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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Effect of dietary protein to energy ratio on performance of nile tilapia and food web enhancement in semi-intensive pond aquaculture
Kabir, K.A. ; Schrama, J.W. ; Verreth, J.A.J. ; Phillips, M.J. ; Verdegem, M.C.J. - \ 2019
Aquaculture 499 (2019). - ISSN 0044-8486 - p. 235 - 242.
Food web - N utilization - P:E ratio - Pond

When fish have only access to formulated feed, the optimal dietary protein to energy ratio (P:E) for tilapia ranges between 18 and 23 g.MJ−1. In pond culture, where natural foods complement administrated feed, increasing the carbon:nitrogen (C:N) ratio stimulates the natural food productivity. This study assessed if lowering the dietary P:E ratio (and thus increasing the C:N ratio of the feed input in the pond) below the optimal P:E ratio affects fish productivity, food web dynamics and nitrogen balances in semi-intensively managed tilapia ponds. Twelve ponds, each divided into three equally-sized compartments, were assigned to test the effect of two diets, which differed in P:E ratio (19 vs. 14 g.MJ−1). Three feeding levels (no, “low” and “high”) were nested in each pond in a split plot design. Initial fish biomass was 1166 (±16) g.compartment−1 and the experiment lasted 60 days. Decreasing P:E ratio enhanced tilapia production and specific growth rate (P <.05; 1195 vs. 985 g.compartment−1 and 1.76 vs 1.55%.d−1). Body composition of tilapia was unaffected by diet and feeding level. Despite the difference in performance, final fat content was 5% of body weight and unaffected by treatments. Averaged over both diets, survival and feed conversion ratio increased with increasing feeding level (P <.001). Diet composition did not alter measured water quality, and abundance and diversity of the related parameters of the food web. The total amount of N accumulated in the pond was lower with the low P:E ratio diet (i.e., low protein diet). The data on N gain and N balance at the pond level suggest that the food web productivity was stimulated by reducing the dietary P:E ratio below the reported optimal levels in the literature. It is hypothesized that the optimal dietary P:E ratio is dependent on the culture intensity (extensive, semi-extensive or intensive pond culture).

Study to support the evaluation of the EU Adaptation Strategy : Final report
Smithers, R. ; Tweed, James ; Phillips-Itty, Ruth ; Nesbit, Martin ; Illes, Andrea ; Smith, Matthew ; Eichler, L. ; Baroni, Laura ; Klostermann, J.E.M. ; Bruin, K. de; Coninx, I. - \ 2018
Brussels : European Commission - 159 p.
A regional benthic fauna assessment method for the Southern North Sea using Margalef diversity and reference value modelling
Loon, Willem M.G.M. van; Walvoort, Dennis J.J. ; Hoey, Gert van; Vina-Herbon, Christina ; Blandon, Abigayil ; Pesch, Roland ; Schmitt, Petra ; Scholle, Jörg ; Heyer, Karin ; Lavaleye, Marc ; Phillips, Graham ; Duineveld, Gerard C.A. ; Blomqvist, Mats - \ 2018
Ecological Indicators 89 (2018). - ISSN 1470-160X - p. 667 - 679.
AMBI - Benthic assessment method - Fishing pressure - Index - ITI - Margalef diversity - Marine benthos - MMI - Model - MSFD - Multi-metric index - Organic enrichment - OSPAR - PIE - Reference value estimation - Sedimentation - Shannon index - SN - SNA - Species richness
The aims of this study are to develop an optimized method for regional benthic fauna assessment of the Southern North Sea which (a) is sensitive and precise (quantified as the slope and the R2 value of the pressure-impact relationships, respectively) for the anthropogenic pressures bottom fishing and organic enrichment, (b) is suitable for estimating and modelling reference values, (c) is transparent, (d) can be efficiently applied using dedicated software; and to apply this method to benthic data from the Southern North Sea. Margalef diversity appeared to be the best performing benthic index regarding these criteria, even better than several Multi-Metric Indices (MMIs) containing e.g. AMBI (AZTI Marine Biotic Index) and ITI (Infaunal Trophic Index). Therefore, this relatively simple and very practical index, including a new reference value estimation and modelling method, and BENMMI software were selected as a common OSPAR (Oslo Paris convention) method for the benthic fauna assessment of the Southern North Sea. This method was applied to benthic fauna data from the Southern North Sea collected during the period 2010–2015. The results in general show lower normalized Margalef values in coastal areas, and higher normalized Margalef values in deeper offshore areas. The following benthic indices were compared in this study: species richness, Margalef diversity, SNA index, Shannon index, PIE index, AMBI, ITI. For each assessment area, the least disturbed benthic dataset was selected as an adjacent 6 year period with, on average, the highest Margalef diversity values. For these datasets, the reference values were primarily set as the 99th percentile values of the respective indices. This procedure results in the highest stable reference values that are not outliers. In addition, a variable percentile method was developed, in which the percentile value is adjusted to the average bottom fishing pressure (according to data from the International Council for the Exploration of the Sea, ICES) in the period 2009–2013. The adjusted percentile values were set by expert judgement, at 75th (low fishing pressure), 95th (medium fishing pressure) and 99th (high fishing pressure) percentile. The estimated reference values for Margalef diversity correlate quite well with the median depth of the assessment areas using a sigmoid model (pseudo-R2 = 0.86). This relationship between depth and Margalef diversity was used to estimate reference values in case an assessment area had insufficient benthic data For testing the effects of bottom fishing pressure, normalized index values (NIV; index value divided by reference value) were used. The rationale for using NIVs is the assumption that, although a certain level of bottom fishing pressure will have a larger absolute effect on more biodiverse benthic communities in deeper waters than on more robust and less biodiverse coastal benthic communities, the relative effects (tested using NIVs) are comparable. A clear exponentially decreasing relationship (R2 = 0.26–0.27, p < 0.00001) was found between both bottom surface and subsurface fishing activity (penetration depth <2 cm and >2 cm, respectively) and normalized Margalef diversity values, with an asymptotic normalized Margalef value of 0.45 at a subsurface fishing activity >2.3 sweeps/year. This asymptotic value is predominantly found in coastal waters, and probably shows that the naturally more robust coastal benthic communities have been transformed into resilient benthic communities, which rapidly recover from increasing fishing pressure.
