Life Sciences Commons^™

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 …

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 …

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: …

Walking For Health During Pregnancy: A Literature Review And Considerations For Future Research, Christopher P. Connelly, Scott A. Conger, Alexander H.K. Montoye, Mallory R. Marshall, Rebecca A. Schlaff, Sylvia E. Badon, James M. Pivarnik

Kinesiology Faculty Publications and Presentations

Walking is the most commonly chosen type of physical activity (PA) during pregnancy and provides several health benefits to both mother and child. National initiatives have promoted the importance of walking in general, but little emphasis is directed toward pregnant women, the majority of whom are insufficiently active. Pregnant women face a variety of dynamic barriers to a physically active lifestyle, some of which are more commonly experienced during specific times throughout the pregnancy experience. Walking is unique in that it appears resistant to a number of these barriers that limit other types of PA participation, and it can be …

Long-Billed Curlew Nest Site Selection And Success In The Intermountain West, Stephanie E. Coates, Benjamin W. Wright, Jay D. Carlisle

Intermountain Bird Observatory Publications and Presentations

Grassland birds have experienced steeper population declines between 1966 and 2015 than any other bird group on the North American continent, and migratory grassland birds may face threats in all stages of their annual cycle. The grassland‐associated long‐billed curlew (Numenius americanus) is experiencing population declines in regional and local portions of their North American breeding range. The nesting period is an important portion of the annual cycle when curlews may face demographic rate limitations from a suite of threats including predators and anthropogenic disturbance. We compared nest sites to random sites within breeding territories to examine nest site …

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 …

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 …

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 …

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 …

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 …

Designing Studies Of Predation Risk For Improved Inference In Carnivore-Ungulate Systems, Mark A. Ditmer

Human-Environment Systems Research Center Faculty Publications and Presentations

Quantifying both the lethal and non-lethal (or “risk”) effects of predation has emerged as a major research focus in carnivore-ungulate systems. While numerous studies have examined predation risk and risk effects in recent decades, a lack of standardization in approaches has impeded progress in the field. We provide an overview of five major study design considerations involved in assessing predation risk and responses of prey in carnivoreungulate systems, highlighting how different design choices can impact the strength and scope of inference. First, we stress the importance of distinguishing measures of predation risk (probability of being killed) from measures of risk …

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 …

High Expression Of Osm And Il-6 Are Associated With Decreased Breast Cancer Survival: Synergistic Induction Of Il-6 Secretion By Osm And Il-1Β, Ken Tawara, Hannah Scott, Jacqueline Emathinger, Cody Wolf, Dollie Lajoie, Danielle Hedeen, Laura Bond, Cheryl Jorcyk

Biomolecular Research Center Publications and Presentations

Chronic inflammation has been recognized as a risk factor for the development and maintenance of malignant disease. Cytokines such as interleukin-6 (IL-6), oncostatin M (OSM), and interleukin-1 beta (IL-1β) promote the development of both acute and chronic inflammation while promoting in vitro metrics of breast cancer metastasis. However, anti-IL-6 and anti-IL-1β therapeutics have not yielded significant results against solid tumors in clinical trials. Here we show that these three cytokines are interrelated in expression. Using the Curtis TCGA™ dataset, we have determined that there is a correlation between expression levels of OSM, IL-6, and IL-1β and reduced breast cancer patient …

Parent Perceptions Of Their Child's Coach: Coaching Knowledge, Behavior, And Interpersonal Relationships, Eric Martin

Kinesiology Faculty Publications and Presentations

The two most significant agents for youth athletes are coaches and parents. Even though the parent-child and coach-athlete relationship has been well explored, the relationship between parents and coaches has remained largely unexamined in the literature. Therefore, the current project surveyed 251 parents of children involved in the USTA 10 & Under tennis program concerning parent perceptions of their coach and the coach-parent relationship. Overall, parents rated their relationship with their coach as positive and communicated with them frequently on several aspects of the tennis environment and their child’s development. Additionally, parents saw their child’s coach as knowledgeable and positive. …

Using Motion-Activated Trail Cameras To Study Diet And Productivity Of Cliff-Nesting Golden Eagles, Jordan T. Harrison, Michael N. Kochert, Benjamin P. Pauli, Julie A. Heath

Raptor Research Center Publications and Presentations

Studies of cliff-nesting raptors can be challenging because direct observations of nest contents are difficult. Our goals were to develop a protocol for installing motion-activated trail cameras at Golden Eagle (Aquila chrysaetos) nests to record diet information and productivity, and to estimate prey detection probability using different diet study methods. In 2014 and 2015, we installed cameras at 12 Golden Eagle nests with 18–42-d-old nestlings. Following installation, we monitored adult behavior using direct observation and post-installation image review. At two nests, adult eagles did not return to nests or exhibited behaviors suggesting avoidance of the cameras, but returned …

