Mammal responses to global changes in human activity vary by trophic group and landscape.

Wildlife must adapt to human presence to survive in the Anthropocene, so it is critical to understand species responses to humans in different contexts. We used camera trapping as a lens to view mammal responses to changes in human activity during the COVID-19 pandemic. Across 163 species sampled in 102 projects around the world, changes in the amount and timing of animal activity varied widely. Under higher human activity, mammals were less active in undeveloped areas but unexpectedly more active in developed areas while exhibiting greater nocturnality. Carnivores were most sensitive, showing the strongest decreases in activity and greatest increases in nocturnality. Wildlife managers must consider how habituation and uneven sensitivity across species may cause fundamental differences in human-wildlife interactions along gradients of human influence.

How landscape traits affect boreal mammal responses to anthropogenic disturbance.

Understanding mammalian responses to anthropogenic disturbance is challenging, as ecological processes and the patterns arising therefrom notoriously change across spatial and temporal scales, and among different landscape contexts. Responses to local scale disturbances are likely influenced by landscape context (e.g., overall landscape-level disturbance, landscape-level productivity). Hierarchical approaches considering small-scale sampling sites as nested holons within larger-scale landscapes, which constrain processes in lower-level holons, can potentially explain differences in ecological processes between multiple locations. We tested hypotheses about mammal responses to disturbance and interactions among holons using collected images from 957 camera sites across 9 landscapes in Alberta from 2007 to 2020 and examined occurrence for 11 mammal species using generalized linear mixed models. White-tailed deer occurred more in higher disturbed sites within lower disturbed landscapes (ß = -0.30 [-0.4 to -0.15]), whereas occurrence was greater in highly disturbed sites within highly disturbed landscapes for moose (ß = 0.20 [0.09-0.31]), coyote (ß = 0.20 [0.08-0.26]), and lynx (ß = 0.20 [0.07-0.26]). High disturbance sites in high productivity landscapes had higher occurrence of black bears (ß = -0.20 [-0.46 to -0.01]), lynx (ß = -0.70 [-0.97 to -0.34]), and wolves (ß = -0.50 [-0.73 to -0.21]). Conversely, we found higher probability of occurrence in low productivity landscapes with increasing site disturbance for mule deer (ß = 0.80 [0.39-1.14]), and white-tailed deer (ß = 0.20 [0.01-0.47]). We found the ecological context created by aggregate sums (high overall landscape disturbance), and by subcontinental hydrogeological processes in which that landscape is embedded (high landscape productivity), alter mammalian responses to anthropogenic disturbance at local scales. These responses also vary by species, which has implications for large-scale conservation planning. Management interventions must consider large-scale geoclimatic processes and geographic location of a landscape when assessing wildlife responses to disturbance.

Cattle grazing management affects soil microbial diversity and community network complexity in the Northern Great Plains.

Soil microbial communities play a vital role in the biogeochemical cycling and ecological functioning of grassland, but may be affected by common land uses such as cattle grazing. Changes in microbial diversity and network complexity can affect key ecosystem functions such as nutrient cycling. However, it is not well known how microbial diversity and network complexity respond to grazing in the Northern Great Plains. Consequently, it is important to understand whether variation in grazing management alters the diversity and complexity of grassland microbial communities. We compared the effect of intensive adaptive multi-paddock (AMP) grazing and conventional grazing practices on soil microbial communities using 16S/ITS amplicon sequencing. Samples were collected from grasslands in 13 AMP ranches and 13 neighboring, conventional ranches located across the Canadian prairies. We found that AMP grazing increased fungal diversity and evenness, and led to more complex microbial associations. Acidobacteria, Actinobacteria, Gemmatimonadetes, and Bacteroidetes were keystone taxa associated with AMP grazing, while Actinobacteria, Acidobacteria, Proteobacteria, and Armatimonadetes were keystone taxa under conventional grazing. Besides overall grazing treatment effects, specific grazing metrics like cattle stocking rate and rest-to-grazing ratio affected microbial richness and diversity. Bacterial and fungal richness increased with elevated stocking rate, and fungal richness and diversity increased directly with the rest-to-grazing ratio. These results suggest that AMP grazing may improve ecosystem by enhancing fungal diversity and increasing microbial network complexity and connectivity.

