environment association - range shift - species distribution - species interactions

Aim: Identifying the underlying drivers of species’ distributional dynamics is critical for predicting change and managing biological diversity. While anthropogenic factors such as climate change can affect species distributions through time, other naturally occurring ecological processes can also have an influence. Theory predicts that interactions between species can influence distributional dynamics, yet empirical evidence remains sparse. A powerful approach is to monitor and model local colonization and extinction—the processes that generate change in distributions over time—and to identify their abiotic and biotic associations. Intensive camera-trap monitoring provides an opportunity to assess the role of temperature and species interactions in the colonization and extinction dynamics of tropical mammals, many of which are species of conservation concern. Using data from a pan-tropical monitoring network, we examined how short-term local temperature change and ecological similarity between species (a proxy for the strength of species interactions) influenced the processes that drive distributional shifts. Location: Tropical forests worldwide. Time period: 2007–2016. Major taxa studied: Terrestrial mammals. Methods: We used dynamic occupancy models to assess the influence of the abiotic and biotic environment on the distributional dynamics of 42 mammal populations from 36 species on 7 tropical elevation gradients around the world. Results: Overall, temperature, ecological similarity, or both, were linked to colonization or extinction dynamics in 29 populations. For six species, the effect of temperature depended upon the local mammal community similarity. This result suggests that the way in which temperature influences local colonization and extinction dynamics depends on local mammal community composition. Main conclusions: These results indicate that varying temperatures influence tropical mammal distributions in surprising ways and suggest that interactions between species mediate distributional dynamics.

Prey availability and temporal partitioning modulate felid coexistence in Neotropical forests
Santos, Fernanda ; Carbone, Chris ; Wearn, Oliver R. ; Rowcliffe, J.M. ; Espinosa, Santiago ; Moreira, Marcela Guimarães ; Ahumada, Jorge A. ; Gonçalves, André Luis Sousa ; Trevelin, Leonardo C. ; Alvarez-Loayza, Patricia ; Spironello, Wilson R. ; Jansen, Patrick A. ; Juen, Leandro ; Peres, Carlos A. - \ 2019
PLoS ONE 14 (2019)3. - ISSN 1932-6203

Carnivores have long been used as model organisms to examine mechanisms that allow coexistence among ecologically similar species. Interactions between carnivores, including competition and predation, comprise important processes regulating local community structure and diversity. We use data from an intensive camera-trapping monitoring program across eight Neotropical forest sites to describe the patterns of spatiotemporal organization of a guild of five sympatric cat species: jaguar (Panthera onca), puma (Puma concolor), ocelot (Leopardus pardalis), jaguarundi (Herpailurus yagouaroundi) and margay (Leopardus wiedii). For the three largest cat species, we developed multi-stage occupancy models accounting for habitat characteristics (landscape complexity and prey availability) and models accounting for species interactions (occupancy estimates of potential competitor cat species). Patterns of habitat-use were best explained by prey availability, rather than habitat structure or species interactions, with no evidence of negative associations of jaguar on puma and ocelot occupancy or puma on ocelot occupancy. We further explore temporal activity patterns and overlap of all five felid species. We observed a moderate temporal overlap between jaguar, puma and ocelot, with differences in their activity peaks, whereas higher temporal partitioning was observed between jaguarundi and both ocelot and margay. Lastly, we conducted temporal overlap analysis and calculated species activity levels across study sites to explore if shifts in daily activity within species can be explained by varying levels of local competition pressure. Activity patterns of ocelots, jaguarundis and margays were similarly bimodal across sites, but pumas exhibited irregular activity patterns, most likely as a response to jaguar activity. Activity levels were similar among sites and observed differences were unrelated to competition or intraguild killing risk. Our study reveals apparent spatial and temporal partitioning for most of the species pairs analyzed, with prey abundance being more important than species interactions in governing the local occurrence and spatial distribution of Neotropical forest felids.

