Owen Leonard Petchey

University of Zurich | UZH · Institut für Evolutionsbiologie und Umweltwissenschaften

Stochasticity is a major cause of compositional β‐diversity in communities that develop at similar environmental conditions. Such communities may exhibit functional similarity due to sympatric taxa with equivalent metabolic capacities in the source assemblage. However, the redundancy of individual physiological traits may differ in the original sou...

Global change increasingly threatens nature, endangering the ecosystem services human wellbeing depends upon. Biodiversity potentially mediates these impacts by providing resilience to ecosystems. While biodiversity has been linked to resilience and ecosystem service supply on smaller scales, we lack understanding of whether mediating interactions...

1)A large obstacle in food web ecology is the time and effort required to adequately describe the structure of a food web using individual predator guts. Food web models such as the allometric diet breadth model (ADBM) can be used to circumvent this problem by predicting the interactions based on easily measured characteristics, such as the size of...

Games as a didactic tool (e. g., puzzles) are gaining recognition in environmental education to promote skill development, but also to develop a specific understanding of the natural world. However, a children’s puzzle containing representations of nature may unwillingly lead to “misconceptions” of biodiversity themes and processes, and an over-sim...

The potential for forecasting the dynamics of ecological systems is currently unclear, with contrasting opinions regarding its feasibility due to ecological complexity. To investigate forecast skill within and across systems, we monitored a microbial system exposed to either constant or fluctuating temperatures in a 5‐month‐long laboratory experime...

Despite substantial progress in understanding global biodiversity loss, major taxonomic and geographic knowledge gaps remain. Decision makers often rely on expert judgement to fill knowledge gaps, but are rarely able to engage with sufficiently large and diverse groups of specialists. To improve understanding of the perspectives of thousands of bio...

Microbial communities in many ecosystems are facing a broad range of global change drivers, such as nutrient enrichment, chemical pollution, and temperature change. These drivers can cause changes in the abundance of taxa, the composition of communities, and the properties of ecosystems. While the influence of single drivers is already described in...

While environmental science, and ecology in particular, is working to provide better understanding to base sustainable decisions on, the way scientific understanding is developed can at times be detrimental to this cause. Locked‐in debates are often unnecessarily polarised and can compromise any common goals of the opposing camps. The present paper...

The ties between a society and its local ecosystem can decouple as societies develop and replace ecosystem services such as food or water regulation via trade and technology. River deltas have developed into important, yet threatened, urban, agricultural and industrial centres. Here, we use global spatial datasets to explore how 49 ecosystem servic...

Understanding how microbial communities of aquatic ecosystems respond to environmental change remains a critical challenge in microbial ecology. In this study, we used light-dependent oxic-anoxic micro-ecosystems to understand how the functioning and diversity of aerobic and anaerobic lake analog communities are affected by a pulse light deprivatio...

The potential for forecasting the dynamics of ecological systems is currently unclear, with contrasting opinions regarding its feasibility due to ecological complexity. To investigate forecast skill within and across system complexity, we monitored a microbial system exposed to either constant or fluctuating temperatures in a five months long labor...

Habitat loss is a significant driver of biodiversity loss, causing fragmentation into small, isolated patches of suitable land cover. This reduces the permeability of landscapes to the movement of individuals and reduces the likelihood of metapopulation persistence. Quantifying functional connectivity, the ability of a focal species to move between...

Three decades of research have demonstrated that biodiversity can promote the functioning of ecosystems. Yet, it is unclear whether the positive effects of biodiversity on ecosystem functioning will persist under various types of global environmental change drivers. We conducted a meta‐analysis of 46 factorial experiments manipulating both species...

Food web models explain and predict the trophic interactions in a food web, and they can infer missing interactions among the organisms. The allometric diet breadth model (ADBM) is a food web model based on the foraging theory. In the ADBM, the foraging parameters are allometrically scaled to body sizes of predators and prey. In Petchey et al. (Pro...

