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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Global distribution of earthworm diversity
Phillips, Helen R.P. ; Guerra, Carlos A. ; Bartz, Marie L.C. ; Briones, Maria J.I. ; Brown, George ; Crowther, Thomas W. ; Ferlian, Olga ; Gongalsky, Konstantin B. ; Hoogen, Johan Van Den; Krebs, Julia ; Orgiazzi, Alberto ; Routh, Devin ; Schwarz, Benjamin ; Bach, Elizabeth M. ; Bennett, Joanne ; Brose, Ulrich ; Decaëns, Thibaud ; König-Ries, Birgitta ; Loreau, Michel ; Mathieu, Jérôme ; Mulder, Christian ; Putten, Wim H. Van Der; Ramirez, Kelly S. ; Rillig, Matthias C. ; Russell, David ; Rutgers, Michiel ; Thakur, Madhav P. ; Vries, Franciska T. De; Wall, Diana H. ; Wardle, David A. ; Arai, Miwa ; Ayuke, Fredrick O. ; Baker, Geoff H. ; Beauséjour, Robin ; Bedano, José C. ; Birkhofer, Klaus ; Blanchart, Eric ; Blossey, Bernd ; Bolger, Thomas ; Bradley, Robert L. ; Callaham, Mac A. ; Capowiez, Yvan ; Caulfield, Mark E. ; Choi, Amy ; Crotty, Felicity V. ; Dávalos, Andrea ; Diaz Cosin, Darío J. ; Dominguez, Anahí ; Duhour, Andrés Esteban ; Eekeren, Nick Van; Emmerling, Christoph ; Falco, Liliana B. ; Fernández, Rosa ; Fonte, Steven J. ; Fragoso, Carlos ; Franco, André L.C. ; Fugère, Martine ; Fusilero, Abegail T. ; Gholami, Shaieste ; Gundale, Michael J. ; Gutiérrez Lopez, Monica ; Hackenberger, Davorka K. ; Hernández, Luis M. ; Hishi, Takuo ; Holdsworth, Andrew R. ; Holmstrup, Martin ; Hopfensperger, Kristine N. ; Lwanga, Esperanza Huerta ; Huhta, Veikko ; Hurisso, Tunsisa T. ; Iannone, Basil V. ; Iordache, Madalina ; Joschko, Monika ; Kaneko, Nobuhiro ; Kanianska, Radoslava ; Keith, Aidan M. ; Kelly, Courtland A. ; Kernecker, Maria L. ; Klaminder, Jonatan ; Koné, Armand W. ; Kooch, Yahya ; Kukkonen, Sanna T. ; Lalthanzara, H. ; Lammel, Daniel R. ; Lebedev, Iurii M. ; Li, Yiqing ; Jesus Lidon, Juan B. ; Lincoln, Noa K. ; Loss, Scott R. ; Marichal, Raphael ; Matula, Radim ; Moos, Jan Hendrik ; Moreno, Gerardo ; Mor n-Ríos, Alejandro ; Muys, Bart ; Neirynck, Johan ; Norgrove, Lindsey ; Novo, Marta ; Nuutinen, Visa ; Nuzzo, Victoria ; Mujeeb Rahman, P. ; Pansu, Johan ; Paudel, Shishir ; Pérès, Guénola ; Pérez-Camacho, Lorenzo ; Piñeiro, Raúl ; Ponge, Jean François ; Rashid, Muhammad Imtiaz ; Rebollo, Salvador ; Rodeiro-Iglesias, Javier ; Rodríguez, Miguel ; Roth, Alexander M. ; Rousseau, Guillaume X. ; Rozen, Anna ; Sayad, Ehsan ; Schaik, Loes Van; Scharenbroch, Bryant C. ; Schirrmann, Michael ; Schmidt, Olaf ; Schröder, Boris ; Seeber, Julia ; Shashkov, Maxim P. ; Singh, Jaswinder ; Smith, Sandy M. ; Steinwandter, Michael ; Talavera, José A. ; Trigo, Dolores ; Tsukamoto, Jiro ; Valença, Anne W. De; Vanek, Steven J. ; Virto, Iñigo ; Wackett, Adrian A. ; Warren, Matthew W. ; Wehr, Nathaniel H. ; Whalen, Joann K. ; Wironen, Michael B. ; Wolters, Volkmar ; Zenkova, Irina V. ; Zhang, Weixin ; Cameron, Erin K. ; Eisenhauer, Nico - \ 2019
Science 366 (2019)6464. - ISSN 0036-8075 - p. 480 - 485.

Soil organisms, including earthworms, are a key component of terrestrial ecosystems. However, little is known about their diversity, their distribution, and the threats affecting them. We compiled a global dataset of sampled earthworm communities from 6928 sites in 57 countries as a basis for predicting patterns in earthworm diversity, abundance, and biomass. We found that local species richness and abundance typically peaked at higher latitudes, displaying patterns opposite to those observed in aboveground organisms. However, high species dissimilarity across tropical locations may cause diversity across the entirety of the tropics to be higher than elsewhere. Climate variables were found to be more important in shaping earthworm communities than soil properties or habitat cover. These findings suggest that climate change may have serious implications for earthworm communities and for the functions they provide.

