iDiv Summer School 2017 – Synthesising and modelling biodiversity data
The German Centre for Integrative Biodiversity Research (iDiv) conducts its third summer school “Synthesising and modelling biodiversity data” from 3 to 15 September 2017 in Leipzig, Germany. Please find more information about the theme, contents and teachers below. Note that the summer school registration has been closed on the 2nd of May 2017; applications are no longer accepted.
The aim of the summer school is to learn about biodiversity synthesis and integrative biodiversity research in a relaxed and constructive atmosphere. The participants will gain practical, relevant skills in conducting synthesis analyses of biodiversity data, and work towards publishing the results of their work in the form of a journal article. The programme combines preparatory work conducted at home, methodological training, plenary lectures, hands-on collaborative work on a research project, as well as plenty of interaction with iDiv scientists. We also offer social programme and a field visit to the 20 selected candidates.
The lead teacher of the summer school 2017 is Nico Eisenhauer, iDiv Professor and Head of the research group Experimental Interaction Ecology. Other lecturers will include senior scientific staff at the iDiv consortium, as well as invited scientists.
3–15 September 2017
iDiv at BioCity Campus Leipzig
Deutscher Platz 5e
04103 Leipzig, Germany
Dr. Mari Bieri
iDiv’s core mission is to provide the scientific foundation for a sustainable management of the earth’s biodiversity. This is especially important as the current biodiversity crisis compromises the functioning and service provisioning of ecosystems to society. Addressing the key questions related to biodiversity and its loss require an approach that integrates across space and time, organizational levels, complexities and scientific disciplines. Along with integration, synthesis is at the heart of iDiv’s mission.
Synthesis of existing information in order to generalize findings or detect new patterns has been important in biological sciences for a long time. However, with the recent rise of IT, new type of synthesis is rising, using previously unknown types and quantities of data and applying novel computational tools to answer fundamental questions of biodiversity sciences. An important aspect of biodiversity synthesis is to understand, map and predict the distribution and shifts of mechanisms that drive biodiversity dynamics and consequences in response to such topics as climate change and land use change on a large scale.
Biodiversity synthesis also means bridging researchers from different disciplines, with the goal to provide a comprehensive and consistent understanding of the underlying processes and mechanisms of biodiversity dynamics. Broad synthesis can only be reached through transdisciplinary research.
The programme of the summer school consists of:
- Plenary lectures
- Methodological course on meta-analysis/structural equation modelling
- Group work on research projects under the supervision of two senior scientists
- Exchange with iDiv researchers
- Social events and celebrations
See the preliminary programme.
Approximately eight weeks prior the course, the preparatory stage takes place. The preparation will take place in the form of e.g. video-conferences, tutorials or weekly homework, and will not exceed four hours per week for each participant.
After the course opening and introductions, two parallel methodological courses will be organised to train the participants skills to use in their project work. The courses will concentrate on Meta-analysis (Prof. Julia Koricheva) and Structural Equation Modelling (Dr. Masha van der Sande and Dr. Andrew Barnes). These are specific tools that are extremely powerful to synthesize data and let theory emerge.
Each of the remaining course days will start with a plenary session. These illustrate the diversity of approaches to study biodiversity, including practical examples of work done at iDiv and our ongoing collaborations.
The hands-on research projects have been designed by iDiv researchers and will apply the skills learnt during the methodological courses. In each project, a small team of course participants work together with the objective of a joint publication. Each project is tutored by the project leader(s), who also plan the work done by the participants during the preparatory stage (see above).
The proposed projects are summarized below (click on + symbol to see full description):
CANCELLED: Project 1: A global understanding of pollination ecology
Project leaders: Tiffany Knight, Joanne Bennett
Most flowering plants (~87%) rely on pollinators for reproduction (Ollerton et al 2011). Thus pollinator declines could threaten native plant biodiversity, ecosystem stability and food security (Goulson et al. 2015). Pollen supplementation experiments, link plant reproductive fitness to pollination; where a plants reproduction is considered limited by pollen receipt if it produces more seeds when supplemented pollen is added compared to a control plant (Knight et al. 2005).
