Life Sciences Commons^™

Gather Round The Tree: Woody Aboveground Biomass Increases Animal Presence And Species Richness In A Tropical Forest-Savanna Ecotone, Merry Vanessa Marshall Davidson

Boise State University Theses and Dissertations

Boundaries between ecosystems are often biodiversity hotspots with relatively high vulnerability to global change. The boundary between tropical rainforest and savanna ecosystems in the Amazon presents an ecotone that is undergoing a shift in ecosystem structure, as a warming climate promotes the expansion of grassland. How animal communities in the Amazon will respond to changes in ecosystem structure is a crucial unanswered question with implications for the many ecosystem services that animals provide, from a food source for Indigenous people to seed dispersal for vulnerable tree populations. Recent modeling work has forecasted that faunal savannization will occur in the Amazon, …

From Microbes To Management: Spatial And Temporal Variations In Available Vegetation Affect The Gut Microbiota In A Population Of Free-Ranging Generalist Herbivores, Olivia K. Rodríguez

Boise State University Theses and Dissertations

The effects of extrinsic environmental factors that shape ecological systems are not only seen at the macroscopic level, but additionally influence and govern the host-associated microbial communities of their mammalian hosts. These microbial communities are susceptible to the fluctuation of abiotic and biotic factors which affect their host organisms. The surge in the research of microbiota–communities of archaea, bacteria, fungi, and viruses residing in various environmental systems–has shown that these communities can profoundly influence animal health. As such, monitoring microbiota has allowed for a new approach to study animal health and physiology. This is of particular benefit in the conservation …

Commentary: The Past, Present, And Future Of The Global Raptor Impact Network, James R. Belthoff, Julie A. Heath

Biology Faculty Publications and Presentations

Most raptor populations are declining and nearly a fifth are threatened with extinction; thus there is a need to increase collaboration to ensure efficient and effective research, management, and conservation. Here, we introduce the Global Raptor Impact Network (GRIN; www.globalraptors.org), a tool to enhance collaboration and conservation impact of the raptor research community. We provide an overview of the history and current state of GRIN, including plans for expansion. Predecessors to GRIN include The African Raptor DataBank, which was launched in 2012 to ascertain the conservation status of raptors across Africa; and the Global Raptor Information Network, which was launched …

Expanding The Conservation Genomics Toolbox: Incorporating Structural Variants To Enhance Genomic Studies For Species Of Conservation Concern, Stephanie J. Galla

Biology Faculty Publications and Presentations

Structural variants (SVs) are large rearrangements (>50 bp) within the genome that impact gene function and the content and structure of chromosomes. As a result, SVs are a significant source of functional genomic variation, that is, variation at genomic regions underpinning phenotype differences, that can have large effects on individual and population fitness. While there are increasing opportunities to investigate functional genomic variation in threatened species via single nucleotide polymorphism (SNP) data sets, SVs remain understudied despite their potential influence on fitness traits of conservation interest. In this future-focused Opinion, we contend that characterizing SVs offers the conservation genomics …

Bio-Acoustic Tracking And Localization Using Heterogeneous, Scalable Microphone Arrays, Erik Verreycken, Ralph Simon, Brandt Quirk-Royal, Walter Daems, Jesse Barber, Jan Steckel

Biology Faculty Publications and Presentations

Microphone arrays are an essential tool in the field of bioacoustics as they provide a non-intrusive way to study animal vocalizations and monitor their movement and behavior. Microphone arrays can be used for passive localization and tracking of sound sources while analyzing beamforming or spatial filtering of the emitted sound. Studying free roaming animals usually requires setting up equipment over large areas and attaching a tracking device to the animal which may alter their behavior. However, monitoring vocalizing animals through arrays of microphones, spatially distributed over their habitat has the advantage that unrestricted/unmanipulated animals can be observed. Important insights have …

Intraspecific Variation Mediates Density Dependence In A Genetically Diverse Plant Species, Andrii Zaiats, Matthew J. Germino, Marcelo D. Serpe, Bryce Richardson, T. Trevor Caughlin

