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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Resilience, Reindeer, Oil, and Climate change : Challenges facing the Nenets Indigenous People in the Russian Arctic
Tysyachnyouk, M. ; Henry, Laura A. ; Tulaeva, Svetlana - \ 2019
In: The Big Thaw / Zubrow, Ezra B.W., Meidinger, Errol, Connolly, Kim Diana, Suny Press. - ISBN 9781438475639 - p. 337 - 360.
Correction to: Genetic variant predictors of gene expression provide new insight into risk of colorectal cancer
Bien, Stephanie A. ; Su, Yu Ru ; Conti, David V. ; Harrison, Tabitha A. ; Qu, Conghui ; Guo, Xingyi ; Lu, Yingchang ; Albanes, Demetrius ; Auer, Paul L. ; Banbury, Barbara L. ; Berndt, Sonja I. ; Bézieau, Stéphane ; Brenner, Hermann ; Buchanan, Daniel D. ; Caan, Bette J. ; Campbell, Peter T. ; Carlson, Christopher S. ; Chan, Andrew T. ; Chang-Claude, Jenny ; Chen, Sai ; Connolly, Charles M. ; Easton, Douglas F. ; Feskens, Edith J.M. ; Gallinger, Steven ; Giles, Graham G. ; Gunter, Marc J. ; Hampe, Jochen ; Huyghe, Jeroen R. ; Hoffmeister, Michael ; Hudson, Thomas J. ; Jacobs, Eric J. ; Jenkins, Mark A. ; Kampman, Ellen ; Kang, Hyun Min ; Kühn, Tilman ; Küry, Sébastien ; Lejbkowicz, Flavio ; Marchand, Loic Le; Milne, Roger L. ; Li, Li ; Li, Christopher I. ; Lindblom, Annika ; Lindor, Noralane M. ; Martín, Vicente ; McNeil, Caroline E. ; Melas, Marilena ; Moreno, Victor ; Newcomb, Polly A. ; Offit, Kenneth ; Pharaoh, Paul D.P. ; Potter, John D. ; Qu, Chenxu ; Riboli, Elio ; Rennert, Gad ; Sala, Núria ; Schafmayer, Clemens ; Scacheri, Peter C. ; Schmit, Stephanie L. ; Severi, Gianluca ; Slattery, Martha L. ; Smith, Joshua D. ; Trichopoulou, Antonia ; Tumino, Rosario ; Ulrich, Cornelia M. ; Duijnhoven, Fränzel J.B. van; Guelpen, Bethany Van; Weinstein, Stephanie J. ; White, Emily ; Wolk, Alicja ; Woods, Michael O. ; Wu, Anna H. ; Abeçasis, Goncalo R. ; Casey, Graham ; Nickerson, Deborah A. ; Gruber, Stephen B. ; Hsu, Li ; Zheng, Wei ; Peters, Ulrike - \ 2019
Human Genetics 138 (2019)7. - ISSN 0340-6717 - p. 789 - 791.

Every author has erroneously been assigned to the affiliation “62”. The affiliation 62 belongs to the author Graham Casey.

Digital mapping of peatlands – A critical review
Minasny, Budiman ; Berglund, Örjan ; Connolly, John ; Hedley, Carolyn ; Vries, Folkert de; Gimona, Alessandro ; Kempen, Bas ; Kidd, Darren ; Lilja, Harry ; Malone, Brendan ; McBratney, Alex ; Roudier, Pierre ; O'Rourke, Sharon ; Rudiyanto, ; Padarian, José ; Poggio, Laura ; Caten, Alexandre ten; Thompson, Daniel ; Tuve, Clint ; Widyatmanti, Wirastuti - \ 2019
Earth-Science Reviews 196 (2019). - ISSN 0012-8252

Peatlands offer a series of ecosystem services including carbon storage, biomass production, and climate regulation. Climate change and rapid land use change are degrading peatlands, liberating their stored carbon (C) into the atmosphere. To conserve peatlands and help in realising the Paris Agreement, we need to understand their extent, status, and C stocks. However, current peatland knowledge is vague—estimates of global peatland extent ranges from 1 to 4.6 million km2, and C stock estimates vary between 113 and 612 Pg (or billion tonne C). This uncertainty mostly stems from the coarse spatial scale of global soil maps. In addition, most global peatland estimates are based on rough country inventories and reports that use outdated data. This review shows that digital mapping using field observations combined with remotely-sensed images and statistical models is an avenue to more accurately map peatlands and decrease this knowledge gap. We describe peat mapping experiences from 12 countries or regions and review 90 recent studies on peatland mapping. We found that interest in mapping peat information derived from satellite imageries and other digital mapping technologies is growing. Many studies have delineated peat extent using land cover from remote sensing, ecology, and environmental field studies, but rarely perform validation, and calculating the uncertainty of prediction is rare. This paper then reviews various proximal and remote sensing techniques that can be used to map peatlands. These include geophysical measurements (electromagnetic induction, resistivity measurement, and gamma radiometrics), radar sensing (SRTM, SAR), and optical images (Visible and Infrared). Peatland is better mapped when using more than one covariate, such as optical and radar products using nonlinear machine learning algorithms. The proliferation of satellite data available in an open-access format, availability of machine learning algorithms in an open-source computing environment, and high-performance computing facilities could enhance the way peatlands are mapped. Digital soil mapping allows us to map peat in a cost-effective, objective, and accurate manner. Securing peatlands for the future, and abating their contribution to atmospheric C levels, means digitally mapping them now.

