Preprints
There are 2712 Preprints listed.
The promise of environmental RNA research beyond mRNA
Published: 2025-05-07
Subjects: Biology, Ecology and Evolutionary Biology, Life Sciences
Environmental RNA (eRNA) studies have primarily focused on species detection and community composition through metabarcoding or metatranscriptomics, and on gene expression through messenger RNA (mRNA) abundance analysis. While valuable, this focus overlooks the broader functional roles of other RNA types in cellular metabolism. Beyond mRNA, non-coding RNAs as well as structural RNAs play critical [...]
Unifying occupancy-detection and local frequency scaling (Frescalo) models
Published: 2025-05-07
Subjects: Life Sciences
Frescalo’s “local frequency scaling” and classical occupancy-detection models both seek to recover true species‐occurrence signals from imperfect data. In this paper, we show that the two approaches rest on the same underlying detection mathematics. Occupancy models treat each site’s repeat visits as independent detection trials and separately estimate occupancy probability and per-visit [...]
Removing dead coral after marine heatwaves can mitigate coral-algae competition and increase viable coral recruitment
Published: 2025-05-07
Subjects: Ecology and Evolutionary Biology, Marine Biology
Ecological disturbance regimes are shifting and leaving behind novel legacies, like the remnant structures of dead foundation species, which have poorly known impacts on ecosystem resilience. We explored how dead coral skeletons produced by marine heatwaves–material legacies of increasingly common disturbances on coral reefs–influence spatial competition between corals and macroalgae, focusing on [...]
Inter-specific relationships and their ecological role in an oceanic elasmobranch community
Published: 2025-05-07
Subjects: Life Sciences
Marine ecosystems support a diverse array of co-occurring species, whose presence and abundance influence the behavior, population dynamics, and distribution of interacting organisms. Elasmobranchs play a central role in marine ecological processes as top and meso-predators across various ecosystems. Previous work has shown that some elasmobranchs are key to ecosystem health and resilience, [...]
Biodiversity science is improved when silent herbaria speak
Published: 2025-05-07
Subjects: Life Sciences
Herbaria represent a global biodiversity heritage essential for botanical research and conservation assessments. Despite their importance, herbaria in many parts of the world—especially in under-resourced regions such as much of Africa—are “silent”. These silent collections are poorly integrated into global research networks and hence underused and especially vulnerable to neglect. Here, we [...]
Predicting high pathogenicity avian influenza H5N1 susceptibility in wild birds
Published: 2025-05-06
Subjects: Ecology and Evolutionary Biology, Immunology and Infectious Disease
High pathogenicity avian influenza (HPAI) has caused widespread sickness and mortality in wildlife, especially since the emergence of a novel H5 virus belonging to clade 2.3.4.4b in 2021. The ongoing panzootic caused by this lineage has infected an unprecedented diversity of species across the globe, seeming capable of impacting all birds. Here, we analyse ecological and phylogenetic patterns in [...]
IQ2MC: A New Framework to Infer Phylogenetic Time Trees Using IQ-TREE 3 and MCMCTree with Mixture Models
Published: 2025-05-05
Subjects: Bioinformatics, Computational Biology, Ecology and Evolutionary Biology, Evolution, Genetics, Genetics and Genomics, Genomics, Life Sciences
IQ-TREE and MCMCTree are two widely used phylogenetic tools to infer phylogenetic trees and estimate divergence times, respectively. As MCMCTree performs fast approximate Markov Chain Monte Carlo sampling to obtain the times along a fixed tree topology, it would be natural to use IQ-TREE to obtain the tree. However, it is currently not possible to integrate these tools seamlessly, as MCMCTree [...]
Evolutionary rate incongruences in squamates reveal contrasting patterns of evolutionary novelties and innovation
Published: 2025-05-05
Subjects: Ecology and Evolutionary Biology, Evolution, Life Sciences
Understanding the rate of phenotypic evolution can reveal fundamental aspects of organismal evolutionary trajectories. Hence, several studies have attempted to detect the tempo of evolution for multiple organisms, although based on radically different datatypes (e.g., discrete and morphometric) and methods (phylodynamic vs comparative methods). Here, we ask whether these competing approaches [...]
Responses of wintering corvids to New Year’s Eve fireworks in Berlin
Published: 2025-05-05
Subjects: Life Sciences
Animals around the globe are strongly affected by anthropogenic disturbances, creating concerns for welfare and conservation. Fireworks during New Year’s eve are a major, regularly recurring anthropogenic disturbance, causing light, noise as well as air pollution. In the present study, we investigated behavioural responses of mixed-species flocks of corvids (hooded crows, Corvus cornix, rooks, [...]
A practical framework for identifying genetic subpopulations and ESUs: insights for IUCN assessments and broader management
Published: 2025-05-05
Subjects: Biodiversity, Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences
Species conservation assessments, such as the International Union for Conservation of Nature (IUCN) Red List and Green Status of Species, guide global conservation priorities by evaluating species’ extinction risk and recovery status. Although such frameworks provide scope to include genetic information, this aspect of biodiversity, which is critical for species’ fitness and adaptive [...]
Genetic load in Evolutionarily Significant Units (ESUs): conservation and management implications
Published: 2025-05-05
Subjects: Biodiversity, Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences
The Conservation Genetics Specialist Group of the International Union for Conservation of Nature (IUCN) proposes introducing Evolutionarily Significant Units (ESUs) as an additional new assessment unit in the IUCN Red List and Green Status. This proposal is made because ESUs possess unique evolutionary trajectories present within species and harbour genetic diversity that requires safeguarding. [...]
Using large language models to address the bottleneck of georeferencing natural history collections
Published: 2025-05-02
Subjects: Biodiversity, Ecology and Evolutionary Biology
Natural history collections are fundamental for biodiversity research. The broad use of them relies on the digitization effort, especially georeferencing that translates textual locality descriptions into geographic coordinates. However, traditional georeferencing approaches are labor-intensive and costly, thus georeferencing is a major bottleneck in the digitization process that prevents the [...]
The bright, the bold and the toxic: do coloration, personality, and toxicity represent an integrated phenotype in fire salamanders?
Published: 2025-05-02
Subjects: Ecology and Evolutionary Biology
Defensive coloration such as bright colors used to advertise secondary defenses (i.e., aposematic coloration) is very common but also shows high intraspecific variation. Similarly, consistent among-individual differences in behavior (i.e., animal personality) are pervasive in the animal kingdom. Therefore, aposematism and personality could be linked to produce an optimal defensive phenotype, [...]
Acclimation to fluctuating hypoxia alters activity and escape performance, but not metabolism, in guppies
Published: 2025-05-02
Subjects: Behavior and Ethology, Life Sciences, Terrestrial and Aquatic Ecology, Zoology
Organisms living in fluctuating environments must cope with constantly changing conditions. Here we investigated how acclimation to either fluctuating or constant oxygen affects behavioural and physiological responses to hypoxia in guppies (Poecilia reticulata). Guppies were acclimated to either fluctuating hypoxia (100% of air saturation during day to 40% at night) or constant normoxia (100% of [...]
“A history of the world imperfectly kept”: Will we ever know how biodiversity has changed over deep time?
Published: 2025-05-02
Subjects: Biodiversity, Evolution, Paleobiology
The fossil record is our only direct source of evidence for how life on Earth has waxed and waned over its long history. However, the fossil record is also incomplete and biased in many ways, after passing through biological, geological, and socio-economic filters. This means that we only possess snapshots of information, relating to specific places and times in Earth history, from which to try [...]