Life Sciences Commons^™

Drone Imagery Protocols To Map Vegetation Are Transferable Between Dryland Sites Across An Elevational Gradient, Anna Roser, Josh Enterkine, Juan M. Requena-Mullor, Nancy F. Glenn, Alex R. Boehm, Marie-Anne De Graaff, Patrick E. Clark, Fred Pierson, T. Trevor Caughlin

Biology Faculty Publications and Presentations

The structure and composition of plant communities in drylands are highly variable across scales, from microsites to landscapes. Fine spatial resolution field surveys of dryland plants are essential to unravel the impact of climate change; however, traditional field data collection is challenging considering sampling efforts and costs. Unoccupied aerial systems (UAS) can alleviate this challenge by providing standardized measurements of plant community attributes with high resolution. However, given widespread heterogeneity in plant communities in drylands, and especially across environmental gradients, the transferability of UAS imagery protocols is unclear. Plant functional types (PFTs) are a classification scheme that aggregates the diversity …

Post-Fire Seed Dispersal Of A Wind-Dispersed Shrub Declined With Distance To Seed Source, Yet Had High Levels Of Unexplained Variation, Cara Applestein, T. Trevor Caughlin, Matthew J. Germino

Biology Faculty Publications and Presentations

Plant-population recovery across large disturbance areas is often seed-limited. An understanding of seed dispersal patterns is fundamental for determining natural-regeneration potential. However, forecasting seed dispersal rates across heterogeneous landscapes remains a challenge. Our objectives were to determine (i) the landscape patterning of post-disturbance seed dispersal, and underlying sources of variation and the scale at which they operate, and (ii) how the natural seed dispersal patterns relate to a seed augmentation strategy. Vertical seed trapping experiments were replicated across 2 years and five burned and/or managed landscapes in sagebrush steppe. Multi-scale sampling and hierarchical Bayesian models were used to determine the …

The Effects Of Cheatgrass Invasion On Us Great Basin Carbon Storage Depend On Interactions Between Plant Community Composition, Precipitation Seasonality, And Soil Climate Regime, Toby M. Maxwell, Matthew J. Germino

Biology Faculty Publications and Presentations

1. Annual-grass invasions are transforming desert ecosystems in ways that affect ecosystem carbon (C) balance, but previous studies do not agree on the pattern, magnitude and direction of changes. A recent meta-analysis of 41 articles and 386 sites concludes that invasion by annual grasses such as cheatgrass (Bromus tectorum L) reduces C in biomass across the Great Basin (Nagy et al., 2021). Reanalysis reveals that whether cheatgrass affects biomass C stocks is not generalizable, but rather depends on the considerable variation in climate across the subject sites. Our analysis suggests that accurate Great Basin-scale estimates of cheatgrass effects on C …

Meta-Analysis Reveals Challenges And Gaps For Genome-To-Phenome Research Underpinning Plant Drought Response, Anthony E. Melton, Stephanie J. Galla, Carlos Dave C. Dumaguit, John M.A. Wojahn, Stephen Novak, Marcelo Serpe, Peggy Martinez, Sven Buerki

Biology Faculty Publications and Presentations

Severe drought conditions and extreme weather events are increasing worldwide with climate change, threatening the persistence of native plant communities and ecosystems. Many studies have investigated the genomic basis of plant responses to drought. However, the extent of this research throughout the plant kingdom is unclear, particularly among species critical for the sustainability of natural ecosystems. This study aimed to broaden our understanding of genome-to-phenome (G2P) connections in drought-stressed plants and identify focal taxa for future research. Bioinformatics pipelines were developed to mine and link information from databases and abstracts from 7730 publications. This approach identified 1634 genes involved in …

Phenology Effects On Productivity And Hatching-Asynchrony Of American Kestrels (Falco Sparverius) Across A Continent, Kathleen R. Callery, Sarah E. Schulwitz, Anjolene R. Hunt, Jason M. Winiarski, Christopher J. W. Mcclure, Richard A. Fischer, Julie A. Heath

Biology Faculty Publications and Presentations

Optimal reproductive performance occurs when birds time reproduction to coincide with peak food availability. Deviation from optimal timing, or mismatch, can affect productivity, though birds may mediate some mismatch effects by altering their incubation behavior. We studied the consequences of nesting timing (i.e., clutch initiation relative to an index of spring start) on productivity across the breeding range of American kestrels (Falco sparverius) in the United States and southern Canada, and associations between nesting timing, incubation behavior, and hatching asynchrony. We used observations from long-term nest box monitoring, remote trail cameras, and community-scientist-based programs to obtain data on …