Response of submerged macrophyte communities to external and internal restoration measures in north temperate shallow lakes
Hilt, Sabine ; Alirangues Nuñez, Marta M. ; Bakker, Elisabeth S. ; Blindow, Irmgard ; Davidson, Thomas A. ; Gillefalk, Mikael ; Hansson, Lars Anders ; Janse, Jan H. ; Janssen, Annette B.G. ; Jeppesen, Erik ; Kabus, Timm ; Kelly, Andrea ; Köhler, Jan ; Lauridsen, Torben L. ; Mooij, Wolf M. ; Noordhuis, Ruurd ; Phillips, Geoff ; Rücker, Jacqueline ; Schuster, Hans Heinrich ; Søndergaard, Martin ; Teurlincx, Sven ; Weyer, Klaus van de; Donk, Ellen van; Waterstraat, Arno ; Willby, Nigel ; Sayer, Carl D. - \ 2018
Frontiers in Plant Science 9 (2018). - ISSN 1664-462X
Aquaticplants - Biomanipulation - Eutrophication - Lakerestoration - Nutrient loadreduction - PCLake - Plant traits - Regime shift
Submerged macrophytes play a key role in north temperate shallow lakes by stabilizing clear-water conditions. Eutrophication has resulted in macrophyte loss and shifts to turbid conditions in many lakes. Considerable efforts have been devoted to shallow lake restoration in many countries, but long-term success depends on a stable recovery of submerged macrophytes. However, recovery patterns vary widely and remain to be fully understood. We hypothesize that reduced external nutrient loading leads to an intermediate recovery state with clear spring and turbid summer conditions similar to the pattern described for eutrophication. In contrast, lake internal restoration measures can result in transient clear-water conditions both in spring and summer and reversals to turbid conditions. Furthermore, we hypothesize that these contrasting restoration measures result in different macrophyte species composition, with added implications for seasonal dynamics due to differences in plant traits. To test these hypotheses, we analyzed data on water quality and submerged macrophytes from 49 north temperate shallow lakes that were in a turbid state and subjected to restoration measures. To study the dynamics of macrophytes during nutrient load reduction, we adapted the ecosystem model PCLake. Our survey and model simulations revealed the existence of an intermediate recovery state upon reduced external nutrient loading, characterized by spring clear-water phases and turbid summers, whereas internal lake restoration measures often resulted in clear-water conditions in spring and summer with returns to turbid conditions after some years. External and internal lake restoration measures resulted in different macrophyte communities. The intermediate recovery state following reduced nutrient loading is characterized by a few macrophyte species (mainly pondweeds) that can resist wave action allowing survival in shallowareas, germinate early in spring, have energy-rich vegetative propagules facilitating rapid initial growth and that can complete their life cycle by early summer. Later in the growing season these plants are, according to our simulations, outcompeted by periphyton, leading to late-summer phytoplankton blooms. Internal lake restoration measures often coincide with a rapid but transient colonization by hornworts, waterweeds or charophytes. Stable clear-water conditions and a diverse macrophyte flora only occurred decades after external nutrient load reduction or when measures were combined.
Recent progress in understanding climate thresholds : Ice sheets, the Atlantic meridional overturning circulation, tropical forests and responses to ocean acidification
Good, Peter ; Bamber, Jonathan ; Halladay, Kate ; Harper, Anna B. ; Jackson, Laura C. ; Kay, Gillian ; Kruijt, Bart ; Lowe, Jason A. ; Phillips, Oliver L. ; Ridley, Jeff ; Srokosz, Meric ; Turley, Carol ; Williamson, Phillip - \ 2018
Progress in Physical Geography 42 (2018)1. - ISSN 0309-1333 - p. 24 - 60.
