Life Sciences Commons^™

Integrating Social Dimensions Into Spatial Connectivity Planning For Grizzly Bears, Abigail Sage

Boise State University Theses and Dissertations

In anthropogenic landscapes, which prevail globally, preserving key habitat corridors or routes between wildlife populations is vital for long-term species persistence. Animals moving through these corridors can encounter a number of barriers, including roads, fences, or other human land-uses. Additionally, people unwilling to cohabitate with wildlife can also kill animals considered nuisances or disturb animals in ways that reduce their fitness. The spatial patterns of human tolerance therefore play an important role in the efficacy of habitat corridors. Although there are large bodies of research on habitat corridors and human attitudes toward wildlife, studies that examine the spatial interaction of …

Human-Carnivore Relations: Conflicts, Tolerance And Coexistence In The American West, Juan M. Requena-Mullor

Biology Faculty Publications and Presentations

Carnivore and humans live in proximity due to carnivore recovery efforts and ongoing human encroachment into carnivore habitats globally. The American West is a region that uniquely exemplifies these human-carnivore dynamics, however, it is unclear how the research community here integrates social and ecological factors to examine human-carnivore relations. Therefore, strategies promoting human-carnivore coexistence are urgently needed. We conducted a systematic review on human-carnivore relations in the American West covering studies between 2000 and 2018. We first characterized human-carnivore relations across states of the American West. Second, we analyzed similarities and dissimilarities across states in terms of coexistence, tolerance, number …

A First Phylogenetic Assessment Of Dictyonemo S.Lat In Southwestern North America Reveals Three New Basidiolichens, Described In Honor James D. Lawrey, Manuel Dal Forno, Laurel Kaminsky, Roger Rosentreter, R. Troy Mcmullin, André Aptroot, Robert Lücking

Biology Faculty Publications and Presentations

Three species of lichenized basidiomycetes in the Dictyonema clade from southeastern North America are described as new to science: Cyphellostereum georgianum, C. jamesianum and Dictyonema lawreyi, all with a crustose-filamentous growth form. Based on ITS sequences, the species form well-supported monophyletic clades in a phylogeny and are represented by at least two specimens each. They are also distinguishable by morphological and anatomical characters. These new findings emphasize the importance of lichenological studies in North America, especially in historically understudied taxonomic groups, such as basidiolichens. This study is dedicated to James D. Lawrey on the occasion of his 70^{th …}

Shotgun Sequencing Decades-Old Lichen Specimens To Resolve Phylogenomic Placement Of Type Material, Steven D. Leavitt, Rachel Kueler, Clayton C. Newberry, Roger Rosentreter, Larry L. St. Clair

Biology Faculty Publications and Presentations

Natural history collections, including name-bearing type specimens, are an important source of genetic information. These data can be critical for appropriate taxonomic revisions in cases where the phylogenetic position of name-bearing type specimens needs to be identified, including morphologically cryptic lichen-forming fungal species. Here, we use high-throughput metagenomic shotgun sequencing to generate genome-scale data from decades-old (i.e., more than 30 years old) isotype specimens representing three vagrant taxa in the lichen-forming fungal genus Rhizoplaca, including one species and two subspecies. We also use data from high-throughput metagenomic shotgun sequencing to infer the phylogenetic position of an enigmatic collection, originally …

Integrating Anthropogenic Factors Into Regional-Scale Species Distribution Models: A Novel Application In The Imperiled Sagebrush Biome, Juan M. Requena-Mullor, Kaitlin C. Maguire, Douglas J. Shinneman, Timothy Trevor Caughlin

Biology Faculty Publications and Presentations

Species distribution models (SDM) that rely on regional-scale environmental variables will play a key role in forecasting species occurrence in the face of climate change. However, in the Anthropocene, a number of local-scale anthropogenic variables, including wildfire history, land-use change, invasive species, and ecological restoration practices can override regional-scale variables to drive patterns of species distribution. Incorporating these human-induced factors into SDMs remains a major research challenge, in part because spatial variability in these factors occurs at fine scales, rendering prediction over regional extents problematic. Here, we used big sagebrush (Artemisia tridentata Nutt.) as a model species to …

Where To Forage When Afraid: Does Perceived Risk Impair Use Of The Foodscape?, Samantha P.H. Dwinnell, Hall Sawyer, Jill E. Randall, Jeffery L. Beck, Jennifer S. Forbey, Gary L. Fralick, Kevin L. Monteith