Genetic variant predictors of gene expression provide new insight into risk of colorectal cancer
Bien, Stephanie A. ; Su, Yu-Ru ; Conti, David V. ; Harrison, Tabitha A. ; Qu, Conghui ; Guo, Xingyi ; Lu, Yingchang ; Albanes, Demetrius ; Auer, Paul L. ; Banbury, Barbara L. ; Berndt, Sonja I. ; Bézieau, Stéphane ; Brenner, Hermann ; Buchanan, Daniel D. ; Caan, Bette J. ; Campbell, Peter T. ; Carlson, Christopher S. ; Chan, Andrew T. ; Chang-Claude, Jenny ; Chen, Sai ; Connolly, Charles M. ; Easton, Douglas F. ; Feskens, Edith J.M. ; Gallinger, Steven ; Giles, Graham G. ; Gunter, Marc J. ; Hampe, Jochen ; Huyghe, Jeroen R. ; Hoffmeister, Michael ; Hudson, Thomas J. ; Jacobs, Eric J. ; Jenkins, Mark A. ; Kampman, Ellen ; Kang, Hyun Min ; Kühn, Tilman ; Küry, Sébastien ; Lejbkowicz, Flavio ; Marchand, Loic Le; Milne, Roger L. ; Li, Christopher I. ; Lindblom, Annika ; Lindor, Noralane M. ; Martín, Vicente ; McNeil, Caroline E. ; Melas, Marilena ; Moreno, Victor ; Newcomb, Polly A. ; Offit, Kenneth ; Pharaoh, Paul D.P. ; Potter, John D. ; Qu, Chenxu ; Riboli, Elio ; Rennert, Gad ; Sala, Núria ; Schafmayer, Clemens ; Scacheri, Peter C. ; Schmit, Stephanie L. ; Severi, Gianluca ; Slattery, Martha L. ; Smith, Joshua D. ; Trichopoulou, Antonia ; Tumino, Rosario ; Ulrich, Cornelia M. ; Duijnhoven, Fränzel J.B. van; Guelpen, Bethany Van; Weinstein, Stephanie J. ; White, Emily ; Wolk, Alicja ; Woods, Michael O. ; Wu, Anna H. ; Abecasis, Goncalo R. ; Casey, Graham ; Nickerson, Deborah A. ; Gruber, Stephen B. ; Hsu, Li ; Zheng, Wei ; Peters, Ulrike - \ 2019
Human Genetics 138 (2019)4. - ISSN 0340-6717 - p. 307 - 326.
Genome-wide association studies have reported 56 independently associated colorectal cancer (CRC) risk variants, most of which are non-coding and believed to exert their effects by modulating gene expression. The computational method PrediXcan uses cis-regulatory variant predictors to impute expression and perform gene-level association tests in GWAS without directly measured transcriptomes. In this study, we used reference datasets from colon (n = 169) and whole blood (n = 922) transcriptomes to test CRC association with genetically determined expression levels in a genome-wide analysis of 12,186 cases and 14,718 controls. Three novel associations were discovered from colon transverse models at FDR ≤ 0.2 and further evaluated in an independent replication including 32,825 cases and 39,933 controls. After adjusting for multiple comparisons, we found statistically significant associations using colon transcriptome models with TRIM4 (discovery P = 2.2 × 10− 4, replication P = 0.01), and PYGL (discovery P = 2.3 × 10− 4, replication P = 6.7 × 10− 4). Interestingly, both genes encode proteins that influence redox homeostasis and are related to cellular metabolic reprogramming in tumors, implicating a novel CRC pathway linked to cell growth and proliferation. Defining CRC risk regions as one megabase up- and downstream of one of the 56 independent risk variants, we defined 44 non-overlapping CRC-risk regions. Among these risk regions, we identified genes associated with CRC (P < 0.05) in 34/44 CRC-risk regions. Importantly, CRC association was found for two genes in the previously reported 2q25 locus, CXCR1 and CXCR2, which are potential cancer therapeutic targets. These findings provide strong candidate genes to prioritize for subsequent laboratory follow-up of GWAS loci. This study is the first to implement PrediXcan in a large colorectal cancer study and findings highlight the utility of integrating transcriptome data in GWAS for discovery of, and biological insight into, risk loci.
The Future of Complementarity : Disentangling Causes from Consequences
Barry, Kathryn E. ; Mommer, Liesje ; Ruijven, Jasper van; Wirth, Christian ; Wright, Alexandra J. ; Bai, Yongfei ; Connolly, John ; Deyn, Gerlinde B. De; Kroon, Hans de; Isbell, Forest ; Milcu, Alexandru ; Roscher, Christiane ; Scherer-Lorenzen, Michael ; Schmid, Bernhard ; Weigelt, Alexandra - \ 2019
Trends in Ecology and Evolution 34 (2019)2. - ISSN 0169-5347 - p. 167 - 180.
Abiotic facilitation - Biodiversity - Biotic feedbacks - Complementarity - Complementarity effect - Ecosystem functioning - Plant-soil feedback - Resource partitioning - Resource tracers - Stress amelioration

Evidence suggests that biodiversity supports ecosystem functioning. Yet, the mechanisms driving this relationship remain unclear. Complementarity is one common explanation for these positive biodiversity–ecosystem functioning relationships. Yet, complementarity is often indirectly quantified as overperformance in mixture relative to monoculture (e.g., ‘complementarity effect’). This overperformance is then attributed to the intuitive idea of complementarity or, more specifically, to species resource partitioning. Locally, however, several unassociated causes may drive this overperformance. Here, we differentiate complementarity into three types of species differences that may cause enhanced ecosystem functioning in more diverse ecosystems: (i) resource partitioning, (ii) abiotic facilitation, and (iii) biotic feedbacks. We argue that disentangling these three causes is crucial for predicting the response of ecosystems to future biodiversity loss.

