Resilience of a deer hunting system in Southeast Alaska: integrating social, ecological, and genetic dimensions

Thesis (Ph.D.) University of Alaska Fairbanks, 2009I examined the interactions of key components of a hunting system of Sitka black-tailed deer (Odocoileus hemionus sitkensis) on Prince of Wales Island, Alaska to address concerns of subsistence hunters and to provide a new tool to more effectively monitor deer populations. To address hunter concerns, I documented local knowledge and perceptions of changes in harvest opportunities of deer over the last 50 years as a result of landscape change (e.g., logging, roads). To improve deer monitoring, I designed an efficient method to sample and survey deer pellets, tested the feasibility of identifying individual deer from fecal DNA, and used DNA-based mark and recapture techniques to estimate population trends of deer. I determined that intensive logging from 1950 into the 1990s provided better hunter access to deer and habitat that facilitated deer hunting. However, recent declines in logging activity and successional changes in logged forests have reduced access to deer and increased undesirable habitat for deer hunting. My findings suggested that using DNA from fecal pellets is an effective method for monitoring deer in southeast Alaska. My sampling protocol optimized encounter rates with pellet groups allowing feasible and efficient estimates of deer abundance. I estimated deer abundance with precision (±20%) each year in 3 distinct watersheds, and identified a 30% decline in the deer population between 2006-2008. My data suggested that 3 consecutive severe winters caused the decline. Further, I determined that managed forest harvested>30 years ago supported fewer deer relative to young-managed forest and unmanaged forest. I provided empirical data to support both the theory that changes in plant composition because of succession of logged forest may reduce habitat carrying capacity of deer over the long-term (i.e., decades), and that severity of winter weather may be the most significant force behind annual changes in deer population size in southeast Alaska. Adaptation at an individual and institutional level may be needed to build resilience into the hunting system as most (>90%) of logged forest in southeast Alaska transitions over the next couple of decades into a successional stage that sustains fewer deer and deer hunting opportunities.1. General introduction -- 2. Influence of hunter adaptability on resilience of subsistence hunting systems -- 3. Linking hunter knowledge with forest change to understand changing deer harvest opportunities in intensively logged landscapes -- 4. Individual identification of Sitka black-tailed deer using DNA from fecal pellets -- 5. A practical approach for sampling along animal trails -- 6. Estimating abundance of Sitka black-tailed deer using DNA from fecal pellets -- 7. Summary -- 8. Future recommendations -- Appendix

Changing Daily Wind Speeds on Alaska’s North Slope: Implications for Rural Hunting Opportunities

Because of their reliance on the harvest of fish and game, Alaskan rural communities have experienced a variety of impacts from climate change, the effects of which are amplified at high latitudes. We collaborated with hunters from the coastal community of Wainwright, Alaska, to document their observations of environmental change (e.g., sea ice, wind, temperature) and the implications of those changes for opportunities to hunt bowhead whale (Balaena mysticetus) during spring and caribou (Rangifer tarandus) during summer. We integrated hunter observations on wind with statistical analysis of daily wind speed data collected in the nearby community of Barrow, Alaska, between 1971 and 2010 to characterize changes in the number of days with suitable hunting conditions. Hunters in Wainwright currently observe fewer days than in previous decades with wind conditions suitable for safely hunting bowhead whales and caribou. The statistical analysis of wind speed data supported these conclusions and suggested that the annual windows of opportunity for hunting each species have decreased by up to seven days since 1971. This study demonstrates the potential power of collaboration between local communities and researchers to characterize the societal impacts of climate change. Continued collaborative research with residents of rural northern Alaskan communities could produce knowledge and develop tools to help rural Alaskans adapt to novel social-ecological conditions.Les collectivités rurales de l’Alaska dépendent de la récolte du poisson et du gibier et à ce titre, elles sont assujetties à une panoplie d’incidences découlant du changement climatique, dont les effets sont amplifiés en haute altitude. Grâce à l’aide des chasseurs de la collectivité côtière de Wainwright, en Alaska, nous avons consigné les observations de ces chasseurs relativement à l’évolution de l’environnement (en ce qui a trait, par exemple, à la glace de mer, au vent et aux températures) de même que les incidences de cette évolution sur les possibilités de chasse de la baleine boréale (Balaena mysticetus) au printemps, et du caribou (Rangifer tarandus) à l’été. Nous avons intégré les observations des chasseurs au sujet du vent à l’analyse statistique des données de la vitesse quotidienne du vent, données recueillies dans la localité avoisinante de Barrow, en Alaska, entre 1971 et 2010, afin de caractériser les changements quant au nombre de jours où les conditions de chasse sont convenables. Comparativement aux décennies précédentes, les chasseurs de Wainwright observent un moins grand nombre de jours, à l’heure actuelle, qu’au cours des décennies précédentes pendant lesquels le régime des vents se prête à la chasse sécuritaire de la baleine boréale et du caribou. L’analyse statistique des données de la vitesse du vent permet de soutenir ces conclusions et suggère qu’annuellement, la période pendant laquelle chacune de ces espèces peut faire l’objet de la chasse a diminué dans une mesure allant jusqu’à sept jours depuis 1971. Cette étude témoigne du pouvoir de collaboration qui pourrait exister entre les collectivités de la région et les chercheurs dans le but de caractériser les incidences du changement climatique sur la société. Les travaux de recherche en collaboration continue avec les habitants des collectivités rurales du nord de l’Alaska pourraient permettre de produire des connaissances et d’élaborer des outils qui aideraient les Alaskiens à s’adapter aux nouvelles conditions socioécologiques