In 2003 Knight et al. (2005) performed a quantitative meta-analysis of 655 pollen supplementation experiments, finding pollen limitation to be common. However, their study and inferences had a North America and European data bias. In 2015, a repeat meta-analysis synthesized ~3000 experiments incorporating and translating research from China, Brazil and South Africa. However, dataset gaps remain in regions expected to experience rapid global change. For example, high latitude regions (North-eastern Europe, e.g., Russia) predicted to experience high rates of climate change (Serreze et al. 2000) and developing regions (e.g., Central Africa) under-going rapid land-use change (Jetz et al. 2007). Much scientific research in these regions is published in local, languages and journals that are not ISI listed, thus difficult to access for non-residents (Amano et al. 2016).
To overcome these issues we propose to perform a meta-analysis of studies on pollen ecology, published in non- English languages utilizing the 2003 global meta-analysis methods. Information gained will be used to determine the breeding system of plant species’, the magnitude by which plant species are pollen limited, and the environmental and plant traits that correlate with pollen limitation.
Students proficient in languages other than Mandarin, English and Portuguese are encouraged to apply.
Project 2: Primary data analysis vs. meta-analysis of summary statistics – hidden biases caused by methodological differences
Project leaders: Katharina Gerstner, Dylan Craven
Large distributed networks of biological experiments (e.g. Nutrient Network1, Drought Net2, TreeDiv Net3, ZenScience4) have been implemented to collect data from a broad range of sites in a consistent manner to allow direct comparisons of relationships among systems around the world. Synthesis across sites, sometimes referred to as 'meta-level' analysis', allows inference about ecological phenomena without worrying about methodological differences. In contrast, meta-analysis offers a subtly different perspective on the outcome of experiments or observational studies. Instead of providing a definitive demonstration of a particular phenomenon, the outcomes of independent research studies, like the primary data from which they are derived, are treated as if they are subject to sampling uncertainties. Whether and how this methodological difference causes biases in the results from data synthesis has not yet been explored.
We will use primary data from standardized forest inventories to study the effect of species richness on standing biomass. In preparation of the course, using the same data we will create scenarios of summary statistics which could have been reported in primary studies of similar but not identical research questions, e.g. some studies are restricted to trees with more than 20 cm dbh others to more than 30 cm dbh. During the course, we will explore how methodological differences affect results from data synthesis using the primary data to fit a null model. To do so, we will use an array of quantitative tools (all using R5) that are relevant for data synthesis: linear mixed-effects models, bayesian hierarchical models, and meta-analytical regression models.
5 e.g. packages ‘lme4’ or ‘nlme’ for linear mixed effects models, ‘metafor’ for traditional meta-analysis, and ‘brms’ for bayesian meta-analysis (https://cran.r-project.org/web/packages/brms/brms.pdf)
Project 3: Historical, environmental, and anthropogenic effects on mammal richness across multiple scale dimensions (geographic, temporal, and phylogenetic)
Project leaders: Carsten Meyer, Antonin Machac
There is a wide consensus that multiple processes influence species richness across scales. In the proposed project, we will evaluate three broad classes of such processes simultaneously (historical, environmental, and anthropogenic) using the structural equation modeling (SEM) framework. The assessment will be conducted across a range of geographic, temporal, and phylogenetic scales. Specifically, we will test a series of scale-specific hypotheses, involving both direct and indirect effects, using mammals as our model system. We will expect that historical factors (time and past geographic area) directly determine species richness over large scales. These large-scale effects will be moderated by meso-scale effects of climate, energy, productivity, and human land-use. The interrelations between these meso-scale effects are perfectly suited for SEM. SEM models will be constructed across a range of geographic (biomes, grid cells), temporal (Eocene, Anthropocene, Present), and phylogenetic scales (classes, families, species) to illuminate the hypothesized effects on richness across multiple scale dimensions. Even though similar efforts have been often been encouraged, multiscale assessments of the processes that together, both directly and indirectly, govern species richness remain surprisingly scarce. Students then will get an excellent opportunity to employ their newly acquired SEM skills toward the resolution of this question. Our project will hopefully yield a more complete and precise understanding of these effects, which might prove qualitatively different from those reported by studies that examined these effects in isolation.
