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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Paying the price for the meat we eat
Allen, Andrew M. ; Hof, Anouschka R. - \ 2019
Environmental Science & Policy 97 (2019). - ISSN 1462-9011 - p. 90 - 94.
Biodiversity offsetting - Climate change - Ecological compensation - Intensive agriculture - Meat consumption

An increasingly gloomy picture is painted by research focusing on the environmental challenges faced by our planet. Biodiversity loss is ongoing, landscapes continue to transform, and predictions on the effects of climate change worsen. Calls have been made for urgent action to avoid pushing our planet into a new system state. One of the principal threats to biodiversity is intensive agriculture, and in particular the livestock industry, which is an important driver of greenhouse gas emissions, habitat degradation and habitat loss. Ongoing intensification of agricultural practices mean that farmland no longer provides a habitat for many species. We suggest the use of a growing policy tool, biodiversity offsetting, to tackle these challenges. Biodiversity offsetting, or ecological compensation, assesses the impacts of new development projects and seeks to avoid, minimise and otherwise compensate for the ecological impacts of these development projects. By applying biodiversity offsetting to agriculture, the impacts of progressively intensifying farming practices can be compensated to achieve conservation outcomes by using tools like environmental taxes or agri-environment schemes. Low intensity, traditional, farming systems provide a number of benefits to biodiversity and society, and we suggest that the consumer and the agriculture industry compensate for the devastating ecological impacts of intensive farming so that we can once again preserve biodiversity in our landscapes and attempt to limit global temperature rise below 2°c.

Dynamics of the Gut Microbiota in Children Receiving Selective or Total Gut Decontamination Treatment during Hematopoietic Stem Cell Transplantation
Bekker, Vincent ; Zwittink, Romy D. ; Knetsch, Cornelis W. ; Sanders, Ingrid M.J.G. ; Berghuis, Dagmar ; Heidt, Peter J. ; Vossen, Jaak M.J.J. ; Vos, Willem M. de; Belzer, Clara ; Bredius, Robbert G.M. ; van‘t Hof, Peter J. ; Lankester, Arjan C. ; Kuijper, Ed J. - \ 2019
Biology of Blood and Marrow Transplantation 25 (2019)6. - ISSN 1083-8791 - p. 1164 - 1171.
Graft-versus-host disease - Gut decontamination - Hematopoietic stem cell transplantation - Microbiota - Pediatrics

Bloodstream infections and graft-versus-host disease are common complications after hematopoietic stem cell transplantation (HSCT) procedures, associated with the gut microbiota that acts as a reservoir for opportunistic pathogens. Selective gut decontamination (SGD) and total gut decontamination (TGD) during HSCT have been associated with a decreased risk of developing these complications after transplantation. However, because studies have shown conflicting results, the use of these treatments remains subject of debate. In addition, their impact on the gut microbiota is not well studied. The aim of this study was to elucidate the dynamics of the microbiota during and after TGD and to compare these with the dynamics of SGD. In this prospective, observational, single-center study fecal samples were longitudinally collected from 19 children eligible for allogenic HSCT (TGD, n=12; SGD, n=7), weekly during hospital admission and monthly after discharge. In addition, fecal samples were collected from 3 family stem cell donors. Fecal microbiota structure of patients and donors was determined by 16S rRNA gene amplicon sequencing. Microbiota richness and diversity markedly decreased during SGD and TGD and gradually increased after cessation of decontamination treatment. During SGD, gut microbiota composition was relatively stable and dominated by Bacteroides, whereas it showed high inter- and intraindividual variation and low Bacteroides abundance during TGD. In some children TGD allowed the genera Enterococcus and Streptococcus to thrive during treatment. A gut microbiota dominated by Bacteroides was associated with increased predicted activity of several metabolic processes. Comparing the microbiota of recipients and their donors indicated that receiving an SCT did not alter the patient's microbiota to become more similar to that of its donor. Overall, our findings indicate that SGD and TGD affect gut microbiota structure in a treatment-specific manner. Whether these treatments affect clinical outcomes via interference with the gut microbiota needs to be further elucidated.