Diverse peptide hormones affecting root growth identified in the Medicago truncatula secreted peptidome
Patel, Neha ; Mohd-Radzman, Nadiatul A. ; Corcilius, Leo ; Crossett, Ben ; Connolly, Angela ; Cordwell, Stuart J. ; Ivanovici, Ariel ; Taylor, Katia ; Williams, James ; Binos, Steve ; Mariani, Michael ; Payne, Richard J. ; Djordjevic, Michael A. - \ 2018
Molecular and Cellular Proteomics 17 (2018)1. - ISSN 1535-9476 - p. 160 - 174.

Multigene families encoding diverse secreted peptide hormones play important roles in plant development. A need exists to efficiently elucidate the structures and post-translational-modifications of these difficult-to-isolate peptide hormones in planta so that their biological functions can be determined. A mass spectrometry and bioinformatics approach was developed to comprehensively analyze the secreted peptidome of Medicago hairy root cultures and xylem sap. We identified 759 spectra corresponding to the secreted products of twelve peptide hormones including four CEP (C-TERMINALLY ENCODED PEPTIDE), two CLE (CLV3/ENDOSPERM SURROUNDING REGION RELATED) and six XAP (XYLEM SAP ASSOCIATED PEPTIDE) peptides. The MtCEP1, MtCEP2, MtCEP5 and MtCEP8 peptides identified differed in post-translational- modifications. Most were hydroxylated at conserved proline residues but some MtCEP1 derivatives were tri-arabinosylated. In addition, many CEP peptides possessed unexpected N- and C-terminal extensions. The pattern of these extensions suggested roles for endo- and exoproteases in CEP peptide maturation. Longer than expected, hydroxylated and homogeneously modified mono- and tri-arabinosylated CEP peptides corresponding to their in vivo structures were chemically synthesized to probe the effect of these post-translational-modifications on function. The ability of CEP peptides to elevate root nodule number was increased by hydroxylation at key positions. MtCEP1 peptides with N-terminal extensions or with tri-arabinosylation modification, however, were unable to impart increased nodulation. The MtCLE5 and MtCLE17 peptides identified were of precise size, and inhibited main root growth and increased lateral root number. Six XAP peptides, each beginning with a conserved DY sulfation motif, were identified including MtXAP1a, MtXAP1b, MtXAP1c, MtXAP3, MtXAP5 and MtXAP7. MtXAP1a and MtXAP5 inhibited lateral root emergence. Transcriptional analyses demonstrated peptide hormone gene expression in the root vasculature and tip. Since hairy roots can be induced on many plants, their corresponding root cultures may represent ideal source materials to efficiently identify diverse peptide hormones in vivo in a broad range of species.

Discovery of common and rare genetic risk variants for colorectal cancer
Huyghe, Jeroen R. ; Bien, Stephanie A. ; Harrison, Tabitha A. ; Kang, Hyun Min ; Chen, Sai ; Schmit, Stephanie L. ; Conti, David V. ; Qu, Conghui ; Jeon, Jihyoun ; Edlund, Christopher K. ; Greenside, Peyton ; Wainberg, Michael ; Schumacher, Fredrick R. ; Smith, Joshua D. ; Levine, David M. ; Nelson, Sarah C. ; Sinnott-armstrong, Nasa A. ; Albanes, Demetrius ; Alonso, M.H. ; Anderson, Kristin ; Arnau-Collell, Coral ; Arndt, Volker ; Bamia, Christina ; Banbury, Barbara L. ; Baron, John A. ; Berndt, Sonja I. ; Bézieau, Stéphane ; Bishop, D.T. ; Boehm, Juergen ; Boeing, Heiner ; Brenner, Hermann ; Brezina, Stefanie ; Buch, Stephan ; Buchanan, Daniel D. ; Burnett-hartman, Andrea ; Butterbach, Katja ; Caan, Bette J. ; Campbell, Peter T. ; Carlson, Christopher S. ; Castellví-Bel, Sergi ; Chan, Andrew T. ; Chang-Claude, Jenny ; Chanock, Stephen J. ; Chirlaque, Maria-Dolores ; Cho, Sang Hee ; Connolly, Charles M. ; Cross, Amanda J. ; Feskens, Edith J.M. ; Li, Li ; Huang, Wen-Yi - \ 2018
Nature Genetics 51 (2018). - ISSN 1061-4036 - p. 76 - 87.
To further dissect the genetic architecture of colorectal cancer (CRC), we performed whole-genome sequencing of 1,439 cases and 720 controls, imputed discovered sequence variants and Haplotype Reference Consortium panel variants into genome-wide association study data, and tested for association in 34,869 cases and 29,051 controls. Findings were followed up in an additional 23,262 cases and 38,296 controls. We discovered a strongly protective 0.3% frequency variant signal at CHD1. In a combined meta-analysis of 125,478 individuals, we identified 40 new independent signals at P < 5 × 10−8, bringing the number of known independent signals for CRC to ~100. New signals implicate lower-frequency variants, Krüppel-like factors, Hedgehog signaling, Hippo-YAP signaling, long noncoding RNAs and somatic drivers, and support a role for immune function. Heritability analyses suggest that CRC risk is highly polygenic, and larger, more comprehensive studies enabling rare variant analysis will improve understanding of biology underlying this risk and influence personalized screening strategies and drug development.