Atlantic meridional overturning circulation - climate change - ice sheets - ocean acidification - thresholds - tropical forests
This article reviews recent scientific progress, relating to four major systems that could exhibit threshold behaviour: ice sheets, the Atlantic meridional overturning circulation (AMOC), tropical forests and ecosystem responses to ocean acidification. The focus is on advances since the Intergovernmental Panel on Climate Change Fifth Assessment Report (IPCC AR5). The most significant developments in each component are identified by synthesizing input from multiple experts from each field. For ice sheets, some degree of irreversible loss (timescales of millennia) of part of the West Antarctic Ice Sheet (WAIS) may have already begun, but the rate and eventual magnitude of this irreversible loss is uncertain. The observed AMOC overturning has decreased from 2004–2014, but it is unclear at this stage whether this is forced or is internal variability. New evidence from experimental and natural droughts has given greater confidence that tropical forests are adversely affected by drought. The ecological and socio-economic impacts of ocean acidification are expected to greatly increase over the range from today’s annual value of around 400, up to 650 ppm CO2 in the atmosphere (reached around 2070 under RCP8.5), with the rapid development of aragonite undersaturation at high latitudes affecting calcifying organisms. Tropical coral reefs are vulnerable to the interaction of ocean acidification and temperature rise, and the rapidity of those changes, with severe losses and risks to survival at 2 °C warming above pre-industrial levels. Across the four systems studied, however, quantitative evidence for a difference in risk between 1.5 and 2 °C warming above pre-industrial levels is limited.
Field methods for sampling tree height for tropical forest biomass estimation
Sullivan, Martin J.P. ; Lewis, Simon L. ; Hubau, Wannes ; Qie, Lan ; Baker, Timothy R. ; Banin, Lindsay F. ; Chave, Jerôme ; Cuni-Sanchez, Aida ; Feldpausch, Ted R. ; Lopez-Gonzalez, Gabriela ; Arets, Eric ; Ashton, Peter ; Bastin, Jean François ; Berry, Nicholas J. ; Bogaert, Jan ; Boot, Rene ; Brearley, Francis Q. ; Brienen, Roel ; Burslem, David F.R.P. ; Canniere, Charles de; Chudomelová, Markéta ; Dančák, Martin ; Ewango, Corneille ; Hédl, Radim ; Lloyd, Jon ; Makana, Jean Remy ; Malhi, Yadvinder ; Marimon, Beatriz S. ; Junior, Ben Hur Marimon ; Metali, Faizah ; Moore, Sam ; Nagy, Laszlo ; Vargas, Percy Nuñez ; Pendry, Colin A. ; Ramírez-Angulo, Hirma ; Reitsma, Jan ; Rutishauser, Ervan ; Salim, Kamariah Abu ; Sonké, Bonaventure ; Sukri, Rahayu S. ; Sunderland, Terry ; Svátek, Martin ; Umunay, Peter M. ; Martinez, Rodolfo Vasquez ; Vernimmen, Ronald R.E. ; Torre, Emilio Vilanova ; Vleminckx, Jason ; Vos, Vincent ; Phillips, Oliver L. - \ 2018
Methods in Ecology and Evolution 9 (2018)5. - ISSN 2041-210X - p. 1179 - 1189.
Above-ground biomass estimation - Allometry - Carbon stocks - Forest inventory - Forest structure - Sample size
Quantifying the relationship between tree diameter and height is a key component of efforts to estimate biomass and carbon stocks in tropical forests. Although substantial site-to-site variation in height-diameter allometries has been documented, the time consuming nature of measuring all tree heights in an inventory plot means that most studies do not include height, or else use generic pan-tropical or regional allometric equations to estimate height. Using a pan-tropical dataset of 73 plots where at least 150 trees had in-field ground-based height measurements, we examined how the number of trees sampled affects the performance of locally derived height-diameter allometries, and evaluated the performance of different methods for sampling trees for height measurement. Using cross-validation, we found that allometries constructed with just 20 locally measured values could often predict tree height with lower error than regional or climate-based allometries (mean reduction in prediction error = 0.46 m). The predictive performance of locally derived allometries improved with sample size, but with diminishing returns in performance gains when more than 40 trees were sampled. Estimates of stand-level biomass produced using local allometries to estimate tree height show no over- or under-estimation bias when compared with biomass estimates using field measured heights. We evaluated five strategies to sample trees for height measurement, and found that sampling strategies that included measuring the heights of the ten largest diameter trees in a plot outperformed (in terms of resulting in local height-diameter models with low height prediction error) entirely random or diameter size-class stratified approaches. Our results indicate that even limited sampling of heights can be used to refine height-diameter allometries. We recommend aiming for a conservative threshold of sampling 50 trees per location for height measurement, and including the ten trees with the largest diameter in this sample.