Detecting tropical wildlife declines through camera-trap monitoring : An evaluation of the Tropical Ecology Assessment and Monitoring protocol
Beaudrot, Lydia ; Ahumada, Jorge ; O'Brien, Timothy G. ; Jansen, Patrick A. - \ 2019
Oryx 53 (2019)1. - ISSN 0030-6053 - p. 126 - 129.
Camera trap - conservation - monitoring - power analysis - sampling design - Tropical Ecology Assessment and Monitoring - wildlife management

Identifying optimal sampling designs for detecting population-level declines is critical for optimizing expenditures by research and monitoring programmes. The Tropical Ecology Assessment and Monitoring (TEAM) network is the most extensive tropical camera-trap monitoring programme, but the effectiveness of its sampling protocol has not been rigorously assessed. Here, we assess the power and sensitivity of the programme's camera-trap monitoring protocol for detecting occupancy changes in unmarked populations using the freely available application PowerSensor!. We found that the protocol is well suited to detect moderate (≥ 5%) population changes within 3-4 years for relatively common species that have medium to high detection probabilities (i.e. p > 0.2). The TEAM protocol cannot, however, detect typical changes in rare and evasive species, a category into which many tropical species and many species of conservation concern fall. Additional research is needed to build occupancy models for detecting change in rare and elusive species when individuals are unmarked.

Novel energy conservation strategies and behaviour of Pelotomaculum schinkii driving syntrophic propionate catabolism
Hidalgo-Ahumada, Catalina A.P. ; Nobu, Masaru K. ; Narihiro, Takashi ; Tamaki, Hideyuki ; Liu, Wen Tso ; Kamagata, Yoichi ; Stams, Alfons J.M. ; Imachi, Hiroyuki ; Sousa, Diana Z. - \ 2018
Environmental Microbiology 20 (2018)12. - ISSN 1462-2912 - p. 4503 - 4511.

Under methanogenic conditions, short-chain fatty acids are common byproducts from degradation of organic compounds and conversion of these acids is an important component of the global carbon cycle. Due to the thermodynamic difficulty of propionate degradation, this process requires syntrophic interaction between a bacterium and partner methanogen; however, the metabolic strategies and behaviour involved are not fully understood. In this study, the first genome analysis of obligately syntrophic propionate degraders (Pelotomaculum schinkii HH and P. propionicicum MGP) and comparison with other syntrophic propionate degrader genomes elucidated novel components of energy metabolism behind Pelotomaculum propionate oxidation. Combined with transcriptomic examination of P. schinkii behaviour in co-culture with Methanospirillum hungatei, we found that formate may be the preferred electron carrier for P. schinkii syntrophy. Propionate-derived menaquinol may be primarily re-oxidized to formate, and energy was conserved during formate generation through newly proposed proton-pumping formate extrusion. P. schinkii did not overexpress conventional energy metabolism associated with a model syntrophic propionate degrader Syntrophobacter fumaroxidans MPOB (i.e., CoA transferase, Fix and Rnf). We also found that P. schinkii and the partner methanogen may also interact through flagellar contact and amino acid and fructose exchange. These findings provide new understanding of syntrophic energy acquisition and interactions.

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.