Biology Faculty Publications and Presentations

Interactions between neighboring plants are critical for biodiversity maintenance in plant populations and communities. Intraspecific trait variation and genome duplication are common in plant species and can drive eco-evolutionary dynamics through genotype-mediated plant-plant interactions. However, few studies have examined how species-wide intraspecific variation may alter interactions between neighboring plants. We investigate how subspecies and ploidy variation in a genetically diverse species, big sagebrush (Artemisia tridentata), can alter the demographic outcomes of plant interactions. Using a replicated, long-term common garden experiment that represents range-wide diversity of A. tridentata, we ask how intraspecific variation, environment, and stand age mediate …

Golden Eagle Dietary Shifts Following Wildfire And Shrub Loss Have Negative Consequences For Nestling Survivorship, Julie A. Heath, Michael N. Kochert, Karen Steenhof

Biology Faculty Publications and Presentations

Wildfires and invasive species have caused widespread changes in western North America’s shrub-steppe landscapes. The bottom–up consequences of degraded shrublands on predator ecology and demography remain poorly understood. We used a before–after paired design to study whether Golden Eagle (Aquila chrysaetos) diet and nestling survivorship changed following wildfires in southwestern Idaho, USA. We assessed burn extents from 1981 to 2013 and vegetation changes between 1979 (pre-burn) and 2014 (post-burn) within 3 km of Golden Eagle nesting centroids. We measured the frequency and biomass of individual prey, calculated diet diversity indexes, and monitored nestling survivorship at 15 territories in …

A Draft Genome Provides Hypotheses On Drought Tolerance In A Keystone Plant Species In Western North America Threatened By Climate Change, Anthony E. Melton, James Beck, Stephanie J. Galla, Marcelo Serpe, Stephen Novak, Sven Buerki

Biology Faculty Publications and Presentations

Climate change presents distinct ecological and physiological challenges to plants as extreme climate events become more common. Understanding how species have adapted to drought, especially ecologically important nonmodel organisms, will be crucial to elucidate potential biological pathways for drought adaptation and inform conservation strategies. To aid in genome-to-phenome research, a draft genome was assembled for a diploid individual of Artemisia tridentata subsp. tridentata, a threatened keystone shrub in western North America. While this taxon has few genetic resources available and genetic/genomics work has proven difficult due to genetic heterozygosity in the past, a draft genome was successfully assembled. Aquaporin …

Intra-Specific Variation In Migration Phenology Of American Kestrels (Falco Sparverius) In Response To Spring Temperatures, Breanna F. Powers, Jason M. Winiarski, Juan M. Requena-Mullor, Julie A. Heath

Biology Faculty Publications and Presentations

In migratory birds, among- and within-species heterogeneity in response to climate change may be attributed to differences in migration distance and environmental cues that affect timing of arrival at breeding grounds. We used eBird observations and a within-species comparative approach to examine whether migration distance (with latitude as a proxy) and weather predictors can explain spring arrival dates at the breeding site in a raptor species with a widespread distribution and diverse migration strategies, the American Kestrel Falco sparverius. We found an interactive effect between latitude and spring minimum temperatures on arrival dates, whereby at lower latitudes (short-distance migrants) …

Authentication Of A Novel Antibody To Zebrafish Collagen Type Xi Alpha 1 Chain (Col11a1a), Jonathon C. Reeck, Makenna J. Hardy, Xinzhu Pu, Cynthia Keller-Peck, Julia Thom Oxford

Biology Faculty Publications and Presentations

Objective: Extracellular matrix proteins play important roles in embryonic development and antibodies that specifically detect these proteins are essential to understanding their function. The zebrafish embryo is a popular model for vertebrate development but suffers from a dearth of authenticated antibody reagents for research. Here, we describe a novel antibody designed to detect the minor fibrillar collagen chain Col11a1a in zebrafish (AB strain).