Rarity of monodominance in hyperdiverse Amazonian forests
Steege, Hans Ter; Henkel, Terry W. ; Helal, Nora ; Marimon, Beatriz S. ; Marimon-Junior, Ben Hur ; Huth, Andreas ; Groeneveld, Jürgen ; Sabatier, Daniel ; Souza Coelho, Luiz de; Andrade Lima Filho, Diogenes de; Salomão, Rafael P. ; Amaral, Iêda Leão ; Almeida Matos, Francisca Dionízia de; Castilho, Carolina V. ; Phillips, Oliver L. ; Guevara, Juan Ernesto ; Jesus Veiga Carim, Marcelo de; Cárdenas López, Dairon ; Magnusson, William E. ; Wittmann, Florian ; Irume, Mariana Victória ; Martins, Maria Pires ; Silva Guimarães, José Renan da; Molino, Jean François ; Bánki, Olaf S. ; Piedade, Maria Teresa Fernandez ; Pitman, Nigel C.A. ; Mendoza, Abel Monteagudo ; Ramos, José Ferreira ; Luize, Bruno Garcia ; Moraes de Leão Novo, Evlyn Márcia ; Núñez Vargas, Percy ; Silva, Thiago Sanna Freire ; Venticinque, Eduardo Martins ; Manzatto, Angelo Gilberto ; Reis, Neidiane Farias Costa ; Terborgh, John ; Casula, Katia Regina ; Honorio Coronado, Euridice N. ; Montero, Juan Carlos ; Feldpausch, Ted R. ; Duque, Alvaro ; Costa, Flávia R.C. ; Arboleda, Nicolás Castaño ; Schöngart, Jochen ; Killeen, Timothy J. ; Vasquez, Rodolfo ; Mostacedo, Bonifacio ; Demarchi, Layon O. ; Assis, Rafael L. ; Baraloto, Chris ; Engel, Julien ; Petronelli, Pascal ; Castellanos, Hernán ; Medeiros, Marcelo Brilhante de; Quaresma, Adriano ; Simon, Marcelo Fragomeni ; Andrade, Ana ; Camargo, José Luís ; Laurance, Susan G.W. ; Laurance, William F. ; Rincón, Lorena M. ; Schietti, Juliana ; Sousa, Thaiane R. ; Sousa Farias, Emanuelle de; Lopes, Maria Aparecida ; Magalhães, José Leonardo Lima ; Mendonça Nascimento, Henrique Eduardo ; Lima de Queiroz, Helder ; Aymard C, Gerardo A. ; Brienen, Roel ; Revilla, Juan David Cardenas ; Vieira, Ima Célia Guimarães ; Cintra, Bruno Barçante Ladvocat ; Stevenson, Pablo R. ; Feitosa, Yuri Oliveira ; Duivenvoorden, Joost F. ; Mogollón, Hugo F. ; Araujo-Murakami, Alejandro ; Ferreira, Leandro Valle ; Lozada, José Rafael ; Comiskey, James A. ; Toledo, José Julio de; Damasco, Gabriel ; Dávila, Nállarett ; Draper, Freddie ; García-Villacorta, Roosevelt ; Lopes, Aline ; Vicentini, Alberto ; Alonso, Alfonso ; Dallmeier, Francisco ; Gomes, Vitor H.F. ; Lloyd, Jon ; Neill, David ; Aguiar, Daniel Praia Portela de; Arroyo, Luzmila ; Carvalho, Fernanda Antunes ; Souza, Fernanda Coelho de; Amaral, Dário Dantas do; Feeley, Kenneth J. ; Gribel, Rogerio ; Pansonato, Marcelo Petratti ; Barlow, Jos ; Berenguer, Erika ; Ferreira, Joice ; Fine, Paul V.A. ; Guedes, Marcelino Carneiro ; Jimenez, Eliana M. ; Licona, Juan Carlos ; Peñuela Mora, Maria Cristina ; Villa, Boris ; Cerón, Carlos ; Maas, Paul ; Silveira, Marcos ; Stropp, Juliana ; Thomas, Raquel ; Baker, Tim R. ; Daly, Doug ; Dexter, Kyle G. ; Huamantupa-Chuquimaco, Isau ; Milliken, William ; Pennington, Toby ; Ríos Paredes, Marcos ; Fuentes, Alfredo ; Klitgaard, Bente ; Pena, José Luis Marcelo ; Peres, Carlos A. ; Silman, Miles R. ; Tello, J.S. ; Chave, Jerome ; Cornejo Valverde, Fernando ; Fiore, Anthony Di; Hilário, Renato Richard ; Phillips, Juan Fernando ; Rivas-Torres, Gonzalo ; Andel, Tinde R. van; Hildebrand, Patricio von; Noronha, Janaína Costa ; Barbosa, Edelcilio Marques ; Barbosa, Flávia Rodrigues ; Matos Bonates, Luiz Carlos de; Sá Carpanedo, Rainiellen de; Dávila Doza, Hilda Paulette ; Fonty, Émile ; GómeZárate Z, Ricardo ; Gonzales, Therany ; Gallardo Gonzales, George Pepe ; Hoffman, Bruce ; Junqueira, André Braga ; Malhi, Yadvinder ; Andrade Miranda, Ires Paula de; Pinto, Linder Felipe Mozombite ; Prieto, Adriana ; Jesus Rodrigues, Domingos de; Rudas, Agustín ; Ruschel, Ademir R. ; Silva, Natalino ; Vela, César I.A. ; Vos, Vincent Antoine ; Zent, Egleé L. ; Zent, Stanford ; Weiss Albuquerque, Bianca ; Cano, Angela ; Carrero Márquez, Yrma Andreina ; Correa, Diego F. ; Costa, Janaina Barbosa Pedrosa ; Flores, Bernardo Monteiro ; Galbraith, David ; Holmgren, Milena ; Kalamandeen, Michelle ; Nascimento, Marcelo Trindade ; Oliveira, Alexandre A. ; Ramirez-Angulo, Hirma ; Rocha, Maira ; Scudeller, Veridiana Vizoni ; Sierra, Rodrigo ; Tirado, Milton ; Umaña Medina, Maria Natalia ; Heijden, Geertje van der; Vilanova Torre, Emilio ; Vriesendorp, Corine ; Wang, Ophelia ; Young, Kenneth R. ; Ahuite Reategui, Manuel Augusto ; Baider, Cláudia ; Balslev, Henrik ; Cárdenas, Sasha ; Casas, Luisa Fernanda ; Farfan-Rios, William ; Ferreira, Cid ; Linares-Palomino, Reynaldo ; Mendoza, Casimiro ; Mesones, Italo ; Torres-Lezama, Armando ; Giraldo, Ligia Estela Urrego ; Villarroel, Daniel ; Zagt, Roderick ; Alexiades, Miguel N. ; Oliveira, Edmar Almeida de; Garcia-Cabrera, Karina ; Hernandez, Lionel ; Palacios Cuenca, Walter ; Pansini, Susamar ; Pauletto, Daniela ; Ramirez Arevalo, Freddy ; Sampaio, Adeilza Felipe ; Valderrama Sandoval, Elvis H. ; Valenzuela Gamarra, Luis ; Levesley, Aurora ; Pickavance, Georgia ; Melgaço, Karina - \ 2019
Scientific Reports 9 (2019). - ISSN 2045-2322