Sarracenia Pitcher Plant-Associated Microbial Communities Differ Primarily By Host Species Across A Longitudinal Gradient, Jacob A. Heil, Charles J. Wolock, Naomi E. Pierce, Anne Pringle, Leonora S. Bittleston

Biology Faculty Publications and Presentations

Plant-associated microbial communities can profoundly affect plant health and success, and research is still uncovering factors driving the assembly of these communities. Here, we examine how geography versus host species affects microbial community structure and differential abundances of individual taxa. We use metabarcoding to characterize the bacteria and eukaryotes associated with five, often co-occurring species of Sarracenia pitcher plants (Sarraceniaceae) and three natural hybrids along the longitudinal gradient of the U.S. Gulf Coast, as well as samples from S. purpurea in Massachusetts. To tease apart the effects of geography versus host species, we focus first on sites with co-occurring …

Near-Infrared Spectroscopy Aids Ecological Restoration By Classifying Variation Of Taxonomy And Phenology Of A Native Shrub, Brecken C. Robb, Peter J. Olsoy, T. Trevor Caughlin, Stephanie J. Galla, Marcella R. Fremgen-Tarantino, Jordan D. Nobler, Jennifer S. Forbey

Biology Faculty Publications and Presentations

Plant communities are composed of complex phenotypes that not only differ among taxonomic groups and habitats but also change over time within a species. Restoration projects (e.g. translocations and reseeding) can introduce new functional variation in plants, which further diversifies phenotypes and complicates our ability to identify locally adaptive phenotypes for future restoration. Near-infrared spectroscopy (NIRS) offers one approach to detect the chemical phenotypes that differentiate plant species, populations, and phenological states of individual plants over time. We use sagebrush (Artemisia spp.) as a case study to test the accuracy by which NIRS can classify variation within taxonomy and …

Interannual Variation In Climate Contributes To Contingency In Post-Fire Restoration Outcomes In Seeded Sagebrush Steppe, Allison B. Simler-Williamson, Cara Applestein, Matthew J. Germino

Biology Faculty Publications and Presentations

Interannual variation, especially weather, is an often-cited reason for restoration “failures”; yet its importance is difficult to experimentally isolate across broad spatiotemporal extents, due to correlations between weather and site characteristics. We examined post-fire treatments within sagebrush-steppe ecosystems to ask: (1) Is weather following seeding efforts a primary reason why restoration outcomes depart from predictions? and (2) Does the management-relevance of weather differ across space and with time since treatment? Our analysis quantified range-wide patterns of sagebrush (Artemisia spp.) recovery, by integrating long-term records of restoration and annual vegetation cover estimates from satellite imagery following thousands of post-fire seeding …

A Haploid Pseudo-Chromosome Genome Assembly For A Keystone Sagebrush Species Of Western North American Rangelands, Anthony E. Melton, Richard S. Beard Jr., Carlos Dave C. Dumaguit, Jennifer S. Forbey, Marie-Anne De Graaff, Peggy Martinez, Stephen J. Novak, Desiree Self, Marcelo Serpe, Sven Buerki

Biology Faculty Publications and Presentations

Increased ecological disturbances, species invasions, and climate change are creating severe conservation problems for several plant species that are widespread and foundational. Understanding the genetic diversity of these species and how it relates to adaptation to these stressors are necessary for guiding conservation and restoration efforts. This need is particularly acute for big sagebrush (Artemisia tridentata; Asteraceae), which was once the dominant shrub over 1,000,000 km² in western North America but has since retracted by half and thus has become the target of one of the largest restoration seeding efforts globally. Here, we present the first reference-quality …

Optimizing Process-Based Models To Predict Current And Future Soil Organic Carbon Stocks At High-Resolution, Marie-Anne De Graaff, Ryan Will

Biology Faculty Publications and Presentations

From hillslope to small catchment scales (< 50 km²), soil carbon management and mitigation policies rely on estimates and projections of soil organic carbon (SOC) stocks. Here we apply a process-based modeling approach that parameterizes the MIcrobial-MIneral Carbon Stabilization (MIMICS) model with SOC measurements and remotely sensed environmental data from the Reynolds Creek Experimental Watershed in SW Idaho, USA. Calibrating model parameters reduced error between simulated and observed SOC stocks by 25%, relative to the initial parameter estimates and better captured local gradients in climate and productivity. The calibrated parameter ensemble was used to produce spatially continuous, high-resolution (10 m …

Anti-Bat Ultrasound Production In Moths Is Globally And Phylogenetically Widespread, Jesse R. Barber, Brian C. Leavell, Krystie A. Miner, Brandt Quirk-Royal

