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  1. Rodents are the largest and most diverse group of mammals. Covering a wide range of structural and functional adaptations, rodents successfully occupy virtually every terrestrial habitat, and they are often found in close association with humans, domestic animals, and wildlife. Although a significant amount of research has focused on rodents’ prominence as known reservoirs of zoonotic viruses, there has been less emphasis on the viral ecology of rodents in general. Here, we utilized a viral metagenomics approach to investigate polyomaviruses in wild rodents from the Baja California peninsula, Mexico, using fecal samples. We identified a novel polyomavirus in fecal samples from two rodent species, a spiny pocket mouse (Chaetodipus spinatus) and a Dulzura kangaroo rat (Dipodomys simulans). These two polyomaviruses represent a new species in the genus Betapolyomavirus. Sequences of this polyomavirus cluster phylogenetically with those of other rodent polyomaviruses and two other non-rodent polyomaviruses (WU and KI) that have been identified in the human respiratory tract. Through our continued work on seven species of rodents, we endeavor to explore the viral diversity associated with wild rodents on the Baja California peninsula and expand on current knowledge of rodent viral ecology and evolution. 
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    Free, publicly-accessible full text available October 1, 2024
  2. Abstract

    There is considerable interest in better understanding how earth processes shape the generation and distribution of life on Earth. This question, at its heart, is one of causation. In this article I propose that at a regional level, earth processes can be thought of as behaving somewhat deterministically and may have an organized effect on the diversification and distribution of species. However, the study of how landscape features shape biology is challenged by pseudocongruent or collinear variables. I demonstrate that causal structures can be used to depict the cause–effect relationships between earth processes and biological patterns using recent examples from the literature about speciation and species richness in montane settings. This application shows that causal diagrams can be used to better decipher the details of causal relationships by motivating new hypotheses. Additionally, the abstraction of this knowledge into structural equation metamodels can be used to formulate theory about relationships within Earth–life systems more broadly. Causal structures are a natural point of collaboration between biologists and Earth scientists, and their use can mitigate against the risk of misassigning causality within studies. My goal is that by applying causal theory through application of causal structures, we can build a systems‐level understanding of what landscape features or earth processes most shape the distribution and diversification of species, what types of organisms are most affected, and why.

     
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  3. Oftentimes, to understand the genetic relatedness and diversity of today's populations requires considering the ancient landscape on which those populations evolved. Nowhere is this clearer than along Earth's coastline, which has been in its present‐day configuration for only about 6.5% of the past 800,000 years (Dolby et al., 2020; Miller et al., 2005). During ice ages when glaciers expanded in the Northern Hemisphere, they stored enough of the planet's water to drop global sea level by ~120 m below present levels (“lowstand”, Figure 1a), and there have been at least eight of these 100,000‐year cycles preceding today. When glaciers melted, ocean water reflooded shorelines, shifting and re‐forming marginal marine habitats globally and shaping the relatedness of populations (Dolby et al., 2016). In a From the Cover article in this issue ofMolecular Ecology, Stiller et al. (2020) integrate population genomic analysis of leafy seadragons in southern Australia with estimates of available seabed area to reveal that the expansion of habitat that accompanied this reflooding led to strong demographic expansions. With statistical models, they also show that western populations were eliminated and then recolonized because the continental shelf there is narrow, leaving little available habitat when sea level was low (Figure 1b). Their results document the dynamic and interrelated nature of a hidden, changing landscape and the evolution of species inhabiting it.

     
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  4. Protti, S. ; Raviola, C. (Ed.)
    This chapter is intended to help make inroads to the role of Intralipid in photodynamic therapy (PDT). In addition to Intralipid’s favorable property as a light scattering agent, we hypothesized that it will be unstable to photosensitized oxidation. To explore this, measurements of total quenching rate constants (kT) of singlet oxygen with Intralipid and its constituents are described. Furthermore, organic phosphines were tested to trap Intralipid peroxides formed in photosensitized oxidation reactions. Our findings indicate that the vulnerability of Intralipid to photooxidation might suggest limits of its use in PDT. 
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