Tropical forests are known for their high diversity. Yet, forest patches do occur in the tropics where a single tree species is dominant. Such "monodominant" forests are known from all of the main tropical regions. For Amazonia, we sampled the occurrence of monodominance in a massive, basin-wide database of forest-inventory plots from the Amazon Tree Diversity Network (ATDN). Utilizing a simple defining metric of at least half of the trees ≥ 10 cm diameter belonging to one species, we found only a few occurrences of monodominance in Amazonia, and the phenomenon was not significantly linked to previously hypothesized life history traits such wood density, seed mass, ectomycorrhizal associations, or Rhizobium nodulation. In our analysis, coppicing (the formation of sprouts at the base of the tree or on roots) was the only trait significantly linked to monodominance. While at specific locales coppicing or ectomycorrhizal associations may confer a considerable advantage to a tree species and lead to its monodominance, very few species have these traits. Mining of the ATDN dataset suggests that monodominance is quite rare in Amazonia, and may be linked primarily to edaphic factors.

Modeling of Soil Functions for Assessing Soil Quality: Soil Biodiversity and Habitat Provisioning
Leeuwen, J.P. van; Creamer, Rachel ; Cluzeau, Daniel ; Debeljak, Marko ; Gatti, Fabio ; Henriksen, Christian Bugge ; Kuzmanovski, Vladimir ; Menta, Cristina ; Pérès, Guénola ; Picaud, Calypso ; Saby, N.P.A. ; Trajanov, Aneta ; Trinsoutrot-Gattin, Isabelle ; Visioli, Giovanna ; Rutgers, M. - \ 2019
Frontiers in Environmental Science 7 (2019). - ISSN 2296-665X - 13 p.
Soil biodiversity and habitat provisioning is one of the soil functions that agricultural land provides to society. This paper describes assessment of the soil biodiversity function (SB function) as a proof of concept to be used in a decision support tool for agricultural land management. The SB function is defined as “the multitude of soil organisms and processes, interacting in an ecosystem, providing society with a rich biodiversity source and contributing to a habitat for aboveground organisms.” So far, no single measure provides the full overview of the soil biodiversity and how a soil supports a habitat for a biodiverse ecosystem. We have assembled a set of attributes for a proxy-indicator system, based on four “integrated attributes”: (1) soil nutrient status, (2) soil biological status, (3) soil structure, and (4) soil hydrological status. These attributes provide information to be used in a model for assessing the capacity of a soil to supply the SB function. A multi-criteria decision model was developed which comprises of 34 attributes providing information to quantify the four integrated attributes and subsequently assess the SB function for grassland and for cropland separately. The model predictions (in terms of low—moderate—high soil biodiversity status) were compared with expert judgements for a collection of 137 grassland soils in the Netherlands and 52 French soils, 29 grasslands, and 23 croplands. For both datasets, the results show that the proposed model predictions were statistically significantly correlated with the expert judgements. A sensitivity analysis indicated that the soil nutrient status, defined by attributes such as pH and organic carbon content, was the most important integrated attribute in the assessment of the SB function. Further progress in the assessment of the SB function is needed. This can be achieved by better information regarding land use and farm management. In this way we may make a valuable step in our attempts to optimize the multiple soil functions in agricultural landscapes, and hence the multifaceted role of soils to deliver a bundle of ecosystem services for farmers and citizens, and support land management and policy toward a more sustainable society.
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.

Simple parametric tests for trait–environment association
Braak, Cajo J.F. ter; Peres-Neto, Pedro R. ; Dray, Stéphane - \ 2018
Journal of Vegetation Science 29 (2018)5. - ISSN 1100-9233 - p. 801 - 811.
community ecology - community-level test - CWM of traits - environmental gradients - fourth-corner - functional traits - modified test - species niche centroid - species-level test - statistical ecology - trait–environment relationship