Mammalian predator and prey responses to recreation and land use across multiple scales provide limited support for the human shield hypothesis.

Outdoor recreation is widespread, with uncertain effects on wildlife. The human shield hypothesis (HSH) suggests that recreation could have differential effects on predators and prey, with predator avoidance of humans creating a spatial refuge 'shielding' prey from people. The generality of the HSH remains to be tested across larger scales, wherein human shielding may prove generalizable, or diminish with variability in ecological contexts. We combined data from 446 camera traps and 79,279 sampling days across 10 landscapes spanning 15,840 km2 in western Canada. We used hierarchical models to quantify the influence of recreation and landscape disturbance (roads, logging) on ungulate prey (moose, mule deer and elk) and carnivore (wolf, grizzly bear, cougar and black bear) site use. We found limited support for the HSH and strong responses to recreation at local but not larger spatial scales. Only mule deer showed positive but weak landscape-level responses to recreation. Elk were positively associated with local recreation while moose and mule deer responses were negative, contrary to HSH predictions. Mule deer showed a more complex interaction between recreation and land-use disturbance, with more negative responses to recreation at lower road density or higher logged areas. Contrary to HSH predictions, carnivores did not avoid recreation and grizzly bear site use was positively associated. We also tested the effects of roads and logging on temporal activity overlap between mule deer and recreation, expecting deer to minimize interaction with humans by partitioning time in areas subject to more habitat disturbance. However, temporal overlap between people and deer increased with road density. Our findings highlight the complex ecological patterns that emerge at macroecological scales. There is a need for expanded monitoring of human and wildlife use of recreation areas, particularly multi-scale and -species approaches to studying the interacting effects of recreation and land-use change on wildlife.

Industrial development alters wolf spatial distribution mediated by prey availability.

Increasing resource extraction and human activity are reshaping species' spatial distributions in human-altered landscape and consequently shaping the dynamics of interspecific interactions, such as between predators and prey. To evaluate the effects of industrial features and human activity on the occurrence of wolves (Canis lupus), we used wildlife detection data collected in 2014 from an array of 122 remote wildlife camera traps in Alberta's Rocky Mountains and foothills near Hinton, Canada. Using generalized linear models, we compared the occurrence frequency of wolves at camera sites to natural land cover, industrial disturbance (forestry and oil/gas exploration), human activity (motorized and non-motorized), and prey availability (moose, Alces alces; elk, Cervus elaphus; mule deer, Odocoileus hemionus; and white-tailed deer, Odocoileus virginianus). Industrial block features (well sites and cutblocks) and prey (elk or mule deer) availability interacted to influence wolf occurrence, but models including motorized and non-motorized human activity were not strongly supported. Wolves occurred infrequently at sites with high densities of well sites and cutblocks, except when elk or mule deer were frequently detected. Our results suggest that wolves risk using industrial block features when prey occur frequently to increase predation opportunities, but otherwise avoid them due to risk of human encounters. Effective management of wolves in anthropogenically altered landscapes thus requires the simultaneous consideration of industrial block features and populations of elk and mule deer.

Diverse migration patterns and seasonal habitat use of Stone's sheep (Ovis dalli stonei).

