Preprints

Filtering by Subject: Research Methods in Life Sciences

Quantifying clearance rates of restored shellfish reefs using modular baskets

Maja Paulina Andersson, Karen L Cheney, Robbie Porter, et al.

Published: 2023-12-08
Subjects: Animal Experimentation and Research, Aquaculture and Fisheries Life Sciences, Biology, Ecology and Evolutionary Biology, Environmental Indicators and Impact Assessment, Environmental Monitoring, Environmental Sciences, Life Sciences, Marine Biology, Oceanography and Atmospheric Sciences and Meteorology, Research Methods in Life Sciences, Terrestrial and Aquatic Ecology, Water Resource Management, Zoology

Shellfish reefs are one of the most degraded marine ecosystems, prompting substantial efforts to restore them. While biodiversity gains of restored reefs are well documented, other ecosystem services such as water filtration remain overlooked. We tested whether modular baskets could provide a practical way to measure water filtration by invertebrate communities on restored reefs and assess [...]

Covariance reaction norms: A flexible approach to estimating continuous environmental effects on quantitative genetic and phenotypic (co)variances

Jordan Scott Martin

Published: 2023-11-21
Subjects: Behavior and Ethology, Biology, Ecology and Evolutionary Biology, Evolution, Genetics, Integrative Biology, Life Sciences, Population Biology, Research Methods in Life Sciences, Zoology

Estimating quantitative genetic and phenotypic (co)variances plays a crucial role in investigating key evolutionary ecological phenomena, such as developmental integration, life history tradeoffs, and niche specialization, as well as in describing selection and predicting multivariate evolution in the wild. While most studies assume (co)variances are fixed over short timescales, environmental [...]

Same data, different analysts: variation in effect sizes due to analytical decisions in ecology and evolutionary biology

Elliot Gould, Hannah S. Fraser, Timothy H Parker, et al.

Published: 2023-10-04
Subjects: Ecology and Evolutionary Biology, Life Sciences, Research Methods in Life Sciences

Although variation in effect sizes and predicted values among studies of similar phenomena is inevitable, such variation far exceeds what might be produced by sampling error alone. One possible explanation for variation among results is differences among researchers in the decisions they make regarding statistical analyses. A growing array of studies has explored this analytical variability in [...]

Growth and opportunities for drone surveillance in pinniped research

Gregory D Larsen, David W. Johnston

Published: 2023-09-03
Subjects: Ecology and Evolutionary Biology, Integrative Biology, Marine Biology, Other Ecology and Evolutionary Biology, Population Biology, Research Methods in Life Sciences, Zoology

Pinniped species undergo uniquely amphibious life histories that make them valuable subjects for many domains of research. Pinniped research has often progressed hand-in-hand with technological frontiers of wildlife biology, and drones represent a leap forward for methods of aerial remote sensing, heralding data collection and integration at new scales of biological importance. Drone methods and [...]

Paws for thought: Impacts of animal husbandry on tundra greening in High Arctic Svalbard

Elise Gallois, Logan Berner, Kristine Bakke Westergaard, et al.

Published: 2023-08-07
Subjects: Animal Sciences, Ecology and Evolutionary Biology, Plant Sciences, Research Methods in Life Sciences

Dog sledding in High Arctic Svalbard is a key tourist attraction, and the keeping of animals and livestock has historically been in practice in the settlements of the archipelago. The resulting waste disposal practices - particularly those involving the disposal of animal faeces and fodder - hugely enrich soils with excess nutrients. Here, we explore how animal husbandry affected changes in [...]

Application of crime theory in urban ecology, evolution and planning: factors influencing the disappearance of field equipment

Ignacy Stadnicki, Marta Szulkin, Michela Corsini

Published: 2023-07-15
Subjects: Ecology and Evolutionary Biology, Other Social and Behavioral Sciences, Research Methods in Life Sciences, Urban Studies and Planning

1. Research in urban ecology and evolution relies on the use of deployable scientific equipment. If left unattended in the field, it may be prone to vandalism and theft, especially in the urban space. We empirically applied crime theory, specifically the Routine Activity Theory (RAT), to predict disappearance rates of scientific equipment in an on-going urban ecology research project. 2. [...]

Developing systems theory in soil agroecology: Incorporating heterogeneity and dynamic instability

Nicholas Medina, John Vandermeer

Published: 2023-03-21
Subjects: Agriculture, Applied Mathematics, Biogeochemistry, Biology, Dynamic Systems, Earth Sciences, Ecology and Evolutionary Biology, Life Sciences, Longitudinal Data Analysis and Time Series, Research Methods in Life Sciences, Soil Science, Sustainability

Ecosystem management is integral to the future of soils, yet anthropogenic drivers represent a key source of uncertainty in ecosystem models. First- and new-generation soil models formulate many soil pools using first-order decomposition, which tends to generate simpler yet numerous parameters. Systems or complexity theory, developed across various scientific and social fields, may help improve [...]

ForageFeeder: a low-cost open source feeder for randomly distributing food

Maggie Zhang, Andrew Kyle Schulz, Josh Meyerchick, et al.

Published: 2022-12-31
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

Edward Richard Ivimey-Cook, Daniel W.A. Noble, Shinichi Nakagawa, et al.

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

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

Published: 2022-08-11
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: 2022-08-06
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: 2022-04-22
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: 2022-04-08
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 [...]

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