Question: The CWM approach is an easy way of analysing trait–environment association by regressing (or correlating) the mean trait per plot against an environmental variable and assessing the statistical significance of the slope or the associated correlation coefficient. However, the CWM approach does not yield valid tests, as random traits (or random indicator values) are far too often judged significantly related to the environmental variable, even when the trait and environmental variable are extrinsic to (not derived from) the community data. Existing solutions are the ZS-modified test (Zelený & Schaffers,) and the max (or sequential) test based on the fourth-corner correlation. Both tests are based on permutations which become cumbersome when many tests need to be carried out and many permutations are required, as in methods that correct for multiple testing. The main goal of this study was to compare these existing permutation-based solutions and to develop a quick and easy parametric test that can replace them. Methods: This study decomposes the fourth-corner correlation in two ways, which suggests a simple parametric approach consisting of assessing the significances of two linear regressions, one plot-level test as in the CWM approach and one species-level test, the reverse of the CWM approach, that regresses the environmental mean per species (i.e. the species niche centroid) on to the trait. The tests are combined by taking the maximum p-value. The type I error rates and power of this parametric max test are examined by simulation of one- and two-dimensional Gaussian models and log-linear models. Results: The ZS-modified test and the fourth-corner max test are conservative in different scenarios, the ZS-modified test being even more conservative than the fourth-corner. The new parametric max test is shown to control the type I error and has equal or even higher power than permutation tests based on the fourth-corner, the ZS-modified test and variants thereof. A weighted version of the new test showed inflated type I error. Conclusion: The combination of two simple regressions is a good alternative to the fourth-corner and the ZS-modified test. This combination is also applicable when multiple trait measurements are made per plot.

Comparison of two widely used sampling methods in assessing earthworm community responses to agricultural intensification
Andriuzzi, Walter S. ; Pulleman, Mirjam M. ; Cluzeau, Daniel ; Pérès, Guénola - \ 2017
Applied Soil Ecology 119 (2017). - ISSN 0929-1393 - p. 145 - 151.
Body size distribution - Data integration - Ecological group - Land use - Lumbricidae - Soil fauna

To assess whether different sampling protocols provide similar results on earthworm community responses to land use, comparisons across different environments are required. Using an ongoing experiment in France, we assessed whether two protocols, widely used in international projects and global databases, provide similar estimates of earthworm abundance, and detect the same community responses to agricultural intensification. Method A consisted of hand-sorting composite samples of three soil monoliths 35 × 35 × 20 cm each, and applying formalin in the resulting holes. Method B consisted of applying formalin over a 1 m2 contiguous area and subsequently hand-sorting a 25 × 25 × 25 cm soil monolith within it. Higher abundance was obtained from Method A than from Method B, but the two methods led to the same ecological conclusions. Firstly, they both showed that earthworm biomass and density decreased with agricultural intensification. Secondly, they showed similar land use effects on earthworm ecological group proportions, age structure, and body size distribution, pointing to a relative loss of large-bodied earthworms with agricultural intensification. These findings suggest that data from the two methods are both suitable to investigate the community response of earthworms, whereas assessments of earthworm abundance per se are more sensitive to the sampling protocol. Merits and drawbacks of the methods in terms of time and labour needed and of statistical variation are discussed.

Pedigree-based analysis in a multiparental population of octoploid strawberry reveals QTL alleles conferring resistance to phytophthora cactorum
Mangandi, Jozer ; Verma, Sujeet ; Osorio, Luis ; Peres, Natalia A. ; Weg, Eric van de; Whitaker, Vance M. - \ 2017
G3 : Genes Genomes Genetics 7 (2017)6. - ISSN 2160-1836 - p. 1707 - 1719.
disease resistance - FaRPc2 - FlexQTL - Fragaria - Haplotype quantitative trait locus - MPP - Multiparental population

Understanding the genetic architecture of traits in breeding programs can be critical for making genetic progress. Important factors include the number of loci controlling a trait, allele frequencies at those loci, and allele effects in breeding germplasm. To this end, multiparental populations offer many advantages for quantitative trait locus (QTL) analyses compared to biparental populations. These include increased power for QTL detection, the ability to sample a larger number of segregating loci and alleles, and estimation of allele effects across diverse genetic backgrounds. Here, we investigate the genetic architecture of resistance to crown rot disease caused by Phytophthora cactorum in strawberry (Fragaria × ananassa), using connected full-sib families from a breeding population. Clonal replicates of > 1100 seedlings from 139 full-sib families arising from 61 parents were control-inoculated during two consecutive seasons. Subgenome-specific single nucleotide polymorphism (SNP) loci were mapped in allo-octoploid strawberry (2n = 8 × = 56), and FlexQTL software was utilized to perform a Bayesian, pedigree-based QTL analysis. A major locus on linkage group (LG) 7D, which we name FaRPc2, accounts for most of the genetic variation for resistance. Four predominant SNP haplotypes were detected in the FaRPc2 region, two of which are strongly associated with two different levels of resistance, suggesting the presence of multiple resistance alleles. The phenotypic effects of FaRPc2 alleles across trials and across numerous genetic backgrounds make this locus a highly desirable target for genetic improvement of resistance in cultivated strawberry.

Linking trait variation to the environment : Critical issues with community-weighted mean correlation resolved by the fourth-corner approach
Peres-Neto, Pedro R. ; Dray, Stéphane ; Braak, Cajo ter - \ 2017
Ecography 40 (2017)7. - ISSN 0906-7590 - p. 806 - 816.

Establishing trait-environment relationships has become routine in community ecology. Here, we demonstrate that the community weighted means correlation (CWM) and its parallel approach in linking trait variation to the environment, the species niche centroid correlation (SNC), have important shortcomings, arguing against their continuing application. Using mathematical derivations and simulations, we show that the two major issues are inconsistent parameter estimation and unacceptable significance rates when only the environment or only traits are structuring species distributions, but they themselves are not linked. We show how both CWM and SNC are related to the fourth-corner correlation and propose to replace all by the Chessel fourth-corner correlation, which is the fourth-corner correlation divided by its maximum attainable value. We propose an appropriate hypothesis testing procedure that is not only unbiased but also has much greater statistical power in detecting trait-environmental relationships. We derive an additive framework in which trait variation is partitioned among and within communities, which can be then modeled against the environment. We finish by presenting a contrast between methods and an application of our proposed framework across 85 lake-fish metacommunities.

