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Transmissible spongiform encephalopathy, or prion disease, poses a serious threat to wildlife; however, the susceptibility of apex predators is still being assessed. We investigated variation in the prion protein gene in Florida panthers (Puma concolor coryi) and found that admixture from Central American pumas probably introduced a novel, albeit benign, prion allele. 

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. 

For nearly 30 years, biologists have documented a striking pattern of intra-species genetic divergence on the Baja California peninsula in dozens of disparate species. Evolutionary theory predicts that when such a pattern is shared among species the cause is extrinsic (e.g., environmental, climatic, physiographic, geological). The leading hypothesis within biological literature has been that genetic divergence was facilitated by flooding across the central peninsula by a seaway between ~3-1 Ma, resulting in separation of northern and southern populations. However, new detailed geologic mapping from the Baja GeoGenomics consortium reveals evidence for continuous terrestrial environments during the last ~30 Myr in a ≥40-km-wide ~E-W region of the central peninsula that straddles the modern-day crest, conclusively refuting the seaway hypothesis. Through integration of tectonic, volcanic, and sedimentological evidence with genomic (DNA) and gene expression (RNA) data for plants and animals, we are developing a new working model for Earth-life evolution on the peninsula over the last ~5 Myr. In this model, rift-related uplift drives the growth and dissection of topography, causing increased microenvironmental heterogeneity that populations differentially adapted to in the north and south. This is evidenced by widespread, statistically significant niche divergence in populations between northern and southern Baja in 21 studied taxa. This pattern is supported by strong differences in gene expression in northern and southern populations of two lizard species, particularly in genes relating to metabolism, which may indicate different diet or energy requirements between the regions. Habitats in the north and south then shifted due to glacial and interglacial periods, indicated by hindcasting the estimated niche conditions of those 21 taxa. With ongoing analyses, we expect to find genomic signatures of differential natural selection and adaptation within these species due in part to monsoon-driven rainfall differences. The significance of this work is twofold: it demonstrates the importance of incorporating geological data into evolutionary hypotheses and it cautions how mis-assigning cause-effect relationships in individual Earth-life systems can bias our fundamental understanding of how Earth processes shape biological evolution writ large.