Project 4: Effects of invasive earthworms on soil biogeochemical characteristics
Project leaders: Nico Eisenhauer, Olga Ferlian, Madhav Thakur
Invasive ecosystem engineers can have disproportionally strong impacts on native ecosystems. Invasive earthworms are a prime example of ecosystem engineers that influence many ecosystems around the world. For instance, invasive earthworms can dramatically alter the physico-chemical characteristics of the soil that were previously earthworm-free. The spatial distribution of soil C and soil N and that of other trace elements progressively change with the introduction of invasive earthworms, mainly due to their feeding and soil mixing activities. However, the current information of invasive earthworm effects on soil physico-chemical characteristics is scattered in the literature. We aim to quantitatively synthesize the effects of invasive earthworms on soil physico-chemical characteristics. With this, we aim to broaden the participants’ knowledge of consequences of earthworm invasion for soil biogeochemical characteristics and ecosystem processes. Furthermore, they will gain skills in carrying out literature search, the evaluation of research data, and application of meta-analysis techniques using R statistical software. Prior to the course, we will organize Skype sessions that will familiarize the participants with the course. During the course, participants will search published studies on earthworm invasion effects on different soil physico-chemical parameters and extend an already existing database created by us with the aim of conducting own meta-analyses. We will provide R codes to perform meta-analyses on the assembled database. Further, we aim to discuss our results with the participants and work together on a joint manuscript. Basic R skills are desirable, but not mandatory.
Participants interested in invasion ecology and biodiversity effects in natural settings are encouraged to apply.
Project 5: Impact of plant diversity on stabilization of soil carbon dynamics after land use change
Project leader: Markus Lange
In the terrestrial ecosphere three-third of all organic carbon is stored in soils 1. The most mobile form of soil carbon is dissolved organic carbon (DOC)2. It is highly biodegradable and is a main factor in the formation of soil organic matter in the soil profile. Plant diversity holds a central position in controlling ecosystem functions3 that are relevant for element cycling and soil carbon storage 4-6. Furthermore, diverse ecosystems are considered to be less vulnerable to environmental changes and disturbances (“Diversity–Stability Hypothesis”7). Fluxes and concentrations of DOC are highly dynamic, because they vary strongly among seasons8, they are strongly affected by human disturbances 9 and also by weather extremes. However, the impact of plant diversity on DOC dynamics its potential to stabilize DOC fluxes and dynamics have been not addressed, yet.
This project aims at revealing the impact of plant diversity on DOC fluxes and DOC concentrations. Based on a comprehensive data set of continuous DOC observations over 14 years from a biodiversity experiment, we will identify how plant diversity influences the seasonal dynamics in DOC concentrations and fluxes, and if higher plant diversity lessens the influence of extreme weather events such as heavy rain or summer drought. Using time series analyses and linear mixed effect models, possible shift in seasonal dynamics as well as break points in the time series will be identified.
1 Lal, R. Soil carbon sequestration impacts on global climate change and food security. Science 304, 1623-1627, doi:10.1126/science.1097396 (2004).
2 Jansen, B., Kalbitz, K. & McDowell, W. H. Dissolved Organic Matter: Linking Soils and Aquatic Systems. Vadose Zone Journal 13, doi:10.2136/vzj2014.05.0051 (2014).
3 Hooper, D. U. et al. Effects of biodiversity on ecosystem functioning: A consensus of current knowledge. Ecological Monographs 75, 3-35, doi:10.1890/04-0922 (2005).
4 De Deyn, G. B. et al. Vegetation composition promotes carbon and nitrogen storage in model grassland communities of contrasting soil fertility. Journal of Ecology 97, 864-875, doi:10.1111/j.1365-2745.2009.01536.x (2009).
5 Lange, M. et al. Plant diversity increases soil microbial activity and soil carbon storage. Nature Communications 6, doi:10.1038/ncomms7707 (2015).
6 Steinbeiss, S. et al. Plant diversity positively affects short-term soil carbon storage in experimental grasslands. Global Change Biology 14, 2937-2949, doi:10.1111/j.1365-2486.2008.01697.x (2008).