Biology Faculty Publications and Presentations

Warning signals are well known in the visual system, but rare in other modalities. Some moths produce ultrasonic sounds to warn bats of noxious taste or to mimic unpalatable models. Here, we report results from a long-term study across the globe, assaying moth response to playback of bat echolocation. We tested 252 genera, spanning most families of large-bodied moths, and document anti-bat ultrasound production in 52 genera, with eight subfamily origins described. Based on acoustic analysis of ultrasonic emissions and palatability experiments with bats, it seems that acoustic warning and mimicry are the raison d'être for sound production in most …

Characterization And Comparison Of Convergence Among Cephalotus Follicularis Pitcher Plant-Associated Communities With Those Of Nepenthes And Sarracenia Found Worldwide, Leonora S. Bittleston, Elizabeth L. Benson, Jessica R. Bernardin, Naomi E. Pierce

Biology Faculty Publications and Presentations

The Albany pitcher plant, Cephalotus follicularis, has evolved cup-shaped leaves and a carnivorous habit completely independently from other lineages of pitcher plants. It is the only species in the family Cephalotaceae and is restricted to a small region of Western Australia. Here, we used metabarcoding to characterize the bacterial and eukaryotic communities living in C. follicularis pitchers at two different sites. Bacterial and eukaryotic communities were correlated in both richness and composition; however, the factors associated with richness were not the same across bacteria and eukaryotes, with bacterial richness differing with fluid color, and eukaryotic richness differing with the …

Reassessment Of Chirita Umbrophila (Gesneriaceae) Based On Molecular And Morphological Evidence, Peng-Wei Li, James F. Smith, Debabrata Maity, Xi-Zuo Shi, Li-Hua Yang

Biology Faculty Publications and Presentations

Chirita umbrophila is a species endemic to Yunnan, China, and its exact systematic position remains a mystery since it was treated as a species with uncertain generic affiliation in the taxonomic revision of Chirita in 1985. In the present study, the phylogenetic relationships between C. umbrophila and its allied species were inferred using two nuclear ribosomal DNA regions (ETS and ITS) and three chloroplast regions (rpl16, rps16, and trnL-F). Additionally, the type locality of C. umbrophila was revisited and flowering specimens were collected and examined. Our phylogenetic analyses showed that Chirita umbrophila is imbedded in three …

Detecting Gold Mining Impacts On Insect Biodiversity In A Tropical Mining Frontier With Smallsat Imagery, Eric Stoll, Anand Roopsind, Gyanpriya Maharaj, Sandra Velazco, T. Trevor Caughlin

Biology Faculty Publications and Presentations

Gold mining is a major driver of Amazonian forest loss and degradation. As mining activity encroaches on primary forest in remote and inaccessible areas, satellite imagery provides crucial data for monitoring mining-related deforestation. High-resolution imagery, in particular, has shown promise for detecting artisanal gold mining at the forest frontier. An important next step will be to establish relationships between satellite-derived land cover change and biodiversity impacts of gold mining. In this study, we set out to detect artisanal gold mining using high-resolution imagery and relate mining land cover to insects, a taxonomic group that accounts for the majority of faunal …

Two New Pendulous Epiphytic Columnea L. (Gesneriaceae) Species From The Chocó Forests Of The Northern Andes, Francisco Tobar, James F. Smith, John L. Clark

Biology Faculty Publications and Presentations

Exploratory field expeditions to the Chocó forests in the northwestern slopes of the Ecuadorian and Colombian Andes resulted in the discovery of two new species of Columnea (Gesneriaceae). Columnea fluidifolia J.L.Clark & F.Tobar, sp. nov., is described as a narrow endemic from Bosque Protector Mashpi and surrounding areas in the province of Pichincha in northern Ecuador. Columnea pendens F.Tobar, J.L.Clark & J.F.Sm., sp. nov., is described from recently discovered populations in the provinces of Carchi and Santo Domingo de los Tsáchilas (Ecuador) and the departments of Cauca and Nariño in southwestern Colombia. The two new species are pendent …

Clock-Linked Genes Underlie Seasonal Migratory Timing In A Diurnal Raptor, Christen M. Bossu, Julie A. Heath, Gregory S. Kaltenecker, Barbara Helm, Kristen C. Ruegg

Biology Faculty Publications and Presentations

Seasonal migration is a dynamic natural phenomenon that allows organisms to exploit favourable habitats across the annual cycle. While the morphological, physiological and behavioural changes associated with migratory behaviour are well characterized, the genetic basis of migration and its link to endogenous biological time-keeping pathways are poorly understood. Historically, genome-wide research has focused on genes of large effect, whereas many genes of small effect may work together to regulate complex traits like migratory behaviour. Here, we explicitly relax stringent outlier detection thresholds and, as a result, discover how multiple biological time-keeping genes are important to migratory timing in an iconic …

