Dylan Childs

• The University of Sheffield

Lack’s seminal work on bird clutch sizes has spurred expansive research on reproductive trade-offs, especially focusing on offspring quantity–quality trade-offs and the potential fitness consequences for the parents. The environment is a critical driver of the expression of individual reproductive traits, influencing them through plastic responses....

Many important ecological processes play out over large geographic ranges, and accurate large-scale monitoring of populations is a requirement for their effective management. Of particular interest are agricultural weeds, which cause widespread economic and ecological damage. However, the scale of weed population data collection is limited by an in...

Climate change‐driven impacts on vegetation productivity have been shown to drive mammalian herbivore population dynamics in Arctic and alpine environments. However, there is less evidence for temperate systems. To address this, we examined the contribution of increasing plant biomass in different vegetation communities (measured by NDVI, normalise...

Life history trade‐offs are one of the central tenets of evolutionary demography. Trade‐offs, depicting negative covariances between individuals' life history traits, can arise from genetic constraints, or from a finite amount of resources that each individual has to allocate in a zero‐sum game between somatic and reproductive functions. While theo...

Organisms have evolved diverse strategies to manage parasite infections. Broadly, hosts may avoid infection by altering behaviour, resist infection by targeting parasites or tolerate infection by repairing associated damage. The effectiveness of a strategy depends on interactions between, for example, resource availability, parasite traits (virulen...

1. Organisms have evolved diverse strategies to manage parasite infections. Broadly, hosts may avoid infection by altering behaviour, resist infection by targeting parasites, or tolerate infection by repairing associated damage. Effectiveness of a strategy depends on interactions between, e.g., resource availability, parasite traits (virulence, lif...

Trade-offs are central to life history theory and play a role in driving life history diversity. They arise from a finite amount of resources that need to be allocated among different functions by an organism. Yet covariation of demographic rates among individuals frequently do not reflect allocation trade-offs because of variation in resource acqu...

Biodiversity faces unprecedented threats from rapid global change¹. Signals of biodiversity change come from time-series abundance datasets for thousands of species over large geographic and temporal scales. Analyses of these biodiversity datasets have pointed to varied trends in abundance, including increases and decreases. However, these analyses...

Globally, pesticides improve crop yields but at great environmental cost, and their overuse has caused resistance. This incurs large financial and production losses but, despite this, very diversified farm management that might delay or prevent resistance is uncommon in intensive farming. We asked farmers to design more diversified cropping strateg...

The widespread and persistent use of herbicides has both selected for dramatically increased levels of herbicide resistance in the weed populations they were designed to control, and increased contamination of non-target ecosystems. Experimental evolution using microbes offers the opportunity to explore basic evolutionary theory, including testing...

Herbicide resistant weeds are an increasing economic and ecological problem worldwide. Evolutionary theory and insight from experiments testing this theory are now a central part of solving resistance problems. More specifically, experimental evolution, where populations are allowed to evolve under specific conditions, can offer substantial insight...

A key challenge in the management of populations is to quantify the impact of interventions in the face of environmental and phenotypic variability. However, accurate estimation of the effects of management and environment, in large‐scale ecological research is often limited by the expense of data collection, the inherent trade‐off between quality...

Life history tradeoffs are one of the central tenets of evolutionary demography. Tradeoffs, depicting negative phenotypic or genetic covariances between individuals’ demographic rates, arise from a finite amount of resources that each individual has to allocate in a zero-sum game between somatic and reproductive functions. While theory predicts tha...

Nest site selection is the principal way secondary cavity‐nesting species mitigate the negative effects of factors such as predation, parasitism and exposure on reproductive success. Large‐bodied secondary cavity‐nesting birds rely on large cavities in mature trees that are often absent or reduced in anthropogenically disturbed forests. Thus, the a...

Next-generation sequencing (NGS) and metabarcoding approaches are increasingly applied to wild animal populations, but there is a disconnect between the widely applied generalized linear mixed model (GLMM) approaches commonly used to study phenotypic variation and the statistical toolkit from community ecology typically applied to metabarcoding dat...