A critical issue in model-based inference for studying trait-based community assembly and a solution
Braak, Cajo J.F. ter; Peres-Neto, Pedro ; Dray, Stéphane - \ 2017
PeerJ 5 (2017). - ISSN 2167-8359
Community composition - Compositional count data - Fourthcorner problem - Generalized linear models - Log-linear model - Negative-binomial response - Poisson regression - Trait-environment association

Statistical testing of trait-environment association from data is a challenge as there is no common unit of observation: the trait is observed on species, the environment on sites and the mediating abundance on species-site combinations. A number of correlation-based methods, such as the community weighted trait means method (CWM), the fourth-corner correlation method and the multivariate method RLQ, have been proposed to estimate such trait-environment associations. In these methods, valid statistical testing proceeds by performing two separate resampling tests, one sitebased and the other species-based and by assessing significance by the largest of the two p-values (the pmax test). Recently, regression-based methods using generalized linear models (GLM) have been proposed as a promising alternative with statistical inference via site-based resampling. We investigated the performance of this new approach along with approaches that mimicked the pmax test using GLM instead of fourth-corner. By simulation using models with additional random variation in the species response to the environment, the site-based resampling tests using GLM are shown to have severely inflated type I error, of up to 90%, when the nominal level is set as 5%. In addition, predictive modelling of such data using site-based cross-validation very often identified trait-environment interactions that had no predictive value. The problem that we identify is not an ``omitted variable bias'' problem as it occurs even when the additional random variation is independent of the observed trait and environment data. Instead, it is a problem of ignoring a random effect. In the same simulations, the GLM-based pmax test controlled the type I error in all models proposed so far in this context, but still gave slightly inflated error in more complex models that included both missing (but important) traits and missing (but important) environmental variables. For screening the importance of single trait-environment combinations, the fourth-corner test is shown to give almost the same results as the GLM-based tests in far less computing time.

Selecting cost effective and policy-relevant biological indicators for European monitoring of soil biodiversity and ecosystem function
Griffiths, B.S. ; Römbke, J. ; Schmelz, R.M. ; Scheffczyk, A. ; Faber, J.H. ; Bloem, J. ; Peres, G. ; Cluzeau, D. ; Chabbi, A. ; Suhadolc, M. ; Sousa, J.P. ; Silva, P.M. da; Carvalho, F. ; Mendes, S. ; Morais, P. ; Francisco, R. ; Pereira, C. ; Bonkowski, M. ; Geisen, Stefan ; Bardgetti, R.D. ; Vries, F.T. De; Bolger, T. ; Dirilgen, T. ; Schmidt, O. ; Winding, Anne ; Hendriksen, Nicolien ; Johansen, A. ; Philippot, L. ; Plassart, P. ; Bru, D. ; Thomson, B.M. ; Griffiths, R.I. ; Bailey, Megan ; Keith, A. ; Rutgers, M. ; Mulder, Christian ; Hannula, S.E. ; Creamer, Rachel ; Stone, D. - \ 2016
Ecological Indicators 69 (2016). - ISSN 1470-160X - p. 213 - 223.
Soils provide many ecosystem services that are ultimately dependent on the local diversity and belowground abundance of organisms. Soil biodiversity is affected negatively by many threats and there is a perceived policy requirement for the effective biological monitoring of soils at the European level. The aim of this study was to evaluate and recommend policy relevant, cost-effective soil biological indicators for biodiversity and ecosystem function across Europe. A total of 18 potential indicators were selected using a logical-sieve based approach. This paper considers the use of indicators from the ‘top down’ (i.e. concerned with the process of indicator selection), rather than from the ‘bottom up’ detail of how individual indicators perform at specific sites and with specific treatments. The indicators assessed a range of microbial, faunal and functional attributes, newer nucleic acids based techniques, morphological approaches and process based measurements. They were tested at 6 European experimental sites already in operation and chosen according to land-use, climatic zone and differences in land management intensity. These were 4 arable sites, one each in Atlantic, Continental, Mediterranean and Pannonian climate zones, and 2 grassland sites, one each in Atlantic and Continental zones. At each site we sampled three replicated plots of contrasting management intensity and, while the treatments varied from site to site, their disturbance effects were quantified in terms of land use intensity. The field sampling and laboratory analysis were standardised through a combination of ISO protocols, or standard operating procedures if the former were not available. Sites were sampled twice, in autumn 2012 and spring or autumn 2013, with relative costs of the different indicators being determined each time. A breakdown of the cost effectiveness of the indicators showed the expected trade-off between effort required in the field and effort required in the laboratory. All the indicators were able to differentiate between the sites but, as no single indicator was sensitive to all the differences in land use intensity, we suggest that an indicator programme should be based upon a suite of different indicators. For monitoring under the European climatic zones and land uses of this study, indicators for ecosystem functions related to the services of water regulation, C-sequestration and nutrient provision would include a minimum suite of: earthworms; functional genes; and bait lamina. For effective monitoring of biodiversity all taxonomic groups would need to be addressed.
Predicting bee community responses to land-use changes : Effects of geographic and taxonomic biases
Palma, Adriana De; Abrahamczyk, Stefan ; Aizen, Marcelo A. ; Albrecht, Matthias ; Basset, Yves ; Bates, Adam ; Blake, Robin J. ; Boutin, Céline ; Bugter, Rob ; Connop, Stuart ; Cruz-López, Leopoldo ; Cunningham, Saul A. ; Darvill, Ben ; Diekötter, Tim ; Dorn, Silvia ; Downing, Nicola ; Entling, Martin H. ; Farwig, Nina ; Felicioli, Antonio ; Fonte, Steven J. ; Fowler, Robert ; Franzén, Markus ; Goulson, Dave ; Grass, Ingo ; Hanley, Mick E. ; Hendrix, Stephen D. ; Herrmann, Farina ; Herzog, Felix ; Holzschuh, Andrea ; Jauker, Birgit ; Kessler, Michael ; Knight, M.E. ; Kruess, Andreas ; Lavelle, Patrick ; Féon, Violette Le; Lentini, Pia ; Malone, Louise A. ; Marshall, Jon ; Pachón, Eliana Martínez ; McFrederick, Quinn S. ; Morales, Carolina L. ; Mudri-Stojnic, Sonja ; Nates-Parra, Guiomar ; Nilsson, Sven G. ; Öckinger, Erik ; Osgathorpe, Lynne ; Parra-H, Alejandro ; Peres, Carlos A. ; Persson, Anna S. ; Petanidou, Theodora ; Poveda, Katja ; Power, Eileen F. ; Quaranta, Marino ; Quintero, Carolina ; Rader, Romina ; Richards, Miriam H. ; Roulston, Tai ; Rousseau, Laurent ; Sadler, Jonathan P. ; Samnegård, Ulrika ; Schellhorn, Nancy A. ; Schüepp, Christof ; Schweiger, Oliver ; Smith-Pardo, Allan H. ; Steffan-Dewenter, Ingolf ; Stout, Jane C. ; Tonietto, Rebecca K. ; Tscharntke, Teja ; Tylianakis, Jason M. ; Verboven, Hans A.F. ; Vergara, Carlos H. ; Verhulst, Jort ; Westphal, Catrin ; Yoon, Hyung Joo ; Purvis, Andy - \ 2016
Scientific Reports 6 (2016). - ISSN 2045-2322 - 14 p.

