Preprints

Filtering by Subject: Ecology and Evolutionary Biology

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 [...]

Social niche shapes social behavior and cortisol concentrations during adolescence in female guinea pigs

Taylor Lynne Rystrom, S. Helene Richter, Norbert Sachser, et al.

Published: 2022-07-15
Subjects: Behavior and Ethology, Biology, Ecology and Evolutionary Biology, Life Sciences

Individualized social niches arise in social groups and are associated with behavior and hormone (e.g. cortisol) concentrations. During sensitive life phases, social interactions can have a profound impact on the development of social behavior. Focusing on adolescence, we aimed to investigate the relationship between the social niche, social behavior, and cortisol concentrations (baseline and [...]

The role of genomics in the future of ESA decision-making

Brenna Forester, Tanya Lama

Published: 2022-07-14
Subjects: Biodiversity, Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences

The U.S. Endangered Species Act (ESA) provides a framework for the protection and recovery of threatened and endangered species and their habitats in the face of anthropogenic threats. Genetic information has played a role in decision-making under the ESA for decades, most commonly informing taxonomy and the designation of distinct population segments, though detection of inbreeding also played [...]

Jointly Modeling the Evolution of Discrete and Continuous Traits

James Boyko, Brian O'Meara, Jeremy Beaulieu

Published: 2022-07-13
Subjects: Ecology and Evolutionary Biology, Evolution, Life Sciences

Whether modeling the evolution of a discrete or continuous character, the focal trait of interest does not evolve in isolation and require comparative methods that model multivariate evolution. Progress along these lines has involved modeling multivariate evolution of the same class of character and there are fewer options when jointly modeling traits when one character is discrete and the other [...]

The brain’s bootstrapping problem and its consequences: Parental provisioning and variation in vertebrate brain sizes

Carel P. van Schaik, Zitan Song, Carolline Schuppli, et al.

Published: 2022-07-05
Subjects: Ecology and Evolutionary Biology, Evolution, Life Sciences

Our understanding of the considerable variation in vertebrate brain size remains incomplete. Large brains are adaptive but brains require unusually high, near-constant energy inputs, and are prioritized energy targets. This trade-off also has understudied developmental consequences: immatures must develop a fully functional brain without already having one. We here propose that energy subsidies [...]

Herodotools: An R package to integrate macroevolution, community ecology, and biogeography

Gabriel Nakamura, Arthur Vinícius Rodrigues, André Luíz Luza, et al.

Published: 2022-07-05
Subjects: Ecology and Evolutionary Biology, Evolution, Life Sciences, Other Ecology and Evolutionary Biology

Aim: Historical processes like speciation, extinction, and historical dispersal are the ultimate factors generating and maintaining biodiversity in space and time. While detecting the effect of those processes on the distribution of biodiversity has great relevance by itself, how to measure them is critical to interpreting the underlying causes of biological patterns. However, metrics of [...]

Methodological inconsistencies define thermal bottlenecks in fish life cycle: a comment on Dahlke et al. 2020

Patrice Pottier, Samantha Burke, Szymon Marian Drobniak, et al.

Published: 2022-07-03
Subjects: Ecology and Evolutionary Biology, Life Sciences, Terrestrial and Aquatic Ecology

Comparative analyses require researchers to not only ensure data quality, but also to make prudent and justifiable assumptions about data comparability. A failure to do so can lead to unreliable conclusions. As a case in point, we comment on a study that estimated the vulnerability of the world’s fish species to climate change using comparison between life stages (Dahlke et al. 2020, Science 369: [...]

When bacteria are phage playgrounds: interactions between viruses, cells and mobile genetic elements

Eugen Pfeifer, Jorge Moura de Sousa, Marie Touchon, et al.

Published: 2022-07-01
Subjects: Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences, Microbiology

Studies of viral adaptation have focused on the selective pressures imposed by hosts. However, there is increasing evidence that interactions between viruses, cells, and other mobile genetic elements (MGEs) are determinant to the success of infections. These interactions are often associated with antagonism and competition, but sometimes involve cooperation or parasitism. They involve mechanism [...]

The coevolutionary mosaic of bat betacoronavirus emergence risk

Norma Forero, Renata L. Muylaert, Stephanie N. Seifert, et al.