The frequency of ecological disturbances, such as fires, is changing due to changing land use and climatic conditions. Disturbance‐adapted species may thus require the manipulation of disturbance regimes to persist. However, the effects of changes in other abiotic factors, such as climatic conditions, are frequently disregarded in studies of such s...

Globally, herbicides improve crop yields but at great environmental cost, and their overuse has caused herbicide resistance. This incurs large financial and production losses but, despite this, truly integrated weed management that might delay or prevent resistance is uncommon in intensive farming. We asked farmers to design more diversified croppi...

Contemporary rates of biodiversity decline emphasize the need for reliable ecological forecasting, but current methods vary in their ability to predict the declines of real-world populations. Acknowledging that stressor effects start at the individual level, and that it is the sum of these individual-level effects that drives populations to collaps...

Stage-based demographic methods, such as matrix population models (MPMs), are powerful tools used to address a broad range of fundamental questions in ecology, evolutionary biology, and conservation science. Accordingly, MPMs now exist for over 3,000 species worldwide. These data are being digitised as an ongoing process and periodically released i...

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...

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...

Monitoring the prevalence and abundance of parasites over time is important for addressing their potential impact on host life histories, immunological profiles and their influence as a selective force. Only long-term ecological studies have the potential to shed light on both the temporal trends in infection prevalence and abundance and the driver...

Weed infestation is a global threat to agricultural productivity, leading to low yields and financial losses. Weed detection, based on applying machine learning to imagery collected by Unmanned Aerial Vehicles (UAV) has shown potential in the past; however, validation on large data-sets (e.g., across a wide number of different fields) remains lacki...

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...

Discrete time structured population projection models are an important tool for studying population dynamics. Within this field, integral projection models (IPMs) have become a popular method for studying populations structured by continuously distributed traits (e.g. height, weight). Databases of discrete time, discrete state structured population...

BACKGROUND Unravelling the genetic architecture of non‐target‐site resistance (NTSR) traits in weed populations can inform questions about the inheritance, trade‐offs and fitness costs associated with these traits. Classical quantitative genetics approaches allow study of the genetic architecture of polygenic traits even where the genetic basis of...

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...

Understanding or predicting the responses of natural populations to climate is an urgent task for ecologists. However, studies linking the temporal dynamics of populations to climate remain limited. In population ecology, studies typically assume that populations respond only to the climate of the most recent growing season or year. However, eviden...

Discrete time structured population projection models are an important tool for studying population dynamics. Within this field, Integral Projection Models (IPMs) have become a popular method for studying populations structured by continuously distributed traits (e.g. height, weight). Databases of discrete time, discrete state structured population...

The social environment in which individuals live affects their fitness and in turn population dynamics as a whole. Birds with facultative cooperative breeding can live in social groups with dominants, subordinate helpers that assist with the breeding of others, and subordinate non‐helpers. Helping behaviour benefits dominants through increased repr...

Integral projection models (IPMs) allow projecting the behaviour of a population over time using information on the vital processes of individuals, their state and that of the environment they inhabit. As with matrix population models (MPMs), time is treated as a discrete variable, but in IPMs state and environmental variables are continuous, and a...

Genetic differentiation and phenotypic plasticity jointly shape intraspecific trait variation, but their roles differ among traits. In short-lived plants, reproductive traits may be more genetically determined due to their impact on fitness, whereas vegetative traits may show higher plasticity to buffer short-term perturbations. Combining a multi-t...

Integral projection models (IPMs) are an important tool for studying the dynamics of populations structured by one or more continuous traits (e.g. size, height, body mass). Researchers use IPMs to investigate questions ranging from linking drivers to population dynamics, planning conservation and management strategies, and quantifying selective pre...

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...

Integral projection models (IPMs) are an important tool for studying the dynamics of populations structured by one or more continuous traits ( e.g. size, height, color). Researchers use IPMs to investigate questions ranging from linking drivers to plant population dynamics, planning conservation and management strategies, and quantifying selective...

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...

Population dynamics can be highly variable in the face of environmental heterogeneity, and understanding this variation is central in the study of ecology. Robust management decisions require that we understand how populations respond to management at a range of scales, and under a broad suite of conditions. Population models are potentially valuab...