7 Chapin, F. S. et al. Consequences of changing biodiversity. Nature 405, 234-242, doi:10.1038/35012241 (2000).
8 Don, A. & Schulze, E. D. Controls on fluxes and export of dissolved organic carbon in grasslands with contrasting soil types. Biogeochemistry 91, 117-131, doi:10.1007/s10533-008-9263-y (2008).
9 Butman, D. E., Wilson, H. F., Barnes, R. T., Xenopoulos, M. A. & Raymond, P. A. Increased mobilization of aged carbon to rivers by human disturbance. Nature Geoscience 8, 112-116, doi:10.1038/ngeo2322 (2015).
Project 6: Landscape effects on the relationship of forest-use intensity and species diversity
Project leader: Stephan Kambach
Human land-use is the main driver for the global decline in biodiversity, also in forests ecosystems that are exploited for timber, food and other products. In this project, we will conduct a global meta-analysis on the effect of different levels of forest-use/forest management intensity on species diversity. We aim to test if these effects are moderated by i) the area of nearby primary forest, ii) the fragmentation of the surrounding forest, iii) the mobility of the focal species and iv) the diversity index reported for which we hypothesize that in case of positive effects on species richness, community evenness still declines significantly.
Prior to the summer school, participants will receive a list with publications relevant to this meta-analysis that was already compiled during the project “Land-Use-BioDiversity-Ecosystem Services-trade-offs” (funded by SESYNC and led by Prof. Ralf Seppelt) and that will be reviewed by the project leader. In 2-3 google hangout meetings the group will discuss the hypotheses, the process of data extraction and the according coding table. During the summer school, participants will then fill this coding table and use QGIS and R (packages metafor, lme4 and ggplot2) to run mixed-effect meta-analysis models and produce publication-quality figures. Expected outputs of the summer school include a filled coding table, an R script providing analyses and figures as well as a structured manuscript.
CANCELLED: Project 7: Investigating the relationship between biodiversity, ecosystem services and human well-being
Project leaders: Isabel M.D. Rosa, Matthias Schröter, Carlos A. Guerra
Ecosystem services are usually conceptualised as a bridge between biodiversity and human wellbeing along a cascade including ecosystem properties that builds the basis for ecosystem services, from which benefits that increase human well-being are derived. However, biodiversity, ecosystem services and human well-being are mostly studied independently - although evidence for their relation is present and accumulating rapidly (2). This undermines our understanding on the extent and complexity of their interlinkages. It is essential to improve this knowledge, given that existing international policy bodies (e.g. IPBES) focus their mission on this relationship. Harrison et al. (3) performed a literature review on the link between biodiversity and ecosystem services, considering 530 research papers, and addressing different measures of biodiversity and ecosystem services. Understanding of the direction and magnitude of the links between ecosystem services and human well-being is however yet missing. Therefore, in this project, students will use the same set of papers reviewed by Harrison et al. (3) to investigate the relationships between the same group of ecosystem services and selected indicators for human well-being (e.g. economic wealth, physical health) (4, 5). In order to perform a meta-analysis, students will extract information regarding the magnitude and direction of these relationships, as well as regarding the relationships established between biodiversity and ecosystem services (only assessed qualitatively in Harrison et al. (3)). Given that these relations are still poorly studied, a complete meta-analysis may not be possible. In this case, students will either produce a structured systematic review following the example provided by Harrison et al. (3) or conduct a new systematic literature search focussing on the link between ecosystem services and human well-being.
1. Haines-Young, R. and M. Potschin, 2010. The links between biodiversity, ecosystem services and human well-being, in: Raffaelli, D., Frid, C. (Ed.), Ecosystem Ecology: a new synthesis.
Cambridge University Press, Cambridge, pp. 110-139.
2. Cardinale, B. J., et al., 2012. Biodiversity loss and its impact on humanity. Nature. 486, 59–67.
3. Harrison, P.A., etal. 2014. Linkages between biodiversity attributes and ecosystem services: A systematic review. Ecosystem Services 9, 191-203.
