346 Works

Models to assess ability to achieve localized areas of reduced white-tailed deer density

Amanda Van Buskirk, Christopher Rosenberry, Bret Wallingford, Emily Just Domoto, Marc McDill, Patrick Drohan & Duane Diefenbach
Localized management of white-tailed deer (Odocoileus virginianus) involves the removal of matriarchal family units with the intent to create areas of reduced deer density. However, application of this approach has not always been successful, possibly because of female dispersal and high deer densities. We developed a spatially explicit, agent-based model to investigate the intensity of deer removal required to locally reduce deer density depending on the surrounding deer density, dispersal behavior, and size and shape...

Data from: User experience methods and maturity in academic libraries

Scott W. H. Young, Zoe Chao & Adam Chandler
This article presents a mixed-methods study of the methods and maturity of user experience (UX) practice in academic libraries. The authors apply qualitative content analysis and quantitative statistical analysis to a research dataset derived from a survey of UX practitioners. Results reveal the type and extent of UX methods currently in use by practitioners in academic libraries. Themes extracted from the survey responses also reveal a set of factors that influence the development of UX...

Pollen defenses negatively impact foraging and fitness in a generalist bee (Bombus impatiens: Apidae)

Kristen Brochu
Plants may benefit from limiting the community of generalist floral visitors if the species that remain are more effective pollinators and less effective pollenivores. Plants can reduce access to pollen through altered floral cues or morphological structures, but can also reduce consumption through direct pollen defenses. We observed that Eucera (Peponapis) pruinosa, a specialist bee on Cucurbita plants, collected pure loads of pollen while generalist honey bees and bumble bees collected negligible amounts of cucurbit...

Genetic connectivity and population structure of African savanna elephants (Loxodonta africana) in Tanzania

George Lohay, Casey Weathers, Anna Estes, Barbara McGrath & Douglas Cavener
Increasing human population growth, exurban development, and associated habitat fragmentation is accelerating the isolation of many natural areas and wildlife populations across the planet. In Tanzania, rapid and ongoing habitat conversion to agriculture has severed many of the country’s former wildlife corridors between protected areas. To identify historically-linked protected areas, we investigated the genetic structure and gene flow of African savanna elephants in Tanzania using microsatellite and mitochondrial DNA markers in 688 individuals. Our results...

Warming and shifting phenology accelerate an invasive plant life cycle

Joseph Keller & Katriona Shea
Numerous studies have documented changes in the seasonal timing of organisms’ growth and reproduction in response to climate warming. These changes correlate with documented changes in species’ abundance, but mechanisms linking these trends remain elusive. We investigated the joint demographic effects of advanced reproductive phenology and warming on a globally invasive plant (Carduus nutans) in a field experiment, documenting a substantial shift toward completion of the life cycle at younger ages. Demographic modeling projected 71%...

Pigmentation Genes Show Evidence of Repeated Divergence and Multiple Bouts of Introgression in Setophaga Warblers

David Toews, Marcella Baiz, Andrew Wood, Alan Brelsford & Irby Lovette
Species radiations have long served as model systems in evolutionary biology. However, it has only recently become possible to study the genetic bases of the traits responsible for diversification, and only in a small number of model systems. Here we use genomes of 36 species of North, Central, and South American warblers to highlight the role of pigmentation genes—involved in melanin and carotenoid processing—in the diversification of this group. We show that agouti signaling protein...

A comparative analysis of the photoprotection hypothesis for the evolution of autumn colors

Marco Archetti
The adaptive value of autumn colors – the seasonal production of red anthocyanins observed in many species of trees and shrubs – is still debated. According to the photoprotection hypothesis, anthocyanins protect leaves from photoinhibition and photooxidation at low temperatures, enabling the tree to reabsorb nutrients more efficiently before leaf fall. Hence, the hypothesis predicts that autumn colors are more likely to evolve in species growing in colder environments. We tested this prediction by comparing...