We describe temporal and spatial patterns of seasonal space-use and migration by 16 GPS-collared Stone's sheep (Ovis dalli stonei) from nine bands in the Cassiar Mountains of northern British Columbia, Canada. Our objectives were to identify the timing of spring and fall migrations, characterize summer and winter ranges, map and describe migration routes and use of stopover sites, and document altitudinal change across seasons. Our last objective was to assess individual migration strategies based on patterns of geographic migration, altitudinal migration, or residency. Median start and end dates of the spring migration were 12 and 17 Jun (range: 20 May to 05 Aug), and of the fall migration were 30 Aug and 22 Sep (range: 21 Aug to 07 Jan). The median area of winter and summer ranges for geographic migrants were 630.8 ha and 2,829.0 ha, respectively, with a broad range from about 233.6 to 10,196.2 ha. Individuals showed high fidelity to winter ranges over the limited duration of the study. The winter and summer ranges of most individuals (n = 15) were at moderate to high elevations with a median summer elevation of 1,709 m (1,563-1,827 m) and 1,673 m (1,478-1,751 m) that varied <150 m between ranges. Almost all collared females (n = 14) exhibited changes in elevation use that coincide with abbreviated altitudinal migration. Specifically, these females descended to lower spring elevations from their winter range (Δ > 150 m), and then gradually moved up to higher-elevation summer ranges (Δ > 150 m). In the fall, they descended to lower elevations (Δ > 100 m) before returning to their higher winter ranges. The median distance travelled along geographic migration routes was 16.3 km (range: 7.6-47.4 km). During the spring migration, most geographic migrants (n = 8) used at least one stopover site (median = 1.5, range: 0-4), while almost all migrants (n = 11) used stopover sites more frequently in the fall (median = 2.5, range: 0-6). Of the 13 migratory individuals that had at least one other collared individual in their band, most migrated at about the same time, occupied the same summer and winter ranges, used similar migration routes and stopover sites, and exhibited the same migration strategy. We found collared females exhibited four different migration strategies which mostly varied across bands. Migration strategies included long-distance geographic migrants (n = 5), short-distance geographic migrants (n = 5), vacillating migrants (n = 2), and abbreviated altitudinal migrants (n = 4). Different migratory strategies occurred within one band where one collared individual migrated and two did not. We conclude that female Stone's sheep in the Cassiar Mountains displayed a diverse assemblage of seasonal habitat use and migratory behaviors. By delineating seasonal ranges, migration routes and stopover sites, we identify potential areas of priority that can help inform land-use planning and preserve the native migrations of Stone's sheep in the region.

Cryogenic electron ptychographic single particle analysis with wide bandwidth information transfer.

Advances in cryogenic transmission electron microscopy have revolutionised the determination of many macromolecular structures at atomic or near-atomic resolution. This method is based on conventional defocused phase contrast imaging. However, it has limitations of weaker contrast for small biological molecules embedded in vitreous ice, in comparison with cryo-ptychography, which shows increased contrast. Here we report a single-particle analysis based on the use of ptychographic reconstruction data, demonstrating that three dimensional reconstructions with a wide information transfer bandwidth can be recovered by Fourier domain synthesis. Our work suggests future applications in otherwise challenging single particle analyses, including small macromolecules and heterogeneous or flexible particles. In addition structure determination in situ within cells without the requirement for protein purification and expression may be possible.

Mule deer fawn recruitment dynamics in an energy disturbed landscape.

Wildlife population dynamics are modulated by abiotic and biotic factors, typically climate, resource availability, density-dependent effects, and predator-prey interactions. Understanding whether and how human-caused disturbances shape these ecological processes is helpful for the conservation and management of wildlife and their habitats within increasingly human-dominated landscapes. However, many jurisdictions lack either long-term longitudinal data on wildlife populations or measures of the interplay between human-mediated disturbance, climate, and predator density. Here, we use a 50-year time series (1962-2012) on mule deer (Odocoileus hemionus) demographics, seasonal weather, predator density, and oil and gas development patterns from the North Dakota Badlands, USA, to investigate long-term effects of landscape-level disturbance on mule deer fawn fall recruitment, which has declined precipitously over the last number of decades. Mule deer fawn fall recruitment in this study represents the number of fawns per female (fawn:female ratio) that survive through the summer to October. We used this fawn recruitment index to evaluate the composite effects of interannual extreme weather conditions, energy development, and predator density. We found that density-dependent effects and harsh seasonal weather were the main drivers of fawn fall recruitment in the North Dakota Badlands. These effects were further shaped by the interaction between harsh seasonal weather and predator density (i.e., lower fawn fall recruitment when harsh weather was combined with higher predator density). Additionally, we found that fawn fall recruitment was modulated by interactions between seasonal weather and energy development (i.e., lower fawn fall recruitment when harsh weather was combined with higher density of active oil and gas wells). Interestingly, we found that the combined effect of predator density and energy development was not interactive but rather additive. Our analysis demonstrates how energy development may modulate fluctuations in mule deer fawn fall recruitment concurrent with biotic (density-dependency, habitat, predation, woody vegetation encroachment) and abiotic (harsh seasonal weather) drivers. Density-dependent patterns emerge, presumably due to limited quality habitat, being the primary factor influencing fall fawn recruitment in mule deer. Secondarily, stochastic weather events periodically cause dramatic declines in recruitment. And finally, the additive effects of human disturbance and predation can induce fluctuations in fawn fall recruitment. Here we make the case for using long-term datasets for setting long-term wildlife management goals that decision makers and the public can understand and support.

