Preprints
Filtering by Subject: Bioinformatics
An operational workflow for producing periodic estimates of species occupancy at large scales
Published: 2022-06-24
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 [...]
A minimum data standard for vector competence experiments
Published: 2022-06-14
Subjects: Bioinformatics, Entomology, Life Sciences, Microbiology, Virology
The growing threat of vector-borne diseases, highlighted by recent epidemics, has prompted increased focus on the fundamental biology of vector-virus interactions. To this end, experiments are often the most reliable way to measure vector competence (the potential for arthropod vectors to transmit certain pathogens). Data from these experiments are critical to understand outbreak risk, but – [...]
EvoPhylo: an R package for pre- and postprocessing of morphological data from relaxed clock Bayesian phylogenetics
Published: 2022-06-06
Subjects: Bioinformatics, Ecology and Evolutionary Biology, Evolution, Life Sciences
1. Relaxed clock Bayesian evolutionary inference (BEI) enables the co-estimation of phylogenetic trees and evolutionary parameters associated with models of character and lineage evolution. Fast advances in new model developments over the past decade have boosted BEI as a major macroevolutionary analytical framework using morphological and/or molecular data across vastly different study systems. [...]
Evolution and impact of socially transferred materials
Published: 2022-05-27
Subjects: Animal Sciences, Biodiversity, Bioinformatics, Cell and Developmental Biology, Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences, Physiology, Systems Biology
Since the dawn of life, transfers of metabolized material between individuals have led to great innovations of evolution. When metabolized material is transferred from one individual’s body to another (as with sperm, eggs, milk, symbionts), secondary manipulative molecules that induce a physiological response in the receiver are often transferred along with the primary cargo. The bioactive and [...]
Towards a cohesive understanding of ecological complexity
Published: 2022-04-15
Subjects: Bioinformatics, Biology, Ecology and Evolutionary Biology, Life Sciences, Systems Biology
Understanding phenomena typical of complex systems is key for progress in ecology and conservation amidst escalating global environmental change. However, myriad definitions of complexity hamper conceptual advancements and synthesis. Ecological complexity may be better understood by following the strong theoretical basis of complexity science. We conduct bibliometric and text-mining analyses to [...]
Handling Character Dependency in Phylogenetic Inference: Extensive Performance Testing of Assumptions and Solutions Using Simulated Data
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 [...]
Past and future uses of text mining in ecology & evolution
Published: 2022-02-16
Subjects: Biodiversity, Bioinformatics, Ecology and Evolutionary Biology, Life Sciences
Ecology and evolutionary biology, like other scientific fields, are experiencing an exponential growth of academic manuscripts. As domain knowledge accumulates, scientists will need new computational approaches for identifying relevant literature to read and include in formal literature reviews and meta-analyses. Importantly, these approaches can also facilitate automated, large-scale data [...]
101 years of biofluorescent animal studies: trends in literature, novel hypotheses, and best practices moving forward
Published: 2022-02-06
Subjects: Animal Sciences, Bioinformatics, Life Sciences
Biofluorescent animals have become a recent trend in natural history publishing. While the functions and origins of biofluorescence in fauna remains somewhat controversial, trends in biofluorescence throughout published literature may elucidate these concepts. Here we review 101 years of biofluorescent studies encompassing 108 published papers and 977 unique species records. Our results provide [...]
Inferring trends in pollinator distributions across the Neotropics from publicly available data remains challenging despite mobilisation efforts
Published: 2022-01-24
Subjects: Bioinformatics, Ecology and Evolutionary Biology, Life Sciences, Other Ecology and Evolutionary Biology
Aim: Aggregated species occurrence data are increasingly accessible through public databases for the analysis of temporal trends in species’ distributions. However, biases in these data present challenges for robust statistical inference. We assessed potential biases in data available through GBIF on the occurrences of four flower-visiting taxa: bees (Anthophila), hoverflies (Syrphidae), [...]
The macroevolutionary consequences of niche construction in microbial metabolism
Published: 2021-05-31
Subjects: Bioinformatics, Computational Biology, Ecology and Evolutionary Biology, Environmental Microbiology and Microbial Ecology Life Sciences, Evolution, Genetics and Genomics, Life Sciences, Microbiology, Population Biology, Systems Biology
Microorganisms display a stunning metabolic diversity. Understanding the origin of this diversity requires understanding how macroevolutionary processes such as innovation and diversification play out in the microbial world. Metabolic networks, which govern microbial resource use, can evolve through different mechanisms, e.g. horizontal gene transfer or de novo evolution of enzymes and pathways. [...]
met v1: Expanding on old estimations of biodiversityfrom eDNA with a new software framework
Published: 2021-04-27
Subjects: Bioinformatics, Computational Biology, Genetics and Genomics, Life Sciences
A long-standing problem in environmental DNA has been the inability to compute across large number of datasets. Here we introduce an open-source software framework that can store a large number of environmental DNA datasets, as well as provide a platform for analysis, in an easily customizable way. We show the utility of such an approach by analyzing over 1400 arthropod metabarcode datasets. This [...]
Phyloreferences: Tree-Native, Reproducible, and Machine-Interpretable Taxon Concepts
Published: 2021-03-06
Subjects: Biodiversity, Bioinformatics, Computer Sciences, Databases and Information Systems, Ecology and Evolutionary Biology, Engineering, Life Sciences, Other Ecology and Evolutionary Biology, Physical Sciences and Mathematics, Software Engineering
Evolutionary and organismal biology have become inundated with data. At the same rate, we are experiencing a surge in broader evolutionary and ecological syntheses for which tree-thinking is the staple for a variety of post-tree analyses. To fully take advantage of this wealth of data to discover and understand large-scale evolutionary and ecological patterns, computational data integration, i.e. [...]
Mobilising molluscan models and genomes in biology
Published: 2020-11-24
Subjects: Biodiversity, Bioinformatics, Biology, Ecology and Evolutionary Biology, Genetics and Genomics, Laboratory and Basic Science Research Life Sciences, Life Sciences
Molluscs are amongst the most ancient, diverse, and important of all animal taxa. Even so, no individual mollusc species has emerged as a broadly applied model system in biology. We here make the case that both perceptual and methodological barriers have played a role in the relative neglect of molluscs as research organisms. We then summarize the current application and potential of molluscs and [...]
Diversity and structure of arbuscular mycorrhizal fungal commmunities and their chemical drivers across dryland habitats in Qatar
Published: 2020-11-22
Subjects: Biodiversity, Bioinformatics, Biotechnology, Desert Ecology, Ecology and Evolutionary Biology, Life Sciences
Qatar is largely characterized by a hyper-arid climate and low soil fertility, which combine to create a stressful soil environment for arbuscular mycorrhizal (AM) fungi. Here we present a study on AM fungi communities and their relationship to soil chemical characteristics. We used high-throughput seqeuncing technique for identifying AM fungal diversity and community composition from different [...]
Removing the bad apples: a simple bioinformatic method to improve loci-recovery in de novo RADseq data for non-model organisms
Published: 2020-08-31
Subjects: Bioinformatics, Computational Biology, Genetics and Genomics, Genomics, Life Sciences
The restriction site-associated DNA (RADseq) family of protocols involves digesting DNA and sequencing the region flanking the cut site, thus providing a cost and time efficient way for obtaining thousands of genomic markers. However, when working with non-model taxa with few genomic resources, optimization of RADseq wet-lab and bioinformatic tools may be challenging, often resulting in allele [...]