4. MA, 2003. Ecosystems and Human Well-Being: A Framework for Assessment. Island Press, Washington D.C.
5. Smith, L.M., Case, J.L., Smith, H.M., Harwell, L.C. and Summers, J.K., 2013. Relating ecoystem services to domains of human well-being: Foundation for a U.S. index. Ecological Indicators 28, 79-90.
Please note that in the electronic application, you will be asked to indicate which project you would like to work in by ranking these projects from favourite to lesser interest.
On the last course day, all groups will present and discuss their findings.
The lecturers and project leaders of this summer school will include senior scientific staff at iDiv as well as visitors; the list will be updated once the participants have chosen their projects.
- Lead teacher Prof. Nico Eisenhauer, Head of Research Group Experimental Interaction Ecology
- Prof. Julia Koricheva, Professor of Ecology, Royal Holloway University of London
- Dr. Masha van der Sande, Postdoc at the Spatial Interaction Ecology group
- Dr. Katharina Gerstner, Postdoc at the synthesis centre sDiv
- Dr. Dylan Craven, Postdoc at the Spatial Interaction Ecology group
- Dr. Carsten Meyer, Head of Research Group Macroecology and Society
- Dr. Antonin Machac, Postdoc at Center for Macroecology, Evolution, and Climate, University of Copenhagen, Denmark
- Dr. Olga Ferlian, Postdoc at the Experimental Interaction Ecology group
- Dr. Madhav Thakur, Postdoc at the Experimental Interaction Ecology group
- Dr. Markus Lange, Postdoc at the Max Planck Institute for Biogeochemistry, Jena
- Stephan Kambach, Doctoral researcher at UFZ Halle
- Prof. Ivo Grosse, Head of Bioinformatics Research Group, Martin Luther University Halle-Wittenberg
- Prof. Henrique Pereira, Head of Research Group Biodiversity Conservation
- Prof. Ulrich Brose, Head of Research Group Theory in Biodiversity Science
- Prof. Nicole van Dam, Head of Research Group Molecular Interaction Ecology
- Dr. Meredith Schuman, Head of Research Group Ecological Functions of Plant Genes
- Dr. Guy Pe'er, Postdoc at the sythesis centre sDiv
- Dr. Marten Winter, Coordinator of synthesis centre sDiv
- Dr. Andrew Barnes, Scientific Guest, Experimental Interaction Ecology
Date and venue
The summer school will take place from 3 to 15 September 2017 at iDiv, which is located at the Biocity Leipzig. The site has good transport connections in the immediate vicinity of the university’s natural science campus and the German National Library. It is surrounded by other cutting-edge research centres in the field of biosciences, including the Max Planck Institute for Evolutionary Anthropology and the Fraunhofer Institute for Cell Therapy and Immunology (IZI). The Leipzig Botanical Garden is also located at a walking distance from iDiv.
Accommodation will take place at a nearby hotel, generally in shared rooms.
As course fee, all participants are expected to pay EUR 150.00 per applicant. This covers the costs of teaching and materials, coffee breaks, lunch, excursion and the cultural programme. Participants are generally asked to cover the costs of the evening meals, except when included as part of the summer school programme.
iDiv is able to offer a travel grant for a limited number of the summer school participants, to cover the full costs of travel and accommodation. Funded positions are primarily aimed for applicants who have limited means to fund their participation via other means.
iDiv is a family-friendly workplace, and we offer various support for young families. For the summer school participants, we are able to offer on-site childcare during the daily programme.
The course will start with a welcome barbeque with iDiv doctoral researchers on 3 September, and end with a farewell celebration on 15 September.
An excursion will be organised to the experimental station of Bad Lauchstädt, where several important biodiversity experiments are conducted (MyDiv experimental forest, Ecotron, Global Change Experiment, Nutrient Network, Drought-Net).
In addition, several joint side events will be offered in the evenings, potentially including a guided city tour, visits to the Schrebergarten of iDiv scientists and to local biergartens. Leipzig is a vibrant city offering a variety of cultural attractions for those participants who would also like to explore the city on their own.
In general we recommend all participants to prepare with all-weather clothing: sunglasses, hats and sun creams will be needed, but you should also pack raincoats and a good backpack.