Preprints
Filtering by Subject: Biology
Inferring the seasonal dynamics and abundance of an invasive species using a spatio-temporal stacked machine learning model
Published: 2023-12-22
Subjects: Biology, Entomology, Life Sciences, Population Biology, Public Health, Virus Diseases
Various modelling techniques are available to understand the temporal and spatial variations of the phenology of species. Scientists often rely on correlative models, which establish a statistical relationship between a response variable (such as species abundance or presence-absence) and a set of predominantly abiotic covariates. The modelling approach choice, i.e. the algorithm, is a crucial [...]
Quantifying clearance rates of restored shellfish reefs using modular baskets
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 among the most degraded ecosystems globally, prompting substantial efforts to restore them. While biodiversity gains of restored reefs are well documented, other ecosystem services such as water filtration remain poorly quantified. We present a novel way of measuring water filtration by restored reefs using modular restoration structures called Robust Oyster Baskets (ROB 400). [...]
Linking biodiversity and nature’s contributions to people (NCP): a macroecological energy flux perspective
Published: 2023-12-08
Subjects: Biology, Ecology and Evolutionary Biology, Life Sciences
Linking biodiversity and the provision of nature’s contribution to people (NCP) remains a challenge. This hinders our ability to properly cope with the decline in biodiversity and the provision of NCP under global climate and land use changes. Here, we propose a framework that combines biodiversity models with food web energy flux approaches to evaluate and map NCP at large spatio-temporal [...]
The Palearctic view on a bat fungal disease
Published: 2023-12-08
Subjects: Animal Sciences, Biology, Immunology and Infectious Disease, Life Sciences, Zoology
The fungal infection causing white-nose disease in hibernating bats in North America has resulted in dramatic population declines of affected species since it was first discovered in 2007. Shortly after, it was demonstrated that the causative agent, Pseudogymnoascus destructans, is native to the Palearctic, where it also infects several bat species. However, infection in the Palearctic rarely [...]
Towards the next generation of species delimitation methods: an overview of Machine Learning applications
Published: 2023-12-07
Subjects: Biology, Computational Biology, Ecology and Evolutionary Biology, Genetics and Genomics
Species delimitation is the process of distinguishing between populations of the same species and distinct species of a particular group of organisms. Various methods exist for inferring species limits, whether based on morphological, molecular, or other types of data. In the case of methods based on DNA sequences, most of them are rooted in the coalescent theory. However, coalescence-based [...]
Functional coherence among miRNA targets: a potential metric for assessing biological signal among target prediction methods in non-model species
Published: 2023-11-30
Subjects: Biology, Ecology and Evolutionary Biology, Life Sciences
Although miRNA regulation of protein production is a likely target of adaptive evolution, high false-positive rates in the identification of mRNAs targeted by miRNAs in non-model species’ complicates interpretation of recent advances. Here we document the challenges and then outline steps for the community to address these challenges.
Vocal Dimorphism in Anna’s Hummingbirds
Published: 2023-11-28
Subjects: Animal Sciences, Behavior and Ethology, Biology, Ecology and Evolutionary Biology, Integrative Biology, Life Sciences, Ornithology, Zoology
Whereas vocal sexual dimorphism is widespread amongst birds, it has been historically overlooked in non-passerines such as hummingbirds. By evaluating correlations among sex, behaviors, and vocalizations, the meaning and utility of intentional sound production may be inferred. Anna's Hummingbirds (Calypte anna) exhibit pronounced sexual dimorphism, with males being larger and having more vibrant [...]
Opinion: Missing half the picture, focus on stony corals during bleaching events has left critical knowledge gaps in our understanding of reef-scale bleaching and recovery
Published: 2023-11-28
Subjects: Biodiversity, Biology, Ecology and Evolutionary Biology, Life Sciences, Marine Biology, Other Ecology and Evolutionary Biology
Covariance reaction norms: A flexible method for estimating complex environmental effects on trait (co)variances
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 is crucial for investigating evolutionary ecological phenomena such as developmental integration, life history tradeoffs, and niche specialization, as well as for describing selection and predicting multivariate evolution in the wild. While most studies assume (co)variances are fixed over short timescales, environmental heterogeneity [...]
The sugar kelp Saccharina latissima II: Recent Advances in farming and applications
Published: 2023-11-20
Subjects: Biology, Life Sciences
The sugar kelp Saccharina latissima has received intense scientific attention over the last decades. In recent years, interest in cultivation of the species has strongly increased in the North Atlantic Ocean and the Eastern Pacific Ocean, driven by the great potential of S. latissima to be utilised for various industrial applications, including food, feed, and biomaterials. Accordingly, current [...]
Impacts of necrotising disease on the Endangered cauliflower soft coral Dendronephthya australis
Published: 2023-11-20
Subjects: Biology, Life Sciences
Context: Diseases have impacted coral populations worldwide, leading to population declines and requiring active restoration efforts. Aims: Describe population and individual impacts of necrotising disease in the Endangered octocoral Dendronephthya australis. Methods: We quantified population loss and recruitment using reference photos, survey, and GPS mapping and described disease lesions [...]
Automated tracking of avian parental care behavior
Published: 2023-11-16
Subjects: Behavior and Ethology, Biology, Life Sciences
1. Parental care may be an important source of phenotypic variation for ecological and evolutionary processes. However, it can be difficult to collect and interpret data on parental care behaviors. To address these challenges, we developed a new hardware and software platform for automated behavioral tracking called ABISSMAL (Automated Behavioral Tracking by Integrating Sensors that Survey [...]
Polyploid plants take cytonuclear perturbations in stride
Published: 2023-11-13
Subjects: Biology, Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences, Plant Biology
Hybridization in plants is often accompanied by nuclear genome doubling (allopolyploidy), which has been hypothesized to perturb interactions between nuclear and cytoplasmic (mitochondrial and plastid) genomes by creating imbalances in the relative copy number of these genomes and producing genetic incompatibilities between maternally derived cytoplasmic genomes and the half of the allopolyploid [...]
Maternal investment and early thermal conditions affect performance and antipredator responses
Published: 2023-10-27
Subjects: Behavior and Ethology, Biology, Evolution, Other Ecology and Evolutionary Biology
Exposure to increased temperatures during early development can lead to phenotypic plasticity in morphology, physiology, and behaviour across a range of ectothermic animals. In addition, maternal effects are known to be important contributors to phenotypic variation in offspring. Whether the two factors interact to shape offspring morphology and behaviour has been barely explored. This is [...]
Applications of Machine Learning in Phylogenetics
Published: 2023-10-15
Subjects: Biology, Life Sciences
Machine learning has increasingly been applied to a wide range of questions in phylogenetic inference. Supervised machine learning approaches that rely on simulated training data have been used to infer tree topologies and branch lengths, to select substitution models, and to perform downstream inferences of introgression and diversification. Here, we review how researchers have used several [...]