Antibiotics can be used to contain drug-resistant bacteria by maintaining sufficiently large sensitive populations

Elsa Hansen, Jason Karslake, Robert Woods, Andrew Read & Kevin Wood
Standard infectious disease practice calls for aggressive drug treatment that rapidly eliminates the pathogen population before resistance can emerge. When resistance is absent, this elimination strategy can lead to complete cure. However, when resistance is already present, removing drug-sensitive cells as quickly as possible removes competitive barriers that may slow the growth of resistant cells. In contrast to the elimination strategy, the containment strategy aims to maintain the maximum tolerable number of pathogens, exploiting competitive...

Temperature and fluid pressurization effects on frictional stability of shale faults reactivated by hydraulic fracturing in the Changning Block, Southwest China

Mengke An, Fengshou Zhang, Zhaowei Chen, Derek Elsworth & Lianyang Zhang
A shale fault reactivated during multi-stage hydraulic fracturing in the Changning block in the Sichuan Basin, southwest China accompanied a cluster of small earthquakes with the largest reaching ML ~0.8. We illuminate the underlying mechanisms of fault reactivation through measurements of frictional properties on simulated fault gouge under hydrothermal conditions. Velocity-stepping experiments were performed at a confining pressure of 60 MPa, temperatures from 30 to 300 ℃, pore fluid pressures from 10 to 55 MPa...

Data from: Spatially-explicit avian frugivory, fruit availability, and seed rain in a latitudinal gradient of the Americas

Tomás Carlo
Network metrics are widely used to infer the roles of mutualistic animals in plant communities and to predict the effect of species' loss. However, their empirical validation is scarce. Here we parameterized a joint species model of frugivory and seed dispersal with bird movement and foraging data from tropical and temperate communities. With this model we investigate the effect of frugivore loss on seed rain, and compare our predictions to those of standard coextinction models...

Data from: VolcanoFinder: genomic scans for adaptive introgression

Derek Setter, Sylvain Mousset, Xiaoheng Cheng, Rasmus Nielsen, Michael DeGiorgio & Joachim Hermisson
Recent research shows that introgression between closely-related species is an important source of adaptive alleles for a wide range of taxa. Typically, detection of adaptive introgression from genomic data relies on comparative analyses that require sequence data from both the recipient and the donor species. However, in many cases, the donor is unknown or the data is not currently available. Here, we introduce a genome-scan method---VolcanoFinder---to detect recent events of adaptive introgression using polymorphism data...

Data from: Insights into the development and evolution of exaggerated traits using de novo transcriptomes of two species of horned scarab beetles

Ian A. Warren, J. Cristobal Vera, Annika Johns, Robert Zinna, James H. Marden, Douglas J. Emlen, Ian Dworkin & Laura C. Lavine
Scarab beetles exhibit an astonishing variety of rigid exo-skeletal outgrowths, known as “horns”. These traits are often sexually dimorphic and vary dramatically across species in size, shape, location, and allometry with body size. In many species, the horn exhibits disproportionate growth resulting in an exaggerated allometric relationship with body size, as compared to other traits, such as wings, that grow proportionately with body size. Depending on the species, the smallest males either do not produce...

Data from: Virus infection influences host plant interactions with non-vector herbivores and predators

Kerry Mauck, Erica Smyers, Consuelo M. De Moraes, Mark Mescher, Kerry E. Mauck & Mark C. Mescher
1. Viruses are widespread in both natural and agricultural plant communities and can significantly alter diverse traits of their host plants that mediate key interactions with other organisms. Yet, the impacts of plant viruses on broader community dynamics remain little studied. 2. Here we explore the effects of Cucumber mosaic virus, a common non-persistently transmitted plant virus, on short and long-term interactions of herbivorous and predatory insects with squash (Cucurbita pepo) plants in a weedy...

