Evolution and diversity of bat and rodent Paramyxoviruses from North America

Paramyxoviruses are a diverse group of negative-sense, single-stranded RNA viruses of which several species cause significant mortality and morbidity. In recent years the collection of paramyxoviruses sequences detected in wild mammals has substantially grown, however little is known about paramyxovirus diversity in North American mammals. To better understand natural paramyxovirus diversity, host range, and host specificity, we sought to comprehensively characterize paramyxoviruses across a range of diverse co-occurring wild small mammals in Southern Arizona. We used highly degenerate primers to screen fecal and urine samples and obtained a total of 55 paramyxovirus sequences from 12 rodent species and 6 bat species. We also performed illumina RNA-seq and de novo assembly on 14 of the positive samples to recover a total of 5 near full-length viral genomes. We show there are at least 2 well-supported clades of rodent-borne paramyxoviruses, while bat-associated paramyxoviruses formed a putative single well-supported clade. Using structural homology modeling of the viral attachment protein, we infer that three of the five novel viruses likely bind sialic acid in a manner similar to other Respiroviruses, while the other two viruses from Heteromyid rodents likely bind a novel host receptor. We find no evidence for cross-species transmission, even among closely related sympatric host species. Taken together, these data suggest paramyxoviruses are a common viral infection in some bat and rodent species present in North America, and illuminate the evolution of these viruses.

Exploitative competition between desert kit foxes and coyotes in the Mojave Desert

Exploitative competition between two sympatric guild members can influence the composition and dynamics of an ecological community. We assessed potential exploitative competition between desert kit foxes (Vulpes macrotis arsipus) and coyotes (Canis latrans) by comparing food habits of the two species from 2009 to 2014 on a study site in the Mojave Desert in California. Desert kit foxes specialised on heteromyid rodents and invertebrates, while the most frequently occurring items consumed by coyotes were lagomorphs and rodents. Both species consumed a variety of food items throughout the study, but relative use of these items varied with year and season. Also, precipitation affected prey abundance, and this influenced prey consumption by the two species. The diets of desert kit foxes and coyotes overlapped extensively, which indicated possible exploitative competition. Desert kit foxes consistently had lower dietary diversity than coyotes, indicating that desert kit foxes are more specialist consumers while coyotes are more generalists. Dietary specialisation by kit foxes on smaller items may help reduce competition with coyotes and facilitate coexistence. Coyotes consumed anthropogenic material at much higher frequencies than desert kit foxes, and this subsidisation could increase competitive pressures on kit foxes if it results in greater coyote abundance. Desert kit foxes in California are not a protected species although formal protection has been proposed due to increasing human encroachment. Conservation strategies should include measures to maintain an abundance and diversity of natural food items and limit anthropogenic subsidisation of coyotes.

Divergent Behavior Amid Convergent Evolution: A Case of Four Desert Rodents Learning to Respond to Known and Novel Vipers

ABSTRACTDesert communities word-wide are used as natural laboratories for the study of convergent evolution, yet inferences drawn from such studies are necessarily indirect. Here, we brought desert organisms together (rodents and vipers) from two deserts (Mojave and Negev). Both predators and prey in the Mojave have adaptations that give them competitive advantage compared to their middle-eastern counterparts. Heteromyid rodents, kangaroo rats and pocket mice, have fur-lined cheek pouches that allow the rodents to carry larger loads under predation risk compared to gerbilline rodents. Sidewinder rattlesnakes have heat-sensing pits, allowing them to hunt better on moonless nights when their Negev sidewinding counterpart, the Saharan horned vipers, are visually impaired. In behavioral-assays, we used giving-up density (GUD) to gage how each species of rodent perceived risk posed by known and novel snakes. We repeated this for the same set of rodents at first encounter and again two months later following intensive “natural” exposure to both snake species. Pre-exposure, all rodents identified their evolutionarily familiar snake as a greater risk than the novel one. However, post-exposure all identified the heat-sensing sidewinder rattlesnake as a greater risk. The heteromyids were more likely to avoid encounters with, and discern the behavioral difference among, snakes than their gerbilline counterparts.

Intercontinental-wide consequences of compromise-breaking adaptations: the case of desert rodents

Desert rodent assemblages from around the world provide convergent, but independent crucibles for testing theory and deducing general ecological principles. The heteromyid rodents of North America and the gerbils of the Middle East and their predators provide such an example. Both sets of rodents face predation from owls and vipers, but the North American species possess unique traits that may represent macroevolutionary breakthroughs: rattlesnakes have infra-red sensitive sensory pits, and heteromyids have cheek pouches. To test their significance, we brought together two gerbils (Middle East), two heteromyid rodents (a kangaroo rat and a pocket mouse; North America) in a common setting (a vivarium in the Negev Desert), and quantified the “opinions” of the rodents towards the North American sidewinder rattlesnake and the Middle Eastern Saharan horned viper and the foraging behavior of each in the face of these snake predators plus owl predators. Gerbils are fairly evenly matched in their anti-predator abilities, while the heteromyids differ widely, and these seem to match well with and may determine the types of mechanisms of species coexistence that operate in the communities of each continent. Evolutionary history, macroevolutionary traits, and risk management therefore combine to determine the characteristics of the organisms and the organization of their communities.