See No, Smell No, Taste No Evil: How Sage-Grouse Detect Toxic Sagebrush

There is increasing evidence that sage-grouse selectively consume individual and species of sagebrush that have the lowest concentrations of chemical defenses, or toxins. We propose that this selection requires the ability to see, smell or taste specific chemicals or groups of chemicals that vary quantitatively and qualitatively in sagebrush available throughout the winter range of sage-grouse. We are developing methods to determine if and how selected and avoided sagebrush may differ in color, smell and taste. We used ultraviolet and near infrared detectors to determine the variation in the color of phenolics in sagebrush. We used gas chromatography to determine the variation in the smell of monoterpenes in sagebrush. We are developing microscopy techniques to determine if sage-grouse possess receptors in the beak and tongue that could taste chemicals in sagebrush. Our goal is to develop detectors that can act as sage-grouse eyes, nose and mouth and allow managers to identify and conserve the least toxic sagebrush for foraging sage-grouse

Ambient Temperature Influences Diet Selection and Physiology of an Herbivorous Mammal, \u3cem\u3eNeotoma albigula\u3c/em\u3e

The whitethroat woodrat (Neotoma albigula) eats juniper (Juniperus monosperma), but the amount of juniper in its diet varies seasonally. We tested whether changes in juniper consumption are due to changes in ambient temperature and what the physiological consequences of consuming plant secondary compounds (PSCs) at different ambient temperatures might be. Woodrats were acclimated to either 20ºC or 28ºC. Later, they were given two diets to choose from (50% juniper and a nontoxic control) for 7 d. Food intake, resting metabolic rate (RMR), and body temperature (Tb) were measured over the last 2 d. Woodrats at 28ºC ate significantly less juniper, both proportionally and absolutely, than woodrats at 20ºC. RMRs were higher for woodrats consuming juniper regardless of ambient temperature, and Tb was higher for woodrats consuming juniper at 28ºC than for woodrats eating control diet at 28ºC. Thus, juniper consumption by N. albigula is influenced by ambient temperature. We conclude that juniper may influence thermoregulation in N. albigula in ways that are helpful at low temperatures but harmful at warmer temperatures in that juniper PSCs may be more toxic at warmer temperatures. The results suggest that increases in ambient temperature associated with climate change could significantly influence foraging behavior of mammalian herbivores

Dietary Partitioning of Toxic Leaves and Fibrous Stems Differs Between Sympatric Specialist and Generalist Mammalian Herbivores

Dietary specialists often reside in habitats that provide a high and predictable abundance of their primary food, which is usually difficult for other herbivores to consume because of high levels of plant toxins or structural impediments. Therefore, sympatric specialist and generalist herbivores may partition food resources within and among plants. We compared how a dietary specialist (pygmy rabbit, Brachylagus idahoensis) and generalist (mountain cottontail, Sylvilagus nuttallii) used sagebrush as a food resource during winter across 3 field sites in Idaho, USA, and in controlled feeding trials with captive rabbits. The proportion of sagebrush consumed by both rabbit species varied among sites, indicating that characteristics of sagebrush plants and the surrounding plant community influenced use of sagebrush. In addition, free-ranging and captive pygmy rabbits consumed a greater proportion of sagebrush and cropped smaller stem diameters with a greater proportion of sagebrush leaves (high monoterpenes, low fiber) relative to stems (low monoterpenes, high fiber) than did cottontails. Cottontails frequently discarded the leafy tips of sagebrush branches. Cottontails are more tolerant of fiber and less tolerant of sagebrush toxins than pygmy rabbits. Cottontails consumed large diameter stems, which diluted toxins in sagebrush but increased fiber intake and reduced digestible nitrogen intake. Pygmy rabbits are less tolerant of fiber but more able to detoxify and eliminate sagebrush toxins than cottontails. Pygmy rabbits consumed small diameter stems, which reduced fiber intake, but increased intake of toxins from sagebrush leaves. Although partitioning of stems and leaves within sagebrush plants may provide a mechanism for coexistence of specialist and generalist rabbits, higher than expected dietary overlap between both free-ranging and captive rabbits in winter might create resource competition in areas with high-density sympatric populations or low availability of sagebrush. In addition, these contrasting foraging strategies have the potential to influence dynamics of sagebrush communities over time