Results: The Col11a1a antibody was raised in rabbit against a peptide comprising a unique sequence within the zebrafish Col11a1a gene product. The antibody was affinity-purified and characterized by ELISA. The antibody is effective for immunoblot and immunohistochemistry …

Artificial Night Light And Anthropogenic Noise Interact To Influence Bird Abundance Over A Continental Scale, Ashley A. Wilson, Mark A. Ditmer, Jesse R. Barber, Neil H. Carter, Eliot T. Miller, Luke P. Tyrell, Clinton D. Francis

Biology Faculty Publications and Presentations

The extent of artificial night light and anthropogenic noise (i.e., “light” and “noise”) impacts is global and has the capacity to threaten species across diverse ecosystems. Existing research involving impacts of light or noise has primarily focused on noise or light alone and single species; however, these stimuli often co-occur and little is known about how co-exposure influences wildlife and if and why species may vary in their responses. Here, we had three aims: (1) to investigate species-specific responses to light, noise, and the interaction between the two using a spatially explicit approach to model changes in abundance of 140 …

Biological Soil Crusts Of The Great Plains: A Review, Steven D. Warren, Roger Rosentreter, Nicole Pietrasiak

Biology Faculty Publications and Presentations

Biological soil crusts (BSCs), or biocrusts, are composed of fungi, bacteria, algae, and bryophytes (mosses, etc.) that occupy bare soil, entwining soil particles with filaments or rootlike structures and/or gluing them together with polysaccharide exudates to form a consolidated surface crust that stabilizes the soil against erosion. BSCs are common in arid and semiarid regions where vascular plant cover is naturally sparse, maximizing the exposure of surface-dwelling organisms to direct sunlight. Although less prominent and less studied there, BSC organisms are also present in more mesic areas such as the Great Plains where they can be found in shortgrass and …

Cellular Activity Of Salmonella Typhimurium Artab Toxin And Its Receptor-Binding Subunit, Elise Overgaard, Brad Morris, Omid Mohammad Mousa, Adriana Rodriguez, Leyla Cufurovic, Richard S. Beard, Juliette K. Tinker

Biology Faculty Publications and Presentations

Salmonellosis is among the most reported foodborne illnesses in the United States. The Salmonella enterica Typhimurium DT104 phage type, which is associated with multidrug-resistant disease in humans and animals, possesses an ADP-ribosylating toxin called ArtAB. Full-length artAB has been found on a number of broad-host-range non-typhoidal Salmonella species and serovars. ArtAB is also homologous to many AB₅ toxins from diverse Gram-negative pathogens, including cholera toxin (CT) and pertussis toxin (PT), and may be involved in Salmonella pathogenesis, however, in vitro cellular toxicity of ArtAB has not been characterized. artAB was cloned into E. coli and initially isolated …

Scaling Up Sagebrush Chemistry With Near-Infrared Spectroscopy And Uas-Acquired Hyperspectral Imagery, Peter J. Olsoy, Brecken C. Robb, Jennifer Sorenson Forbey, T. Trevor Caughlin, Chelsea Merriman, Jordan D. Nobler

Biology Faculty Publications and Presentations

Sagebrush ecosystems (Artemisia spp.) face many threats including large wildfires and conversion to invasive annuals, and thus are the focus of intense restoration efforts across the western United States. Specific attention has been given to restoration of sagebrush systems for threatened herbivores, such as Greater Sage-Grouse (Centrocercus urophasianus) and pygmy rabbits (Brachylagus idahoensis), reliant on sagebrush as forage. Despite this, plant chemistry (e.g., crude protein, monoterpenes and phenolics) is rarely considered during reseeding efforts or when deciding which areas to conserve. Near-infrared spectroscopy (NIRS) has proven effective in predicting plant chemistry under laboratory conditions in …

Exploring Microbiome Functional Dynamics Through Space And Time With Trait-Based Theory, Leonora S. Bittleston, Jessica R. Bernardin

Biology Faculty Publications and Presentations

Microbiomes play essential roles in the health and function of animal and plant hosts and drive nutrient cycling across ecosystems. Integrating novel trait-based approaches with ecological theory can facilitate the prediction of microbial functional traits important for ecosystem functioning and health. In particular, the yield-acquisition-stress (Y-A-S) framework considers dominant microbial life history strategies across gradients of resource availability and stress. However, microbiomes are dynamic, and spatial and temporal shifts in taxonomic and trait composition can affect ecosystem functions. We posit that extending the Y-A-S framework to microbiomes during succession and across biogeographic gradients can lead to generalizable rules for how …