There is an urgent need to synthesize the state of our knowledge on plant responses to climate. The availability of open-access data provide opportunities to examine quantitative generalizations regarding which biomes and species are most responsive to climate drivers. Here, we synthesize time series of structured population models from 162 populat...

The spatial scale at which demographic performance (e.g., net reproductive output) varies can profoundly influence landscape‐level population growth and persistence, and many demographically pertinent processes such as species interactions and resource acquisition vary at fine scales. We compared the magnitude of demographic variation associated wi...

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...

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...

BACKGROUND Arable weeds threaten farming and food production, impacting on productivity. Large‐scale data on weed populations are typically lacking, and changes are frequently undocumented until they reach problem levels. Managing the future spread of weeds requires that we understand the factors that influence current densities and distributions....

Phylogenetically informed imputation methods have rarely been applied to estimate missing values in demographic data but may be a powerful tool for reconstructing vital rates of survival, maturation, and fecundity for species of conservation concern. Imputed vital rates could be used to parameterize demographic models to explore how populations res...

Phenotypic plasticity can mask population genetic differentiation, reducing the predictability of trait-environment relationships. In short-lived plants, reproductive traits may be more genetically determined due to their direct impact on fitness, whereas vegetative traits may show higher plasticity to buffer short-term perturbations. Combining a m...

IPMs, Bayesian demographic models, latent states

Environmental change influences fitness‐related traits and demographic rates, which in herbivores are often linked to resource‐driven variation in body condition. Coupled body condition‐demographic responses may therefore be important for herbivore population dynamics in fluctuating environments, such as the Arctic. We applied a transient Life‐Tabl...

Species range limits are thought to result from a decline in demographic performance at range edges. However, recent studies reporting contradictory patterns in species demographic performance at their edges cast doubt on our ability to predict climate change demographic impacts. To understand these inconsistent demographic responses, we need to sh...

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

A changing environment directly influences birth and mortality rates, and thus population growth rates. However, population growth rates in the short term are also influenced by population age‐structure. Despite its importance, the contribution of age‐structure to population growth rates has rarely been explored empirically in wildlife populations...

Significance Climate change is altering the seasonal environmental conditions to which animals have adapted, but the outcome may differ between seasons for a particular species. Demographic responses therefore need disentangling on a seasonal basis to make accurate forecasts. Our study shows that climate change is causing seasonally divergent demog...

To mitigate and adapt to climate change, there is an urgent need to synthesize the state of our knowledge on plant responses to climate. The availability of open-access data, combined with our understanding of plant physiology and life history theory provide opportunities to examine quantitative generalizations regarding which biomes and species ar...

Intense selection by pesticides and antibiotics has resulted in a global epidemic of evolved resistance. In agriculture and medicine, using mixtures of compounds from different classes is widely accepted as optimal resistance management. However, this strategy may promote the evolution of more generalist resistance mechanisms. Here we test this hyp...

Infection by macroparasites, such as nematodes, varies within vertebrate host systems; elevated infection is commonly observed in juveniles and males, and, for females, with different reproductive states. However, while such patterns are widely recognized in short-lived model systems, how they apply to long-lived hosts is comparatively understudied...

When plants establish outside their native range, their ability to adapt to the new environment is influenced by both demography and dispersal. However, the relative importance of these two factors is poorly understood. To quantify the influence of demography and dispersal on patterns of genetic diversity underlying adaptation, we used data from a...

Natural populations are exposed to seasonal variation in environmental factors that simultaneously affect several demographic rates (survival, development and reproduction). The resulting covariation in these rates determines population dynamics, but accounting for its numerous biotic and abiotic drivers is a significant challenge. Here, we use a f...

Pesticides have underpinned significant improvements in global food security, albeit with associated environmental costs. Currently, the yield benefits of pesticides are threatened as overuse has led to wide-scale evolution of resistance. Despite this threat, there are no large-scale estimates of crop yield losses or economic costs due to resistanc...

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...