Implications of various effort-sharing approaches for national carbon budgets and emission pathways
Berg, Nicole J. van den; Soest, Heleen L. van; Hof, Andries F. ; Elzen, Michel G.J. den; Vuuren, Detlef P. van; Chen, Wenying ; Drouet, Laurent ; Emmerling, Johannes ; Fujimori, Shinichiro ; Höhne, Niklas ; Kõberle, Alexandre C. ; McCollum, David ; Schaeffer, Roberto ; Shekhar, Swapnil ; Vishwanathan, Saritha Sudharmma ; Vrontisi, Zoi ; Blok, Kornelis - \ 2019
Climatic Change (2019). - ISSN 0165-0009

The bottom-up approach of the Nationally Determined Contributions (NDCs) in the Paris Agreement has led countries to self-determine their greenhouse gas (GHG) emission reduction targets. The planned ‘ratcheting-up’ process, which aims to ensure that the NDCs comply with the overall goal of limiting global average temperature increase to well below 2 °C or even 1.5 °C, will most likely include some evaluation of ‘fairness’ of these reduction targets. In the literature, fairness has been discussed around equity principles, for which many different effort-sharing approaches have been proposed. In this research, we analysed how country-level emission targets and carbon budgets can be derived based on such criteria. We apply novel methods directly based on the global carbon budget, and, for comparison, more commonly used methods using GHG mitigation pathways. For both, we studied the following approaches: equal cumulative per capita emissions, contraction and convergence, grandfathering, greenhouse development rights and ability to pay. As the results critically depend on parameter settings, we used the wide authorship from a range of countries included in this paper to determine default settings and sensitivity analyses. Results show that effort-sharing approaches that (i) calculate required reduction targets in carbon budgets (relative to baseline budgets) and/or (ii) take into account historical emissions when determining carbon budgets can lead to (large) negative remaining carbon budgets for developed countries. This is the case for the equal cumulative per capita approach and especially the greenhouse development rights approach. Furthermore, for developed countries, all effort-sharing approaches except grandfathering lead to more stringent budgets than cost-optimal budgets, indicating that cost-optimal approaches do not lead to outcomes that can be regarded as fair according to most effort-sharing approaches.

An uncertain future for the endemic Galliformes of the Caucasus
Hof, Anouschka R. ; Allen, Andrew M. - \ 2019
Science of the Total Environment 651 (2019). - ISSN 0048-9697 - p. 725 - 735.
Birds - Climate change - Conservation - Land use - Species distribution modelling

Impacts of climate change are already evident in ecosystems worldwide. High-latitude and altitude regions are at greatest risk because the effects of climate change are greater in these regions, and species from these areas have limited ability to track their climate envelopes. The Caucasian snowcock (Tetraogallus caucasicus) and the Caucasian grouse (Lyrurus mlokosiewiczi) are both high-altitude specialists that are endemic to a restricted range in the Caucasus mountains of Europe. Little research has been performed to determine the status of the populations or the potential impacts of climate change. We investigated how climate and land use change may impact both species in future and determined whether their life history traits may increase their vulnerability using a combined exposure and trait-based index. We compared several climate models, and in all instances, both species showed drastic range contractions although the extent of the contraction varied with each model. Traits like habitat specialism, ground nesting and incubation period meant that both species may be considered “most vulnerable” in the exposure and trait-based index. Given that both species already occur near the maximum elevations of the Caucasus, and that they lack any dispersal capabilities due to the isolation from alternative mountainous areas, research efforts need to be prioritized to improve our knowledge about their population status, to monitor future trends and to begin developing species action plans that conserve these endemic and iconic species of Europe. Both species are flagship and umbrella species and may serve as indicator species, their protection may therefore benefit a whole range of other species inhabiting this vulnerable Alpine ecosystem. Especially the Caucasian grouse has a high aesthetic value and is favoured by hunters in the region. The potential demise of this species may therefore also be negative for local communities.

Een kleine geschiedenis van tarweteelt in Nederland
Bas, Noortje - \ 2018
Bijeenkomst van boeren, molenaars, bakkers op Het Geweide Hof, Garmerwolde, 2 juli.
Simulating long-term effects of bioenergy extraction on dead wood availability at a landscape scale in Sweden
Hof, Anouschka R. ; Löfroth, Therese ; Rudolphi, Jörgen ; Work, Timothy ; Hjältén, Joakim - \ 2018
Forests 9 (2018)8. - ISSN 1999-4907
Biodiversity - Biofuel - Boreal forest - Modelling - Saproxylic species