An Open Standard for Camera Trap Data
Forrester, Tavis ; O'Brien, Tim ; Fegraus, Eric ; Jansen, P.A. ; Palmer, Jonathan ; Kays, Roland ; Ahumada, Jorge ; Stern, Beth ; McShea, William - \ 2016
Biodiversity Data Journal 4 (2016). - ISSN 1314-2828 - 8 p.
Camera traps that capture photos of animals are a valuable tool for monitoring biodiversity. The use of camera traps is rapidly increasing and there is an urgent need for standardization to facilitate data management, reporting and data sharing. Here we offer the Camera Trap Metadata Standard as an open data standard for storing and sharing camera trap data, developed by experts from a variety of organizations. The standard captures information necessary to share data between projects and offers a foundation for collecting the more detailed data needed for advanced analysis. The data standard captures information about study design, the type of camera used, and the location and species names for all detections in a standardized way. This information is critical for accurately assessing results from individual camera trapping projects and for combining data from multiple studies for meta-analysis. This data standard is an important step in aligning camera trapping surveys with best practices in data-intensive science. Ecology is moving rapidly into the realm of big data, and central data repositories are becoming a critical tool and are emerging for camera trap data. This data standard will help researchers standardize data terms, align past data to new repositories, and provide a framework for utilizing data across repositories and research projects to advance animal ecology and conservation.
Standardized Assessment of Biodiversity Trends in Tropical Forest Protected Areas: The End Is Not in Sight
Beaudrot, Lydia ; Ahumada, J.A. ; O’Brien, Timothy ; Alvarez-Loayza, Patricia ; Boekee, Kelly ; Campos-Arceiz, Ahimsa ; Eichberg, David ; Espinosa, Santiago ; Fegraus, Eric ; Fletcher, Christine ; Jansen, P.A. - \ 2016
PloS Biology 14 (2016)1. - ISSN 1545-7885
Extinction rates in the Anthropocene are three orders of magnitude higher than background and disproportionately occur in the tropics, home of half the world’s species. Despite global efforts to combat tropical species extinctions, lack of high-quality, objective information on tropical biodiversity has hampered quantitative evaluation of conservation strategies. In particular, the scarcity of population-level monitoring in tropical forests has stymied assessment of biodiversity outcomes, such as the status and trends of animal populations in protected areas. Here, we evaluate occupancy trends for 511 populations of terrestrial mammals and birds, representing 244 species from 15 tropical forest protected areas on three continents. For the first time to our knowledge, we use annual surveys from tropical forests worldwide that employ a standardized camera trapping protocol, and we compute data analytics that correct for imperfect detection. We found that occupancy declined in 22%, increased in 17%, and exhibited no change in 22% of populations during the last 3–8 years, while 39% of populations were detected too infrequently to assess occupancy changes. Despite extensive variability in occupancy trends, these 15 tropical protected areas have not exhibited systematic declines in biodiversity (i.e., occupancy, richness, or evenness) at the community level. Our results differ from reports of widespread biodiversity declines based on aggregated secondary data and expert opinion and suggest less extreme deterioration in tropical forest protected areas. We simultaneously fill an important conservation data gap and demonstrate the value of large-scale monitoring infrastructure and powerful analytics, which can be scaled to incorporate additional sites, ecosystems, and monitoring methods. In an era of catastrophic biodiversity loss, robust indicators produced from standardized monitoring infrastructure are critical to accurately assess population outcomes and identify conservation strategies that can avert biodiversity collapse.
Mexico - Pilot Program PNA. Design Phase 1A
Waldhauer, N. ; Ahumada, O. ; Cabildo, Monica ; Soethoudt, J.M. ; Groot, J.J. - \ 2015
Wageningen : Wageningen UR - Food & Biobased Research - ISBN 9789462577084 - 66 p.
TEAM: a standardised camera trap survey to monitor terrestrial vertebrate communities in tropical forests
Jansen, P.A. ; Ahumada, J. ; Fegraus, E. ; O'Brien, T.G. - \ 2014
In: Camera trapping : wildlife management and research / Meek, P.D., Fleming, P.J.S., Melbourne, Australia : CSIRO Publishing - ISBN 9781486300396 - p. 263 - 270.
Carbon storage in tropical forests correlates with taxonomic diversity and functional dominance on global scales
Cavanaugh, K.C. ; Gosnell, S. ; Davis, S.L. ; Ahumada, J. ; Boundja, P. ; Clark, D.B. ; Mugerwa, B. ; Jansen, P.A. ; O'Brien, T.G. ; Rovero, F. ; Sheil, D. ; Vasquez, R. ; Andelman, S. - \ 2014
Global Ecology and Biogeography 23 (2014)5. - ISSN 1466-822X - p. 563 - 573.
ecosystem function - species richness - plant diversity - wood density - aboveground biomass - amazonian forest - spatial-patterns - multiple traits - productivity - biodiversity
We examined (1) the relationships between aboveground tropical forest C storage, biodiversity and environmental drivers and (2) how these relationships inform theory concerning ecosystem function and biodiversity. Experiments have shown that there is a positive relationship between biodiversity and ecosystem functioning, but intense debate exists on the underlying mechanisms. While some argue that mechanisms such as niche complementarity increase ecosystem function, others argue that these relationships are a selection effect.
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