Food Quality, Security, And Thermal Refuge Influence The Use Of Microsites And Patches By Pygmy Rabbits (Brachylagus Idahoensis) Across Landscapes And Seasons, Peter J. Olsoy, Charlotte R. Milling, Jordan D. Nobler, Meghan J. Camp, Lisa A. Shipley, Jennifer S. Forbey, Janet L. Rachlow, Daniel H. Thornton

Biology Faculty Publications and Presentations

How intensely animals use habitat features depends on their functional properties (i.e., how the feature influences fitness) and the spatial and temporal scale considered. For herbivores, habitat use is expected to reflect the competing risks of starvation, predation, and thermal stress, but the relative influence of each functional property is expected to vary in space and time. We examined how a dietary and habitat specialist, the pygmy rabbit (Brachylagus idahoensis), used these functional properties of its sagebrush habitat—food quality, security, and thermal refuge—at two hierarchical spatial scales (microsite and patch) across two seasons (winter and summer). At the …

Seasonal Trends In Adult Apparent Survival And Reproductive Trade-Offs Reveal Potential Constraints To Earlier Nesting In A Migratory Bird, Kathleen R. Callery, John A. Smallwood, Anjolene R. Hunt, Emilie R. Snyder, Julie A. Heath

Biology Faculty Publications and Presentations

Birds aim to optimize resources for feeding young and self-maintenance by timing reproduction to coincide with peak food availability. When reproduction is mistimed, birds could incur costs that affect their survival. We studied whether nesting phenology correlated with the apparent survival of American kestrels (Falco sparverius) from two distinct populations and examined trends in clutch-initiation dates. We estimated apparent survival using multi-state mark-recapture models with nesting timing, nesting success, sex, age, and weather covariates. Nesting timing predicted the apparent survival of successful adults; however, the effect differed between populations. Early nesting kestrels had higher apparent survival than later …

Centralized Project-Specific Metadata Platforms: Toolkit Provides New Perspectives On Open Data Management Within Multi-Institution And Multidisciplinary Research Projects, Andrew Wright Child, Jennifer Hinds, Lucas Sheneman, Sven Buerki

Biology Faculty Publications and Presentations

Open science and open data within scholarly research programs are growing both in popularity and by requirement from grant funding agencies and journal publishers. A central component of open data management, especially on collaborative, multidisciplinary, and multi-institutional science projects, is documentation of complete and accurate metadata, workflow, and source code in addition to access to raw data and data products to uphold FAIR (Findable, Accessible, Interoperable, Reusable) principles. Although best practice in data/metadata management is to use established internationally accepted metadata schemata, many of these standards are discipline-specific making it difficult to catalog multidisciplinary data and data products in a …

Nonhistone Lysine Methylation As A Protein Degradation Signal, Nicholas A. Lehning, Brad E. Morrison

Biology Faculty Publications and Presentations

Protein degradation is a fundamental feature of cellular life, and malfunction of this process is implicated in human disease. Ubiquitin tagging is the best characterized mechanism of targeting a protein for degradation; however, there are a growing number of distinct mechanisms which have also been identified that carry out this essential function. For example, covalent tagging of proteins with sequestosome-1 targets them for selective autophagy. Degradation signals are not exclusively polypeptides such as ubiquitin, NEDD8, and sequestosome-1. Phosphorylation, acetylation, and methylation are small covalent additions that can also direct protein degradation. The diversity of substrate sequences and overlap with other …

Importance Of Local Weather And Environmental Gradients On Demography Of A Broadly Distributed Temperate Frog, Hallie Lingo, James C. Munger

Biology Faculty Publications and Presentations

Amphibian populations are sensitive to environmental temperatures and moisture, which vary with local weather conditions and may reach new norms and extremes as contemporary climate change progresses. Using long-term (11–16 years) mark-recapture data from 10 populations of the Columbia spotted frog (Rana luteiventris) from across its U.S. range, we addressed hypotheses about how demographic relationships to weather depend upon a population’s position along climate gradients. We estimated the effect of seasonal weather on annual survival probability and recruitment rates both within populations and across the species’ range from subalpine forests to semi-arid deserts. We calculated population-specific weather variables …

Endemism, Projected Climate Change, And Identifying Species Of Critical Concern In The Scrub Mint Clade (Lamiaceae), Andre A. Naranjo, Anthony E. Melton, Douglas E. Soltis, Pamela S. Soltis

