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Abstract Climate change is increasing temperature, decreasing precipitation, and increasing atmospheric CO₂concentrations in many ecosystems. As atmospheric carbon rises, plants may increase carbon‐based defenses, such as phenolics, thereby potentially affecting food quality, foraging habits, and habitat suitability for mammalian herbivores. In alpine habitats, the American pika (Ochotona princeps) is a model species for studying effects of changing plant chemistry on mammals. To survive between growing seasons, pikas cache “haypiles” of plants rich in phenolics. Although they are toxic to pikas, phenolic compounds facilitate retention of plant biomass and nutrition during storage, and they degrade over time. Alpine avens (Geum rossii, Rosales: Rosaceae) is a high‐phenolic plant species that comprises up to 75% of pika haypiles in Colorado. Here, we tested the hypothesis that contemporary climate change has affected the nutritional value of alpine avens to pikas in the last 30 years. Specifically, we compared phenolic activity, nutritional quality, and overwinter preservation of plants collected at Niwot Ridge, Colorado (USA), in 1992 to those collected between 2010 and 2018, spanning nearly three decades of climate change. Phenolic activity increased in alpine avens since 1992, while fiber and nitrogen content decreased. Importantly, overwinter preservation of plant biomass also increased, particularly on windblown slopes without long‐lasting snow cover. Previous studies indicate that pikas at this site still depend on alpine avens for their winter food caches. Higher phenolic content in alpine avens could therefore enhance the preservation of haypiles over winter; however, if pikas must further delay consuming these plants to avoid toxicity or invest extra energy in detoxification, then the nutritional gains from enhanced preservation may not be beneficial. This study provides important insights into how climate‐driven changes in plant chemistry will affect mammalian herbivores in the future. 

Abstract Hybridization is a common process that has broadly impacted the evolution of multicellular eukaryotes; however, how ecological factors influence this process remains poorly understood. Here, we report the findings of a 3-year recapture study of the Bryant’s woodrat (Neotoma bryanti) and desert woodrat (Neotoma lepida), two species that hybridize within a creosote bush (Larrea tridentata) shrubland in Whitewater, CA, USA. We used a genotype-by-sequencing approach to characterize the ancestry distribution of individuals across this hybrid zone coupled with Cormack–Jolly–Seber modeling to describe demography. We identified a high frequency of hybridization at this site with ~40% of individuals possessing admixed ancestry, which is the result of multigenerational backcrossing and advanced hybrid-hybrid crossing. F1, F2, and advanced generation hybrids had apparent survival rates similar to parental N. bryanti, while parental and backcross N. lepida had lower apparent survival rates and were far less abundant. Compared to bimodal hybrid zones where hybrids are often rare and selected against, we find that hybrids at Whitewater are common and have comparable survival to the dominant parental species, N. bryanti. The frequency of hybridization at Whitewater is therefore likely limited by the abundance of the less common parental species, N. lepida, rather than selection against hybrids. 

Abstract Little is known about the tolerances of mammalian herbivores to plant specialized metabolites across landscapes.We investigated the tolerances of two species of herbivorous woodrats,Neotoma lepida(desert woodrat) andNeotoma bryanti(Bryant's woodrat) to creosote bushLarrea tridentata, a widely distributed shrub with a highly toxic resin. Woodrats were sampled from 13 locations both with and without creosote bush across a 900 km transect in the US southwest. We tested whether these woodrat populations consume creosote bush using plant metabarcoding of faeces and quantified their tolerance to creosote bush through feeding trials using chow amended with creosote resin.Toxin tolerance was analysed in the context of population structure across collection sites with microsatellite analyses. Genetic differentiation among woodrats collected from different locations was minimal within either species. Tolerance differed substantially between the two species, withN. lepidapersisting 20% longer thanN. bryantiin feeding trials with creosote resin. Furthermore, in both species, tolerance to creosote resin was similar among woodrats near or within creosote bush habitat. In both species, woodrats collected >25 km from creosote had markedly lower tolerances to creosote resin compared to animals from within the range of creosote bush.The results imply that mammalian herbivores are adapted to the specialized metabolites of plants in their diet, and that this tolerance can extend several kilometres outside of the range of dietary items. That is, direct ecological exposure to the specialized chemistry of particular plant species is not a prerequisite for tolerance to these compounds. These findings lay the groundwork for additional studies to investigate the genetic mechanisms underlying toxin tolerance and to identify how these mechanisms are maintained across landscape‐level scales in mammalian herbivores. Read the freePlain Language Summaryfor this article on the Journal blog. 

Significance Understanding the factors that sculpt gut microbial communities in mammals is of great interest. Here, we studied a diverse clade of herbivorous rodents (woodrats,Neotoma) with variable but well-characterized diets and habitats to quantify the relative contributions of host genetics, geography, and diet, alongside neutral processes, in structuring the gut microbiome under natural and controlled conditions. While diet and geography made significant contributions to microbiome structure, host phylogeny explained the greatest proportion of observed variation. Provision of a common diet in captivity altered natural microbial communities, with communities from different species varying in their resistance to this perturbation. Captivity increased the amount of variation explained by host phylogeny, further emphasizing the extent to which host genetics structure mammalian microbiomes. 

Abstract Measurements of fecal pellet size can provide important information about wild mammals, such as body size and demographic information. Previous studies have not rigorously tested whether diet can confound these measurements. Furthermore, it is unknown whether diet might alter fecal dimensions directly or through changes in animal physiology. Here, we studied three closely related rodent species that differ in natural feeding strategies. Individuals were fed diets that varied in protein and fiber content for 5 weeks. We then measured body size, fecal widths and lengths, and the radius of the large intestine. Diet composition significantly changed fecal widths in all species. High-fiber content significantly increased fecal widths and would cause overestimations of body size if applied to wild feces. Using path analysis, we found that fiber can increase fecal widths both directly and indirectly through increasing the large intestine radius. Protein affected each species differently, suggesting that protein effects vary by species feeding strategy and existing physiology. Overall, diet and large intestine morphology can alter fecal pellet measurements. Studies using fecal measurements therefore must consider these effects in their conclusions.