Stoking the flame: Subsistence and wood energy in rural Alaska, United States

Energy costs are large and increasing in rural Alaska communities, so communities are turning to renewable energy. While, many of these communities have a mixed subsistence-cash economy, the relationship between renewable energy and subsistence has not been studied. Tanana, Alaska has a biomass program and we conducted interviews with 61 households in 2017 to understand how residents perceive the program and its association with subsistence activities. We analyzed Alaska Department of Fish & Game subsistence surveys from 89 communities to estimate differences in subsistence harvest between households that harvest wood and those that do not. Interviews indicated that people who harvest wood for the biomass program were six times more likely to engage in subsistence. Subsistence harvests were nearly double (184 kg/per capita) in households that harvested wood for personal use versus those that did not (101 kg/per capita). Equipment used for both activities was similar, and 57% respondents combined wood harvesting with other activities (e.g. subsistence, travel, etc.). Higher household incomes and employment were positively associated with subsistence participation (p < 0.001) while only household incomes was positively associated with wood harvest through the biomass program (p < 0.001). Overall, the program was perceived as having a positive effect (69%) for the community because it has created jobs (36%), saved people money (23%), promoted sharing (16%), and reduced fuel use by the community (15%). Our research shows that biomass programs have the potential to complement subsistence activities and enhance the sustainability of communities in rural Alaska that are faced with high energy costs

Effects of Plant Phenology and Vertical Height on Accuracy of Radio-telemetry Locations

The use of very high frequency (VHF) radio-telemetry remains wide-spread in studies of wildlife ecology andmanagement. However, few studies have evaluated the influence of vegetative obstruction on accuracy in differing habitats with varying transmitter types and heights. Using adult and fawn collars at varying heights above the ground (0, 33, 66 and 100 cm) to simulate activities (bedded, feeding and standing) and ages (neonate, juvenile and adult) of deer Odocoileus spp., we collected 5,767 bearings and estimated 1,424 locations (28-30 for each of 48 subsamples) in three habitat types (pasture, grassland and forest), during two stages of vegetative growth (spring and late summer). Bearing error was approximately twice as large at a distance of 900mfor fawn (9.98) than for adult deer collars (4.98). Of 12 models developed to explain the variation in location error, the analysis of covariance model (HT*D + C*D + HT*TBA + C*TBA) containing interactions of height of collar above ground (HT), collar type (C), vertical height of understory vegetation (D) and tree basal area (TBA) was the best model (wi¼0.92) and explained ; 71% of the variation in location error. Location error was greater for both collar types at 0 and 33 cmabove the ground compared to 66 and 100 cm above the ground; however, location error was less for adult than fawn collars. Vegetation metrics influenced location error, which increased with greater vertical height of understory vegetation and tree basal area. Further, interaction of vegetation metrics and categorical variables indicated significant effects on location error. Our results indicate that researchers need to consider study objectives, life history of the study animal, signal strength of collar (collar type), distance from transmitter to receiver, topographical changes in elevation, habitat composition and season when designing telemetry protocols. Bearing distances in forested habitat should be decreased (approximately 23% in our study) compared to bearing distances in open habitat to maintain a consistent bearing error across habitats. Additionally, we believe that field biologists monitoring neonate ungulates for habitat selection should rely on visual locations rather than using VHF-collars and triangulation

