Preprints
Filtering by Subject: Research Methods in Life Sciences
ForageFeeder: a low-cost open source feeder for randomly distributing food
Published: 2022-12-30
Subjects: Animal Experimentation and Research, Life Sciences, Research Methods in Life Sciences
Automated feeders have long fed mice, livestock, and poultry, but are incapable of feeding zoo animals such as gorillas. Gorilla food, consisting of cut vegetables and fruits, is too large to be dispensed by automated feeders. Instead gorillas are manually at a set time and location, which decreases the exercise and enrichment that accompanies their natural foraging. We designed and built [...]
A framework for improving the reproducibility of data extraction for meta-analysis
Published: 2022-12-14
Subjects: Ecology and Evolutionary Biology, Life Sciences, Psychology, Research Methods in Life Sciences
Extracting data from studies is the norm in meta-analyses, enabling researchers to generate effect sizes when raw data are otherwise not available. While there has been a general push for increased reproducibility in meta-analysis, the transparency and reproducibility of the data extraction phase is still lagging behind. Unfortunately, there is little guidance of how to make this process more [...]
Repeatability of performance within and across contexts measuring behavioral flexibility
Published: 2022-08-10
Subjects: Animal Experimentation and Research, Behavior and Ethology, Ecology and Evolutionary Biology, Life Sciences, Research Methods in Life Sciences
Research into animal cognitive abilities is increasing quickly and often uses methods where behavioral performance on a task is assumed to represent variation in the underlying cognitive trait. However, because these methods rely on behavioral responses as a proxy for cognitive ability, it is important to validate that the task structure does, in fact, target the cognitive trait of interest [...]
Characterizing the Vector Data Ecosystem
Published: 2022-08-05
Subjects: Entomology, Life Sciences, Research Methods in Life Sciences
A growing body of information on vector-borne diseases has arisen as increasing research focus has been directed towards the need for anticipating risk, optimizing surveillance, and understanding the fundamental biology of vector-borne diseases to direct efforts to control and mitigation. The scope and scale of this information, in the form of data, comprising database efforts, data storage, and [...]
fundiversity: a modular R package to compute functional diversity indices
Published: 2022-07-18
Subjects: Biodiversity, Ecology and Evolutionary Biology, Life Sciences, Other Ecology and Evolutionary Biology, Research Methods in Life Sciences
1. Functional diversity is widely used and widespread. However, the main package used to compute functional diversity indices FD is not flexible and not adapted to the volume of data used in modern ecological analyses. 2. We here present fundiversity, an R package that eases the computation of classical functional diversity indices. It leverages parallelization and memoization (caching results [...]
Multi-population analysis reveals spatial consistency in drivers of population dynamics of a declining migratory bird
Published: 2022-04-21
Subjects: Biodiversity, Biology, Biostatistics, Ecology and Evolutionary Biology, Life Sciences, Longitudinal Data Analysis and Time Series, Physical Sciences and Mathematics, Population Biology, Research Methods in Life Sciences, Statistical Methodology, Statistical Models, Statistics and Probability, Survival Analysis, Terrestrial and Aquatic Ecology
Many migratory species are in decline across their geographical ranges. Single-population studies can provide important insights into drivers at a local scale, but effective conservation requires multi-population perspectives. This is challenging because relevant data are often hard to consolidate, and state-of-the-art analytical tools are typically tailored to specific datasets. We capitalized [...]
Handling Character Dependency in Phylogenetic Inference: Extensive Performance Testing of Assumptions and Solutions Using Simulated Data
Published: 2022-04-07
Subjects: Animal Sciences, Bioinformatics, Ecology and Evolutionary Biology, Evolution, Life Sciences, Research Methods in Life Sciences
Character dependency is a major conceptual and methodological problem in phylogenetic inference of morphological datasets, as it violates the assumption of characters independency that is common to all phylogenetic methods. It is more frequently observed in higher-level phylogenies or in datasets characterizing major evolutionary transitions, as these represent parts of the tree of life where [...]
Intergenerational effects of overfeeding on aversive learning in zebrafish (Danio rerio)
Published: 2022-02-07
Subjects: Animal Experimentation and Research, Behavior and Ethology, Ecology and Evolutionary Biology, Life Sciences, Research Methods in Life Sciences
The obesity epidemic is among the most serious and rapidly growing public health challenges of the 21st century. This rapid increase is concerning as obesity appears to negatively impact cognition and behaviour. Furthermore, some studies suggest that this negative effect could be carried across generations from both mothers and fathers although evidence is not consistent. Here, we attempt to [...]