Land-use change and intensification threaten bee populations worldwide, imperilling pollination services. Global models are needed to better characterise, project, and mitigate bees' responses to these human impacts. The available data are, however, geographically and taxonomically unrepresentative; most data are from North America and Western Europe, overrepresenting bumblebees and raising concerns that model results may not be generalizable to other regions and taxa. To assess whether the geographic and taxonomic biases of data could undermine effectiveness of models for conservation policy, we have collated from the published literature a global dataset of bee diversity at sites facing land-use change and intensification, and assess whether bee responses to these pressures vary across 11 regions (Western, Northern, Eastern and Southern Europe; North, Central and South America; Australia and New Zealand; South East Asia; Middle and Southern Africa) and between bumblebees and other bees. Our analyses highlight strong regionally-based responses of total abundance, species richness and Simpson's diversity to land use, caused by variation in the sensitivity of species and potentially in the nature of threats. These results suggest that global extrapolation of models based on geographically and taxonomically restricted data may underestimate the true uncertainty, increasing the risk of ecological surprises.

FaRXf1 : a locus conferring resistance to angular leaf spot caused by Xanthomonas fragariae in octoploid strawberry
Roach, Jack A. ; Verma, Sujeet ; Peres, Natalia A. ; Jamieson, Andrew R. ; Weg, Eric W. van de; Bink, Marco C.A.M. ; Bassil, Nahla V. ; Lee, Seonghee ; Whitaker, Vance M. - \ 2016
Theoretical and Applied Genetics (2016). - ISSN 0040-5752 - p. 1191 - 1201.

Key message: Angular leaf spot is a devastating bacterial disease of strawberry. Resistance from two wild accessions is highly heritable and controlled by a major locus on linkage group 6D.Abstract: Angular leaf spot caused by Xanthomonas fragariae is the only major bacterial disease of cultivated strawberry (Fragaria ×ananassa). While this disease may cause reductions of up to 8 % of marketable yield in Florida winter annual production, no resistant cultivars have been commercialized. Wild accessions US4808 and US4809 were previously identified as resistant to the four genetic clades of X. fragariae, and introgression of the trait into commercial quality perennial-type germplasm was initiated. Previous reports indicated high heritability for the trait but proposed both single-locus and multi-locus inheritance models. The objective of this study was to determine the mode of inheritance of resistance, to identify causal loci, and to begin introgression of resistance into Florida-adapted germplasm. Resistance was observed in two years of field trials with inoculated plants that assayed four full-sib families descended from US4808 to US4809. Resistance segregated 1:1 in all families indicating control by a dominant allele at a single locus. Using a selective genotyping approach with the IStraw90 Axiom® SNP array and pedigree-based QTL detection, a single major-effect QTL was identified in two full-sib families, one descended from each resistant accession. High-resolution melt curve analysis validated the presence of the QTL in separate populations. The QTL was delimited to the 33.1–33.6 Mbp (F. vesca vesca v1.1 reference) and 34.8–35.3 Mbp (F. vesca bracteata v2.0 reference) regions of linkage group 6D for both resistance sources and was designated FaRXf1. Characterization of this locus will facilitate marker-assisted selection toward the development of resistant cultivars.