Characterization of the rotavirus assembly pathway in situ using cryoelectron tomography.

Rotavirus assembly is a complex process that involves the stepwise acquisition of protein layers in distinct intracellular locations to form the fully assembled particle. Understanding and visualization of the assembly process has been hampered by the inaccessibility of unstable intermediates. We characterize the assembly pathway of group A rotaviruses observed in situ within cryo-preserved infected cells through the use of cryoelectron tomography of cellular lamellae. Our findings demonstrate that the viral polymerase VP1 recruits viral genomes during particle assembly, as revealed by infecting with a conditionally lethal mutant. Additionally, pharmacological inhibition to arrest the transiently enveloped stage uncovered a unique conformation of the VP4 spike. Subtomogram averaging provided atomic models of four intermediate states, including a pre-packaging single-layered intermediate, the double-layered particle, the transiently enveloped double-layered particle, and the fully assembled triple-layered virus particle. In summary, these complementary approaches enable us to elucidate the discrete steps involved in forming an intracellular rotavirus particle.

In Utero Exposure to Maternal Electronic Nicotine Delivery System use Demonstrate Alterations to Craniofacial Development.

OBJECTIVE: Develop a model for the study of Electronic Nicotine Device (ENDS) exposure on craniofacial development. DESIGN: Experimental preclinical design followed as pregnant murine dams were randomized and exposed to filtered air exposure, carrier exposure consisting of 50% volume of propylene glycol and vegetable glycine (ENDS Carrier) respectively, or carrier exposure with 20 mg/ml of nicotine added to the liquid vaporizer (ENDS carrier with nicotine). SETTING: Preclinical murine model exposure using the SciReq exposure system. PARTICIPANTS: C57BL6 adult 8 week old female pregnant mice and exposed in utero litters. INTERVENTIONS: Exposure to control filtered air, ENDS carrier or ENDS carrier with nicotine added throughout gestation at 1 puff/minute, 4 h/day, five days a week. MAIN OUTCOME MEASURES: Cephalometric measures of post-natal day 15 pups born as exposed litters. RESULTS: Data suggests alterations to several facial morphology parameters in the developing offspring, suggesting electronic nicotine device systems may alter facial growth if used during pregnancy. CONCLUSIONS: Future research should concentrate on varied formulations and exposure regimens of ENDS to determine timing windows of exposures and ENDS formulations that may be harmful to craniofacial development.

In utero exposure to selective serotonin re-uptake inhibitor affects murine mandibular development.

OBJECTIVES: Antidepressants, specifically Selective Serotonin Re-uptake Inhibitors (SSRIs), that alter serotonin metabolism are currently the most commonly prescribed drugs for the treatment of depression. There is some evidence to suggest these drugs contribute to birth defects. As jaw development is often altered in craniofacial birth defects, the purpose of this study was to interrogate the effects of in utero SSRI exposure in a preclinical model of mandible development. MATERIALS AND METHODS: Wild-type C57BL6 mice were used to produce litters that were exposed in utero to an SSRI, Citalopram (500 µg/day). Murine mandibles from P15 pups were analysed for a change in shape and composition. RESULTS: Analysis indicated an overall shape change with total mandibular length and ramus height being shorter in exposed pups as compared to controls. Histomorphometric analysis revealed that first molar length was longer in exposed pups while third molar length was shorter in exposed as compared to control. Histological investigation of molars and surrounding periodontium revealed no change in collagen content of the molar in exposed pups, some alteration in collagen composition in the periodontium, increased alkaline phosphatase in molars and periodontium and decreased mesenchymal cell marker presence in exposed mandibles. CONCLUSION: The results of this study reveal SSRI exposure may interrupt mandible growth as well as overall dental maturation in a model of development giving insight into the expectation that children exposed to SSRIs may require orthodontic intervention.