Wood bioenergy may decrease the reliance on fossil carbon and mitigate anticipated increases in temperature. However, increased use of wood bioenergy may have large impacts on forest biodiversity primarily through the loss of dead wood habitats. We evaluated both the large-scale and long-term effects of different bioenergy extraction scenarios on the availability of dead wood and the suitability of the resulting habitat for saproxylic species, using a spatially explicit forest landscape simulation framework applied in the Swedish boreal forest. We demonstrate that bioenergy extraction scenarios, differing in the level of removal of biomass, can have significant effects on dead wood volumes. Although all of the scenarios led to decreasing levels of dead wood, the scenario aimed at species conservation led to highest volumes of dead wood (about 10 m3 ha-1) and highest connectivity of dead wood patches (mean proximity index of 78), whilst the scenario aimed at reaching zero fossil fuel targets led to the lowest levels (about 8 m3 ha-1) and least connectivity (mean proximity index of 7). Our simulations stress that further exploitation of dead wood from sites where volumes are already below suggested habitat thresholds for saproxylic species will very likely have further negative effects on dead wood dependent species.

The ecology of Black Guillemot Cepphus grylle grylle chicks in the Baltic Sea region : insights into their diet, survival, nest predation and moment of fledging
Hof, Anouschka R. ; Crombag, Joep A.H.M. ; Allen, Andrew M. - \ 2018
Bird Study 65 (2018)3. - ISSN 0006-3657 - p. 357 - 364.

Capsule: The diet of Black Guillemot Cepphus grylle grylle chicks in the Baltic Sea region was dominated by Viviparous Eelpout Zoarces viviparus. Risk of nest predation by avian and mammalian predators was perceived to be low, and hatching and fledging success were high. Aims: To gain insight into the ecology of nestling Black Guillemots in the Baltic Sea region to fill knowledge gaps and benefit its conservation. Methods: Two island groups in the Baltic Sea were visited several times during the breeding season of 2014 and 2015 to monitor nestling survival and fledging. In addition, camera traps were used in 2014 to monitor prey brought to chicks by adults and record possible nest predation events. Results: Hatching success was 0.89 and 0.73 in 2014 and 2015, respectively, and fledging success was very high (0.95 and 0.97). No incidences of avian or mammalian predation were observed. Chicks fledged at night between 32 and 38 days after hatching. Viviparous Eelpout made up 95% of the prey items brought to the chicks by adults. Conclusions: The hatching rate and fledging rate of the Black Guillemot was high in our study region. Juveniles seemed highly dependent on the availability of eelpout. Changes in the abundance of this species may therefore have negative effects on chick survival.

Europees Hof remt kwekers vanwege genetische modificatie
Smulders, Rene - \ 2018

smulders

Landscape planning-paving theway for effective conservation of forest biodiversity and a diverse forestry?
Michanek, Gabriel ; Bostedt, Göran ; Ekvall, Hans ; Forsberg, Maria ; Hof, Anouschka R. ; Jong, Johnny de; Rudolphi, Jörgen ; Zabel, Astrid - \ 2018
Forests 9 (2018)9. - ISSN 1999-4907
Aichi targets - Biodiversity - Birds directive - Boreal forest - Compensation - Fragmentation - Habitat protection - Habitats directive - Landscape planning - Tax-fund

Globally, intensive forestry has led to habitat degradation and fragmentation of the forest landscape. Taking Sweden as an example, this development is contradictory to international commitments, EU obligations, and to the fulfillment of the Parliament's environmental quality objective "Living Forests", which according to Naturvårdsverket (The Swedish Environmental Protection Agency) will not be achieved in 2020 as stipulated. One important reason for the implementation deficit is the fragmented forestry management. In a forest landscape, felling and other measures are conducted at different times on separate forest stands (often relatively small units) by different operators. Consequently, the authorities take case by case decisions on felling restrictions for conservation purposes. In contrast, conservation biology research indicates a need for a broad geographical and strategical approach in order to, in good time, select the most appropriate habitats for conservation and to provide for a functioning connectivity between different habitats. In line with the EU Commission, we argue that landscape forestry planning could be a useful instrument to achieve ecological functionality in a large area. Landscape planning may also contribute to the fulfilment of Sweden's climate and energy policy, by indicating forest areas with insignificant conservation values, where intensive forestry may be performed for biomass production etc. Forest owners should be involved in the planning and would, under certain circumstances, be entitled to compensation. As state resources for providing compensation are scarce, an alternative could be to introduce a tax-fund system within the forestry sector. Such a system may open for voluntary agreements between forest owners for the protection of habitats within a large area.