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 …

Examining Interactions Between And Among Predictors Of Net Ecosystem Exchange: A Machine Learning Approach In A Semi-Arid Landscape, Qingtao Zhou, Aaron Fellows, Gerald N. Flerchinger, Alejandro N. Flores

Geosciences Faculty Publications and Presentations

Net ecosystem exchange (NEE) is an essential climate indicator of the direction and magnitude of carbon dioxide (CO₂) transfer between land surfaces and the atmosphere. Improved estimates of NEE can serve to better constrain spatiotemporal characteristics of terrestrial carbon fluxes, improve verification of land models, and advance monitoring of Earth’s terrestrial ecosystems. Spatiotemporal NEE information developed by combining ground-based flux tower observations and spatiotemporal remote sensing datasets are of potential value in benchmarking land models. We apply a machine learning approach (Random Forest (RF)) to develop spatiotemporally varying NEE estimates using observations from a flux tower and several …

Sex And Limb Impact Biomechanics Associated With Risk Of Injury During Drop Landing With Body Borne Load, Kayla D. Seymore, Auralea C. Fain, Nicholas J. Lobb, Tyler N. Brown

Kinesiology Faculty Publications and Presentations

Increasing lower limb flexion may reduce risk of musculoskeletal injury for military personnel during landing. This study compared lower limb biomechanics between sexes and limbs when using normal and greater lower limb flexion to land with body borne load. Thirty-three participants (21 male, 12 female, age: 21.6±2.5 years, height: 1.7±0.1 m, weight: 74.5±9.0 kg) performed normal and flexed lower limb landings with four body borne loads: 20, 25, 30 and 35 kg. Hip and knee biomechanics, peak vertical ground reaction force (GRF), and the magnitude and direction of the GRF vector in frontal plane were submitted to two separate repeated …

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 Ethics Of Eliminating Harmful Species: The Case Of The Tsetse Fly, Jérémy Bouyer, Neil H. Carter, Chelsea Batavia, Michael Paul Nelson

Human-Environment Systems Research Center Faculty Publications and Presentations

Wildlife species harmful to humans are often targets of control and elimination programs. A contemporary example is the tsetse fly, a vector of sleeping sickness and African animal trypanosomosis. Tsetse flies have recently been targeted by a pan-African eradication campaign. If it is successful, the campaign could push the entire tsetse family to extinction. With the emergence of effective and efficient elimination technologies, ethical assessment of proposed elimination campaigns is urgently needed. We examine the ethics of tsetse fly elimination by considering arguments predicated on both the instrumental and the intrinsic values of the species at local and global scales. …

Measurement Invariance And Latent Mean Differences Of The Chinese Version Physical Activity Self-Efficacy Scale Across Gender And Education Levels, Han Chen, Jun Dai, Yong Gao

Kinesiology Faculty Publications and Presentations

Background: Self-efficacy has been identified as an important determinant of youth’s behavior change including physical activity (PA) participation. However, the dimensionality check of a PA self-efficacy scale has rarely been conducted in China. The current study aims to examine (1) the unidimensionality of a shortened Chinese version of PA self-efficacy scale (S-PASESC); (2) the measurement invariance of S-PASESC across gender and levels of education; (3) the latent factor mean difference between gender and levels of education; (4) the direct effects of self-efficacy on PA by different gender and education levels; and (5) the comparisons of the direct effects of self-efficacy …

Increased Sod2 In The Diaphragm Contributes To Exercise-Induced Protection Against Ventilator-Induced Diaphragm Dysfunction, Stephanie E. Hall

Kinesiology Faculty Publications and Presentations

Mechanical ventilation (MV) is a life-saving intervention for many critically ill patients. Unfortunately, prolonged MV results in rapid diaphragmatic atrophy and contractile dysfunction, collectively termed ventilator-induced diaphragm dysfunction (VIDD). Recent evidence reveals that endurance exercise training, performed prior to MV, protects the diaphragm against VIDD. While the mechanism(s) responsible for this exercise-induced protection against VIDD remain unknown, increased diaphragm antioxidant expression may be required. To investigate the role that increased antioxidants play in this protection, we tested the hypothesis that elevated levels of the mitochondrial antioxidant enzyme superoxide dismutase 2 (SOD2) is required to achieve exercise-induced protection against VIDD. Cause …

Assessment, Evaluation, Metacognition, And Grading In Pogil, Shawn R. Simonson

Kinesiology Faculty Publications and Presentations

I truly believe no matter the level of student, all students can participate and learn in this form. Set your expectations that all students can learn this way and don't underestimate them. By doing POGIL you can actually see your students learning and it is wonderful!

—A POGIL practitioner

How does POGIL fit inro grading schemes for assignments, tests, and the course? POGIL activities are not designed robe graded as assessments; rather, they are intended as learning tools. However, one of the principle process skills targeted by POGIL is assessment—specifically self-assessment. Thus, much of the grading and assessment in a …

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 …