Data from: Immune response and insulin signalling alter mosquito feeding behaviour to enhance malaria transmission potential

Jose E. Pietri, Lauren J. Cator, Courtney C. Murdock, Johanna R. Ohm, Edwin E. Lews, Andrew F. Read, Shirley Luckhart & Matthew B. Thomas
Malaria parasites alter mosquito feeding behaviour in a way that enhances parasite transmission. This is widely considered a prime example of manipulation of host behaviour to increase onward transmission, but transient immune challenge in the absence of parasites can induce the same behavioural phenotype. Here, we show that alterations in feeding behaviour depend on the timing and dose of immune challenge relative to blood ingestion and that these changes are functionally linked to changes in...

Data from: Population and genetic outcomes 20 years after reintroducing bobcats (Lynx rufus) to Cumberland Island, Georgia USA

Duane Diefenbach, Leslie Hansen, Justin Bohling & Cassandra Miller-Butterworth
In 1988–1989, 32 bobcats Lynx rufus were reintroduced to Cumberland Island (CUIS), Georgia, USA, from which they had previously been extirpated. They were monitored intensively for 3 years immediately post-reintroduction, but no estimation of the size or genetic diversity of the population had been conducted in over 20 years since reintroduction. We returned to CUIS in 2012 to estimate abundance and effective population size of the present-day population, as well as to quantify genetic diversity...

Data from: Chemotherapy, within-host ecology and the fitness of drug-resistant malaria parasites

Silvie Huijben, William A. Nelson, Andrew R. Wargo, Derek G. Sim, Damien R. Drew & Andrew F. Read
A major determinant of the rate at which drug-resistant malaria parasites spread through a population is the ecology of resistant and sensitive parasites sharing the same host. Drug treatment can significantly alter this ecology by removing the drug-sensitive parasites, leading to competitive release of resistant parasites. Here, we test the hypothesis that the spread of resistance can be slowed by reducing drug treatment and hence restricting competitive release. Using the rodent malaria model Plasmodium chabaudi,...

Data from: The population history of endogenous retroviruses in mule deer (Odocoileus hemionus)

Pauline L. Kamath, Daniel Elleder, Le Bao, Paul C. Cross, John H. Powell & Mary Poss
Mobile elements are powerful agents of genomic evolution and can be exceptionally informative markers for investigating species and population-level evolutionary history. While several studies have utilized retrotransposon-based insertional polymorphisms to resolve phylogenies, few population studies exist outside of humans. Endogenous retroviruses are LTR-retrotransposons derived from retroviruses that have become stably integrated in the host genome during past infections and transmitted vertically to subsequent generations. They offer valuable insight into host-virus co-evolution and a unique perspective...

Accommodating the role of site memory in dynamic species distribution models

Graziella DiRenzo, David Miller, Blake Hossack, Brent Sigafus, Paige Howell, Erin Muths & Evan Grant
First-order dynamic occupancy models (FODOMs) are a class of state-space model in which the true state (occurrence) is observed imperfectly. An important assumption of FODOMs is that site dynamics only depend on the current state and that variations in dynamic processes are adequately captured with covariates or random effects. However, it is often difficult to understand and/or measure the covariates that generate ecological data, which are typically spatio-temporally correlated. Consequently, the non-independent error structure of...

Data from: Testing the depth-differentiation hypothesis in a deepwater octocoral

Andrea M. Quattrini, Iliana B. Baums, Timothy M. Shank, Cheryl L. Morrison & Erik E. Cordes
The depth-differentiation hypothesis proposes that the bathyal region is a source of genetic diversity and an area where there is a high rate of species formation. Genetic differentiation should thus occur over relatively small vertical distances, particularly along the upper continental slope (200–1000 m) where oceanography varies greatly over small differences in depth. To test whether genetic differentiation within deepwater octocorals is greater over vertical rather than geographical distances, Callogorgia delta was targeted. This species...