Conservation of Sharp-Tailed Grouse (\u3cem\u3eTympanuchus phasianellus columbianus\u3c/em\u3e) Through Fecal DNA Extraction

Columbian Sharp-tailed Grouse (Tympanuchus phasianellus columbianus) are the rarest of the six extant Sharp-tailed Grouse subspecies. This subspecies experienced a 90% range contraction over the last century and have been extirpated from several states (Figure 1). In Washington alone, populations that once numbered hundreds of thousands of individuals now consist of fewer than 1,000 birds. Conservation efforts—including conservation translocations and habitat management—are underway to help bolster this imperiled subspecies across their range. However, little is known about the ecology of this charismatic species and the factors that may be contributing towards higher rates of decline. The collection of fecal pellets presents an opportunity to better understand Columbian Sharp-tailed Grouse across their range, by providing information on their diet and host ID. As a HERC Fellow in the Conservation Genetics Lab at Boise State University, I have been exploring the potential to use non-invasively collected fecal samples to understand how we can best capture different DNA types, which can be used to better inform the conservation and management of this charismatic grouse

Seasonal temperature acclimatization in a semi-fossorial mammal and the role of burrows as thermal refuges.

Small mammals in habitats with strong seasonal variation in the thermal environment often exhibit physiological and behavioral adaptations for coping with thermal extremes and reducing thermoregulatory costs. Burrows are especially important for providing thermal refuge when above-ground temperatures require high regulatory costs (e.g., water or energy) or exceed the physiological tolerances of an organism. Our objective was to explore the role of burrows as thermal refuges for a small endotherm, the pygmy rabbit (Brachylagus idahoensis), during the summer and winter by quantifying energetic costs associated with resting above and below ground. We used indirect calorimetry to determine the relationship between energy expenditure and ambient temperature over a range of temperatures that pygmy rabbits experience in their natural habitat. We also measured the temperature of above- and below-ground rest sites used by pygmy rabbits in eastern Idaho, USA, during summer and winter and estimated the seasonal thermoregulatory costs of resting in the two microsites. Although pygmy rabbits demonstrated seasonal physiological acclimatization, the burrow was an important thermal refuge, especially in winter. Thermoregulatory costs were lower inside the burrow than in above-ground rest sites for more than 50% of the winter season. In contrast, thermal heterogeneity provided by above-ground rest sites during summer reduced the role of burrows as a thermal refuge during all but the hottest periods of the afternoon. Our findings contribute to an understanding of the ecology of small mammals in seasonal environments and demonstrate the importance of burrows as thermal refuge for pygmy rabbits

Fearscapes: Mapping Functional Properties of Cover for Prey with Terrestrial LiDAR

Heterogeneous vegetation structure can create a variable landscape of predation risk—a fearscape—that influences the use and selection of habitat by animals. Mapping the functional properties of vegetation that influence predation risk (e.g., concealment and visibility) across landscapes can be challenging. Traditional ground-based measures of predation risk are location specific and limited in spatial resolution. We demonstrate the benefits of terrestrial laser scanning (TLS) to map the properties of vegetation structure that shape fearscapes. We used TLS data to estimate the concealment of prey from multiple vantage points, representing predator sightlines, as well as the visibility of potential predators from the locations of prey. TLS provides a comprehensive data set that allows an exploration of how habitat changes may affect prey and predators. Together with other remotely sensed imagery, TLS could facilitate the scaling up of fearscape analyses to promote the management and restoration of landscapes

A Haploid Pseudo-Chromosome Genome Assembly for a Keystone Sagebrush Species of Western North American Rangelands