Biodiversity may increase ecosystem resilience. However, we have limited understanding if this holds true for ecosystems that respond to gradual environmental change with abrupt shifts to an alternative state. We used a mathematical model of anoxic-oxic regime shifts and explored how trait diversity in three groups of bacteria influences resilience...

Microbial communities in many ecosystems are facing a broad range of global change scenarios, resulting in microbial changes and possibly regime shifts with unknown ecological consequences. While the influence of single stressors is already described in numerous studies, the effects of multiple stressors working simultaneously are still poorly unde...

Theory and some evidence suggest that biodiversity promotes stability. However, evidence of how trophic interactions and environmental changes modulate this relationship in multitrophic communities is lacking. Given the current scenario of biodiversity loss and climate changes, where top predators are disproportionately more affected, filling these...

The interspecific interactions within and between adjacent ecosystems strongly depend on the changes in their abiotic and biotic components. However, little is known about how climate change and biodiversity loss in a specific ecosystem can impact the multiple trophic interactions of different biological groups within and across ecosystems. We used...

Non-consumptive effects (NCEs) of predators on prey, such as induced defensive strategies, are frequently neglected in the analysis of predator-prey interactions. Yet these effects can have demographic impacts as strong as consumption. As a counterpart to NCEs, resource-availability effects (RAEs) can prompt changes in predators as well, e.g., in t...

Ecological communities face a variety of environmental and anthropogenic stressors acting simultaneously. Stressor impacts can combine additively or can interact, causing synergistic or antagonistic effects. Our knowledge of when and how interactions arise is limited, as most models and experiments only consider the effect of a small number of non-...

Understanding how microbial communities as key drivers of global biogeochemical cycles respond to environmental change remains a critical challenge in microbial ecology. In this study, we used phototrophic oxic-anoxic micro-ecosystems to understand how aerobic and anaerobic lake analog communities responded towards stressful light removal. Continuo...

Aquatic ecosystems are often stratified, with cyanobacteria in oxic layers and phototrophic sulfur bacteria in anoxic zones. Changes in stratification caused by the global environmental change are an ongoing concern. Increasing understanding of how such aerobic and anaerobic microbial communities, and associated abiotic conditions, respond to multi...

• Metadata plays an essential role in the long-term preservation, reuse, and interoperability of data. Nevertheless, creating useful metadata can be sufficiently difficult and weakly enough incentivized that many datasets may be accompanied by little or no metadata. One key challenge is, therefore, how to make metadata creation easier and more valu...

In the previous chapter we looked at individual variables; however, a sample may involve more than one variable. Moreover, data analysis is usually concerned with the relationships among two or more variables. These relationships might involve the same (e.g. numeric versus numeric) or different (e.g. numeric versus categorical) types of variable. I...

In the previous two chapters we experienced/demonstrated a data analysis workflow about variation in the diets of bats. In this and the next few chapters we will take a deeper dive into the details of R and of concepts. In this chapter, you will become much better acquainted with the wonderful world of the dplyr package. We look more carefully at t...

Before working through a real example of getting insights from data, we need to become acquainted with some tools we will use. Learning a bit about the tools first can help us feel more confident and comfortable when we then come to use them for real. Hence this chapter takes some time to introduce you to R and RStudio, including writing some simpl...

In this chapter, we gain our first real insights about the data. We use visualizations and summarize the data to show how it is distributed and, among other things, that female bats eat larger prey on average than males. We also look at the data from a different perspective and show that the composition of prey species taken differs among female an...

In this chapter we go through some miscellaneous R topics, all of which you experienced briefly in the bat diet workflow demonstration. These include pipes, a mechanism for moving data from one operation to another; strings, how words and text are represented in computers using ‘stringr’; dates and times, until recently a proper pain anywhere on a...