Biology Faculty Publications and Presentations

The availability and quality of forage on the landscape constitute the foodscape within which animals make behavioral decisions to acquire food. Novel changes to the foodscape, such as human disturbance, can alter behavioral decisions that favor avoidance of perceived risk over food acquisition. Although behavioral changes and population declines often coincide with the introduction of human disturbance, the link(s) between behavior and population trajectory are difficult to elucidate. To identify a pathway by which human disturbance may affect ungulate populations, we tested the Behaviorally Mediated Forage‐Loss Hypothesis, wherein behavioral avoidance is predicted to reduce use of available forage adjacent to …

Phylogenomics Resolves Major Relationships And Reveals Significant Diversification Rate Shifts In The Evolution Of Silk Moths And Relatives, J. R. Barber

Biology Faculty Publications and Presentations

Background: Silkmoths and their relatives constitute the ecologically and taxonomically diverse superfamily Bombycoidea, which includes some of the most charismatic species of Lepidoptera. Despite displaying spectacular forms and diverse ecological traits, relatively little attention has been given to understanding their evolution and drivers of their diversity. To begin to address this problem, we created a new Bombycoidea-specific Anchored Hybrid Enrichment (AHE) probe set and sampled up to 571 loci for 117 taxa across all major lineages of the Bombycoidea, with a newly developed DNA extraction protocol that allows Lepidoptera specimens to be readily sequenced from pinned natural history collections.

Results: …

Genetic Variability Of Cultivars Shape Biochemical Profiles In A Bioenergy Cropping System, Megan Kelly-Slatten

Boise State University Theses and Dissertations

The largest terrestrial carbon (C) pool on Earth is the soil, surpassing both biotic and atmospheric C pools combined. The majority of C stabilized in soil is root-derived, and root derived C is the preferred food source for the soil microbial community. Recent studies have indicated that the perennial bioenergy crops Panicum Virgatum (hereafter: switchgrass) and Andropogon Gerardii (hereafter: big bluestem) accumulate significant amounts of soil C owing to their extensive root systems, and that soil C accumulation rates are driven by inter- and intra-specific variability in plant traits. While soil C accumulation in the short term (i.e. after two …

Seed Predation By Owyhee Harvester Ants And The Potential Of Seed Introductions In Recovery Efforts For Slickspot Peppergrass, Jennifer A. Brown

Boise State University Theses and Dissertations

Slickspot peppergrass (Lepidium papilliferum) is a rare plant endemic to the sagebrush-steppe habitat in southwestern Idaho. Within sagebrush-steppe, the plant is restricted to microsites known as “slick spots”– shallow depressions of soil characterized by distinct clay layers and surface water retention that is higher than that of surrounding areas. Having one of the highest extirpation rates among rare plant taxa in Idaho, and considering its unique habitat requirements, limited range, and declining numbers, land managers and conservationists have voiced concern regarding the species’ long-term viability. While range-wide declines in slickspot peppergrass have been attributed largely to the loss …

Old Enemies With New Problems?: Investigating The Ecological Relationship Between Ridgway’S Hawk And The Parasitic Nest Fly Philornis Pici, Christine Deegear Hayes

Boise State University Theses and Dissertations

Modern conservation efforts tend not to focus on individual species, but rather on the entire ecosystem of a species in peril. Many ecological factors can affect a species’ ability to maintain healthy populations. Parasites, which derive nutrients at the expense of their hosts, can reduce host fitness and limit population growth, acting as biological controls in healthy ecosystems. The negative impacts of parasites on their hosts can be exacerbated by climate change and anthropogenic land-use practices in ways that may limit recovery or drive host species to extinction. Introduced parasitic nest flies in the genus Philornis (Diptera: Muscidae) are threatening …

Methodological Advances For Understanding Social Connectivity And Environmental Implications In Multi-Use Landscapes, Matthew Clark

Boise State University Theses and Dissertations

Integrated social-ecological systems research is challenging; complicated feedback and interactions across scales in multi-use landscapes are difficult to decouple. Novel methods and innovative data sources are needed to advance social-ecological systems research. In this thesis, we use network science as a means of explicitly assessing feedback between social and ecological systems, and internet search data to better predict visitation in protected areas. This thesis seeks to provide empirical examples of emerging social-ecological systems science methods as a precedent for resource managers on-the-ground, as well as extending the line of scientific inquiry on the subject