Weed suppression greatly increased by plant diversity in intensively managed grasslands: a continental-scale experiment
Connolly, J. ; Sebastià, M.T. ; Kirwan, L. ; Finn, John A. ; Llurba, Rosa ; Suter, M. ; Collins, Rosemary P. ; Porqueddu, C. ; Helgadóttir, A. ; Baadshaug, Ole H. ; Bélanger, Gilles ; Black, A. ; Brophy, C. ; Čop, Jure ; Dalmannsdóttir, S. ; Delgado, I. ; Elgersma, A. ; Fothergill, M. ; Frankow-Lindberg, Bodil E. ; Ghesquiere, A. ; Golinski, P. ; Grieu, P. ; Gustavsson, A.M. ; Höglind, M. ; Huguenin-Elie, O. ; Jørgensen, M. ; Kadziuliene, Z. ; Lunnan, T. ; Nykanen-Kurki, P. ; Ribas, A. ; Taube, F. ; Thumm, U. ; Vliegher, A. de; Lüscher, A. - \ 2018
Journal of Applied Ecology 55 (2018)2. - ISSN 0021-8901 - p. 852 - 862.
1.Grassland diversity can support sustainable intensification of grassland production through increased yields, reduced inputs and limited weed invasion. We report the effects of diversity on weed suppression from three years of a 31-site continental-scale field experiment.

2.At each site, fifteen grassland communities comprising four monocultures and 11 4-species mixtures based on a wide range of species’ proportions were sown at two densities and managed by cutting. Forage species were selected according to two crossed functional traits, ‘method-of-nitrogen-acquisition’ and ‘pattern-of-temporal- development’.

3.Across sites, years, and sown densities, annual weed biomass in mixtures and monocultures was 0.5 and 2.0 t DM ha−1 (7% and 33% of total biomass respectively). Over 95% of mixtures had weed biomass lower than the average of monocultures, and, in two thirds of cases, lower than in the most suppressive monoculture (transgressive suppression). Suppression was significantly transgressive for 58% of site-years. Transgressive suppression by mixtures was maintained across years, independent of site productivity.

4.Based on models, average weed biomass in mixture over the whole experiment was 52% less (95% confidence interval 30% to 75%) than in the most suppressive monoculture. Transgressive suppression of weed biomass was significant at each year across all mixtures and for each mixture.

5.Weed biomass was consistently low across all mixtures and years and was in some cases significantly but not largely different from that in the equiproportional mixture. The average variability (standard deviation) of annual weed biomass within a site was much lower for mixtures (0.42) than for monocultures (1.77).

6.Synthesis and applications. Weed invasion can be diminished through a combination of forage species selected for complementarity and persistence traits in systems designed to reduce reliance on fertilizer nitrogen. In this study, effects of diversity on weed suppression were consistently strong across mixtures varying widely in species proportions and over time. The level of weed biomass did not vary greatly across mixtures varying widely in proportions of sown species. These diversity benefits in intensively managed grasslands are relevant for the sustainable intensification of agriculture and, importantly, are achievable through practical farm-scale actions.
The peatland map of Europe
Tanneberger, Franziska ; Tegetmeyer, C. ; Busse, S. ; Barthelmes, A. ; Shumka, S. ; Mariné, A.M. ; Jenderedjian, K. ; Steiner, G.M. ; Essl, F. ; Etzold, J. ; Mendes, C. ; Kozulin, A. ; Frankard, P. ; Milanović, ; Ganeva, A. ; Apostolova, I. ; Alegro, A. ; Delipetrou, P. ; Navrátilová, J. ; Risager, M. ; Leivits, A. ; Fosaa, A.M. ; Tuominen, S. ; Muller, F. ; Bakuradze, T. ; Sommer, M. ; Christanis, K. ; Szurdoki, E. ; Oskarsson, H. ; Brink, S.H. ; Connolly, J. ; Bragazza, L. ; Martinelli, G. ; Aleksāns, O. ; Priede, A. ; Sungaila, D. ; Melovski, L. ; Belous, T. ; Saveljić, D. ; Vries, F. De; Moen, A. ; Dembek, W. ; Mateus, J. ; Hanganu, J. ; Sirin, A. ; Markina, A. ; Napreenko, M. ; Lazarević, P. ; Stanová, V.Š. ; Skoberne, P. ; Pérez, P.H. ; Pontevedra-Pombal, X. ; Lonnstad, J. ; Küchler, M. ; Wüst-Galley, C. ; Kirca, S. ; Mykytiuk, O. ; Lindsay, R. ; Joosten, H. - \ 2017
Mires and Peat 19 (2017). - ISSN 1819-754X
Drained peatland - GIS - Histosol - Mire - Organic soil - Peat
Based on the ‘European Mires Book’ of the International Mire Conservation Group (IMCG), this article provides a composite map of national datasets as the first comprehensive peatland map for the whole of Europe. We also present estimates of the extent of peatlands and mires in each European country individually and for the entire continent. A minimum peat thickness criterion has not been strictly applied, to allow for (often historically determined) country-specific definitions. Our ‘peatland’ concept includes all ‘mires’, which are peatlands where peat is being formed. The map was constructed by merging national datasets in GIS while maintaining the mapping scales of the original input data. This ‘bottom-up’ approach indicates that the overall area of peatland in Europe is 593,727 km2. Mires were found to cover more than 320,000 km2 (around 54 % of the total peatland area). If shallow-peat lands (< 30 cm peat) in European Russia are also taken into account, the total peatland area in Europe is more than 1,000,000 km2 which is almost 10 % of the total surface area. Composite inventories of national peatland information, as presented here for Europe, may serve to identify gaps and priority areas for field survey, and help to cross-check and calibrate remote sensing based mapping approaches.