Long-Term Crop Rotation Diversification Enhances Maize Drought Resistance Through Soil Organic Matter, Leah L.R. Renwick, William Deen, Lucas Silva, Matthew E. Gilbert, Toby Maxwell, Timothy M. Bowles, Amélie C.M. Gaudin

Biology Faculty Publications and Presentations

Climate change adaptation requires building agricultural system resilience to warmer, drier climates. Increasing temporal plant diversity through crop rotation diversification increases yields of some crops under drought, but its potential to enhance crop drought resistance and the underlying mechanisms remain unclear. We conducted a drought manipulation experiment using rainout shelters embedded within a 36-year crop rotation diversity and no-till experiment in a temperate climate and measured a suite of soil and crop developmental and eco-physiological traits in the field and laboratory. We show that diversifying maize-soybean rotations with small grain cereals and cover crops mitigated maize water stress at the …

The Role Of Genome Duplication In Big Sagebrush Growth And Fecundity, Bryce A. Richardson, Matthew J. Germino, Marcus V. Warwell, Sven Buerki

Biology Faculty Publications and Presentations

Premise: Adaptive traits can be dramatically altered by genome duplication. The study of interactions among traits, ploidy, and the environment are necessary to develop an understanding of how polyploidy affects niche differentiation and to develop restoration strategies for resilient native ecosystems.

Methods: Growth and fecundity were measured in common gardens for 39 populations of big sagebrush (Artemisia tridentata) containing two subspecies and two ploidy levels. General linear mixed-effect models assessed how much of the trait variation could be attributed to genetics (i.e., ploidy and climatic adaptation), environment, and gene–environment interactions.

Results: Growth and fecundity variation were explained well …

Using An Ultraviolet Light Test To Improve Sagebrush Identification And Predict Forage Quality For Wildlife, Roger Rosentreter, Brecken C. Robb, Jennifer S. Forbey

Biology Faculty Publications and Presentations

Sagebrush identification can be improved by using a relatively easy ultraviolet (UV) light test on specimens. Sagebrush produces a variety of water-soluble polyphenols called coumarins, which fluoresce a blue color under UV light and can help differentiate species, subspecies, and hybrids. We tested 16 different sagebrush taxa (including species and subspecies) from herbarium specimens and found 3 taxa (low sagebrush, Artemisia arbuscula; Wyoming sagebrush, A. tridentata wyomingensis; and basin sagebrush, A. t. tridentata) that were often misidentified. We show that the UV light test can greatly improve identification of these species. Moreover, given that the UV+ chemicals …

A Higher-Level Nuclear Phylogenomic Study Of The Carrot Family (Apiaceae), James F. Smith

Biology Faculty Publications and Presentations

PREMISE: The carrot family (Apiaceae) comprises 466 genera, which include many well-known crops (e.g., aniseed, caraway, carrots, celery, coriander, cumin, dill, fennel, parsley, and parsnips). Higher-level phylogenetic relationships among subfamilies, tribes, and other major clades of Apiaceae are not fully resolved. This study aims to address this important knowledge gap.

METHODS: Target sequence capture with the universal Angiosperms353 probe set was used to examine phylogenetic relationships in 234 genera of Apiaceae, representing all four currently recognized subfamilies (Apioideae, Azorelloideae, Mackinlayoideae, and Saniculoideae). Recovered nuclear genes were analyzed using both multispecies coalescent and concatenation approaches.

RESULTS: We recovered hundreds of nuclear …

An Updated Infra-Familial Classification Of Sapindaceae Based On Targeted Enrichment Data, Sven Buerki

Biology Faculty Publications and Presentations

Premise: The economically important, cosmopolitan soapberry family (Sapindaceae) comprises ca. 1900 species in 144 genera. Since the seminal work of Radlkofer, several authors have attempted to overcome challenges presented by the family’s complex infra-familial classification. With the advent of molecular systematics, revisions of the various proposed groupings have provided significant momentum, but we still lack a formal classification system rooted in an evolutionary framework.