Species Distribution Modelling: Contrasting presence-only models with plot abundance data
Gomes, Vitor H.F. ; Ijff, Stéphanie D. ; Raes, Niels ; Amaral, Iêda Leão ; Salomão, Rafael P. ; Coelho, Luiz De Souza ; Matos, Francisca Dionízia De Almeida ; Castilho, Carolina V. ; Filho, Diogenes De Andrade Lima ; López, Dairon Cárdenas ; Guevara, Juan Ernesto ; Magnusson, William E. ; Phillips, Oliver L. ; Wittmann, Florian ; Carim, Marcelo De Jesus Veiga ; Martins, Maria Pires ; Irume, Mariana Victória ; Sabatier, Daniel ; Molino, Jean François ; Bánki, Olaf S. ; Guimarães, José Renan Da Silva ; Pitman, Nigel C.A. ; Piedade, Maria Teresa Fernandez ; Mendoza, Abel Monteagudo ; Luize, Bruno Garcia ; Venticinque, Eduardo Martins ; de Leão Novo, E.M.M. ; Vargas, Percy Núñez ; Silva, Thiago Sanna Freire ; Manzatto, Angelo Gilberto ; Terborgh, John ; Reis, Neidiane Farias Costa ; Montero, Juan Carlos ; Montero, Juan Carlos ; Casula, Katia Regina ; Marimon, Beatriz S. ; Marimon, Ben Hur ; Honorio Coronado, Euridice N. ; Feldpausch, Ted R. ; Duque, Alvaro ; Zartman, Charles Eugene ; Arboleda, Nicolás Castaño ; Killeen, Timothy J. ; Mostacedo, Bonifacio ; Vasquez, Rodolfo ; Schöngart, Jochen ; Assis, Rafael L. ; Medeiros, Marcelo Brilhante ; Simon, Marcelo Fragomeni ; Andrade, Ana ; Laurance, William F. ; Camargo, José Luís ; Demarchi, Layon O. ; Laurance, Susan G.W. ; Farias, Emanuelle De Sousa ; Nascimento, Henrique Eduardo Mendonça ; Revilla, Juan David Cardenas ; Quaresma, Adriano ; Costa, Flavia R.C. ; Vieira, Ima Célia Guimarães ; Cintra, Bruno Barçante Ladvocat ; Cintra, Bruno Barçante Ladvocat ; Castellanos, Hernán ; Brienen, Roel ; Stevenson, Pablo R. ; Feitosa, Yuri ; Duivenvoorden, Joost F. ; Aymard, Gerardo A.C. ; Mogollón, Hugo F. ; Targhetta, Natalia ; Comiskey, James A. ; Vicentini, Alberto ; Lopes, Aline ; Damasco, Gabriel ; Dávila, Nállarett ; García-Villacorta, Roosevelt ; Levis, Carolina ; Levis, Carolina ; Schietti, Juliana ; Souza, Priscila ; Emilio, Thaise ; Alonso, Alfonso ; Neill, David ; Dallmeier, Francisco ; Ferreira, Leandro Valle ; Araujo-Murakami, Alejandro ; Praia, Daniel ; Amaral, Dário Dantas Do; Carvalho, Fernanda Antunes ; Souza, Fernanda Coelho De - \ 2018
Scientific Reports 8 (2018)1. - ISSN 2045-2322
Species distribution models (SDMs) are widely used in ecology and conservation. Presence-only SDMs such as MaxEnt frequently use natural history collections (NHCs) as occurrence data, given their huge numbers and accessibility. NHCs are often spatially biased which may generate inaccuracies in SDMs. Here, we test how the distribution of NHCs and MaxEnt predictions relates to a spatial abundance model, based on a large plot dataset for Amazonian tree species, using inverse distance weighting (IDW). We also propose a new pipeline to deal with inconsistencies in NHCs and to limit the area of occupancy of the species. We found a significant but weak positive relationship between the distribution of NHCs and IDW for 66% of the species. The relationship between SDMs and IDW was also significant but weakly positive for 95% of the species, and sensitivity for both analyses was high. Furthermore, the pipeline removed half of the NHCs records. Presence-only SDM applications should consider this limitation, especially for large biodiversity assessments projects, when they are automatically generated without subsequent checking. Our pipeline provides a conservative estimate of a species' area of occupancy, within an area slightly larger than its extent of occurrence, compatible to e.g. IUCN red list assessments.
Modeling Agricultural Suitability Along Soil Transects Under Current Conditions and Improved Scenario of Soil Factors
Abd-Elmabod, Sameh K. ; Jordán, Antonio ; Fleskens, Luuk ; Phillips, Jonathan D. ; Muñoz-Rojas, Miriam ; Ploeg, Martine van der; Anaya-Romero, María ; El-Ashry, Soad ; Rosa, Diego de la - \ 2017
In: Soil Mapping and Process Modeling for Sustainable Land Use Management Elsevier Inc. Academic Press - ISBN 9780128052006 - p. 193 - 219.