Mapping earthworm communities in Europe
Rutgers, M. ; Orgiazzi, A. ; Gardi, C. ; Römbke, J. ; Jansch, S. ; Keith, A. ; Neilson, R. ; Boag, B. ; Schmidt, O. ; Murchie, A.K. ; Blackshaw, R.P. ; Pérès, G. ; Cluzeau, D. ; Guernion, M. ; Briones, M.J.I. ; Rodeiro, J. ; Pineiro, R. ; Diaz Cosin, D.J. ; Sousa, J.P. ; Suhadolc, M. ; Kos, I. ; Krogh, P.H. ; Faber, J.H. ; Mulder, C. ; Bogte, J.J. ; Wijnen, H.J. van; Schouten, A.J. ; Zwart, D. de - \ 2016
Applied Soil Ecology 97 (2016). - ISSN 0929-1393 - p. 98 - 111.
Existing data sets on earthworm communities in Europe were collected, harmonized, collated, modelled and depicted on a soil biodiversity map. Digital Soil Mapping was applied using multiple regressions relating relatively low density earthworm community data to soil characteristics, land use, vegetation and climate factors (covariables) with a greater spatial resolution. Statistically significant relationships were used to build habitat–response models for maps depicting earthworm abundance and species diversity. While a good number of environmental predictors were significant in multiple regressions, geographical factors alone seem to be less relevant than climatic factors. Despite differing sampling protocols across the investigated European countries, land use and geological history were the most relevant factors determining the demography and diversity of the earthworms. Case studies from country-specific data sets (France, Germany, Ireland and The Netherlands) demonstrated the importance and efficiency of large databases for the detection of large spatial patterns that could be subsequently applied at smaller (local) scales.
Mapping earthworm communities in Europe
Rutgers, Michiel ; Orgiazzi, A. ; Gardi, C. ; Rombke, J. ; Jänsch, S. ; Keith, A.M. ; Neilson, R. ; Boag, B. ; Schmidt, O. ; Murchie, A.K. ; Blackshaw, R.P. ; Rod, P. ; Pérès, G. ; Cluzeau, D. ; Guernion, M. ; Briones, M.J.I. ; Rodeiro, J. ; Pineiro, R. ; Diaz Cosin, D.J. ; Trigo, Dolores ; Sousa, Paulo J. ; Suhadolc, M. ; Kos, I. ; Krogh, Paul Henning ; Faber, J.H. ; Mulder, Christian ; Bogte, J.J. ; Wijnen, H.J. van; Schouten, A.J. ; Zwart, D. de - \ 2015
Existing data sets on earthworm communities in Europe were collected, harmonized and
modelled to illustrate our current knowledge on their European diversity and geographical
distribution. Digital Soil Mapping was applied using multiple regression techniques relating
relatively low density earthworm community data to soil characteristics, land use, vegetation
type and climate factors, that had a greater spatial resolution. Statistically significant
relationships were used to build habitat-response models to construct earthworm maps for
abundance, species richness, and diversity data. Although a number of environmental
predictors were significant in our multiple regressions, geographical factors alone were less
relevant than climatic factors. Despite differing earthworm sampling protocols, land use and
geological history were the main factors determining demography and diversity of the
earthworms across Europe. Case studies from country-specific data sets (France, Germany,
Ireland and The Netherlands) demonstrated the importance and efficiency of these large
databases for the detection of large spatial patterns that could be subsequently applied at
smaller (local) scales. Additional datasets have been later incorporated (e.g. Portugal, Italy,
England, Wales, Belgium, Finland, Austria and some countries from Eastern Europe) to
improve our predictions of earthworm geographical patterns. The improved maps will be
submitted for publication in the Global Soil Biodiversity Atlas.
Land use intensity impact on functional diversity in earthworms regarding regulation of soil structure and water infiltration
Faber, J.H. ; Pérès, G. ; Groot, Arjen de; Krogh, P.H. - \ 2015
Earthworms can be distinguished into three groups that represent different clusters of morphological and behavioural traits. These so-called ecological groups (sensu Bouché 1977) have traditionally been considered to represent different functional groups with respect to soil processes. In this context, one aim of our study was to assess the impact of agronomic intensification across a range of land-use systems on the relationships between earthworm
community composition and soil processes. Secondly, we quantified the relationships between earthworm ecological groups and individual species with soil aggregate formation,macroporosity and water infiltration capacity. In a comparison between permanent grassland, permanent arable land with conventional ploughing, and a 3:3 years rotation system the stability of soil aggregates in the top layer was higher under grass cover, and the stability of 2-
4mm soil aggregates significantly increased with increasing biomass of both anecic and endogeic earthworms. Earthworm burrow distribution over the soil profile was strongly impacted by land management (e.g. total number was higher under grassland vs crop), and specific relationships were identified between some earthworm species and larger macropores.
Water infiltration rates significantly increased with increasing earthworm biomass, and this effect was significant for the group of anecic species. The role of endogeic species appears to be inconsistent between sites or management practices. We discuss the functional ecology of earthworms at the level of functional group and the individual species, focussing on burrow
morphology and vulnerability towards agricultural management practices. Results contribute to the understanding of the linkage between soil biodiversity and provision of ecosystem services.
Our quantitative results can be used in ecohydrological modelling (forecasting) and economic valuation studies.
Earthworm functioning in soil ecosystem services in relation to land use intensity
Faber, J.H. ; Groot, G.A. de; Andriuzzi, Walter ; Peres, G. ; Henning Krogh, P. ; Sudaholc, Marjetka ; Mihelic, Rok ; Rombke, J. ; Jaensch, S. ; Schmeltz, R. ; Keith, A.K. ; Schmidt, O. ; Chabbi, A. - \ 2014
- 1 p.
Selecting cost effective and policy-relevant biological indicators for European monitoring of soil biodiversity and ecosystem function
Griffiths, B.S. ; Creamer, R. ; Stone, D. ; Römbke, J. ; Schmelz, R. ; Faber, J.H. ; Bloem, J. ; Peres, G. ; Chabbi, A. ; Cluzeau, D. - \ 2014