DNA methylation as a mediator of the association between prenatal adversity and risk factors for metabolic disease in adulthood
Tobi, Elmar W. ; Slieker, Roderick C. ; Luijk, René ; Dekkers, Koen F. ; Stein, Aryeh D. ; Xu, Kate M. ; Slagboom, P.E. ; Zwet, Erik W. Van; Lumey, L.H. ; Heijmans, Bastiaan T. ; T'Hoen, Peter A. ; Pool, René ; Greevenbroek, Marleen M. Van; Stehouwer, Coen D. ; Kallen, Carla J. Van Der; Schalkwijk, Casper G. ; Wijmenga, Cisca ; Zhernakova, Sasha ; Tigchelaar, Ettje F. ; Beekman, Marian ; Deelen, Joris ; Heemst, Diana Van; Veldink, Jan H. ; Berg, Leonard H. Van Den; Duijn, Cornelia M. Van; Hofman, Albert ; Uitterlinden, André G. ; Jhamai, P.M. ; Verbiest, Michael ; Verkerk, Marijn ; Breggen, Ruud Van Der; Rooij, Jeroen Van; Lakenberg, Nico ; Mei, Hailiang ; Bot, Jan ; Zhernakova, Dasha V. ; Hof, Peter Van 't; Deelen, Patrick ; Nooren, Irene ; Moed, Matthijs ; Vermaat, Martijn ; Jan Bonder, Marc ; Dijk, Freerk Van; Arindrarto, Wibowo ; Kielbasa, Szymon M. ; Swertz, Morris A. ; Isaacs, Aaron ; Franke, Lude - \ 2018
Science Advances 4 (2018)1. - ISSN 2375-2548
Although it is assumed that epigenetic mechanisms, such as changes in DNA methylation (DNAm), underlie the relationship between adverse intrauterine conditions and adult metabolic health, evidence from human studies remains scarce. Therefore, we evaluated whether DNAm in whole blood mediated the association between prenatal famine exposure and metabolic health in 422 individuals exposed to famine in utero and 463 (sibling) controls. We implemented a two-step analysis, namely, a genome-wide exploration across 342, 596 cytosine-phosphate-guanine dinucleotides (CpGs) for potential mediators of the association between prenatal famine exposure and adult body mass index (BMI), serum triglycerides (TG), or glucose concentrations, which was followed by formalmediation analysis.DNAm mediated the association of prenatal famine exposure with adult BMI and TG but not with glucose. DNAm at PIM3 (cg09349128), a gene involved in energy metabolism, mediated 13.4% [95% confidence interval (CI), 5 to 28%] of the association between famine exposure and BMI. DNAm at six CpGs, including TXNIP (cg19693031), influencing b cell function, and ABCG1 (cg07397296), affecting lipid metabolism, together mediated 80% (95% CI, 38.5 to 100%) of the association between famine exposure and TG. Analyses restricted to those exposed to famine during early gestation identified additional CpGs mediating the relationship with TG near PFKFB3 (glycolysis) and METTL8 (adipogenesis). DNAm at the CpGs involved was associated with gene expression in an external data set and correlated with DNAm levels in fat depots in additional postmortem data. Our data are consistent with the hypothesis that epigenetic mechanisms mediate the influence of transient adverse environmental factors in early life on long-termmetabolic health. The specific mechanism awaits elucidation.
Are we restoring enough? : Simulating impacts of restoration efforts on the suitability of forest landscapes for a locally critically endangered umbrella species
Hof, A.R. ; Hjältén, J. - \ 2018
Restoration Ecology 26 (2018)4. - ISSN 1061-2971 - p. 740 - 750.
Habitat restoration is often implemented to mitigate the negative effects of intensive forestry on biodiversity. It may be increasingly adopted in future to alleviate additional negative effects of climate change. Ascertaining the restoration effort needed to fulfill project goals is difficult. Insights may be gained through simulating the effects of restoration efforts on landscape dynamics through time. Here we used a spatially explicit landscape simulation model to simulate the effects of different restoration efforts on forest landscapes in Sweden to assess the level of mitigation that is needed to allow viable populations of the locally critically endangered White-backed Woodpecker (Dendrocopos leucotos); an umbrella species whose protection may serve the protection of a range of other species. Based on the goals of the protection plan for the species, which reflect its habitat requirements, we evaluated which of several restoration scenarios could fulfill goals with respect to (1) the amount of deciduous forest; (2) the amount of dead wood; and (3) the age of the forest. We found that whereas it may be relatively easy and quick to acquire high levels of dead wood, increasing the proportions of deciduous forest and of old forests require considerably more time and effort. Also, current management actions would not be sufficient to create the required amount of habitat to conserve the White-backed Woodpecker in our study region. Simulations like ours can provide valuable information about the levels of restoration needed through time to fulfill project goals and may prevent wasting valuable resources, time, effort, and money.
Assessing the ambition of post-2020 climate targets : a comprehensive framework
Höhne, Niklas ; Fekete, Hanna ; Elzen, Michel G.J. den; Hof, Andries F. ; Kuramochi, Takeshi - \ 2018
Climate Policy 18 (2018)4. - ISSN 1469-3062 - p. 425 - 441.
ambition - global stocktake - INDCs - NDCs - Paris agreement - UNFCCC
One of the most fundamental questions surrounding the new Paris Agreement is whether countries’ proposals to reduce GHG emissions after 2020 are equally ambitious, considering differences in circumstances between countries. We review a variety of approaches to assess the ambition of the GHG emission reduction proposals by countries. The approaches are applied illustratively to the mitigation part of the post-2020 climate proposals (nationally determined contributions, or NDCs) by China, the EU, and the US. The analysis reveals several clear trends, even though the results differ per individual assessment approach. We recommend that such a comprehensive ambition assessment framework, employing a large variety of approaches, is used in the future to capture a wide spectrum of perspectives on ambition. POLICY RELEVANCE Assessing the ambition of the national climate proposals is particularly important as the Paris Agreement asks for regular reviews of national contributions, keeping in mind that countries raise their ambition over time. Such an assessment will be an important part of the regular global stocktake that will take place every five years, starting with a ‘light’ version in 2018. However, comprehensive methods to assess the proposals are lacking. This article provides such a comprehensive assessment framework.