Digital elevation model - Mediterranean region - MicroLEIS DSS - Toposequence
Agricultural land suitability evaluation is a good way to distinguish soil suitability in order to improve the soils by addressing major limitations. This study investigated the influence of soil factors variability on the suitability of 12 Mediterranean crops in southern Spain. To represent the variability in elevation, lithology, and soil, two latitudinal and longitudinal soil transects (TA and TB) were considered and sampled in 63 representative points at regular 4. km intervals. This research also aimed to determine how to maximize soil potential by improving limiting factors as drainage, carbonate content, salinity, and sodium saturation. Soil suitability evaluation ranged between optimum and not suitable classes along TA and TB. The decrease in the severity of soil limiting factors in the improved scenario leads to an increase in soil suitability for the 12 crops along TA and TB transects, except in segments with shallow soils and very coarse texture. Soil evaluation and spatial analyses of soil suitability for the 12 crops under current situation and improved scenario, including optimum and not suitable soils, are helpful to achieve a sustainable land management in the studied area. The improvement of soil limitation it could be as adaptation strategies for the long term of environmental changes as climate changes, this work has a real impact, which means the results valuable and easy to grasp for the decision makers.
Integrated systems research in nutrition-sensitive landscapes : A theoretical methodological framework
Groot, Jeroen C.J. ; Kennedy, Gina ; Remans, Roseline ; Estrada-Carmona, Natalia ; Raneri, Jessica ; DeClerck, Fabrice ; Alvarez, Stéphanie ; Mashingaidze, Nester ; Timler, Carl ; Stadler, Minke ; Río Mena, Trinidad del; Horlings, Lummina ; Brouwer, Inge ; Cole, Steven M. ; Descheemaeker, Katrien - \ 2017
In: Sustainable Intensification in Smallholder Agriculture / Oborn, Ingrid, Vanlauwe, Bernard, Phillips, Michael, Thomas, Richard, Atta-Krah, Kwesi, Brooijmans, Willemien, New York : Routledge / Earthscan - ISBN 9781138668089 - p. 259 - 274.
South Asia and sub-Saharan Africa are two regions of the world with the highest concentration of nutritionally vulnerable populations that depend to a large extent on agriculture as an important source of livelihood (Gillespie et al., 2015). The vast majority of farmers in these regions have small landholdings due to land fragmentation (Jayne et al., 2014; Valbuena et al., 2015) and are often constrained in their access to resources and agricultural inputs (Herrero et al., 2010), especially women (e.g., Cole et al., 2015). As a consequence, productivity levels are low, and because income sources are also limited, dependence on surrounding landscapes and ecosystem services is high in terms of safeguarding supplies of clean water, human and animal foods, construction materials and fuel wood. People shape their physical landscapes (Ellis, 2015), influenced by cultures, values and livelihood opportunities (Horlings, 2015). People’s utilization of their physical landscapes is shaped by various conditions such as soil properties, topography, climate and flooding patterns. People’s dependence on their physical landscapes is strong and expected to increase due to climate change, resulting in gradual but persistent changes including adjustments in frequency, timing and severity of anomalies such as droughts and floods (Naylor et al., 2007; Gornall et al., 2010).
Exploring options for sustainable intensification through legume integration in different farm types in eastern Zambia
Timler, Carl ; Michalscheck, Mirja ; Alvarez, Stéphanie ; Descheemaeker, Katrien ; Groot, Jeroen C.J. - \ 2017
In: Sustainable Intensification in Smallholder Agriculture: An Integrated Systems Research Approach / Oborn, Ingrid, Vanlauwe, Bernard, Phillips, Michael, Thomas, Richard, AttaKrah, Kwesi, Brooijmans, Willemien, Taylor and Francis Inc. - ISBN 9781138668089 - p. 196 - 209.
In Zambia maize is the main staple food crop and, with a share of 52% in the daily calorie intake of the local population, it is critical for ensuring the national food security (FAOSTAT, 2013). Of the total maize consumed in Zambia, smallholder farmers produce 80% in rain-fed systems under low soil fertility, frequent drought and with a limited use of high yielding varieties or inorganic fertiliser (Sitko et al., 2011). In eastern Zambia, the livelihoods of small-scale farmers depend largely on maize-legume mixed systems characterised by low productivity, extreme poverty and environmental degradation (Sitko et al., 2011). Thus, there seems to be a great need for sustainable intensification of these farming systems, for instance through promoting best practices in maize–legume integration. Maize–legume cropping provides protein-rich food for humans, residues for animal feed, composting and soil amendments and nitrogen inputs through symbiotic fixation by the legume. Sustainable intensification of farming systems can take place through changes in resource use and allocation that increase farm productivity while reducing pressure on local ecosystems and safeguarding social relations. According to Pretty et al. (2011), this entails the efficient use of all inputs to produce more outputs while reducing damage to the environment and building a resilient natural capital from which environmental services can be obtained. Sustainable intensification results from the application of technological and socio-economic approaches that may be categorised into genetic, ecological and socio-economic intensification (The Montpellier Panel, 2013).