Increased ecological disturbances, species invasions, and climate change are creating severe conservation problems for several plant species that are widespread and foundational. Understanding the genetic diversity of these species and how it relates to adaptation to these stressors are necessary for guiding conservation and restoration efforts. This need is particularly acute for big sagebrush (Artemisia tridentata; Asteraceae), which was once the dominant shrub over 1,000,000 km2 in western North America but has since retracted by half and thus has become the target of one of the largest restoration seeding efforts globally. Here, we present the first reference-quality genome assembly for an ecologically important subspecies of big sagebrush (A. tridentata subsp. tridentata) based on short and long reads, as well as chromatin proximity ligation data analyzed using the HiRise pipeline. The final 4.2-Gb assembly consists of 5,492 scaffolds, with nine pseudo-chromosomal scaffolds (nine scaffolds comprising at least 90% of the assembled genome; n = 9). The assembly contains an estimated 43,377 genes based on ab initio gene discovery and transcriptional data analyzed using the MAKER pipeline, with 91.37% of BUSCOs being completely assembled. The final assembly was highly repetitive, with repeat elements comprising 77.99% of the genome, making the Artemisia tridentata subsp. tridentata genome one of the most highly repetitive plant genomes to be sequenced and assembled. This genome assembly advances studies on plant adaptation to drought and heat stress and provides a valuable tool for future genomic research

A haploid pseudo-chromosome genome assembly for a keystone sagebrush species of western North American rangelands

Increased ecological disturbances, species invasions, and climate change are creating severe conservation problems for several plant species that are widespread and foundational. Understanding the genetic diversity of these species and how it relates to adaptation to these stressors are necessary for guiding conservation and restoration efforts. This need is particularly acute for big sagebrush (Artemisia tridentata; Asteraceae), which was once the dominant shrub over 1,000,000 km2 in western North America but has since retracted by half and thus has become the target of one of the largest restoration seeding efforts globally. Here, we present the first reference-quality genome assembly for an ecologically important subspecies of big sagebrush (A. tridentata subsp. tridentata) based on short and long reads, as well as chromatin proximity ligation data analyzed using the HiRise pipeline. The final 4.2-Gb assembly consists of 5,492 scaffolds, with nine pseudo-chromosomal scaffolds (nine scaffolds comprising at least 90% of the assembled genome; n = 9). The assembly contains an estimated 43,377 genes based on ab initio gene discovery and transcriptional data analyzed using the MAKER pipeline, with 91.37% of BUSCOs being completely assembled. The final assembly was highly repetitive, with repeat elements comprising 77.99% of the genome, making the Artemisia tridentata subsp. tridentata genome one of the most highly repetitive plant genomes to be sequenced and assembled. This genome assembly advances studies on plant adaptation to drought and heat stress and provides a valuable tool for future genomic research.This research was made possible by 2 NSF Idaho EPSCoR grants (award numbers OIA-1757324 and OIA-1826801), as well as a Dovetail Genomics Tree of Life Award.Introduction Materials and methods Sample collection, in vitro tissue propagation, and biomass production Flow cytometry and genome complexity analysis PacBio and Omni-C sequence data generation PacBio long-read de novo assembly and validation Pseudomolecule construction with HiRise Genome annotation RNA sequencing Repeat identification Functional annotation Results and discussion Validation of genome assembly and annotation Genome complexity and evidence of past polyploidization Comparing the A. tridentata and A. annua genome assemblies Applications of the sagebrush reference genome Data availability Acknowledgments Literature cite

Location of studies and evidence of effects of herbivory on Arctic vegetation: a systematic map