In the first chapter of this …

Correcting Forensic Dna Errors, Greg Hampikian

Biology Faculty Publications and Presentations

DNA mixture interpretation can produce opposing conclusions by qualified forensic analysts, even within the same laboratory. The long-delayed publication of the National Institutes of Standards and Technology (NIST) study of 109 North American crime laboratories in this journal demonstrates this most clearly. This latest study supports earlier work that shows common methods such as the Combined Probability of Inclusion (CPI) have wrongly included innocent people as contributors to DNA mixtures.The 2016 President’s Council of Advisors on Science and Technology report concluded,“In summary, the interpretation of complex DNA mixtures with the CPI statistic has been an inadequately specified—and thus inappropriately subjective—method. …

Conservation Genomics In The Sagebrush Sea: Population Divergence, Demographic History, And Local Adaptation In Sage-Grouse (Centrocercus Spp.), Kevin P. Oh, Cameron L. Aldridge, Jennifer S. Forbey, Carolyn Y. Dadabay, Sara J. Oyler-Mccance

Biology Faculty Publications and Presentations

Sage-grouse are two closely related iconic species of the North American West, with historically broad distributions across sagebrush-steppe habitat. Both species are dietary specialists on sagebrush during winter, with presumed adaptations to tolerate the high concentrations of toxic secondary metabolites that function as plant chemical defenses. Marked range contraction and declining population sizes since European settlement have motivated efforts to identify distinct population genetic variation, particularly that which might be associated with local genetic adaptation and dietary specialization of sage-grouse. We assembled a reference genome and performed whole-genome sequencing across sage-grouse from six populations, encompassing both species and including several …

Phylogeny Of The Ciliate Family Psilotrichidae (Protista, Ciliophora), A Curious And Poorly-Known Taxon, With Notes On Two Algae-Bearing Psilotrichids From Guam, Usa, Xiaotian Luo, Jie A. Huang, Lifang Li, Weibo Song, William A. Bourland

Biology Faculty Publications and Presentations

Background: The classification of the family Psilotrichidae, a curious group of ciliated protists with unique morphological and ontogenetic features, is ambiguous and poorly understood particularly due to the lack of molecular data. Hence, the systematic relationship between this group and other taxa in the subclass Hypotrichia remains unresolved. In this paper the morphology and phylogenetics of species from two genera of Psilotrichida are studied to shed new light on the phylogeny and species diversity of this group of ciliates.

Results: The 18S rRNA gene sequences of species from two psilotrichid genera were obtained. In the phylogenetic trees, the available psilotrichid …

Dietary Plasticity In A Specialist Predator, The Gyrfalcon (Falco Rusticolus): New Insights Into Diet During Brood Rearing, Bryce W. Robinson, Travis L. Booms, Marc J. Bechard, David L. Anderson

Biology Faculty Publications and Presentations

Climate and landscape change are expected to affect species’ distributions and interactions, with potentially harmful consequences for specialist predators. Availability of optimal prey can affect reproductive success in raptors, especially in the Arctic, where dramatic differences in prey availability occur both within and between years. However, behavioral responses of dietary specialist, resident predators such as Gyrfalcons (Falco rusticolus) to changes in prey availability remain poorly understood. To improve understanding of how climate-driven changes in prey availability may affect diet of avian predators in the Arctic, we characterized Gyrfalcon diet on the Seward Peninsula, Alaska, in 2014 and 2015 …

Trophic Interactions And Abiotic Factors Drive Functional And Phylogenetic Structure Of Vertebrate Herbivore Communities Across The Arctic Tundra Biome, Jennifer Forbey

Biology Faculty Publications and Presentations

Communities are assembled from species that evolve or colonise a given geographic region, and persist in the face of abiotic conditions and interactions with other species. The evolutionary and colonisation histories of communities are characterised by phylogenetic diversity, while functional diversity is indicative of abiotic and biotic conditions. The relationship between functional and phylogenetic diversity infers whether species functional traits are divergent (differing between related species) or convergent (similar among distantly related species). Biotic interactions and abiotic conditions are known to influence macroecological patterns in species richness, but how functional and phylogenetic diversity of guilds vary with biotic factors, and …

Genotype Network Intersections Promote Evolutionary Innovation, Devin P. Bendixsen, James Collet, Bjørn Østman, Eric J. Hayden