We have made quite a few graphs already but only briefly explained how we did so, specifically using ggplot. We need a deeper understanding… hence this chapter. We focus on making graphs with ggplot2 . The ggplot2 package can help us to produce quite complex visualizations, with elements such as graphical keys, without the need to write lines and l...

Knowledge of how to get useful information from data is essential in the life and environmental sciences. This book provides learners with knowledge, experience, and confidence about how to efficiently and reliably discover useful information from data. The content is developed from first- and second-year undergraduate-level courses taught by the a...

After reading this book, what comes next? There is a lot that we decided to leave out of the book that we would have loved to put in. This chapter includes some pointers about what we left out, and what you could now start exploring. We also include a section on reproducibility, which covers the basics of what reproducibility is, why we might care...

Data analysis is not just about physically performing the analyses. We also need to think carefully about our data, and various issues that they might have. In this chapter, we explore conceptual issues raised by the bat diet workflow demonstration. This chapter discusses statistical variables, populations and samples, independence and non-independ...

This and the next chapter involve us working through the process of getting insights from data. We have chosen a research subject that should have some interest to us all: food. More specifically, what bats eat. In this chapter you will experience a clearly specified set of research questions, learn how the study was performed and why it was done t...

In this perspective article we start from the theories of constructivism and conceptual change within the field of education to develop and present hypotheses about how understandings of biodiversity and diversity more generally are formed. We argue that extrinsic and circumstantial elements from everyday experiences are relevant in shaping underst...

Environmental change can alter species’ abundances within communities consistently; for example, increasing all abundances by the same percentage, or more idiosyncratically. Here, we show how comparing effects of temperature on species grown in isolation and when grown together helps our understanding of how ecological communities more generally re...

Theory predicts that organism–environment feedbacks play a central role in how ecological communities respond to environmental change. Strong feedback causes greater nonlinearity between environmental change and ecosystem state, increases the likelihood of hysteresis in response to environmental change, and augments the possibility of alternative s...

In this paper we will discuss the way in which we experience (bio)diversity in our daily lives. And we raise awareness of some situations in which we implicitly generate a negative experience of biodiversity. I upload this private prepint so as to generate a URL associated with the project. However, it will hopefully soon be available for sharing...

Losses and gains in species diversity affect ecological stability1–7 and the sustainability of ecosystem functions and services8–13. Experiments and models have revealed positive, negative and no effects of diversity on individual components of stability, such as temporal variability, resistance and resilience2,3,6,11,12,14. How these stability com...

Successfully predicting the future states of systems that are complex, stochastic and potentially chaotic is a major challenge. Model forecasting error (FE) is the usual measure of success; however model predictions provide no insights into the potential for improvement. In short, the realized predictability of a specific model is uninformative abo...

Global biodiversity is eroding due to anthropogenic causes such as climate change, habitat loss, and trophic simplification of biological communities. Most studies address only isolated causes within a single group of organisms; however, biological groups of different trophic levels may respond in particular ways to different environmental impacts....

Much of life's diversity has arisen through ecological opportunity and adaptive radiations, but the mechanistic underpinning of such diversification is not fully understood. Competition and predation can affect adaptive radiations, but contrasting theoretical and empirical results show that they can both promote and interrupt diversification. A mec...

Understanding and monitoring pressures on ecosystems and their consequences for ecosystem services (ES) is essential for management decisions and verification of progress towards national and international policies (e.g. Aichi Biodiversity Targets, Sustainable Development Goals). Remote sensing (RS) offers a unique capability to assess ES systemati...

Global sustainability initiatives are gaining momentum and impact, and place-based research can provide complementary insights to strengthen them. Here, we explore the current and potential role of place-based research into informing global sustainability initiatives by assessing the strengths, challenges, and opportunities. We show that place-base...

Global environmental change and biodiversity loss are closely linked through different feedback mechanisms. The University of Zurich Research Priority Programme on ‘Global Change and Biodiversity’ approach is to work with interdisciplinarity and transdisciplinarity to integrate mechanisms of interactions, feedback and scale and improve our understa...

