Preprints

Filtering by Subject: Research Methods in Life Sciences

Repeatability of performance within and across contexts measuring behavioral flexibility

Kelsey McCune, Aaron Blaisdell, Zoe Johnson-Ulrich, et al.

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

Catherine A. Lippi, Samuel SC Rund, Sadie Jane Ryan

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

Matthias Grenié, Hugo Gruson

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

Chloé Rebecca Nater, Malcolm D. Burgess, Peter Coffey, et al.

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

Tiago R. Simões, Oksana V. Vernygora, Bruno A.S. de Medeiros, et al.

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)

Hamza Anwer, Dominic Mason, Susanne Zajitschek, et al.

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

Hamza Anwer, Rose E O'Dea, Dominic Mason, et al.

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

Irene Di Lecce, Joanna Sudyka, David F. Westneat, et al.

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

Derek Jon Nies Young, Michael J Koontz, Jonah Weeks

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

Cédric Sueur, Martin Quque, Alexandre Naud, et al.

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

Yong Zhi Foo, Rose E O'Dea, Julia Koricheva, et al.

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

Rachel Renne, Daniel Schlaepfer, Kyle Palmquist, et al.

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

Hamza Anwer, Dominic Mason, Susanne Zajitschek, et al.

Published: 2020-11-18
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 [...]

Workflow for constructing social networks from automated telemetry systems

Daizaburo Shizuka, Sahas Barve, Allison E. Johnson, et al.

Published: 2020-11-02
Subjects: Animal Experimentation and Research, Behavior and Ethology, Ecology and Evolutionary Biology, Life Sciences, Research Methods in Life Sciences

1. Advances in datalogging technologies have provided a way to monitor the movement of individual animals at unprecedented spatial and temporal scales, both large and small. When used in conjunction with social network analyses, these data can provide insight into fine scale associative behaviors. The variety of technologies demand continuous progress in workflows to translate data streams from [...]

Participatory mapping of aquatic invasive species: a demonstration in a coastal lagoon

Jacopo Cerri, Ernesto Azzurro

Published: 2020-10-15
Subjects: Biodiversity, Life Sciences, Marine Biology, Other Life Sciences, Research Methods in Life Sciences

Aquatic Invasive species (AIS) are a growing driver of change across marine and freshwater ecosystems but spatially-explicit information is seldom available for supporting management actions and decision making. Here we conceived and tested a new participatory method to map the distribution of three invasive species (Callinectes sapidus, Procambarus clarkii and Oreochromis niloticus) in the [...]

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