Published: 2022-07-01
Subjects: Biodiversity, Bioinformatics, Biology, Biotechnology, Cell and Developmental Biology, Ecology and Evolutionary Biology, Immunology and Infectious Disease, Life Sciences, Other Ecology and Evolutionary Biology, Other Life Sciences

Pathogen evolution is one of the least predictable components of disease emergence, particularly in nature. Here, building on principles established by the geographic mosaic theory of coevolution, we develop a quantitative, spatially-explicit framework for mapping the evolutionary risk of viral emergence. Driven by interest in diseases like SARS, MERS, and COVID-19, we examine the global [...]

PHENOTYPIC PLASTICITY MADE SIMPLE, BUT NOT TOO SIMPLE

Richard Gomulkiewicz, John R Stinchcombe

Published: 2022-06-29
Subjects: Biology, Ecology and Evolutionary Biology, Evolution, Life Sciences

Phenotypic plasticity refers to environment-dependent trait expression (Dewitt and Scheiner, 2004). Knowledge of phenotypic plasticity is important in virtually all areas of basic and applied biology. Researchers in applied fields (such as agriculture, medicine, public health, wildlife management, and conservation biology) have a vested interest in knowing how traits are or will be expressed [...]

Ecological networks of an Antarctic ecosystem: a full description of non-trophic interactions

Vanesa Salinas, Tomas Ignacio Marina, Georgina Cordone, et al.

Published: 2022-06-29
Subjects: Ecology and Evolutionary Biology, Life Sciences, Terrestrial and Aquatic Ecology

Interactions between organisms are very diverse and attend to multiple biological demands, hence understanding ecological communities requires considering different types of species interactions beyond predation. In this work, we assemble for the first time the non-trophic networks of an Antarctic ecosystem. We report mutualistic (+/+), competitive (-/-), commensalistic (+/0) and amensalistic [...]

The community-function landscape of microbial consortia

Alvaro Sanchez, Djordje Bajic, Juan Diaz-Colunga, et al.

Published: 2022-06-28
Subjects: Ecology and Evolutionary Biology, Life Sciences, Population Biology

Quantitatively and predictively linking the composition and function of microbial communities is a major aspiration of microbial ecology. It is also a critical step in the path toward engineering synthetic consortia and manipulating natural microbiomes. The functions of microbial communities are collective properties that emerge from a complex web of molecular interactions between individual [...]

A simple conceptual framework and nomenclature for studying repeated, parallel and convergent evolution

José Cerca

Published: 2022-06-28
Subjects: Ecology and Evolutionary Biology, Evolution, Life Sciences

Parallel and convergent evolution are textbook examples of the role of natural selection in evolution. However, these terms are used interchangeably, and sometimes with conflicting meanings. This has resulted in confusion, which hampers the understanding of the processes underlying these important forms of evolution. In this synthesis, I discuss the issues with current definitions of parallel, [...]

Dispersal and space use of captive-reared and wild-rehabilitated Harpy Eagles released in Central American landscapes: Implications for reintroduction and reinforcement management

Adrian Naveda-Rodriguez, Edwin Campbell-Thompson, Richard T. Watson, et al.

Published: 2022-06-23
Subjects: Ecology and Evolutionary Biology, Life Sciences, Terrestrial and Aquatic Ecology

Understanding the spatial context of animal movements is fundamental for establishment and management of protected areas (PA). However, these data are not readily available for large raptors, particularly for tropical species. We telemetry-tracked 36 captive-reared and wild-rehabilitated Harpia harpyja and estimated dispersal and space use after release in Mesoamerica. We evaluated the [...]

An operational workflow for producing periodic estimates of species occupancy at large scales

Rob James Boyd, Tom August, Robert Cooke, et al.

Published: 2022-06-23
Subjects: Biodiversity, Bioinformatics, Ecology and Evolutionary Biology, Life Sciences

Policy makers require high-level summaries of biodiversity change. However, deriving such summaries from raw biodiversity data is a complex process involving several intermediary stages. In this paper, we describe a workflow for generating annual estimates of species’ occupancy at national scales from raw species occurrence data, which can be used to construct a range of policy-relevant [...]

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