Assessing functional diversity from space can help predict productivity and stability of forest ecosystems at global scale using biodiversity–ecosystem functioning relationships. We present a new spatially continuous method to map regional patterns of tree functional diversity using combined laser scanning and imaging spectroscopy. The method does...

Spatially well-informed decisions are essential to sustain and regulate processes and ecosystem services (ES), and to maintain the capacity of ecosystems to supply services. However, spatially explicit ES information is often lacking in decision-making, or exists only as ES maps based on categorical land cover data. Remote sensing (RS) opens new pa...

Global change affects ecosystem functioning both directly by modifications in physicochemical processes, and indirectly, via changes in biotic metabolism and interactions. Unclear, however, is how multiple anthropogenic drivers affect different components of community structure and the performance of multiple ecosystem functions (ecosystem multifun...

Intraspecific trait change, including altered behaviour or morphology, can drive temporal variation in inter-specific interactions and population dynamics. In turn, variation in species’ interactions and densities can alter the strength and direction of trait change. The resulting feedback between species′ traits and abundance permits a wide range...

Computer science offers a large set of tools for prototyping, writing, running, testing, validating, sharing and reproducing results, however computational science lags behind. In the best case, authors may provide their source code as a compressed archive and they may feel confident their research is reproducible. But this is not exactly true. Jam...

Urban development is rapidly expanding across the globe and is a major driver of environmental change. Despite considerable improvements in our understanding of how species richness responds to urbanization, there is still insufficient knowledge of how other measures of assemblage composition and structure respond to urban development. Functional d...

Global environmental change has negative impacts on ecological systems, impacting the stable provision of functions, goods and services. Whereas effects of individual environmental changes (e.g. temperature change or change in resource availability) are reasonably well understood, we lack information about if and how multiple changes interact. We e...

Scatterplot of trajectories in principal component space from videos of three experimental units (Tetra = Tetrahymena thermophila, none = control (no ciliates), and Loxo = Loxocephalus sp.). A 90% confidence interval ellipse is fitted to each of the three experimental units to identify background noise in component space. The observations that fall...

Morphological boundaries for training data. (PDF)

Output model 1. (PDF)

Output model 4. (PDF)

Sensitivity and specificity of alternative classifiers such as support vector machines (SVM) and Naive Bayes (NB), compared to random forest (RF) and manual classifiers. All provide similar classification success for the ciliate species. SVM and NB are even slightly better than RF in terms of classifying noise. (TIF)

A single frame of one video, with particles labeled by their trajectory ID. For each trajectory, we obtained morphology and movement properties that were later used for classification into the respective species. (JPG)

In each panel, a point is a trajectory, with its position on PC1 corresponding to overall size, and PC2 to variability in size, and turning behaviour. Trajectories from microcosms containing ciliates are shown in black, yellow dots are trajectories from the controls (no ciliates). Panel codes: Colp = Colpidium striatum, Dexio = Dexiostoma campylum,...

Initial densities (individuals mL−1) for different richness treatments. (PDF)

Scatterplot of trajectories in principal component space from videos of three experimental units. Trajectories reclassified as noise by the Gaussian Mixture Model (GMM) are outlined in black. In this example, only some of the trajectories from the Tetrahymena thermophila culture were classified as noise (i.e. are outlined in black and have their co...

Output model 2. (PDF)

Output model 3. (PDF)

The development of video-based monitoring methods allows for rapid, dynamic and accurate monitoring of individuals or communities, compared to slower traditional methods, with far reaching ecological and evolutionary applications. Large amounts of data are generated using video-based methods, which can be effectively processed using machine learnin...

Ecological networks are tightly interconnected, such that loss of a single species can trigger additional species extinctions. Theory predicts that such secondary extinctions are driven primarily by loss of species from intermediate or basal trophic levels. In contrast, most cases of secondary extinctions from natural systems have been attributed t...