Major shifts in species’ relative abundance in grassland mixtures alongside positive effects of species diversity in yield: a continental-scale experiment
Brophy, Caroline ; Finn, John A. ; Lüscher, Andreas ; Suter, Matthias ; Kirwan, Laura ; Sebastià, Maria Teresa ; Helgadóttir, Áslaug ; Baadshaug, Ole H. ; Bélanger, Gilles ; Black, Alistair ; Collins, Rosemary P. ; Čop, Jure ; Dalmannsdottir, Sigridur ; Delgado, Ignacio ; Elgersma, Anjo ; Fothergill, Michael ; Frankow-Lindberg, Bodil E. ; Ghesquiere, A. ; Golinska, Barbara ; Golinski, Piotr ; Grieu, Philippe ; Gustavsson, Anne Maj ; Höglind, Mats ; Huguenin-Elie, Olivier ; Jørgensen, Marit ; Kadziuliene, Zydre ; Kurki, Päivi ; Llurba, Rosa ; Lunnan, Tor ; Porqueddu, Claudio ; Thumm, Ulrich ; Connolly, John - \ 2017
Journal of Ecology 105 (2017)5. - ISSN 0022-0477 - p. 1210 - 1222.
Increased species diversity promotes ecosystem function; however, the dynamics of multi-species grassland systems over time and their role in sustaining higher yields generated by increased diversity are still poorly understood. We investigated the development of species’ relative abundances in grassland mixtures over 3 years to identify drivers of diversity change and their links to yield diversity effects.
A continental-scale field experiment was conducted at 31 sites using 11 different four-species mixtures each sown at two seed abundances. The four species consisted of two grasses and two legumes, of which one was fast establishing and the other temporally persistent. We modelled the dynamics of the four-species mixtures, and tested associations with diversity effects on yield.
We found that species’ dynamics were primarily driven by differences in the relative growth rates (RGRs) of competing species, and secondarily by density dependence and climate. The temporally persistent grass species typically had the highest RGRs and hence became dominant over time. Density dependence sometimes induced stabilising processes on the dominant species and inhibited shifts to monoculture. Legumes persisted at most sites at low or medium abundances and persistence was improved at sites with higher annual minimum temperature.
Significant diversity effects were present at the majority of sites in all years and the strength of diversity effects was improved with higher legume abundance in the previous year. Observed diversity effects, when legumes had declined, may be due to (i) important effects of legumes even at low abundance, (ii) interaction between the two grass species or (iii) a store of N because of previous presence of legumes.
Synthesis. Alongside major compositional changes driven by RGR differences, diversity effects were observed at most sites, albeit at reduced strength as legumes declined. This evidence strongly supports the sowing of multi-species mixtures that include legumes over the long-standing practice of sowing grass monocultures. Careful and strategic selection of the identity of the species used in mixtures is suggested to facilitate the maintenance of species diversity and especially persistence of legumes over time, and to preserve the strength of yield increases associated with diversity.
Biodiversity increases the resistance of ecosystem productivity to climate extremes
Isbell, F. ; Craven, D. ; Connolly, J. ; Bezemer, T.M. ; Putten, W.H. van der; Ruijven, J. van - \ 2015
Nature 526 (2015). - ISSN 0028-0836 - p. 574 - 577.
It remains unclear whether biodiversity buffers ecosystems against climate extremes, which are becoming increasingly frequent worldwide1. Early results suggested that the ecosystem productivity of diverse grassland plant communities was more resistant, changing less during drought, and more resilient, recovering more quickly after drought, than that of depauperate communities2. However, subsequent experimental tests produced mixed results. Here we use data from 46 experiments that manipulated grassland plant diversity to test whether biodiversity provides resistance during and resilience after climate events. We show that biodiversity increased ecosystem resistance for a broad range of climate events, including wet or dry, moderate or extreme, and brief or prolonged events. Across all studies and climate events, the productivity of low-diversity communities with one or two species changed by approximately 50% during climate events, whereas that of high-diversity communities with 16–32 species was more resistant, changing by only approximately 25%. By a year after each climate event, ecosystem productivity had often fully recovered, or overshot, normal levels of productivity in both high- and low-diversity communities, leading to no detectable dependence of ecosystem resilience on biodiversity. Our results suggest that biodiversity mainly stabilizes ecosystem productivity, and productivity-dependent ecosystem services, by increasing resistance to climate events. Anthropogenic environmental changes that drive biodiversity loss thus seem likely to decrease ecosystem stability14, and restoration of biodiversity to increase it, mainly by changing the resistance of ecosystem productivity to climate events.
