Andrew P Beckerman

The University of Sheffield | Sheffield · Department of Animal and Plant Sciences

Acquisition and allocation of resources are central to life-history theory. However, empirical work typically focuses only on allocation despite the fact that relationships between fitness components may be governed by differences in the ability of individuals to acquire resources across environments. Here, we outline a statistical framework to par...

Phenotypic plasticity is the ability of a genotype to produce more than one phenotype in order to match the environment. Recent theory proposes that the major axis of genetic variation in a phenotypically plastic population can align with the direction of selection. Therefore, theory predicts that plasticity directly aids adaptation by increasing g...

Food webs, the networks of feeding links between species, are central to our understanding of ecosystem structure, stability, and function. One of the key aspects of food web structure is complexity, or connectance, the number of links expressed as a proportion of the total possible number of links. Connectance (complexity) is linked to the stabili...

Understanding what structures ecological communities is vital to answering questions about extinctions, environmental change, trophic cascades, and ecosystem functioning. Optimal foraging theory was conceived to increase such understanding by providing a framework with which to predict species interactions and resulting community structure. Here, w...

Nest site selection is the principal way secondary cavity-nesting species mitigate the negative effects of factors such as predation, parasitism and exposure on productivity. High-quality cavities could then be expected to be selected in response to the primary threat to nest success. Understanding how demographic rates are affected by anthropogeni...

Most conservation relies on being able to estimate population size accurately. The development, implementation and adaptation of effective conservation strategies rely on quantifying the impacts of different threats on population dynamics, identifying species that need conservation management, and providing feedback on the effectiveness of any mana...

Passive acoustic monitoring (PAM) - the use of autonomous recording units to record ambient sound - offers the potential to dramatically increase the scale and robustness of species monitoring in rainforest ecosystems. PAM generates large volumes of data that require automated methods of target species detection. Species-specific recognisers, which...

A key challenge for ecological and ecotoxicological risk assessment is to predict the risk of organisms when exposed simultaneously to multiple stressors in sub-lethal concentrations. Here, we assessed whether sub-lethal concentrations of an anthropogenic stressors, the heavy metal copper (Cu), mediates the impacts of a natural ecological threat to...

In the face of rapid global change and an uncertain fate for biodiversity, it is vital to quantify trends in wild populations. These trends are typically estimated from abundance time series for suites of species across large geographic and temporal scales. Such data implicitly contain phylogenetic, spatial, and temporal structure which, if not pro...

The adaptive nature of phenotypic plasticity is widely documented. However, little is known about the evolutionary forces that shape genetic variation of plasticity within populations. Whether genetic variation in plasticity is driven by stabilizing or diversifying selection and whether the strength of such forces remains constant through time, rem...

Patterns of biological diversity across the tree of life are the result of millions of years of evolutionary history and are shaped by natural selection. A long-standing proposal is that most morphological diversity among species arises along "an evolutionary line of least resistance", where new phenotypes arise primarily by elaboration - evolution...

Microbial experimental evolution allows studying evolutionary dynamics in action and testing theory predictions in the lab. Experimental evolution in chemostats (i.e. continuous flow through cultures) has recently gained increased interest as it allows tighter control of selective pressures compared to static batch cultures, with a growing number o...

Biotic interactions and community structure are seldom examined in mass extinction studies but must be considered if we are to truly understand extinction and recovery dynamics at the ecosystem scale. Here, we model shallow marine food web structure across the Toarcian extinction event in the Cleveland Basin, UK using a trait-based inferential mode...

Microbial experimental evolution allows studying evolutionary dynamics in action and testing theory predictions in the lab. Experimental evolution in chemostats (i.e. continuous flow through cultures) has recently gained increased interest as it allows tighter control of selective pressures compared to static batch cultures, with a growing number o...

Local adaptation is a fundamental evolutionary process generating biological diversity and potentially enabling ecological speciation. Divergent selection underlies the evolution of local adaptation in spatially structured populations by driving their adaptation toward local optima. Environments rarely differ along just one environmental axis; ther...

Trapliners are pollinators that visit widely dispersed flowers along circuitous foraging routes. The evolution of traplining in hummingbirds is thought to entail morphological specialization through the reciprocal coevolution of longer bills with the long-tubed flowers of widely dispersed plant species. Specialization, such as that exhibited by tra...

Anthropogenic activity is changing Earth's climate and ecosystems in ways that are potentially dangerous and disruptive to humans. Greenhouse gas concentrations in the atmosphere continue to rise, ensuring that these changes will be felt for centuries beyond 2100, the current benchmark for projection. Estimating the effects of past, current, and po...

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-...

The adaptive nature of phenotypic plasticity is widely documented in natural populations. However, little is known about the evolutionary forces that shape genetic variation in plasticity within populations. Here we empirically address this issue by testing the hypothesis that stabilizing selection shapes genetic variation in the anti-predator deve...

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...

Approximately 25% of mammals are currently threatened with extinction, a risk that is amplified under climate change. Species persistence under climate change is determined by the combined effects of climatic factors on multiple demographic rates (survival, development and reproduction), and hence, population dynamics. Thus, to quantify which speci...

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...

Gut microbiota communities are fundamental ecological components in the aquatic food web. Their potential to mediate how organisms respond to multiple environmental stressors remains understudied. Here we explored how manipulations of the gut microbiome of Daphnia pulex, a keystone species in aquatic communities, influenced life history (size at ma...

Valuing, managing and conserving marine biodiversity and a full range of ecosystem services is at the forefront of research and policy agendas. However, biodiversity is being lost at up to a thousand times the average background rate. Traditional disciplinary and siloed conservation approaches are not able to tackle this massive loss of biodiversit...

Anthropogenic activity is changing Earth’s climate and ecosystems in ways that are potentially dangerous and disruptive to humans . Greenhouse gas concentrations in the atmosphere continue to rise, ensuring these changes will be felt for centuries beyond 2100, the current benchmark for prediction emissions to only 2100 is therefore shortsighted. Cr...

Indirect interactions are central to ecological and evolutionary dynamics in pollination communities, yet we have little understanding about the processes determining patterns of indirect interactions, such as those between pollinators through shared flowering plants. Instead, research has concentrated on the processes responsible for direct intera...

Population responses to threats such as habitat loss, climate change and overexploitation are usually explored using demographic models parameterized with estimates of vital rates of survival, maturation and fecundity. However, the vital rate estimates required to construct such models are often unavailable, particularly for species of conservation...

The eco-evolutionary dynamics of microbial communities are predicted to affect both the tempo and trajectory of evolution in constituent species [1]. While community composition determines available niche space, species sorting dynamically alters composition, changing over time the distribution of vacant niches to which species adapt [2], altering...

Rapid evolution can influence the ecology of populations, communities, and ecosystems, but the importance of evolution for ecological dynamics remains unclear, largely because the contexts in which evolution is powerful are poorly resolved. Here, we carry out a large observational study to test hypotheses about context dependency of eco‐evolutionar...

Microalgae can respond to natural cues from crustacean grazers, such as Daphnia, by forming colonies and aggregations called flocs. Combining microalgal biology, physiological ecology, and quantitative proteomics, we identified how infochemicals from Daphnia trigger physiological and cellular level changes in the microalga Scenedesmus subspicatus,...

Indirect interactions are central to ecological and evolutionary dynamics in pollination communities, yet we have little understanding about the processes determining patterns of indirect interactions, such as those between pollinators through shared flowering plants. Instead, research has concentrated on the processes responsible for direct intera...

Microalgae can respond to natural cues from crustacean grazers, such as Daphnia, by forming colonies and aggregations called flocs. Combining microalgal biology, physiological ecology, and quantitative proteomics, we identified how infochemicals from Daphnia trigger physiological and cellular level changes in the microalga Scenedesmus subspicatus,...

Growing population and industrialization have resulted in a significant contamination of freshwater by a variety of micropollutants including endocrine disrupting chemicals (EDCs). Wastewater treatment plants cannot completely remove EDC yet, which then end up in wastewater effluents, and they are discharged directly into the environment. Rising co...

A key challenge of standard ecotoxicological risk assessment is to predict the sub-lethal risk of multiple contaminants on aquatic organisms. Our study assessed the sub-lethal mixture toxicity of copper (Cu) and cadmium (Cd) on Daphnia pulex and included manipulations of food level and assessment of three genotypes. We investigated the interaction...

Approximately 25 % of mammals are threatened globally with extinction, a risk that is amplified under climate change. Persistence under climate change is determined by the combined effects of climatic factors on multiple demographic rates (survival, development, reproduction), and hence, on population dynamics. Thus, to quantify which species and p...

Approximately 25 % of mammals are threatened globally with extinction, a risk that is amplified under climate change1. Persistence under climate change is determined by the combined effects of climatic factors on multiple demographic rates (survival, development, reproduction), and hence, on population dynamics2. Thus, to quantify which species and...

Recent advances in metaproteomics have provided us a link between genomic expression and functional characterization of environmental microbial communities. Therefore, the large-scale identification of proteins expressed by environmental microbiomes allows an unprecedented view of their in situ metabolism and function. However, one of the main chal...

The performance of microbial communities exploited by industry are largely optimised by manipulating process parameters, such as flow rates, growth conditions, and reactor parameters. Conversely, the composition of microorganisms used are often viewed as a “black box”. This is mostly due to the relatively high costs and technical expertise required...

The effect of sublethal concentrations of heavy metals on cladoceran growth and reproduction is a cornerstone of modern ecotoxicology. However, the literature contains assays across numerous concentrations, on numerous species and genotypes, and conditions are far from consistent. We undertook a systematic review of the sublethal effects of copper...

Eutrophication and climate change are two of the most pressing environmental issues affecting up to 50% of aquatic ecosystems worldwide. Mitigation strategies to reduce the impact of environmental change are complicated by inherent difficulties of predicting the long-term impact of multiple stressors on natural populations. Here, we investigated th...

Accounting for the variation that occurs within species in food webs can theoretically result in significant changes in both network structure and dynamics. However, there has been little work exploring their role with empirical data. In particular, the variation associated with species’ life cycles, which is prevalent and represents both trait var...

Front Cover: Ten days old female gray mouse lemur on a stick of beech (6 mm diameter). This 14 grams baby weighted 5.6 grams at birth and belonged to a clutch with one male and one other female. The photo credit should be Grégoire BOULINGUEZ-AMBROISE.

Phenotypic plasticity is the ability of an individual genotype to alter aspects of its phenotype depending on the current environment. It is central to the persistence, resistance and resilience of populations facing variation in physical or biological factors. Genetic variation in plasticity is pervasive, which suggests its local adaptation is pla...

An Empirical Orthogonal Function (EOF) variance analysis was performed to map in detail the spatiotemporal variability in individual stake mass-balances (ba) on Mittivakkat Gletscher (MG) – in a region where at present five out of ~20.000 glaciers have mass-balance observations. The EOF analysis suggested that observed ba was summarized by two mode...

Knowledge about variations in runoff from Greenland to adjacent fjords and seas is important for the hydrochemistry and ocean research communities to understand the link between terrestrial and marine Arctic environments. Here, we simulate the Greenland Ice Sheet (GrIS) surface mass balance (SMB), including refreezing and retention, and runoff toge...

Inducible, anti-predator traits are a classic example of phenotypic plasticity. Their evolutionary dynamics depend on their genetic basis, the historical pattern of predation risk that populations have experienced and current selection gradients. When populations experience predators with contrasting hunting strategies and size preferences, theory...

This is a correction of the 2016 paper.