Comparative analysis of microbiota along the length of the gastrointestinal tract of two tree squirrel species (Sciurus aberti and S. niger) living in sympatry.

Microbiota inhabiting the gastrointestinal (GI) tract of animals has important impacts on many host physiological processes. Although host diet is a major factor influencing the composition of the gut micro-organismal community, few comparative studies have considered how differences in diet influence community composition across the length of the GI tract. We used 16S sequencing to compare the microbiota along the length of the GI tract in Abert's (Sciurus aberti) and fox squirrels (S. niger) living in the same habitat. While fox squirrels are generalist omnivores, the diet of Abert's squirrels is unusually high in plant fiber, particularly in winter when they extensively consume fiber-rich inner bark of ponderosa pine (Pinus ponderosa). Consistent with previous studies, microbiota of the upper GI tract of both species consisted primarily of facultative anaerobes and was less diverse than that of the lower GI tract, which included mainly obligate anaerobes. While we found relatively little differentiation between the species in the microbiota of the upper GI tract, the community composition of the lower GI tract was clearly delineated. Notably, the Abert's squirrel lower GI community was more stable in composition and enriched for microbes that play a role in the degradation of plant fiber. In contrast, overall microbial diversity was higher in fox squirrels. We hypothesize that these disparities reflect differences in diet quality and diet breadth between the species.

Host biology and environmental variables differentially predict flea abundances for two rodent hosts in a plague-relevant system.

While rodents frequently host ectoparasites that can vector zoonotic diseases, often little is known about their ectoparasite communities, even in places where hosts frequently interact with humans. Yosemite National Park is an area of high human-wildlife interaction and high potential zoonotic disease transfer. Nonetheless, relatively few studies have surveyed the flea communities on mammalian hosts in this area, and even fewer have characterized the environmental and host factors that predict infestation. We focused on two species, the alpine chipmunk (Tamias alpinus) and the lodgepole chipmunk (T. speciosus), which inhabit Yosemite and surrounding areas and can host fleas that vector plague. Because these hosts are exhibiting differential responses to environmental change, it is valuable to establish baselines for their flea communities before further changes occur. We surveyed fleas on these chipmunk hosts during three years (2013-2015), including in the year of a plague epizootic (2015), and documented significant inter-host differences in flea communities and changes across years. Flea abundance was associated with host traits including sex and fecal glucocorticoid metabolite levels. The average number of fleas per individual and the proportion of individuals carrying fleas increased across years for T. speciosus but not for T. alpinus. To better understand these patterns, we constructed models to identify environmental predictors of flea abundance for the two most common flea species, Ceratophyllus ciliatus mononis and Eumolpianus eumolpi. Results showed host-dependent differences in environmental predictors of flea abundance for E. eumolpi and C. ciliatus mononis, with notable ties to ambient temperature variation and elevation. These results provide insight into factors affecting flea abundance on two chipmunk species, which may be linked to changing climate and possible future plague epizootics.

Genome-wide markers reveal a complex evolutionary history involving divergence and introgression in the Abert's squirrel (Sciurus aberti) species group.

BACKGROUND: Genetic introgression between divergent lineages is now considered more common than previously appreciated, with potentially important consequences for adaptation and speciation. Introgression is often asymmetric between populations and patterns can vary for different types of loci (nuclear vs. organellar), complicating phylogeographic reconstruction. The taxonomy of the ecologically specialized Abert's squirrel species group has been controversial, and previous studies based on mitochondrial data have not fully resolved the evolutionary relationships among populations. Moreover, while these studies identified potential areas of secondary contact between divergent lineages, the possibility for introgression has not been tested. RESULTS: We used RAD-seq to unravel the complex evolutionary history of the Abert's squirrel species group. Although some of our findings reinforce inferences based on mitochondrial data, we also find significant areas of discordance. Discordant signals generally arise from previously undetected introgression between divergent populations that differentially affected variation at mitochondrial and nuclear loci. Most notably, our results support earlier claims (disputed by mitochondrial data) that S. aberti kaibabensis, found only on the north rim of the Grand Canyon, is highly divergent from other populations. However, we also detected introgression of S. aberti kaibabensis DNA into other S. aberti populations, which likely accounts for the previously inferred close genetic relationship between this population and those south of the Grand Canyon. CONCLUSIONS: Overall, the evolutionary history of Abert's squirrels appears to be shaped largely by divergence during periods of habitat isolation. However, we also found evidence for interbreeding during periods of secondary contact resulting in introgression, with variable effects on mitochondrial and nuclear markers. Our results support the emerging view that populations often diversify under scenarios involving both divergence in isolation and gene flow during secondary contact, and highlight the value of genome-wide datasets for resolving such complex evolutionary histories.