Evaluating expert-based habitat suitability information of terrestrial mammals with GPS-tracking data.

Aim: Macroecological studies that require habitat suitability data for many species often derive this information from expert opinion. However, expert-based information is inherently subjective and thus prone to errors. The increasing availability of GPS tracking data offers opportunities to evaluate and supplement expert-based information with detailed empirical evidence. Here, we compared expert-based habitat suitability information from the International Union for Conservation of Nature (IUCN) with habitat suitability information derived from GPS-tracking data of 1,498 individuals from 49 mammal species. Location: Worldwide. Time period: 1998-2021. Major taxa studied: Forty-nine terrestrial mammal species. Methods: Using GPS data, we estimated two measures of habitat suitability for each individual animal: proportional habitat use (proportion of GPS locations within a habitat type), and selection ratio (habitat use relative to its availability). For each individual we then evaluated whether the GPS-based habitat suitability measures were in agreement with the IUCN data. To that end, we calculated the probability that the ranking of empirical habitat suitability measures was in agreement with IUCN's classification into suitable, marginal and unsuitable habitat types. Results: IUCN habitat suitability data were in accordance with the GPS data (> 95% probability of agreement) for 33 out of 49 species based on proportional habitat use estimates and for 25 out of 49 species based on selection ratios. In addition, 37 and 34 species had a > 50% probability of agreement based on proportional habitat use and selection ratios, respectively. Main conclusions: We show how GPS-tracking data can be used to evaluate IUCN habitat suitability data. Our findings indicate that for the majority of species included in this study, it is appropriate to use IUCN habitat suitability data in macroecological studies. Furthermore, we show that GPS-tracking data can be used to identify and prioritize species and habitat types for re-evaluation of IUCN habitat suitability data.

Sustainable elk harvests in Alberta with increasing predator populations.

Large predators often are believed to cause declines in hunter harvests of ungulates due to direct competition for prey with hunters. In Alberta, predators of elk (Cervus elaphus), including grizzly bear (Ursus arctos), cougar (Puma concolor), and wolf (Canis lupus), have increased in recent years. We used trend analysis replicated by Wildlife Management Unit (WMU) to examine regional trends in elk harvest and hunter success. Over a 26-yr period, average harvest of elk increased by 5.46% per year for unrestricted bull and by 6.64% per year for limited-quota seasons. Also, over the same time frame, average hunter success increased by 0.2% per year for unrestricted bull and by 0.3% per year for limited-quota seasons, but no trend was detected in hunter effort (P>0.05). Our results show that increasing large-predator populations do not necessarily reduce hunter harvest of elk, and we only found evidence for this in Alberta's mountain WMUs where predation on elk calves has reduced recruitment. Furthermore, data indicate that Alberta's elk harvest management has been sustainable, i.e., hunting has continued while populations of elk have increased throughout most of the province. Wildlife agencies can justify commitments to long-term population monitoring because data allow adaptive management and can inform stakeholders on the status of populations.

Nonlytic cellular release of hepatitis A virus requires dual capsid recruitment of the ESCRT-associated Bro1 domain proteins HD-PTP and ALIX.