The agrodiversity experiment : three years of data from a multisite study in intensively managed grasslands
Kirwan, L. ; Connolly, J. ; Brophy, C. ; Elgersma, A. - \ 2014
grasslands
Intensively managed grasslands are globally prominent ecosystems. We investigated whether experimental increases in plant diversity in intensively managed grassland communities can increase their resource use efficiency. This work consisted of a coordinated, continental-scale 33-site experiment. The core design was 30 plots, representing 15 grassland communities at two seeding densities. The 15 communities were comprised of four monocultures (two grasses and two legumes) and 11 four-species mixtures that varied in the relative abundance of the four species at sowing. There were 1028 plots in the core experiment, with another 572 plots sown for additional treatments. Sites agreed a protocol and employed the same experimental methods with certain plot management factors, such as seeding rates and number of cuts, determined by local practice. The four species used at a site depended on geographical location, but the species were chosen according to four functional traits: a fast-establishing grass, a slow-establishing persistent grass, a fast-establishing legume, and a slow-establishing persistent legume. As the objective was to maximize yield for intensive grassland production, the species chosen were all high-yielding agronomic species. The data set contains species-specific biomass measurements (yield per species and of weeds) for all harvests for up to four years at 33 sites. Samples of harvested vegetation were also analyzed for forage quality at 26 sites. Analyses showed that the yield of the mixtures exceeded that of the average monoculture in >97% of comparisons. Mixture biomass also exceeded that of the best monoculture (transgressive overyielding) at about 60% of sites. There was also a positive relationship between the diversity of the communities and aboveground biomass that was consistent across sites and persisted for three years. Weed invasion in mixtures was very much less than that in monocultures. These data should be of interest to ecologists studying relationships between diversity and ecosystem function and to agronomists interested in sustainable intensification. The large spatial scale of the sites provides opportunity for analyses across spatial (and temporal) scales. The database can also complement existing databases and meta-analyses on biodiversity–ecosystem function relationships in natural communities by focusing on those same relationships within intensively managed agricultural grasslands.
The agrodiversity experiment : three years of data from a multisite study in intensively managed grasslands
Kirwan, L. ; Connolly, J. ; Brophy, C. ; Elgersma, A. - \ 2014
Ecology 95 (2014)9. - ISSN 0012-9658 - p. 2680 - 2680.
Intensively managed grasslands are globally prominent ecosystems. We investigated whether experimental increases in plant diversity in intensively managed grassland communities can increase their resource use efficiency. This work consisted of a coordinated, continental-scale 33-site experiment. The core design was 30 plots, representing 15 grassland communities at two seeding densities. The 15 communities comprised four monocultures (two grasses and two legumes) and 11 four-species mixtures that varied in the relative abundance of the four species at sowing. There were 1028 plots in the core experiment, with another 572 plots sown for additional treatments. Sites followed a protocol and employed the same experimental methods with certain plot management factors, such as seeding rates and number of cuts, determined by local practice. The four species used at a site depended on geographical location, but the species were chosen according to four functional traits: a fast-establishing grass, a slow-establishing persistent grass, a fast-establishing legume, and a slow-establishing persistent legume. As the objective was to maximize yield for intensive grassland production, the species chosen were all highyielding agronomic species. The data set contains species-specific biomass measurements (yield per species and of weeds) for all harvests for up to four years at 33 sites. Samples of harvested vegetation were also analyzed for forage quality at 26 sites. These data should be of interest to ecologists studying relationships between diversity and ecosystem function and to agronomists interested in sustainable intensification. The large spatial scale of the sites provides opportunity for analyses across spatial (and temporal) scales. The database can also complement existing databases and meta-analyses on biodiversity– ecosystem function relationships in natural communities by focusing on those same relationships within intensively managed agricultural grasslands.
Ecosystem function enhanced by combining four functional types of plant species in intensively managed grassland mixtures: a 3-year continental-scale field experiment
Finn, J.A. ; Connolly, J. ; Sebastià, M.T. ; Elgersma, A. - \ 2013
Journal of Applied Ecology 50 (2013)2. - ISSN 0021-8901 - p. 365 - 375.
nitrogen-fixation - diversity - biodiversity - systems - forage - productivity - pasture - richness - evenness - impacts
1.A coordinated continental-scale field experiment across 31 sites was used to compare the biomass yield of monocultures and four species mixtures associated with intensively managed agricultural grassland systems. To increase complementarity in resource use, each of the four species in the experimental design represented a distinct functional type derived from two levels of each of two functional traits, nitrogen acquisition (N2-fixing legume or nonfixing grass) crossed with temporal development (fast-establishing or temporally persistent). Relative abundances of the four functional types in mixtures were systematically varied at sowing to vary the evenness of the same four species in mixture communities at each site and sown at two levels of seed density. 2.Across multiple years, the total yield (including weed biomass) of the mixtures exceeded that of the average monoculture in >97% of comparisons. It also exceeded that of the best monoculture (transgressive overyielding) in about 60% of sites, with a mean yield ratio of mixture to best-performing monoculture of 1·07 across all sites. Analyses based on yield of sown species only (excluding weed biomass) demonstrated considerably greater transgressive overyielding (significant at about 70% of sites, ratio of mixture to best-performing monoculture = 1·18). 3.Mixtures maintained a resistance to weed invasion over at least 3 years. In mixtures, median values indicate
High plant diversity is needed tomaintain ecosystem services
Isbell, F. ; Calcagno, V. ; Hector, A. ; Connolly, J. ; Harpole, W.S. ; Reich, P.B. ; Scherer-Lorenzen, M. ; Ruijven, J. van - \ 2011
Nature 477 (2011)7363. - ISSN 0028-0836 - p. 199 - 202.