Methods: Nuclear DNA sequence data were generated for 123 genera (86%) of Sapindaceae using target sequence capture with the Angiosperms353 universal probe set. HybPiper was used to produce aligned DNA matrices. Phylogenetic inferences were obtained using …

Resolving Species Boundaries In A Recent Radiation With The Angiosperms353 Probe Set: The Lomatium Packardiae/L. Anomalum Clade Of The L. Triternatum (Apiaceae) Complex, Michael V. Ottenlips, Sven Buerki, James F. Smith

Biology Faculty Publications and Presentations

Premise: Speciation not associated with morphological shifts is challenging to detect unless molecular data are employed. Using Sanger-sequencing approaches, the Lomatium packardiae/L. anomalum subcomplex within the larger Lomatium triternatum complex could not be resolved. Therefore, we attempt to resolve these boundaries here.

Methods: The Angiosperms353 probe set was employed to resolve the ambiguity within Lomatium triternatum species complex using 48 accessions assigned to L. packardiae, L. anomalum, or L. triternatum. In addition to exon data, 54 nuclear introns were extracted and were complete for all samples. Three approaches were used to estimate evolutionary relationships and define species …

Data Management Tools To Measure The Impact Of Core Facilities, Diane B. Smith, Tracy L. Yarnell, Barbara J. Jibben, Linda E. Liou, Carolyn J. Hovde, Julia Thom Oxford

Biology Faculty Publications and Presentations

The Biomolecular Research Center at Boise State University is a research core facility that supports the study of biomolecules with an emphasis on protein structure and function, molecular interactions, and imaging. The mission of the core is to facilitate access to instrumentation that might otherwise be unavailable because of the cost, training for new users, and scientific staff with specialized skills to support early-stage investigators, as well as more established senior investigators. Data collection and management of users and their research output is essential to understand the impact of the center on the research environment and research productivity. However, challenges …

Poor Vector Competence Of The Human Flea, Pulex Irritans, To Transmit Yersinia Pestis, Adélaïde Miarinjara, David M. Bland, James R. Belthoff, B. Joseph Hinnebusch

Biology Faculty Publications and Presentations

Background: The human flea, Pulex irritans, is widespread globally and has a long association with humans, one of its principal hosts. Its role in plague transmission is still under discussion, although its high prevalence in plague-endemic regions and the presence of infected fleas of this species during plague outbreaks has led to proposals that it has been a significant vector in human-to-human transmission in some historical and present-day epidemiologic situations. However, based on a limited number of studies, P. irritans is considered to be a poor vector and receives very little attention from public health policymakers. In this study …

Decellularized Porcine Cartilage Scaffold: Validation Of Decellularization And Evaluation Of Biomarkers Of Chondrogenesis, Roxanne N. Stone, Stephanie M. Frahs, Makenna J. Hardy, Akina Fujimoto, Xinzhu Pu, Cynthia Keller-Peck, Julia Thom Oxford

Biology Faculty Publications and Presentations

Osteoarthritis is a major concern in the United States and worldwide. Current non-surgical and surgical approaches alleviate pain but show little evidence of cartilage restoration. Cell-based treatments may hold promise for the regeneration of hyaline cartilage-like tissue at the site of injury or wear. Cell–cell and cell–matrix interactions have been shown to drive cell differentiation pathways. Biomaterials for clinically relevant applications can be generated from decellularized porcine auricular cartilage. This material may represent a suitable scaffold on which to seed and grow chondrocytes to create new cartilage. In this study, we used decellularization techniques to create an extracellular matrix scaffold …

Linking Behavioral States To Landscape Features For Improved Conservation Management, Maitreyi Sur, Jim R. Belthoff

Biology Faculty Publications and Presentations

1. A central theme for conservation is understanding how animals differentially use, and are affected by change in, the landscapes they inhabit. However, it has been challenging to develop conservation schemes for habitat-specific behaviors.
2. Here we use behavioral change point analysis to identify behavioral states of golden eagles (Aquila chrysaetos) in the Sonoran and Mojave Deserts of the southwestern United States, and we identify, for each behavioral state, conservation-relevant habitat associations.
3. We modeled behavior using 186,859 GPS points from 48 eagles and identified 2,851 distinct segments comprising four behavioral states. Altitude above ground level (AGL) best differentiated behavioral states, …