Although picornaviruses are conventionally considered 'nonenveloped', members of multiple picornaviral genera are released nonlytically from infected cells in extracellular vesicles. The mechanisms underlying this process are poorly understood. Here, we describe interactions of the hepatitis A virus (HAV) capsid with components of host endosomal sorting complexes required for transport (ESCRT) that play an essential role in release. We show release of quasi-enveloped virus (eHAV) in exosome-like vesicles requires a conserved export signal located within the 8 kDa C-terminal VP1 pX extension that functions in a manner analogous to late domains of canonical enveloped viruses. Fusing pX to a self-assembling engineered protein nanocage (EPN-pX) resulted in its ESCRT-dependent release in extracellular vesicles. Mutational analysis identified a 24 amino acid peptide sequence located within the center of pX that was both necessary and sufficient for nanocage release. Deleting a YxxL motif within this sequence ablated eHAV release, resulting in virus accumulating intracellularly. The pX export signal is conserved in non-human hepatoviruses from a wide range of mammalian species, and functional in pX sequences from bat hepatoviruses when fused to the nanocage protein, suggesting these viruses are released as quasi-enveloped virions. Quantitative proteomics identified multiple ESCRT-related proteins associating with EPN-pX, including ALG2-interacting protein X (ALIX), and its paralog, tyrosine-protein phosphatase non-receptor type 23 (HD-PTP), a second Bro1 domain protein linked to sorting of ubiquitylated cargo into multivesicular endosomes. RNAi-mediated depletion of either Bro1 domain protein impeded eHAV release. Super-resolution fluorescence microscopy demonstrated colocalization of viral capsids with endogenous ALIX and HD-PTP. Co-immunoprecipitation assays using biotin-tagged peptides and recombinant proteins revealed pX interacts directly through the export signal with N-terminal Bro1 domains of both HD-PTP and ALIX. Our study identifies an exceptionally potent viral export signal mediating extracellular release of virus-sized protein assemblies and shows release requires non-redundant activities of both HD-PTP and ALIX.

Soil greenhouse gas emissions and grazing management in northern temperate grasslands.

Adaptive multi-paddock (AMP) grazing, a grazing system in which individual paddocks are grazed for a short duration at a high stock density and followed by a long rest period, is claimed to be an effective tool to sustainably manage and improve grasslands and enhance their ecosystem services. However, whether AMP grazing is superior to conventional grazing (n-AMP) in reducing soil greenhouse gas (GHG) emissions is unclear. Here, we measured CO2, CH4, and N2O fluxes between August 2017 and August 2019 in 12 pairs of AMP vs. n-AMP ranches distributed across an agro-climatic gradient in Alberta, Canada. We found that field GHG fluxes did not differ between AMP and n-AMP grazing systems, but instead were regulated by specific management attributes, environmental conditions, and soil properties, including cattle stocking rate, cultivation history, soil moisture content, and soil bulk density. Specifically, we found that seasonal mean CO2 emissions increased with increasing cattle stocking rates, while CH4 uptake was lower in grasslands with a history of cultivation. Seasonal mean CO2 emissions increased while CH4 uptake decreased with increasing soil moisture content. In addition, CH4 uptake decreased with increasing soil bulk density. Observed N2O emissions were poorly predicted by the management, environmental conditions, and soil properties investigated in our study. We conclude that AMP grazing does not have an advantage over n-AMP grazing in reducing GHG fluxes from grasslands. Future efforts to develop optimal management strategies (e.g., the use of sustainable stocking rates and avoided cultivation) that reduce GHG emissions should also consider the environmental conditions and soil properties unique to every grassland ecosystem.

Predation landscapes influence migratory prey ecology and evolution.

Migratory prey experience spatially variable predation across their life cycle. They face unique challenges in navigating this predation landscape, which affects their perception of risk, antipredator responses, and resulting mortality. Variable and unfamiliar predator cues during migration can limit accurate perception of risk and migrants often rely on social information and learning to compensate. The energetic demands of migration constrain antipredator responses, often through context-dependent patterns. While migration can increase mortality, migrants employ diverse strategies to balance risks and rewards, including life history and antipredator responses. Humans interact frequently with migratory prey across space and alter both mortality risk and antipredator responses, which can scale up to affect migratory populations and should be considered in conservation and management.