grassland experiment - biomass production - current knowledge - elevated co2 - biodiversity - productivity - communities - ecology - insurance - stability
Biodiversity is rapidly declining worldwide1, and there is consensus that this can decrease ecosystem functioning and services2, 3, 4, 5, 6, 7. It remains unclear, though, whether few8 or many9 of the species in an ecosystem are needed to sustain the provisioning of ecosystem services. It has been hypothesized that most species would promote ecosystem services if many times, places, functions and environmental changes were considered9; however, no previous study has considered all of these factors together. Here we show that 84% of the 147 grassland plant species studied in 17 biodiversity experiments promoted ecosystem functioning at least once. Different species promoted ecosystem functioning during different years, at different places, for different functions and under different environmental change scenarios. Furthermore, the species needed to provide one function during multiple years were not the same as those needed to provide multiple functions within one year. Our results indicate that even more species will be needed to maintain ecosystem functioning and services than previously suggested by studies that have either (1) considered only the number of species needed to promote one function under one set of environmental conditions, or (2) separately considered the importance of biodiversity for providing ecosystem functioning across multiple years10, 11, 12, 13, 14, places15, 16, functions14, 17, 18 or environmental change scenarios12, 19, 20, 21, 22. Therefore, although species may appear functionally redundant when one function is considered under one set of environmental conditions7, many species are needed to maintain multiple functions at multiple times and places in a changing world.
The application of reporter gene assays for the detection of endocrine disruptors in sport supplements
Plotan, M. ; Elliot, C.T. ; Scippo, M.L. ; Müller, M. ; Antignac, J.P. ; Malone, E. ; Bovee, T.F.H. ; Mitchell, S. ; Connolly, L. - \ 2011
Analytica Chimica Acta 700 (2011)1-2. - ISSN 0003-2670 - p. 34 - 40.
dietary-supplements - anabolic-steroids - androgen receptor - sex-hormones - chemicals - estrogen - health - urine
The increasing availability and use of sports supplements is of concern as highlighted by a number of studies reporting endocrine disruptor contamination in such products. The health food supplement market, including sport supplements, is growing across the Developed World. Therefore, the need to ensure the quality and safety of sport supplements for the consumer is essential. The development and validation of two reporter gene assays coupled with solid phase sample preparation enabling the detection of estrogenic and androgenic constituents in sport supplements is reported. Both assays were shown to be of high sensitivity with the estrogen and androgen reporter gene assays having an EC50 of 0.01 ng mL-1 and 0.16 ng mL-1 respectively. The developed assays were applied in a survey of 63 sport supplements samples obtained across the Island of Ireland with an additional seven reference samples previously investigated using LC–MS/MS. Androgen and estrogen bio-activity was found in 71% of the investigated samples. Bio-activity profiling was further broken down into agonists, partial agonists and antagonists. Supplements (13) with the strongest estrogenic bio-activity were chosen for further investigation. LC–MS/MS analysis of these samples determined the presence of phytoestrogens in seven of them. Supplements (38) with androgen bio-activity were also selected for further investigation. Androgen agonist bio-activity was detected in 12 supplements, antagonistic bio-activity was detected in 16 and partial antagonistic bio-activity was detected in 10. A further group of supplements (7) did not present androgenic bio-activity when tested alone but enhanced the androgenic agonist bio-activity of dihydrotestosterone when combined. The developed assays offer advantages in detection of known, unknown and low-level mixtures of endocrine disruptors over existing analytical screening techniques. For the detection and identification of constituent hormonally active compounds the combination of biological and physio-chemical techniques is optimal.
The changing landscape of Clara Bog: the history of an Irish raised bog
Crushell, P.H. ; Connolly, A. ; Schouten, M.G.C. ; Mitchell, F.J.G. - \ 2008
Irish Geography 41 (2008)1. - ISSN 0075-0778 - p. 89 - 111.
Clara Bog is one of the few raised bogs that has not been fully exploited in the Irish midlands and is a reminder of how the landscape of this region once appeared. This paper describes how the Clara Bog landscape has been changing since the commencement of the Holocene 11,500 years ago. Initially change was relatively slow as the bog naturally developed from its origins in an early Holocene lake, which became in-filled to form a fen circa 8000 years ago, before it continued to develop into an acid raised bog reaching its maximum extent by the beginning of the nineteenth century. Clara Bog has changed dramatically in the last 200 years due to human activity. Today less than 50% of its original bog surface remains. The changes in the bog during the historic past have been driven by population change, poverty, economic growth, construction of the Grand Canal, the building of roads, the need for fuel and farmland, nature conservation and tourism. The prehistoric development of the bog and land use in its hinterland was reconstructed from a detailed analysis of published archaeological records, palaeoecological studies and stratigraphical studies. Published maps and historical records have been vital in establishing a chronology for the changes that have occurred on Clara Bog since the beginning of the nineteenth century
Evenness drives consistent diversity effects in intensive grassland systems across 28 European sites
Kirwan, L. ; Lüscher, A. ; Sebastià, M.T. ; Finn, F.A. ; Collins, R.P. ; Porqueddu, C. ; Helgadottir, A. ; Baadshaug, O.H. ; Brophy, C. ; Coran, C. ; Dalmannsdóttir, S. ; Delgado, I. ; Elgersma, A. ; Fothergill, M. ; Frankow-Lindberg, B.E. ; Golinski, P. ; Grieu, P. ; Gustavsson, A.M. ; Höglind, M. ; Huguenin-Elie, O. ; Iliadis, C. ; Jøgensen, M. ; Kadziuliene, Z. ; Karyotis, T. ; Lunnan, T. ; Malengier, M. ; Maltoni, S. ; Meyer, V. ; Nyfeler, D. ; Nykanen-Kurki, P. ; Parente, J. ; Smit, H.J. ; Thumm, U. ; Connolly, J. - \ 2007
Journal of Ecology 95 (2007)3. - ISSN 0022-0477 - p. 530 - 539.