The effects of an obesogenic diet on behaviour and cognition in zebrafish (Danio rerio): traits average, variability, repeatability, and behavioural syndromes
Published: 2022-02-07
Subjects: Animal Experimentation and Research, Behavior and Ethology, Ecology and Evolutionary Biology, Life Sciences, Research Methods in Life Sciences
The obesity epidemic, largely driven by the accessibility of ultra-processed high-energy foods, is one of the most pressing public health challenges of the 21st century. Consequently, there is increasing concern about the impacts of diet-induced obesity on behaviour and cognition. While research on this matter continues, to date, no study has explicitly investigated the effect of obesogenic diet [...]
Preserving avian blood and DNA sampled in the wild: a survey of personal experiences
Published: 2021-12-21
Subjects: Ecology and Evolutionary Biology, Life Sciences, Research Methods in Life Sciences
Collecting and storing biological material from wild animals in a way that does not deteriorate data quality for analyses using DNA is instrumental for research in ecology and evolution. Our aims were to collect methods commonly used by researchers for the field collection and long-term storage of blood samples and DNA extracts from wild birds and gather reports on their effectiveness. Personal [...]
Optimizing aerial imagery collection and processing parameters for drone-based individual tree mapping in structurally complex conifer forests
Published: 2021-09-11
Subjects: Ecology and Evolutionary Biology, Forest Sciences, Life Sciences, Research Methods in Life Sciences, Terrestrial and Aquatic Ecology
Recent advances in remotely piloted aerial systems (“drones”) and imagery processing enable individual tree mapping in forests across broad areas with low-cost equipment and minimal ground-based data collection. One such method involves collecting many partially overlapping aerial photos, processing them using “structure from motion” (SfM) photogrammetry to create a digital 3D representation, and [...]
Social capital: an independent dimension of healthy ageing
Published: 2021-05-24
Subjects: Animal Sciences, Ecology and Evolutionary Biology, Evolution, Life Sciences, Medicine and Health Sciences, Other Social and Behavioral Sciences, Physiology, Public Health, Research Methods in Life Sciences, Social and Behavioral Sciences, Zoology
Resources that are embedded in social relationships, such as shared knowledge, access to food, services, social support or cooperation, are all examples of social capital. Social capital is recognized as an important age-related mediator of health in humans and of fitness-related traits in animals. A rich social capital in humans can slow senescence and reverse age-related deficits. Animals have [...]
A practical guide to question formation, systematic searching and study screening for literature reviews in ecology and evolution
Published: 2021-05-12
Subjects: Ecology and Evolutionary Biology, Life Sciences, Other Ecology and Evolutionary Biology, Research Methods in Life Sciences
1. Well-conducted systematic reviews are invaluable for synthesizing research findings. The conclusions of a review depend on how the research question was formulated, how relevant studies were found, and how studies were selected for synthesis. 2. Here, we present a practical guide for ecologists and evolutionary biologists on formulating a question for a systematic review, and finding a [...]
Estimating complex ecological variables at high resolution in heterogeneous terrain using multivariate matching algorithms
Published: 2021-04-16
Subjects: Ecology and Evolutionary Biology, Life Sciences, Multivariate Analysis, Physical Sciences and Mathematics, Research Methods in Life Sciences, Statistics and Probability
1. Simulation models are valuable tools for estimating ecosystem structure and function under various climatic and environmental conditions and disturbance regimes, and are particularly relevant for investigating the potential impacts of climate change on ecosystems. However, because computational requirements can restrict the number of feasible simulations, they are often run at coarse scales or [...]
An efficient new assay for measuring zebrafish anxiety: tall tanks that better characterize between-individual differences
Published: 2020-11-17
Subjects: Animal Experimentation and Research, Life Sciences, Research Methods in Life Sciences
Zebrafish (Danio rerio) are increasingly being used to model anxiety. A common behavioral assay employed for assessing anxiety-like behaviors in zebrafish is the “novel tank test”. We hypothesized that using deeper tanks in this test would result in greater between-individual variation in behavioral responses and a more ‘repeatable’ assay. After mapping the literature and identifying common [...]