Biology Faculty Publications and Presentations

Evolutionary innovations are qualitatively novel traits that emerge through evolution and increase biodiversity. The genetic mechanisms of innovation remain poorly understood. A systems view of innovation requires the analysis of genotype networks—the vast networks of genetic variants that produce the same phenotype. Innovations can occur at the intersection of two different genotype networks. However, the experimental characterization of genotype networks has been hindered by the vast number of genetic variants that need to be functionally analyzed. Here, we use high-throughput sequencing to study the fitness landscape at the intersection of the genotype networks of two catalytic RNA molecules (ribozymes). We …

The Endosymbiotic Gut Fungus Zancudomyces Culisetae Influences Transstadial Transmission Of Host-Associated Microbiota In The Yellow Fever Mosquito (Aedes Aegypti), Jonas Frankel-Bricker

Boise State University Theses and Dissertations

Mosquitoes are vectors for a variety of human pathogens and have a significant impact on human health worldwide. There is growing evidence that host-associated microbiota influence mosquito vector competence for certain viruses. Transstadial transmission of bacteria from larvae through pupae to adults could affect these interactions, though further studies are needed to fully unravel the mechanisms involved. Current microbiome research primarily focuses on bacterial communities, whereas the potential role endosymbiotic gut fungi have in transstadial transmission dynamics remains largely unknown. Trichomycetes is an ecological group of endosymbiotic microfungi that colonize the digestive tracts of arthropod hosts, including the Yellow Fever …

Evolution Of The Caribbean Species Of Columnea (Gesneriaceae) With An Emphasis On The Jamaican Species, James F. Smith, Maggie T.-Y. Ooi, Lacie J. Schulte, Keron C. St.E. Campbell, Judeen Meikle, John L. Clark

Biology Faculty Publications and Presentations

Premise of research. Biogeography has improved understanding of evolution and diversification of organisms on both continental and island systems. One complicated island group in terms of geological history and biogeographic pattern is the Caribbean island system. A comparison across taxonomic groups does not result in overarching patterns for this group of islands. Columnea has the greatest number of species endemic to the Caribbean for any genus in Gesneriaceae that is not mostly endemic to the Caribbean with 16 species. Thirteen of these species are found on Jamaica, the remaining three each endemic to Cuba, Hispaniola, and Puerto Rico. In …

Reduced-Impact Logging For Climate Change Mitigation (Ril-C) Can Halve Selective Logging Emissions From Tropical Forests, Anand Roopsind

Biology Faculty Publications and Presentations

Selective logging causes at least half of the emissions from tropical forest degradation. Reduced-impact logging for climate (RIL-C) is proposed as a way to maintain timber production while minimizing forest damage. Here we synthesize data from 61 coordinated field-based surveys of logging impacts in seven countries across the tropics. We estimate that tropical selective logging emitted 834 Tg CO₂ in 2015, 6% of total tropical greenhouse gas emissions. Felling, hauling, and skidding caused 59%, 31%, and 10% of these emissions, respectively. We suggest that RIL-C incentive programs consider a feasible target carbon impact factor of 2.3 Mg emitted per …

Morpho-Molecular Characterization Of The Litostomatean Predatory Ciliate Phialina Pupula (Müller, 1773) Foissner, 1983 (Haptoria, Lacrymariidae), Ľubomír Rajter, William Bourland, Peter Vďačný

Biology Faculty Publications and Presentations

The morphology and phylogenetic position of a haptorian ciliate, Phialina pupula (Müller, 1773) Foissner, 1983, isolated from microaerobic sandy sediments of the floodplain area of the Boise River, Idaho, U.S.A., were studied using live observation, protargol impregnation, scanning electron microscopy, and the 18S rRNA gene as well as the ITS region. The Boise population of P. pupula is characterized by a size of about 60–130 × 20–50 μm, an elliptical macronucleus with a single micronucleus, highly refractive dumbbell-shaped inclusions scattered throughout the cytoplasm and concentrated in the anterior body half, a single subterminal/terminal contractile vacuole, about 10 μm long rod-shaped …

Contributions Of Vps35 Mutations To Parkinson’S Disease, Abir A. Rahman, Brad E. Morrison

Biology Faculty Publications and Presentations

Parkinson’s Disease (PD) is a multi-system neurodegenerative disease where approximately 90% of cases are idiopathic. The remaining 10% of the cases can be traced to a genetic origin and research has largely focused on these associated genes to gain a better understanding of the molecular and cellular pathogenesis for PD. The gene encoding vacuolar protein sorting protein 35 (VPS35) has been definitively linked to late onset familial PD following the identification of a point mutation (D620N) as the causal agent in a Swiss family. Since its discovery, numerous studies have been undertaken to characterize the role of VPS35 in cellular …