Learning system for agricultural research for development (LESARD) : Documenting, reporting, and analysis of performance factors in multi-stakeholder processes
Sartas, Murat ; Schut, Marc ; Leeuwis, Cees - \ 2017
In: Sustainable Intensification in Smallholder Agriculture: An Integrated Systems Research Approach / Oborn, Ingrid, Vanlauwe, Bernard, Phillips, Michael, Thomas, Richard, AttaKrah, Kwesi, Brooijmans, Wilemien, Taylor and Francis Inc. - ISBN 9781138668089 - p. 367 - 380.
Nutrition-sensitive landscapes : Approach and methods to assess food availability and diversification of diets
Kennedy, Gina ; Raneri, Jessica ; Termote, Celine ; Nowak, Verena ; Remans, Roseline ; Groot, Jeroen C.J. ; Thilsted, Shakuntala H. - \ 2017
In: Sustainable Intensification in Smallholder Agriculture: An Integrated Systems Research Approach / Oborn, Ingrid, Vanlauwe, Bernard, Phillips, Michael, Thomas, Richard, AttaKrah, Kwesi, Brooijmans, Willemien, Taylor and Francis Inc. - ISBN 9781138668089 - p. 247 - 258.
Sustainable intensification has recently been developed and adopted as a key concept and driver for research and policy in sustainable agriculture. It includes ecological, economic and social dimensions, where food and nutrition security, gender and equity are crucial components. This book describes different aspects of systems research in agriculture in its broadest sense, where the focus is moved from farming systems to livelihoods systems.
How can external interventions build on local innovations? : Lessons from an assessment of innovation experiences in African smallholder agriculture
Triomphe, Bernard ; Floquet, Anne ; Letty, Brigid ; Kamau, Geoffrey ; Almekinders, Conny ; Waters-Bayer, Ann - \ 2017
In: Sustainable Intensification in Smallholder Agriculture: An Integrated Systems Research Approach / Oborn, Ingrid, Vanlauwe, Bernard, Phillips, Michael, Thomas, Richard, AttaKrah, Kwesi, Brooijmans, Willemien, Taylor and Francis Inc. - ISBN 9781138668089 - p. 334 - 366.
Integrated systems research for sustainable intensification of smallholder agriculture
Öborn, Ingrid ; Vanlauwe, Bernard ; Atta-Krah, Kwesi ; Thomas, Richard J. ; Phillips, Michael ; Schut, Marc - \ 2017
In: Sustainable Intensification in Smallholder Agriculture: An Integrated Systems Research Approach / Oborn, Ingrid, Vanlauwe, Bernard, Phillips, Michael, Thomas, Richard, Atta-Krah, Kwesi, Brooijmans, Willemien, Taylor and Francis Inc. - ISBN 9781138668089 - p. 1 - 15.
In sub-Saharan Africa (SSA), increases in yields of the major crops in smallholder farming systems have failed to match population growth, with increased production resulting rather from agricultural area expansion (Worldbank, 2007), very often at the expense of the natural resource base, such as carbon-rich and biodiverse forest land (e.g. Gockowski and Sonwa, 2011). Intensification of smallholder agriculture is a must under high population densities but also desirable in less populated areas in order to protect natural ecosystems. Smallholder farming communities and systems in SSA are heterogeneous, both at the community and farm level, driven by varying and often limited access for production resources (land, labour, capital) (Tittonell et al., 2010). At the community level, variable resource endowments and production objectives are often conceptualized through the construction of farm typologies. At farm level, preferential management of specific plots within a farm has resulted in within-farm soil fertility gradients, often with soils of higher fertility near the homestead, and more degraded soils towards the outer limits of the farm. For many households and regions, agriculture alone will not be able to provide rural populations with adequate livelihoods due to limited farm size and access to land (Harris and Orr, 2014; Jayne et al., 2014). Besides heterogeneity at farm and community level, enabling conditions for intensification, often expressed as access to agro-inputs, markets, and credit, quality of rural infrastructure, or conducive policies, also vary considerably. Intensification of smallholder farming systems will thus require co-learning among research, development, and private sector actors for the tailored integration of both technical and institutional innovations (Giller et al., 2011; Coe et al., 2014).
Comment on "Marine plastic debris emits a keystone infochemical for olfactory foraging seabirds" by Savoca et al.
dell'Ariccia, Gaia ; Phillips, Richard A. ; Franeker, J.A. van; Gaidet, Nicolas ; Catrey, Paulo ; Granadeiro, Jose P. ; Ryan, Peter G. ; Bonadonna, Franceso - \ 2017
Science Advances 3 (2017)6. - ISSN 2375-2548 - 3 p.
In their recent paper, Savoca and collaborators (2016) showed that plastic debris in the ocean may acquire a dimethyl sulfide (DMS) signature from biofouling developing on their surface. According to them, DMS emission may represent an olfactory trap for foraging seabirds, which explains patterns of plastic ingestion among procellariiform seabirds. This hypothesis is appealing, but some of the data that Savoca et al. used to support their claim are questionable, resulting in a misclassification of species, as well as other decisions regarding the variables
to include in their models. Furthermore, with their focus on a single lifestyle trait (nesting habit) of dubious relevance for explaining plastic ingestion, Savoca et al. neglect the opportunity to explore other factors that might provide better ecological insight. Finally, we are deeply concerned by the conservation policy recommendation proposed by Savoca et al.—to increase antifouling properties of consumer plastics—which constitutes a substantial environmental risk and delivers the wrong message to decision-makers. The reduction of plastic consumption, waste prevention, and proactive reuse through a circular economy should be at the heart of policy recommendations for future mitigation efforts.
Diversity and carbon storage across the tropical forest biome
Sullivan, Martin J.P. ; Talbot, Joey ; Lewis, Simon L. ; Phillips, Oliver L. ; Qie, Lan ; Begne, Serge K. ; Chave, Jerôme ; Cuni-Sanchez, Aida ; Hubau, Wannes ; Lopez-Gonzalez, Gabriela ; Bongers, Frans ; Peña-Claros, Marielos ; Sheil, Douglas - \ 2017
Scientific Reports 7 (2017). - ISSN 2045-2322

Tropical forests are global centres of biodiversity and carbon storage. Many tropical countries aspire to protect forest to fulfil biodiversity and climate mitigation policy targets, but the conservation strategies needed to achieve these two functions depend critically on the tropical forest tree diversity-carbon storage relationship. Assessing this relationship is challenging due to the scarcity of inventories where carbon stocks in aboveground biomass and species identifications have been simultaneously and robustly quantified. Here, we compile a unique pan-Tropical dataset of 360 plots located in structurally intact old-growth closed-canopy forest, surveyed using standardised methods, allowing a multi-scale evaluation of diversity-carbon relationships in tropical forests. Diversity-carbon relationships among all plots at 1 ha scale across the tropics are absent, and within continents are either weak (Asia) or absent (Amazonia, Africa). A weak positive relationship is detectable within 1 ha plots, indicating that diversity effects in tropical forests may be scale dependent. The absence of clear diversity-carbon relationships at scales relevant to conservation planning means that carbon-centred conservation strategies will inevitably miss many high diversity ecosystems. As tropical forests can have any combination of tree diversity and carbon stocks both require explicit consideration when optimising policies to manage tropical carbon and biodiversity.

The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project
Hudson, Lawrence N. ; Newbold, Tim ; Contu, Sara ; Hill, Samantha L.L. ; Lysenko, Igor ; Palma, Adriana De; Phillips, Helen R.P. ; Alhusseini, Tamera I. ; Bedford, Felicity E. ; Bennett, Dominic J. ; Bugter, R.J.F. - \ 2017
Ecology and Evolution 7 (2017)1. - ISSN 2045-7758 - p. 145 - 188.
The PREDICTS project—Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)—has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.
Seasonal drought limits tree species across the Neotropics
Esquivel-Muelbert, Adriane ; Baker, Timothy R. ; Dexter, Kyle G. ; Lewis, Simon L. ; Steege, Hans ter; Lopez-Gonzalez, Gabriela ; Monteagudo Mendoza, Abel ; Brienen, Roel ; Feldpausch, Ted R. ; Pitman, Nigel ; Alonso, Alfonso ; Heijden, Geertje van der; Peña-Claros, Marielos ; Ahuite, Manuel ; Alexiaides, Miguel ; Álvarez Dávila, Esteban ; Murakami, Alejandro Araujo ; Arroyo, Luzmila ; Aulestia, Milton ; Balslev, Henrik ; Barroso, Jorcely ; Boot, Rene ; Cano, Angela ; Chama Moscoso, Victor ; Comiskey, James A. ; Cornejo, Fernando ; Dallmeier, Francisco ; Daly, Douglas C. ; Dávila, Nallarett ; Duivenvoorden, Joost F. ; Duque Montoya, Alvaro Javier ; Erwin, Terry ; Fiore, Anthony Di; Fredericksen, Todd ; Fuentes, Alfredo ; García-Villacorta, Roosevelt ; Gonzales, Therany ; Guevara Andino, Juan Ernesto ; Honorio Coronado, Euridice N. ; Huamantupa-Chuquimaco, Isau ; Killeen, Timothy J. ; Malhi, Yadvinder ; Mendoza, Casimiro ; Mogollón, Hugo ; Jørgensen, Peter Møller ; Montero, Juan Carlos ; Mostacedo, Bonifacio ; Nauray, William ; Neill, David ; Vargas, Percy Núñez ; Palacios, Sonia ; Palacios Cuenca, Walter ; Pallqui Camacho, Nadir Carolina ; Peacock, Julie ; Phillips, Juan Fernando ; Pickavance, Georgia ; Quesada, Carlos Alberto ; Ramírez-Angulo, Hirma ; Restrepo, Zorayda ; Reynel Rodriguez, Carlos ; Paredes, Marcos Ríos ; Sierra, Rodrigo ; Silveira, Marcos ; Stevenson, Pablo ; Stropp, Juliana ; Terborgh, John ; Tirado, Milton ; Toledo, Marisol ; Torres-Lezama, Armando ; Umaña, María Natalia ; Urrego, Ligia Estela ; Vasquez Martinez, Rodolfo ; Gamarra, Luis Valenzuela ; Vela, César I.A. ; Vilanova Torre, Emilio ; Vos, Vincent ; Hildebrand, Patricio von; Vriesendorp, Corine ; Wang, Ophelia ; Young, Kenneth R. ; Zartman, Charles Eugene ; Phillips, Oliver L. - \ 2017
Ecography 40 (2017)5. - ISSN 0906-7590 - p. 618 - 629.