Introduction – There is a demand for reliable tools to design and implement strategies for sustainable management of soils, including the design of policy-relevant and cost-effective indicators for monitoring soil biodiversity and ecosystem function. Our goal, which forms part of an EU-funded project called EcoFINDERS, was to develop and evaluate novel approaches for monitoring of soil biodiversity and functioning across a broad range of European environments and land-use systems. Methods – Eighteen existing and potential biological indicators were selected using a logical sieve approach, combined with meta-analysis of European soil monitoring schemes. All indicators were evaluated at six, long-term field sites offering replicated plots of different agricultural management scenarios. The sites covered the major European climatic zones and land use types, while the replicated treatments spanned a wide range of management intensification. Soil sampling was standardised and coordinated across all sites. Results – The response of the indicators was analysed with respect to the intensity gradient of applied treatments. All the indicators tested were sensitive between the different sites, but showed variable sensitivity to the imposed management practices. Preliminary analysis showed greater effects of intensification on biodiversity and function in arable than grassland systems.. Cost-effectiveness of the indicators was assessed from their labour intensity, practicability and ease of interpretation. Conclusion – Results clearly demonstrated strengths and weaknesses to each type of indicator, confirming that no single indicator will be appropriate for a large scale monitoring scheme. A scheme should aim for the lowest number of indicators in order to be efficient with limited resources, but with enough power to address the specific question. Some of the developing methods, especially next-generation sequencing and functional gene analysis, look increasingly favourable from cost-effective and ease of interpretation perspectives. The ‘toolkit’ of biological indicators can be adapted according to the priorities of the monitoring scheme. Keywords: Monitoring, Indicators, Land use intensity, Sustainability
Impact of agricultural extensification on the relation between soil biodiversity and ecosystem services (soil structure maintenance, water regulation)
Faber, J.H. ; Pérès, G. ; Groot, G.A. de; Krogh, P.H. ; Suhadol, M. ; Jaensch, S. ; Keith, A.K. ; Schmidt, O. ; Andriuzzi, W.S. ; Chabbi, A. - \ 2014
In: Book of Abstracts of the First Global Soil Biodiversity Conference. - - p. 517 - 517.
Introduction – There are increasing pressures on soil biodiversity and soil degradation remains a pertinent issue. In this context, one aim of the EcoFINDERS European project was to assess the impact of agricultural extensification, across a broad range of European land-use systems, on the relationships between soil biodiversity and ecosystem services. Special attention was given to the relation between i) soil biodiversity and aggregate stability, and ii) earthworms and soil macroporosity and water infiltration. Method - Data from seven long-term field studies (France, Germany, United-Kingdom, Slovenia, Denmark) on replicated plots of different land management scenarios (grassland, arable cropping, mixed crop-grassland, reduced or conventional tillage) were analysed. Earthworms were sampled using hand sorting and chemical extraction. Aggregate stability was measured using wet sieving method. Macropore distribution (i.e. numbers and diameter of earthworm burrows) was quantified at different horizontal layers. Infiltration rates were measured as the saturated hydraulic conductivity. Results – Data analysis demonstrated that earthworm community (species, ecological groups) was affected by land use and management practices. Aggregate stability in the top layer was significantly different among management treatments: higher under grassland than crop, and higher under reduced tillage than conventional tillage. Moreover, aggregate stability could significantly increase with earthworm biomass (anecic, endogeic). Burrow distribution was impacted by managements, likewise water infiltration capacity (permanent arable <mixed cropgrassland <permanent grassland; conventional <reduced or minimal tillage). Water infiltration capacity was related to functional diversity in earthworms, through the mediation of specific soil macropores by various species; pore systems and burrows that were connected to the soil surface contributed most efficiently to water infiltration rates. Conclusion – These observations indicate that less intensive managements result in increasing earthworm functional biodiversity, providing better soil structure and water infiltration. These results provide more quantitative insights that allow for ecohydrological modelling (forecasting) and economic valuation.
Functional soil biodiversity; the contribution of reduced tillage systems to ecosystem services and sustainable farming.
Pulleman, M.M. ; Pérès, G. ; Faber, J. - \ 2014
Combining the fourth-corner and the RLQ methods for assessing trait responses to environmental variation
Dray, S. ; Choler, P. ; Dolédec, S. ; Peres-Neto, P.R. ; Thuiller, W. ; Pavoine, S. ; Braak, C.J.F. ter - \ 2014
Ecology 95 (2014). - ISSN 0012-9658 - p. 14 - 21.
co-inertia analysis - species traits - community ecology - plant - variables - linking
Assessing trait responses to environmental gradients requires the simultaneous analysis of the information contained in three tables: L (species distribution across samples), R (environmental characteristics of samples) and Q (species traits). Among the available methods, the so-called fourth-corner and RLQ methods are two appealing alternatives that provide a direct way to test and estimate trait-environment relationships. Both methods are based on the analysis of the fourth-corner matrix which crosses traits and environmental variables weighted by species abundances. However, they greatly differ in their outputs: RLQ is a multivariate technique that provides ordination scores to summarize the joint structure among the three tables, whereas the fourth-corner method mainly tests for individual trait-environment relationships (i.e. one trait and one environmental variable at a time). Here, we illustrate how the complementarity between these two methods can be exploited to promote new ecological knowledge and to improve the study of trait-environment relationships. After a short description of each method, we apply them to real ecological data to present their different outputs and provide hints about the gain resulting from their combined use. Read More: http://www.esajournals.org/doi/abs/10.1890/13-0196.1
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