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  1. Free, publicly-accessible full text available June 12, 2025
  2. Free, publicly-accessible full text available June 1, 2025
  3. Abstract

    Biological soil crusts represent a rich habitat for diverse and complex eukaryotic microbial communities. A unique but extremely common habitat is the urban sidewalk and its cracks that collect detritus. While these habitats are ubiquitous across the globe, little to no work has been conducted to characterize protists found there. Amoeboid protists are major predators of bacteria and other microbial eukaryotes in these microhabitats and therefore play a substantial ecological role. From sidewalk crack soil crusts, we have isolated three naked amoebae with finely tapered subpseudopodia, and a simple life cycle consisting of a trophic amoeba and a cyst stage. Using a holistic approach including light, electron, and fluorescence microscopy as well as phylogenetics using the ribosomal small subunit rRNA gene and phylogenomics using 230 nuclear genes, we find that these amoeboid organisms fail to match any previously described eukaryote genus. However, we determined the amoebae belong to the amoebozoan lineage Variosea based on phylogenetics. The molecular analyses place our isolates in two novel genera forming a grade at the base of the variosean group Protosteliida. These three novel varioseans among two novel genera and species are herein named “Kanabo kenzan” and “Parakanabo toge.”

     
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    Free, publicly-accessible full text available January 19, 2025
  4. Abstract

    PhyloFisher is a software package written primarily in Python3 that can be used for the creation, analysis, and visualization of phylogenomic datasets that consist of protein sequences from eukaryotic organisms. Unlike many existing phylogenomic pipelines, PhyloFisher comes with a manually curated database of 240 protein‐coding genes, a subset of a previous phylogenetic dataset sampled from 304 eukaryotic taxa. The software package can also utilize a user‐created database of eukaryotic proteins, which may be more appropriate for shallow evolutionary questions. PhyloFisher is also equipped with a set of utilities to aid in running routine analyses, such as the prediction of alternative genetic codes, removal of genes and/or taxa based on occupancy/completeness of the dataset, testing for amino acid compositional heterogeneity among sequences, removal of heterotachious and/or fast‐evolving sites, removal of fast‐evolving taxa, supermatrix creation from randomly resampled genes, and supermatrix creation from nucleotide sequences. © 2024 Wiley Periodicals LLC.

    Basic Protocol 1: Constructing a phylogenomic dataset

    Basic Protocol 2: Performing phylogenomic analyses

    Support Protocol 1: Installing PhyloFisher

    Support Protocol 2: Creating a custom phylogenomic database

     
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    Free, publicly-accessible full text available January 1, 2025
  5. Free, publicly-accessible full text available October 1, 2024
  6. Abstract Fine-resolution computer models of supercell storms generate realistic tornadic vortices. Like real tornadoes, the origins of these virtual vortices are mysterious. To diagnose the origin of a tornado, typically a near-ground material circuit is drawn around it. This circuit is then traced back in time using backward trajectories. The rate of change of the circulation around the circuit is equal to the total force circulation. This circulation theorem is used to deduce the origins of the tornado’s large vorticity. However, there is a well-known problem with this approach; with staggered grids parcel trajectories become uncertain as they dip into the layer next to the ground where horizontal wind cannot be interpolated. To circumvent this dilemma, we obtain a generalized circulation theorem that pertains to any circuit. We apply this theorem either to moving circuits that are constrained to simple surfaces or to a ‘hybrid’ circuit defined next. Let A be the horizontal surface at one grid spacing off the ground. Above A the circuit moves as a material circuit. Horizontal curve segments that move in A with the horizontal wind replace segments of the material circuit that dip below A . The circulation equation for the modified circuit includes the force circulation of the inertial force that is required to keep the curve segments horizontal. This term is easily evaluated on A . Use of planar or circular circuits facilitates explanation of some simple flows. The hybrid-circuit method significantly improves the accuracy of the circulation budget in an idealized supercell simulation. 
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  7. Hejnol, Andreas (Ed.)
    Phylogenomic analyses of hundreds of protein-coding genes aimed at resolving phylogenetic relationships is now a common practice. However, no software currently exists that includes tools for dataset construction and subsequent analysis with diverse validation strategies to assess robustness. Furthermore, there are no publicly available high-quality curated databases designed to assess deep (>100 million years) relationships in the tree of eukaryotes. To address these issues, we developed an easy-to-use software package, PhyloFisher ( https://github.com/TheBrownLab/PhyloFisher ), written in Python 3. PhyloFisher includes a manually curated database of 240 protein-coding genes from 304 eukaryotic taxa covering known eukaryotic diversity, a novel tool for ortholog selection, and utilities that will perform diverse analyses required by state-of-the-art phylogenomic investigations. Through phylogenetic reconstructions of the tree of eukaryotes and of the Saccharomycetaceae clade of budding yeasts, we demonstrate the utility of the PhyloFisher workflow and the provided starting database to address phylogenetic questions across a large range of evolutionary time points for diverse groups of organisms. We also demonstrate that undetected paralogy can remain in phylogenomic “single-copy orthogroup” datasets constructed using widely accepted methods such as all vs. all BLAST searches followed by Markov Cluster Algorithm (MCL) clustering and application of automated tree pruning algorithms. Finally, we show how the PhyloFisher workflow helps detect inadvertent paralog inclusions, allowing the user to make more informed decisions regarding orthology assignments, leading to a more accurate final dataset. 
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  8. null (Ed.)
    Recognition of environmental cues is essential for the survival of all organisms. Transcriptional changes occur to enable the generation and function of the neural circuits underlying sensory perception. To gain insight into these changes, we generated single-cell transcriptomes of Drosophila olfactory- (ORNs), thermo-, and hygro-sensory neurons at an early developmental and adult stage using single-cell and single-nucleus RNA sequencing. We discovered that ORNs maintain expression of the same olfactory receptors across development. Using receptor expression and computational approaches, we matched transcriptomic clusters corresponding to anatomically and physiologically defined neuron types across multiple developmental stages. We found that cell-type-specific transcriptomes partly reflected axon trajectory choices in development and sensory modality in adults. We uncovered stage-specific genes that could regulate the wiring and sensory responses of distinct ORN types. Collectively, our data reveal transcriptomic features of sensory neuron biology and provide a resource for future studies of their development and physiology. 
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