Within the tropics, the species richness of tree communities is strongly and positively associated with precipitation. Previous research has suggested that this macroecological pattern is driven by the negative effect of water-stress on the physiological processes of most tree species. This implies that the range limits of inventory plots of closed canopy forest distributed across the western Neotropics taxa are defined by their ability to occur under dry conditions, and thus in terms of species distributions predicts a nested pattern of taxa distribution from wet to dry areas. However, this 'dry-tolerance' hypothesis has yet to be adequately tested at large spatial and taxonomic scales. Here, using a dataset of 531 we investigated how precipitation, evaluated both as mean annual precipitation and as the maximum climatological water deficit, influences the distribution of tropical tree species, genera and families. We find that the distributions of tree taxa are indeed nested along precipitation gradients in the western Neotropics. Taxa tolerant to seasonal drought are disproportionally widespread across the precipitation gradient, with most reaching even the wettest climates sampled; however, most taxa analysed are restricted to wet areas. Our results suggest that the 'dry tolerance' hypothesis has broad applicability in the world's most species-rich forests. In addition, the large number of species restricted to wetter conditions strongly indicates that an increased frequency of drought could severely threaten biodiversity in this region. Overall, this study establishes a baseline for exploring how tropical forest tree composition may change in response to current and future environmental changes in this region.
The 2016 release of the PREDICTS database
Hudson, Lawrence N. ; Newbold, Tim ; Contu, Sara ; Hill, Samantha L.L. ; Lysenko, Igor ; Palma, Adriana De; Phillips, Helen R.P. ; Alhusseini, Tamera I. ; Bedford, Felicity E. ; Bennett, Dominic J. ; Bugter, R.J.F. - \ 2016
alpha diversity - global diversity modelling - global change - habitat destruction - land cover - land use - terrestrial biodiversity
Evolutionary heritage influences amazon tree ecology
Souza, Fernanda Coelho De; Dexter, Kyle G. ; Phillips, Oliver L. ; Brienen, Roel J.W. ; Chave, Jerome ; Galbraith, David R. ; Gonzalez, Gabriela Lopez ; Mendoza, Abel Monteagudo ; Toby Pennington, R. ; Poorter, Lourens ; Arets, E.J.M.M. ; Boot, Rene G.A. ; Meer, Peter J. van der - \ 2016
Proceedings of the Royal Society. B: Biological Sciences 283 (2016)1844. - ISSN 0962-8452
Convergent evolution - Divergent selection - Phylogenetic signal - Trait - Tropical tree

Lineages tend to retain ecological characteristics of their ancestors through time. However, for some traits, selection during evolutionary history may have also played a role in determining trait values. To address the relative importance of these processes requires large-scale quantification of traits and evolutionary relationships among species. The Amazonian tree flora comprises a high diversity of angiosperm lineages and species with widely differing life-history characteristics, providing an excellent system to investigate the combined influences of evolutionary heritage and selection in determining trait variation. We used trait data related to the major axes of life-history variation among tropical trees (e.g. growth and mortality rates) from 577 inventory plots in closed-canopy forest, mapped onto a phylogenetic hypothesis spanning more than 300 genera including all major angiosperm clades to test for evolutionary constraints on traits. We found significant phylogenetic signal (PS) for all traits, consistent with evolutionarily related genera having more similar characteristics than expected by chance. Although there is also evidence for repeated evolution of pioneer and shade tolerant lifehistory strategies within independent lineages, the existence of significant PS allows clearer predictions of the links between evolutionary diversity, ecosystem function and the response of tropical forests to global change.

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