Biology Faculty Publications and Presentations

Recent studies have revealed that narrow endemics, particularly those native to the North American Coastal Plain, are experiencing range contractions due to human development and anthropogenic-driven climate warming. We model how the projected distributions of a group of scrub-adapted plant species with similar evolutionary histories change in response to warming climates. The Scrub Mint clade (Lamiaceae) (SMC), which comprises 24 species in Dicerandra, Conradina, Stachydeoma, Piloblephis, and Clinopodium, including federally or state-listed threatened and endangered species, occurs in the scrub and sandhill biomes of the North American Coastal Plain. Georeferenced occurrence points were used to …

Drivers Of Flight Performance Of California Condors (Gymnogyps Californianus), Sophie R. Bonner, Sharon A. Poessel, Joseph C. Brandt, Molly T. Astell, James R. Belthoff, Todd E. Katzner

Biology Faculty Publications and Presentations

Flight behavior of soaring birds depends on a complex array of physiological, social, demographic, and environmental factors. California Condors (Gymnogyps californianus) rely on thermal and orographic updrafts to subsidize extended bouts of soaring flight, and their soaring flight performance is expected to vary in response to environmental variation and, potentially, with experience. We collected 6298 flight tracks described by high-frequency GPS telemetry data from five birds ranging in age from 1 to 19 yr old and followed over 32 d in summer 2016. Using these data, we tested the hypothesis that climb rate, an indicator of flight performance, …

Interactions Between Strains Govern The Eco-Evolutionary Dynamics Of Microbial Communities, Akshit Goyal, Leonora S. Bittleston, Gabriel E. Leventhal, Lu Lu, Otto X. Cordero

Biology Faculty Publications and Presentations

Genomic data has revealed that genotypic variants of the same species, that is, strains, coexist and are abundant in natural microbial communities. However, it is not clear if strains are ecologically equivalent, and at what characteristic genetic distance they might exhibit distinct interactions and dynamics. Here, we address this problem by tracking 10 taxonomically diverse microbial communities from the pitcher plant Sarracenia purpurea in the laboratory for more than 300 generations. Using metagenomic sequencing, we reconstruct their dynamics over time and across scales, from distant phyla to closely related genotypes. We find that most strains are not ecologically equivalent and …

Mule Deer Do More With Less: Comparing Their Nutritional Requirements And Tolerances With White-Tailed Deer, Anna R. Staudenmaier, Lisa A. Shipley, Meghan J. Camp, Jennifer S. Forbey, Ann E. Hagerman, Abigail E. Brandt, Daniel H. Thornton

Biology Faculty Publications and Presentations

Congeneric species often share ecological niche space resulting in competitive interactions that either limit co-occurrence or lead to niche partitioning. Differences in fundamental nutritional niches mediated through character displacement or isolation during evolution are potential mechanisms that could explain overlapping distribution patterns of congenerics. We directly compared nutritional requirements and tolerances that influence the fundamental niche of mule (Odocoileus hemionus) and white-tailed deer (O. virginianus), which occur in allopatry and sympatry in similar realized ecological niches across their ranges in North America. Digestible energy and protein requirements and tolerances for plant fiber and plant secondary …

The Relevance Of Pedigrees In The Conservation Genomics Era, Stephanie J. Galla, Julie A. Heath

Biology Faculty Publications and Presentations

Over the past 50 years conservation genetics has developed a substantive toolbox to inform species management. One of the most long-standing tools available to manage genetics—the pedigree—has been widely used to characterize diversity and maximize evolutionary potential in threatened populations. Now, with the ability to use high throughput sequencing to estimate relatedness, inbreeding, and genome-wide functional diversity, some have asked whether it is warranted for conservation biologists to continue collecting and collating pedigrees for species management. In this perspective, we argue that pedigrees remain a relevant tool, and when combined with genomic data, create an invaluable resource for conservation genomic …

The Nutritional Condition Of Moose Co-Varies With Climate, But Not With Density, Predation Risk, Or Diet Composition, Jennifer S. Forbey, Daniel P. Melody

Biology Faculty Publications and Presentations

A fundamental question about the ecology of herbivore populations pertains to the relative influence of biotic and abiotic processes on nutritional condition. Nutritional condition is influenced in important, yet poorly understood, ways by plant secondary metabolites (PSMs) which can adversely affect a herbivore’s physiology and energetics. Here we assess the relative influence of various abiotic (weather) and biotic (intraspecific competition, predation risk and diet composition) factors on indicators of nutritional condition and the energetic costs of detoxifying PSMs for the moose population in Isle Royale National Park (U.S.A.). Specifically, we observed interannual variation in the ratio of urea nitrogen to …

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 …