Unifying Community Detection Across Scales From Genomes To Landscapes, Stephanie F. Hudon, Andrii Zaiats, Anna Roser, Anand Roopsind, Cristina Barber, Brecken Robb, Britt Pendleton, Merry M. Davidson, Jonas Frankel-Bricker, Marcella Fremgen-Tarantino, Jennifer Sorensen Forbey, Eric Hayden, Olivia K. Rodriguez, T. Trevor Caughlin

Biology Faculty Publications and Presentations

Biodiversity science encompasses multiple disciplines and biological scales from molecules to landscapes. Nevertheless, biodiversity data are often analyzed separately with discipline-specific methodologies, constraining resulting inferences to a single scale. To overcome this, we present a topic modeling framework to analyze community composition in cross-disciplinary datasets, including those generated from metagenomics, metabolomics, field ecology and remote sensing. Using topic models, we demonstrate how community detection in different datasets can inform the conservation of interacting plants and herbivores. We show how topic models can identify members of molecular, organismal and landscape-level communities that relate to wildlife health, from gut microbes to forage …

Phantom Rivers Filter Birds And Bats By Acoustic Niche, D. G. E. Gomes, C. A. Toth, H. J. Cole, C. D. Francis, J. R. Barber

Biology Faculty Publications and Presentations

Natural sensory environments, despite strong potential for structuring systems, have been neglected in ecological theory. Here, we test the hypothesis that intense natural acoustic environments shape animal distributions and behavior by broadcasting whitewater river noise in montane riparian zones for two summers. Additionally, we use spectrally-altered river noise to explicitly test the effects of masking as a mechanism driving patterns. Using data from abundance and activity surveys across 60 locations, over two full breeding seasons, we find that both birds and bats avoid areas with high sound levels, while birds avoid frequencies that overlap with birdsong, and bats avoid higher …

Sodah: The Soils Data Harmonization Database, An Open-Source Synthesis Of Soil Data From Research Networks, Version 1.0, Marie-Anne De Graaff

Biology Faculty Publications and Presentations

Data collected from research networks present opportunities to test theories and develop models about factors responsible for the long-term persistence and vulnerability of soil organic matter (SOM). Synthesizing datasets collected by different research networks presents opportunities to expand the ecological gradients and scientific breadth of information 55 available for inquiry. Synthesizing these data, are challenging, especially considering the legacy of soils data that has already been collected and an expansion of new network science initiatives. To facilitate this effort, here we present the SOils DAta Harmonization database (SoDaH; https://lter.github.io/som-website, last accessed 15 July 2020), a flexible database designed to harmonize …

New Applications For The Kinetic Exclusion Assay (Kinexa), Mark Harrison Smith

Boise State University Theses and Dissertations

This dissertation examines the fundamental principles and applicability of the kinetic exclusion assay (KinExA), developed and marketed by Sapidyne Instruments of Boise, Idaho, since 1995. Chapter One reviews and consolidates the manufacturer’s guidance and many early papers that delineate the practical and theoretical aspects of the technology. In brief, KinExA is a two stage analytical system. In stage one, a number of solutions are prepared, whereby one of the partners is kept constant (the constant binding partner, or CBP), while the other (the titrant) is varied, usually in serial dilution. As the titrant is increased, the free CBP decreases, and …

Natural Noise Can Influence Bird Foraging And Vigilance Behavior, Kate Antonia Sweet

Boise State University Theses and Dissertations

Natural sounds are an often overlooked, yet important component of an animal’s habitat. The acoustic environment may be especially significant during foraging, because a noisy world can limit auditory surveillance. Here, we investigated how natural noise structures the foraging vigilance trade-off to understand how intense acoustic environments may have shaped antipredator behavior across the evolutionary past, and better inform conservation efforts in the present.

First, in Chapter 1, I directly compared the foraging and vigilance behaviors of captive song sparrows (Melospiza melodia) in anthropogenic and natural noise. We recorded foraging trials in 4 playback conditions (roadway traffic, whitewater …