Data from: Amyloid precursor protein translation is regulated by a 3'UTR guanine quadruplex

Ezekiel Crenshaw, Brian P. Leung, Chun Kit Kwok, Michal Sharoni, Kalee Olson, Neeraj P. Sebastian, Sara Ansaloni, Reinhard Schweitzer-Stenner, Michael R. Akins, Philip C. Bevilacqua & Aleister J. Saunders
A central event in Alzheimer’s disease is the accumulation of amyloid β (Aβ) peptides generated by the proteolytic cleavage of the amyloid precursor protein (APP). APP overexpression leads to increased Aβ generation and Alzheimer’s disease in humans and altered neuronal migration and increased long term depression in mice. Conversely, reduction of APP expression results in decreased Aβ levels in mice as well as impaired learning and memory and decreased numbers of dendritic spines. Together these...

Data from: Phosphorus amendment mitigates nitrogen addition-induced phosphorus limitation in two plant species in a desert steppe, China

Huang Juying, Hailong Yu, Henry Lin, Yu Zhang, Eric B. Searle, Zhiyou Yuan & Juying Huang
Background and aims: The increasing deposition of atmospheric nitrogen (N) due to anthropogenic activities has significantly enhanced N inputs to ecosystems, resulting in an imbalance in the N: phosphorus (P) ratios in plants and soils. This study aimed to determine whether, and to what extent, P addition alleviates N-induced P limitation in a desert steppe ecosystem. Methods: We conducted a multi-level N:P supply experiment (i.e., constant N with varied P-addition levels) for a grass species,...

Data from: Effects of land use on lake nutrients: the importance of scale, hydrologic connectivity, and region

Patricia A. Soranno, Kendra Spence Cheruvelil, Tyler Wagner, Katherine E. Webster & Mary Tate Bremigan
Catchment land uses, particularly agriculture and urban uses, have long been recognized as major drivers of nutrient concentrations in surface waters. However, few simple models have been developed that relate the amount of catchment land use to downstream freshwater nutrients. Nor are existing models applicable to large numbers of freshwaters across broad spatial extents such as regions or continents. This research aims to increase model performance by exploring three factors that affect the relationship between...

Data from: The first organ-based ontology for arthropods (Ontology of Arthropod Circulatory Systems - OArCS) and its integration into a novel formalization scheme for morphological descriptions

Christian S. Wirkner, Torben Göpel, Jens Runge, Jonas Keiler, Bastian-Jesper Klussmann-Fricke, Katarina Huckstorf, Stephan Scholz, István Mikó, Matthew J. Yoder & Stefan Richter
Morphology, the oldest discipline in the biosciences, is currently experiencing a renaissance in the field of comparative phenomics. However, morphological/phenotypic research still suffers on various levels from a lack of standards. This shortcoming, first highlighted as the “linguistic problem of morphology”, concerns the usage of terminology and also the need for formalization of morphological descriptions themselves, something of paramount importance not only to the field of morphology but also when it comes to the use...

Data from: A nutrient mediates intraspecific competition between rodent malaria parasites in vivo

Nina Wale, Derek G. Sim & Andrew F. Read
Hosts are often infected with multiple strains of a single parasite species. Within-host competition between parasite strains can be intense and has implications for the evolution of traits that impact patient health, such as drug resistance and virulence. Yet the mechanistic basis of within-host competition is poorly understood. Here, we demonstrate that a parasite nutrient, para-aminobenzoic acid (pABA), mediates competition between a drug resistant and drug susceptible strain of the malaria parasite, Plasmodium chabaudi. We...

Data from: Individual and non-additive effects of exotic sap-feeders on root functional and mycorrhizal traits of a shared conifer host

Robert N. Schaeffer, Claire M. Wilson, Laura Radville, Mauri Barrett, Elizabeth Whitney, Sofia Roitman, Esther R. Miller, Benjamin E. Wolfe, Carol S. Thornber, Colin M. Orians & Evan L. Preisser
Forest pests drive tree mortality through disruption of functional traits linked to nutrient acquisition, growth, and reproduction. The impacts of attack by individual or multiple aboveground herbivores on root functional traits critical to tree health have received little attention. This is especially true for exotic herbivores, organisms often found in disturbed forests. We excavated whole-root systems from eastern hemlock (Tsuga canadensis) individuals experimentally infested with hemlock woolly adelgid (HWA: Adelges tsugae) and elongate hemlock scale...

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