Background: Herbivores modify the structure and function of tundra ecosystems. Understanding their impacts is necessary to assess the responses of these ecosystems to ongoing environmental changes. However, the effects of herbivores on plants and ecosystem structure and function vary across the Arctic. Strong spatial variation in herbivore effects implies that the results of individual studies on herbivory depend on local conditions, i.e., their ecological context. An important first step in assessing whether generalizable conclusions can be produced is to identify the existing studies and assess how well they cover the underlying environmental conditions across the Arctic. This systematic map aims to identify the ecological contexts in which herbivore impacts on vegetation have been studied in the Arctic. Specifically, the primary question of the systematic map was: “What evidence exists on the effects of herbivores on Arctic vegetation?”. Methods: We used a published systematic map protocol to identify studies addressing the effects of herbivores on Arctic vegetation. We conducted searches for relevant literature in online databases, search engines and specialist websites. Literature was screened to identify eligible studies, defined as reporting primary data on herbivore impacts on Arctic plants and plant communities. We extracted information on variables that describe the ecological context of the studies, from the studies themselves and from geospatial data. We synthesized the findings narratively and created a Shiny App where the coded data are searchable and variables can be visually explored. Review findings: We identified 309 relevant articles with 662 studies (representing different ecological contexts or datasets within the same article). These studies addressed vertebrate herbivory seven times more often than invertebrate herbivory. Geographically, the largest cluster of studies was in Northern Fennoscandia. Warmer and wetter parts of the Arctic had the largest representation, as did coastal areas and areas where the increase in temperature has been moderate. In contrast, studies spanned the full range of ecological context variables describing Arctic vertebrate herbivore diversity and human population density and impact. Conclusions: The current evidence base might not be sufficient to understand the effects of herbivores on Arctic vegetation throughout the region, as we identified clear biases in the distribution of herbivore studies in the Arctic and a limited evidence base on invertebrate herbivory. In particular, the overrepresentation of studies in areas with moderate increases in temperature prevents robust generalizations about the effects of herbivores under different climatic scenarios

Location of studies and evidence of effects of herbivory on Arctic vegetation : a systematic map

Background: Herbivores modify the structure and function of tundra ecosystems. Understanding their impacts is necessary to assess the responses of these ecosystems to ongoing environmental changes. However, the effects of herbivores on plants and ecosystem structure and function vary across the Arctic. Strong spatial variation in herbivore effects implies that the results of individual studies on herbivory depend on local conditions, i.e., their ecological context. An important first step in assessing whether generalizable conclusions can be produced is to identify the existing studies and assess how well they cover the underlying environmental conditions across the Arctic. This systematic map aims to identify the ecological contexts in which herbivore impacts on vegetation have been studied in the Arctic. Specifically, the primary question of the systematic map was: "What evidence exists on the effects of herbivores on Arctic vegetation?". Methods: We used a published systematic map protocol to identify studies addressing the effects of herbivores on Arctic vegetation. We conducted searches for relevant literature in online databases, search engines and specialist websites. Literature was screened to identify eligible studies, defined as reporting primary data on herbivore impacts on Arctic plants and plant communities. We extracted information on variables that describe the ecological context of the studies, from the studies themselves and from geospatial data. We synthesized the findings narratively and created a Shiny App where the coded data are searchable and variables can be visually explored. Review findings We identified 309 relevant articles with 662 studies (representing different ecological contexts or datasets within the same article). These studies addressed vertebrate herbivory seven times more often than invertebrate herbivory. Geographically, the largest cluster of studies was in Northern Fennoscandia. Warmer and wetter parts of the Arctic had the largest representation, as did coastal areas and areas where the increase in temperature has been moderate. In contrast, studies spanned the full range of ecological context variables describing Arctic vertebrate herbivore diversity and human population density and impact. Conclusions: The current evidence base might not be sufficient to understand the effects of herbivores on Arctic vegetation throughout the region, as we identified clear biases in the distribution of herbivore studies in the Arctic and a limited evidence base on invertebrate herbivory. In particular, the overrepresentation of studies in areas with moderate increases in temperature prevents robust generalizations about the effects of herbivores under different climatic scenarios.Peer reviewe