Co-Expression Of Vegf And Il-6 Family Cytokines Is Associated With Decreased Survival In Her2 Negative Breast Cancer Patients: Subtype-Specific Il-6 Family Cytokine-Mediated Vegf Secretion, Ken Tawara, Hannah Scott, Jacqueline Emathinger, Alex Ide, Ryan Fox, Daniel Greiner, Dollie Lajoie, Danielle Hedeen, Madhuri Nandakumar, Andrew J. Oler, Ryan Holzer, Cheryl Jorcyk

Biology Faculty Publications and Presentations

Breast cancer cell-response to inflammatory cytokines such as interleukin-6 (IL-6) and oncostatin M (OSM) may affect the course of clinical disease in a cancer subtype-dependent manner. Furthermore, vascular endothelial growth factor A (VEGF) secretion induced by IL-6 and OSM may also be subtype-dependent. Utilizing datasets from Oncomine, we show that poor survival of invasive ductal carcinoma (IDC) breast cancer patients is correlated with both high VEGF expression and high cytokine or cytokine receptor expression in tumors. Importantly, epidermal growth factor receptor-negative (HER2-), but not HER2-positive (HER2+), patient survival is significantly lower with high tumor co-expression of VEGF and OSM, OSMRβ, …

The Role Of Antarctica In Biogeographical Reconstruction: A Point Of View, Manuel De La Estrella, Sven Buerki, Thais Vasconcelos, Eve J. Lucas, Félix Forest

Biology Faculty Publications and Presentations

Premise of research. The opening of the Drake Passage in the Miocene (disconnecting Antarctica and South America and resulting in the establishment of the Circumpolar Current preventing warm waters from the north to reach the polar continent) has led to the formation of the ice sheets and the retreat of the temperate to tropical vegetation that had covered Antarctica for millions of years. With only two current native vascular plant species, Antarctica has been virtually ignored in biogeographical reconstructions and, when considered, only a posteriori invoked as a route of dispersal to reconcile inferred disjunct biogeographical patterns.

Methodology. Here, we …

Preferences Of Specialist And Generalist Mammalian Herbivores For Mixtures Versus Individual Plant Secondary Metabolites, Jordan D. Nobler, Jennifer S. Forbey

Biology Faculty Publications and Presentations

Herbivores that forage on chemically defended plants consume complex mixtures of plant secondary metabolites (PSMs). However, the mechanisms by which herbivores tolerate mixtures of PSMs are relatively poorly understood. As such, it remains difficult to predict how PSMs, singly or as complex mixtures, influence diet selection by herbivores. Although relative rates of detoxification of PSMs have been used to explain tolerance of PSMs by dietary specialist herbivores, few studies have used the rate of detoxification of individual PSMs to understand dietary preferences of individual herbivores for individual versus mixtures of PSMs. We coupled in vivo experiments using captive feeding trials …

Gateway Scholarships In Biological Sciences: Year 2 Annual Report, Vicki Stieha, Julia Oxford, Amy Ulappa, Brittnee Earl, Jennifer Forbey, Kevin Feris, Jocelyn Cullers

Biology Faculty Publications and Presentations

This report summarizes grant activities, progress toward goals, and broader impacts of the Gateway Scholars Program in the Boise State Department of Biological Sciences during the 2018-19 academic year.

A Fragment Of Apolipoprotein E4 Leads To The Downregulation Of A Cxorf56 Homologue, A Novel Er-Associated Protein, And Activation Of Bv2 Microglial Cells, Tanner B. Pollock, Jacob M. Mack, Noail F. Isho, Raquel J. Brown, Alexandra E. Oxford, Brad E. Morrison, Eric J. Hayden, Troy T. Rohn

Biology Faculty Publications and Presentations

Despite the fact that harboring the apolipoprotein E4 (APOE4) allele represents the single greatest risk factor for late-onset Alzheimer’s disease (AD), the exact mechanism by which apoE4 contributes to disease progression remains unknown. Recently, we demonstrated that a 151 amino-terminal fragment of apoE4 (nApoE4_1-151) localizes within the nucleus of microglia in the human AD brain, suggesting a potential role in gene expression. In the present study, we investigated this possibility utilizing BV2 microglia cells treated exogenously with nApoE4_1-151. The results indicated that nApoE4_1-151 leads to morphological activation of microglia cells through, at least in part, …