Gene expression profiling in control, heat-shock, and recovery treatment in a RIL population of Caenorhabditis elegans L4 larvae
Snoek, L.B. ; Sterken, M.G. ; Bevers, R.P.J. ; Volkers, J.M. ; Hof, Arjen van 't; Brenchley, Rachel ; Riksen, J.A.G. ; Cossins, Andrew ; Kammenga, J.E. - \ 2017
Caenorhabditis elegans - transcription profiling by array - stimulus or stress design - strain or line design - E-MTAB-5779
This experiment investigates the genetic architecture of gene expression (eQTL) in three different treatments in a N2xCB4856 RIL population of Caenorhabditis elegans. The goal is to identify genetic variation linked to differences in gene expression. We exposed 48 RILs per treatment to a control, heat-stress, and recovery treatment. More specifically these three conditions can be characterized as: (i) the control treatment was grown for 48 hours at 20C, (ii) the heat-stress treatment was grown for 46 hours at 20C followed by 2 hours at 35C, and (iii) the recovery treatment was grown for 46 hours at 20C, followed by 2 hours at 35C and thereafter 2 hours at 20C. Thereafter RNA was isolated, labelled and hybridized on microarray. The gene expression profiles were used for eQTL mapping.
Contribution of trans regulatory eQTL to cryptic genetic variation in C. elegans
Snoek, L.B. ; Sterken, M.G. ; Bevers, R.P.J. ; Volkers, J.M. ; Hof, Arjen van 't; Brenchley, Rachel ; Riksen, J.A.G. ; Cossins, Andrew ; Kammenga, J.E. - \ 2017
Caenorhabditis elegans - genetical genomics - eQTL - heat stress - cryptic genetic variation - trans-band - eQTL hotspot
Background Cryptic genetic variation (CGV) is the hidden genetic variation that can be unlocked by perturbing normal conditions. CGV can drive the emergence of novel complex phenotypes through changes in gene expression. Although our theoretical understanding of CGV has thoroughly increased over the past decade, insight into polymorphic gene expression regulation underlying CGV is scarce. Here we investigated the transcriptional architecture of CGV in response to rapid temperature changes in the nematode Caenorhabditis elegans. We analyzed regulatory variation in gene expression (and mapped eQTL) across the course of a heat stress and recovery response in a recombinant inbred population. Results We measured gene expression over three temperature treatments: i) control, ii) heat stress, and iii) recovery from heat stress. Compared to control, exposure to heat stress affected the transcription of 3305 genes, whereas 942 were affected in recovering animals. These affected genes were mainly involved in metabolism and reproduction. The gene expression pattern in recovering animals resembled both the control and the heat-stress treatment. We mapped eQTL using the genetic variation of the recombinant inbred population and detected 2626 genes with an eQTL in the heat-stress treatment, 1797 in the control, and 1880 in the recovery. The cis-eQTL were highly shared across treatments. A considerable fraction of the trans-eQTL (40–57%) mapped to 19 treatment specific trans-bands. In contrast to cis-eQTL, trans-eQTL were highly environment specific and thus cryptic. Approximately 67% of the trans-eQTL were only induced in a single treatment, with heat-stress showing the most unique trans-eQTL. Conclusions These results illustrate the highly dynamic pattern of CGV across three different environmental conditions that can be evoked by a stress response over a relatively short time-span (2 h) and that CGV is mainly determined by response related trans regulatory eQTL.
Data from: How bird clades diversify in response to climatic and geographic factors
Rodríguez-Castañeda, Genoveva ; Hof, A.R. ; Jansson, Roland - \ 2017
climate stability - ecological niche modelling - energy availability - geographic area - habitat diversity - phylogenetic independent contrasts - sister group comparisons - species richness - temperate - tropical - Aves
While the environmental correlates of global patterns in standing species richness are well understood, it is poorly known which environmental factors promote diversification (speciation minus extinction) in clades. We tested several hypotheses for how geographic and climatic variables should affect diversification using a large dataset of bird sister genera endemic to the New World. We found support for the area, evolutionary speed, environmental predictability and climatic stability hypotheses, but productivity and topographic complexity were rejected as explanations. Genera that had accumulated more species tend to occupy wider niche space, manifested both as occurrence over wider areas and in more habitats. Genera with geographic ranges that have remained more stable in response to glacial-interglacial changes in climate were also more species rich. Since many relevant explanatory variables vary latitudinally, it is crucial to control for latitude when testing alternative mechanistic explanations for geographic variation in diversification among clades.
Assessing the impacts of 1.5°C global warming - Simulation protocol of the Inter-Sectoral Impact Model Intercomparison Project (ISIMIP2b)
Frieler, Katja ; Lange, Stefan ; Piontek, Franziska ; Reyer, Christopher P.O. ; Schewe, Jacob ; Warszawski, Lila ; Zhao, Fang ; Chini, Louise ; Denvil, Sebastien ; Emanuel, Kerry ; Geiger, Tobias ; Halladay, Kate ; Hurtt, George ; Mengel, Matthias ; Murakami, Daisgbre ; Ostberg, Sebastian ; Popp, Alexander ; Riva, Riccardo ; Stevanovic, Miodrag ; SuzGBRi, Tatsuo ; Volkholz, Jan ; Burke, Eleanor ; Ciais, Philippe ; Ebi, Kristie ; Eddy, Tyler D. ; Elliott, Joshua ; Galbraith, Eric ; Gosling, Simon N. ; Hattermann, Fred ; Hickler, Thomas ; Hinkel, Jochen ; Hof, Christian ; Huber, Veronika ; Jägermeyr, Jonas ; Krysanova, Valentina ; Marcé, Rafael ; Müller Schmied, Hannes ; Mouratiadou, Ioanna ; Pierson, Don ; Tittensor, Derek P. ; Vautard, Robert ; Vliet, Michelle Van; Biber, Matthias F. ; Betts, Richard A. ; Leon Bodirsky, Benjamin ; Deryng, Delphine ; Frolking, Steve ; Jones, Chris D. ; Lotze, Heike K. ; Lotze-Campen, Hermann ; Sahajpal, Ritvik ; Thonicke, Kirsten ; Tian, Hanqin ; Yamagata, Yoshiki - \ 2017
Geoscientific Model Development 10 (2017)12. - ISSN 1991-959X - p. 4321 - 4345.
In Paris, France, December 2015, the Conference of the Parties (COP) to the United Nations Framework Convention on Climate Change (UNFCCC) invited the Intergovernmental Panel on Climate Change (IPCC) to provide a <q>special report in 2018 on the impacts of global warming of 1.5ĝ€°C above pre-industrial levels and related global greenhouse gas emission pathways</q>. In Nairobi, Kenya, April 2016, the IPCC panel accepted the invitation. Here we describe the response devised within the Inter-Sectoral Impact Model Intercomparison Project (ISIMIP) to provide tailored, cross-sectorally consistent impact projections to broaden the scientific basis for the report. The simulation protocol is designed to allow for (1) separation of the impacts of historical warming starting from pre-industrial conditions from impacts of other drivers such as historical land-use changes (based on pre-industrial and historical impact model simulations); (2) quantification of the impacts of additional warming up to 1.5ĝ€°C, including a potential overshoot and long-term impacts up to 2299, and comparison to higher levels of global mean temperature change (based on the low-emissions Representative Concentration Pathway RCP2.6 and a no-mitigation pathway RCP6.0) with socio-economic conditions fixed at 2005 levels; and (3) assessment of the climate effects based on the same climate scenarios while accounting for simultaneous changes in socio-economic conditions following the middle-of-the-road Shared Socioeconomic Pathway (SSP2, Fricko et al., 2016) and in particular differential bioenergy requirements associated with the transformation of the energy system to comply with RCP2.6 compared to RCP6.0. With the aim of providing the scientific basis for an aggregation of impacts across sectors and analysis of cross-sectoral interactions that may dampen or amplify sectoral impacts, the protocol is designed to facilitate consistent impact projections from a range of impact models across different sectors (global and regional hydrology, lakes, global crops, global vegetation, regional forests, global and regional marine ecosystems and fisheries, global and regional coastal infrastructure, energy supply and demand, temperature-related mortality, and global terrestrial biodiversity).
Climate change mitigation through adaptation : The effectiveness of forest diversification by novel tree planting regimes
Hof, Anouschka R. ; Dymond, Caren C. ; Mladenoff, David J. - \ 2017
Ecosphere 8 (2017)11. - ISSN 2150-8925
Assisted migration - Boreal forest - Carbon stocks - Climate change - Ecosystem services - Forestry - Modeling - Temperate forest
Climate change is projected to have negative implications for forest ecosystems and their dependent communities and industries. Adaptation studies of forestry practices have focused on maintaining the provisioning of ecosystem services; however, those practices may have implications for climate change mitigation as well by increasing biological sinks or reducing emissions. Assessments of the effectiveness of adaptation strategies to mitigate climate change are therefore needed; however, they have not been done for the world’s northern coniferous forests. Diversifying the forest by planting tree species more likely suited to a future climate is a potential adaptation strategy to increase resilience. The efficacy of this strategy to reduce the risks of climate change is uncertain, and other ecosystem services provided by the forest are also likely to be affected. We used a spatially explicit forest landscape modeling framework (LANDIS-II) to simulate the effects of planting a range of native tree species in colder areas than where they are currently planted in a managed temperate coniferous forest landscape in British Columbia, Canada. We investigated impacts on carbon pools, fluxes, tree species diversity, and harvest levels under different climate scenarios for 100 yr (2015–2115) and found that the capacity of our forest landscape to sequester carbon would largely depend on the precipitation rates in the future, rather than on temperature. We further found that, irrespective of the climate prediction model, current planting standards led to relatively low levels of resilience as indicated by carbon fluxes and stocks, net primary productivity (NPP), and species diversity. In contrast, planting a mix of alternative tree species was generally superior in increasing the resilience indicators: carbon stocks and fluxes, NPP, and tree species diversity, but not harvest rates. The second best novel planting regime involved adding Pinus contorta to the stocking standard in three ecoregions; however, that species is susceptible to a high number of insects and pathogens. We conclude that although the capacity of temperate coniferous forest landscapes to sequester carbon in the future is largely dependent on the precipitation regime, negative effects may be counteracted to some extent by increasing resilience through tree species diversity in forests.
What Limits the Distribution of Liriomyza huidobrensis and Its Congener Liriomyza sativae in Their Native Niche : When Temperature and Competition Affect Species' Distribution Range in Guatemala
Rodríguez-Castañeda, Genoveva ; MacVean, C. ; Cardona, C. ; Hof, A.R. - \ 2017
Journal of Insect Science 17 (2017)4. - ISSN 1536-2442 - 13 p.
introduced species - Liriomyza huidobrensis - Liriomyza sativae - native niche - physiological limit

Factors limiting distribution range for most species are generally unknown regardless of whether they are native or invasive. We studied factors that could enable or restrict the distribution of two cosmopolitan invasive leafminer fly species, Liriomyza huidobrensis (Blanchard) and Liriomyza sativae (Blanchard) in their native niche. In order to test which ecological and environmental factors affect leafminer distribution we conducted thermal tolerance assays, sampled along elevation gradients and modeled species distribution. Findings from the field and rearing chambers showed a physiological restriction due to high temperatures for L. huidobrensis at 28-29 °C, above which adult emergence is compromised. We also found that maximum temperatures below 22 °C, typical of tropical highlands, favored L. huidobrensis. L. sativae was found across a wider temperature range (i.e., from 21 to 36 °C) in Guatemala. Our finding of a physiological threshold in temperature for L. huidobrensis may enable us to predict its invasive risk when combined with the environmental conditions at horticultural ports of entry and the global agricultural landscape. Further, it strengthens our predictions on shifts in distribution of the leafminer fly under future climate. We also found a temperature mediated competitive exclusion interaction between the two herbivore species, where L. sativae occurred at temperatures < 22 °C only in the absence of L. huidobrensis. We show that parasitoids had a negative effect on the leafminer flies, which varied with host plant. Finally, we show the importance of taking a multiaspect approach when investigating what limits distribution and invasiveness of a species.

Future breeding and foraging sites of a southern edge population of the locally endangered Black Guillemot Cepphus grylle
Buchadas, Ana R.C. ; Hof, Anouschka R. - \ 2017
Bird Study 64 (2017)3. - ISSN 0006-3657 - p. 306 - 316.
Capsule: One of the southernmost populations of the Black Guillemot Cepphus grylle is currently endangered, and the risk may be exacerbated by climate change. Aims: We evaluated the future vulnerability of the Black Guillemot by predicting the impact of climate change on the geographic distribution of its breeding and foraging range in the Baltic Sea. Methods: We used MaxEnt, a species distribution modelling technique, to predict the current and future breeding grounds and foraging sites. Results: We found that although the foraging range is expected to increase in the southern Baltic Sea in future, these areas will no longer be suitable as breeding grounds due to a changing climate, creating a spatial mismatch. Conclusion: Our predictions indicate where threats to the species may be most severe and can be used to guide conservation planning. We advocate conservation measures which integrate potential future threats and focus on breeding sites across the current and future potential geographic range of the Black Guillemot.
A high-coverage draft genome of the mycalesine butterfly Bicyclus anynana
Nowell, Reuben W. ; Elsworth, Ben ; Oostra, Vicencio ; Zwaan, Bas J. ; Wheat, Christopher W. ; Saastamoinen, Marjo ; Saccheri, Ilik J. ; Hof, Arjen E. van 't; Wasik, Bethany R. ; Connahs, Heidi ; Aslam, Muhammad L. ; Kumar, Sujai ; Challis, Richard J. ; Monteiro, Antónia ; Brakefield, Paul M. ; Blaxter, Mark - \ 2017
GigaScience 6 (2017)7. - ISSN 2047-217X
Bicyclus anynana - Lepidopteran genome - Nymphalid - Nymphalidae - Satyrid - Squinting bush brown

The mycalesine butterfly Bicyclus anynana, the "Squinting bush brown," is a model organism in the study of lepidopteran ecology, development, and evolution. Here, we present a draft genome sequence for B. anynana to serve as a genomics resource for current and future studies of this important model species. Seven libraries with insert sizes ranging from 350 bp to 20 kb were constructed using DNA from an inbred female and sequenced using both Illumina and PacBio technology; 128 Gb of raw Illumina data was filtered to 124 Gb and assembled to a final size of 475 Mb (~×260 assembly coverage). Contigs were scaffolded using mate-pair, transcriptome, and PacBio data into 10 800 sequences with an N50 of 638 kb (longest scaffold 5 Mb). The genome is comprised of 26% repetitive elements and encodes a total of 22 642 predicted protein-coding genes. Recovery of a BUSCO set of core metazoan genes was almost complete (98%). Overall, these metrics compare well with other recently published lepidopteran genomes. We report a high-quality draft genome sequence for Bicyclus anynana. The genome assembly and annotated gene models are available at LepBase (http://ensembl.lepbase.org/index.html).

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