Rotavirus NSP1 Inhibits Type I and Type III Interferon Induction.

Type I interferons (IFNs) are produced by most cells in response to virus infection and stimulate a program of anti-viral gene expression in neighboring cells to suppress virus replication. Type III IFNs have similar properties, however their effects are limited to epithelial cells at mucosal surfaces due to restricted expression of the type III IFN receptor. Rotavirus (RV) replicates in intestinal epithelial cells that respond predominantly to type III IFNs, and it has been shown that type III rather than type I IFNs are important for controlling RV infections in vivo. The RV NSP1 protein antagonizes the host type I IFN response by targeting IRF-3, IRF-5, IRF-7, or ß-TrCP for proteasome-mediated degradation in a strain-specific manner. Here we provide the first demonstration that NSP1 proteins from several human and animal RV strains antagonize type III as well as type I IFN induction. We also show that NSP1 is a potent inhibitor of IRF-1, a previously undescribed property of NSP1 which is conserved among human and animal RVs. Interestingly, all NSP1 proteins were substantially more effective inhibitors of IRF-1 than either IRF-3 or IRF-7 which has significance for evasion of basal anti-viral immunity and type III IFN induction in the intestinal epithelium.

The smell of success: Reproductive success related to rub behavior in brown bears.

Several species of bears are known to rub deliberately against trees and other objects, but little is known about why bears rub. Patterns in rubbing behavior of male and female brown bears (Ursus arctos) suggest that scent marking via rubbing functions to communicate among potential mates or competitors. Using DNA from bear hairs collected from rub objects in southwestern Alberta from 2011-2014 and existing DNA datasets from Montana and southeastern British Columbia, we determined sex and individual identity of each bear detected. Using these data, we completed a parentage analysis. From the parentage analysis and detection data, we determined the number of offspring, mates, unique rub objects where an individual was detected, and sampling occasions during which an individual was detected for each brown bear identified through our sampling methods. Using a Poisson regression, we found a positive relationship between bear rubbing behavior and reproductive success; both male and female bears with a greater number of mates and a greater number of offspring were detected at more rub objects and during more occasions. Our results suggest a fitness component to bear rubbing, indicate that rubbing is adaptive, and provide insight into a poorly understood behaviour.

Assembly intermediates of orthoreovirus captured in the cell.

Traditionally, molecular assembly pathways for viruses are inferred from high resolution structures of purified stable intermediates, low resolution images of cell sections and genetic approaches. Here, we directly visualise an unsuspected 'single shelled' intermediate for a mammalian orthoreovirus in cryo-preserved infected cells, by cryo-electron tomography of cellular lamellae. Particle classification and averaging yields structures to 5.6 Å resolution, sufficient to identify secondary structural elements and produce an atomic model of the intermediate, comprising 120 copies each of protein λ1 and σ2. This λ1 shell is 'collapsed' compared to the mature virions, with molecules pushed inwards at the icosahedral fivefolds by ~100 Å, reminiscent of the first assembly intermediate of certain prokaryotic dsRNA viruses. This supports the supposition that these viruses share a common ancestor, and suggests mechanisms for the assembly of viruses of the Reoviridae. Such methodology holds promise for dissecting the replication cycle of many viruses.

Low-dose phase retrieval of biological specimens using cryo-electron ptychography.

Cryo-electron microscopy is an essential tool for high-resolution structural studies of biological systems. This method relies on the use of phase contrast imaging at high defocus to improve information transfer at low spatial frequencies at the expense of higher spatial frequencies. Here we demonstrate that electron ptychography can recover the phase of the specimen with continuous information transfer across a wide range of the spatial frequency spectrum, with improved transfer at lower spatial frequencies, and as such is more efficient for phase recovery than conventional phase contrast imaging. We further show that the method can be used to study frozen-hydrated specimens of rotavirus double-layered particles and HIV-1 virus-like particles under low-dose conditions (5.7 e/Å2) and heterogeneous objects in an Adenovirus-infected cell over large fields of view (1.14 × 1.14 µm), thus making it suitable for studies of many biologically important structures.