plant-species diversity - ecosystem function - current knowledge - productivity - biodiversity - richness - communities - legumes
1 Ecological and agronomic research suggests that increased crop diversity in species-poor intensive systems may improve their provision of ecosystem services. Such general predictions can have critical importance for worldwide food production and agricultural practice but are largely untested at higher levels of diversity. 2 We propose new methodology for the design and analysis of experiments to quantify diversity-function relationships. Our methodology can quantify the relative strength of inter-specific interactions that contribute to a functional response, and can disentangle the separate contributions of species richness and relative abundance. 3 Applying our methodology to data from a common experiment at 28 European sites, we show that the above-ground biomass of four-species mixtures (two legumes and two grasses) in intensive grassland systems was consistently greater than that expected from monoculture performance, even at high productivity levels. The magnitude of this effect generally resulted in transgressive overyielding. 4 A combined analysis of first-year results across sites showed that the additional performance of mixtures was driven by the number and strength of pairwise inter-specific interactions and the evenness of the community. In general, all pairwise interactions contributed equally to the additional performance of mixtures; the grass-grass and legume-legume interactions were as strong as those between grasses and legumes. 5 The combined analysis across geographical and temporal scales in our study provides a generality of interpretation of our results that would not have been possible from individual site analyses or experimentation at a single site. 6 Our four-species agricultural grassland communities have proved a simple yet relevant model system for experimentation and development of methodology in diversity-function research. Our study establishes that principles derived from biodiversity research in extensive, semi-natural grassland systems are applicable in intensively managed grasslands with agricultural plant species.
Erratum: Postglacial migration of Populus nigra L.: Lessons learnt from chloroplast DNA
Cottrell, J.E. ; Krystufek, V. ; Tabbener, H.E. ; Milner, A.D. ; Connolly, T. ; Sing, L. ; Fluch, S. ; Burg, K. ; Lefèvre, F. ; Achard, P. ; Bordács, S. ; Gebhardt, K. ; Vornam, B. ; Smulders, M.J.M. ; Vanden Broeck, A.H. ; Slycken, J. Van; Storme, V. ; Boerjan, W. ; Castiglione, S. ; Fossati, T. ; Alba, N. ; Agúndez, D. ; Maestro, C. ; Notivol, E. ; Bovenschen, J. ; Dam, B.C. van - \ 2005
Forest Ecology and Management 219 (2005)2-3. - ISSN 0378-1127 - p. 292 - 312.
Eleven laboratories have collaborated to study chloroplast DNA (cpDNA) variation in black poplar (Populus nigra L.) across Europe in order to improve our understanding of the location of glacial refugia and the subsequent postglacial routes of recolonisation. A common analysis based on the restricted fragments produced by five primer pairs was used to determine the cpDNA haplotype of 637 samples obtained from genebank collections established in nine European countries. Haplotype 2 was particularly common and was found in 46% of the non-hybrid samples. A total of 81 non-hybrid chloroplast variants were detected. Three haplotypes (from four trees believed to originate from Eastern Europe) clustered together and were very different from the rest of the samples. The remaining samples were divided into two groups, one of which had a largely eastern distribution and samples from the other group were mostly located in the west. This, along with the fact that Spain in the southwest and Austria and Italy in the southeast had high diversity, suggest that there were ice age refugia of black poplar in both southwestern (Spain) and southeastern Europe (Italy and/or Balkan). Results also indicate that the Pyrenees formed a significant
barrier, since only 7 of the 45 haplotypes in Spain exist elsewhere in Europe
Postglacial migration of Populus nigra L.: lessons learnt from chloroplast DNA
Cottrell, J.E. ; Krystufek, V. ; Tabbener, H.E. ; Milner, A.D. ; Connolly, T. ; Sing, L. ; Fluch, S. ; Burg, K. ; Lefèvre, F. ; Achard, P. ; Bordács, S. ; Gebhardt, K. ; Vornam, B. ; Smulders, M.J.M. ; Vanden Broeck, A.H. ; Slycken, J. Van; Storme, V. ; Boerjan, W. ; Castiglione, S. ; Fossati, T. ; Alba, N. ; Agúndez, D. ; Maestro, C. ; Notivol, E. ; Bovenschen, J. ; Dam, B.C. van - \ 2005
Forest Ecology and Management 206 (2005)1-3. - ISSN 0378-1127 - p. 71 - 90.
european white oaks - genetic-variation - colonization routes - noncoding regions - universal primers - x-canadensis - phylogeography - polymorphisms - deltoides - diversity
Eleven laboratories have collaborated to study chloroplast DNA (cpDNA) variation in black poplar (Populus nigra L.) across Europe in order to improve our understanding of the location of glacial refugia and the subsequent postglacial routes of recolonisation. A common analysis based on the restricted fragments produced by five primer pairs was used to determine the cpDNA haplotype of 637 samples obtained from genebank collections established in nine European countries. Haplotype 2 was particularly common and was found in 46% of the non-hybrid samples. A total of 81 non-hybrid chloroplast variants were detected. Three haplotypes (from four trees believed to originate from Eastern Europe) clustered together and were very different from the rest of the samples. The remaining samples were divided into two groups, one of which had a largely eastern distribution and samples from the other group were mostly located in the west. This, along with the fact that Spain in the southwest and Austria and Italy in the southeast had high diversity, suggest that there were ice age refugia of black poplar in both southwestern (Spain) and southeastern Europe (Italy and/or Balkan). Results also indicate that the Pyrenees formed a significant barrier, since only 7 of the 45 haplotypes in Spain exist elsewhere in Europe
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