Environmental factors drive the persistence of natural populations by causing complex, covarying responses in demographic processes (i.e., survival, growth, and reproduction). As most natural populations inhabit seasonal environments, overlooking seasonal differences in this covariation may obscure the mechanisms that buffer or amplify population r...

Predicting how species will be affected by future climatic change requires the underlying environmental drivers to be identified. As vital rates vary over the lifecycle, structured population models derived from statistical environment‐demography relationships are often used to inform such predictions. Environmental drivers are typically identified...

BACKGROUND It is important to map agricultural weed populations to improve management and maintain future food security. Advances in data collection and statistical methodology have created new opportunities to aid in the mapping of weed populations. We set out to apply these new methodologies (unmanned aerial systems; UAS) and statistical techniqu...

The evolution of resistance to herbicides is a striking example of rapid, human‐directed adaptation with major consequences for food production. Most studies of herbicide resistance are performed reactively and focus on post hoc determination of resistance mechanisms following the evolution of field resistance. If the evolution of resistance can be...

Maintaining sustainable populations in captivity without supplementation through wild-capture is a major challenge in conservation that zoos and aquaria are working towards. However, the capture of wild animals continues for many purposes where conservation is not the primary focus. Wild-capture hinders long-term conservation goals by reducing rema...

Populations are formed of their constituent interacting individuals, each with their own respective within‐host biological processes. Infection not only spreads within the host organism but also spreads between individuals. Here we propose and study a multilevel model which links the within‐host statuses of immunity and parasite density to populati...

Temporal variation in environmental conditions affects population growth directly via its impact on vital rates, and indirectly through induced variation in demographic structure and phenotypic trait distributions. We currently know very little about how these processes jointly mediate population responses to their environment. To address this gap,...

Data S1. Materials and methods. Table S1. The 124 pre‐submitted research questions that address fundamental and applied issues in weed ecology, evolution and management

Temporal variability in the environment drives variation in vital rates, with consequences for population dynamics and life‐history evolution. Integral projection models ( IPM s) are data‐driven structured population models widely used to study population dynamics and life‐history evolution in temporally variable environments. However, many dataset...

Restricting application rates is an attractive way for funders to reduce time and money wasted evaluating uncompetitive applications. However, mathematical models show that this could induce chaotic cycles in total application numbers, increasing uncertainty in the funding process. One emergent property is that smaller institutions spend disproport...

Few facets of biology vary more than functional traits and life‐history traits. To explore this vast variation, functional ecologists and population ecologists have developed independent approaches that identify the mechanisms behind and consequences of trait variation. Collaborative research between researchers using trait‐based and demographic ap...

Accurate information on the growth rates of fish is crucial for fisheries stock assessment and management. Empirical life history parameters (von Bertalanffy growth) are widely fitted to cross-sectional size-at-age data sampled from fish populations. This method often assumes that environmental factors affecting growth remain constant over time. Th...

Four linear mixed effects models, each with a differing temperature variable. (DOCX)

Dissolved oxygen concentrations and surface water temperatures of the four major coastal lagoons in the Gulf of Lions; Salses-Leucate (Salses), Bages-Sigean (Bages), Thau and Mauguio, for the years 2002–2012. (TIFF)

Linear relationship between the logged total fish weight (g) and the logged age (in months) in Sparus aurata. The linear model was calculated to be log(weight) = 1.18 + 1.32*(log(age)), where weight in measured in grams and age in months. Otolith radius refers to the dorsal axis radius measure of the otolith (Z4 in Fig 3). R2 = 0.78, p < 0.001. (TI...

Weedy plants pose a major threat to food security, biodiversity, ecosystem services and consequently to human health and wellbeing. However, many currently used weed management approaches are increasingly unsustainable. To address this knowledge and practice gap, in June 2014, 35 weed and invasion ecologists, weed scientists, evolutionary biologist...

Repeated use of xenobiotic chemicals has selected for the rapid evolution of resistance threatening health and food security at a global scale. Strategies for preventing the evolution of resistance include cycling and mixtures of chemicals and diversification of management. We currently lack large-scale studies that evaluate the efficacy of these d...