Universal Quake Statistics: From Compressed Nanocrystals to Earthquakes

Slowly-compressed single crystals, bulk metallic glasses (BMGs), rocks, granular materials, and the earth all deform via intermittent slips or “quakes”. We find that although these systems span 12 decades in length scale, they all show the same scaling behavior for their slip size distributions and other statistical properties. Remarkably, the size distributions follow the same power law multiplied with the same exponential cutoff. The cutoff grows with applied force for materials spanning length scales from nanometers to kilometers. The tuneability of the cutoff with stress reflects “tuned critical” behavior, rather than self-organized criticality (SOC), which would imply stress-independence. A simple mean field model for avalanches of slipping weak spots explains the agreement across scales. It predicts the observed slip-size distributions and the observed stress-dependent cutoff function. The results enable extrapolations from one scale to another, and from one force to another, across different materials and structures, from nanocrystals to earthquakes

Integrating snow science and wildlife ecology in Arctic-boreal North America

Snow covers Arctic and boreal regions (ABRs) for approximately 9 months of the year, thus snowscapes dominate the form and function of tundra and boreal ecosystems. In recent decades, Arctic warming has changed the snowcover\u27s spatial extent and distribution, as well as its seasonal timing and duration, while also altering the physical characteristics of the snowpack. Understanding the little studied effects of changing snowscapes on its wildlife communities is critical. The goal of this paper is to demonstrate the urgent need for, and suggest an approach for developing, an improved suite of temporally evolving, spatially distributed snow products to help understand how dynamics in snowscape properties impact wildlife, with a specific focus on Alaska and northwestern Canada. Via consideration of existing knowledge of wildlife-snow interactions, currently available snow products for focus region, and results of three case studies, we conclude that improving snow science in the ABR will be best achieved by focusing efforts on developing data-model fusion approaches to produce fit-for-purpose snow products that include, but are not limited to, wildlife ecology. The relative wealth of coordinated in situ measurements, airborne and satellite remote sensing data, and modeling tools being collected and developed as part of NASA\u27s Arctic Boreal Vulnerability Experiment and SnowEx campaigns, for example, provide a data rich environment for developing and testing new remote sensing algorithms and retrievals of snowscape properties

A Semantic Problem Solving Environment for Integrative Parasite Research: Identification of Intervention Targets for Trypanosoma cruzi

Effective research in parasite biology requires analyzing experimental lab data in the context of constantly expanding public data resources. Integrating lab data with public resources is particularly difficult for biologists who may not possess significant computational skills to acquire and process heterogeneous data stored at different locations. Therefore, we develop a semantic problem solving environment (SPSE) that allows parasitologists to query their lab data integrated with public resources using ontologies. An ontology specifies a common vocabulary and formal relationships among the terms that describe an organism, and experimental data and processes in this case. SPSE supports capturing and querying provenance information, which is metadata on the experimental processes and data recorded for reproducibility, and includes a visual query-processing tool to formulate complex queries without learning the query language syntax. We demonstrate the significance of SPSE in identifying gene knockout targets for T. cruzi. The overall goal of SPSE is to help researchers discover new or existing knowledge that is implicitly present in the data but not always easily detected. Results demonstrate improved usefulness of SPSE over existing lab systems and approaches, and support for complex query design that is otherwise difficult to achieve without the knowledge of query language syntax

Linearized esculentin-2EM shows pH dependent antibacterial activity with an alkaline optimum

Here the hypothesis that linearized esculentin 2EM (E2EM-lin) from Glandirana emeljanovi possesses pH dependent activity is investigated. The peptide showed weak activity against Gram-negative bacteria (MLCs ≥ 75.0 μM) but potent efficacy towards Gram-positive bacteria (MLCs ≤ 6.25 μM). E2EM-lin adopted an α-helical structure in the presence of bacterial membranes that increased as pH was increased from 6 to 8 (↑ 15.5 to 26.9 %), while similar increases in pH enhanced the ability of the peptide to penetrate (↑ 2.3 to 5.1 mN m-1) and lyse (↑ 15.1 to 32.5%) these membranes. Theoretical analysis predicted that this membranolytic mechanism involved a tilted segment, that increased along the α-helical long axis of E2EM-lin (1-23) in the N → C direction, with - increasing overall from circa - 0.8 to - 0.3. In combination, these data showed that E2EM-lin killed bacteria via novel mechanisms that were enhanced by alkaline conditions and involved the formation of tilted and membranolytic, α-helical structure. The preference of E2EM-lin for Gram-positive bacteria over Gram-negative organisms was primarily driven by the superior ability of phosphatidylglycerol to induce α-helical structure in the peptide as compared to phosphatidylethanolamine. These data were used to generate a novel pore-forming model for the membranolytic activity of E2EM-lin, which would appear to be the first, major reported instance of pH dependent AMPs with alkaline optima using tilted structure to drive a pore-forming process. It is proposed that E2EM-lin has the potential for development to serve purposes ranging from therapeutic usage, such as chronic wound disinfection, to food preservation by killing food spoilage organisms

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts