230 Works

Data from: Local context drives infection of grasses by vector-borne generalist viruses

Elizabeth T. Borer, Eric W. Seabloom, Charles E. Mitchell & Alison G. Power
Host characteristics commonly determine infection risk, but infection can also be mediated by regional- or local-scale variation in the biotic and abiotic environment. Experiments can clarify the relative importance of these factors. We quantified drivers of infection by barley and cereal yellow dwarf viruses (B/CYDV), a group of generalist, vector-borne grass pathogens, at hierarchically nested spatial scales (105–1 m) by planting individuals of six common grass species into five Pacific Coast grassland sites spanning 7°...

Data from: The ability of Drosophila hybrids to locate food declines with parental divergence.

David A. Turissini, Aaron A. Comeault, Geoffrey Liu, Yuh Chwen G. Lee & Daniel R. Matute
Hybrids between two species are generally less fit than the parental species, and the mechanisms underlying their fitness reductions can manifest through different traits and at different life history stages. For example, hybrids can have physiological, behavioral, or ecological defects, resulting in postzygotic isolation between their parental species. However, mechanisms of postzygotic isolation other than sterility and inviability have remained largely uninvestigated. Isolated studies have found that other postzygotic defects are not only possible but...

Data from: Coral reef degradation is not correlated with local human population density

John F. Bruno
The global decline of reef-building corals is understood to be due to a combination of local and global stressors. However, many reef scientists assume that local factors predominate and that isolated reefs, far from human activities, are generally healthier and more resilient. Here we show that coral reef degradation is not correlated with human population density. This suggests that local factors such as fishing and pollution are having minimal effects or that their impacts are...

Data from: Three-dimensional simulation for fast forward flight of a calliope hummingbird

Jialei Song, Bret W. Tobalske, Donald R. Powers, Tyson L. Hedrick & Haoxiang Luo
We present a computational study of flapping-wing aerodynamics of a calliope hummingbird (Selasphorus calliope) during fast forward flight. Three-dimensional wing kinematics were incorporated into the model by extracting time-dependent wing position from high-speed videos of the bird flying in a wind tunnel at 8.3 m s−1. The advance ratio, i.e. the ratio between flight speed and average wingtip speed, is around one. An immersed-boundary method was used to simulate flow around the wings and bird...

Data from: Relatedness and resource diversity interact to influence the intensity of competition

Ryan A. Martin & Sara C. Garnett
When resource competition occurs between close relatives the negative effects of competition are potentially amplified. However, kin selection theory predicts that natural selection should promote the evolution of mechanisms that minimize the intensity of competition between kin. Experimental tests of these hypotheses are mixed, however. Moreover, there is little consensus regarding the generality of either outcome, suggesting that the conditions important in determining the effects of competition between kin are likely complex and not fully...

Data from: Reproductive aging patterns in primates reveal that humans are distinct

Susan C. Alberts, Jeanne Altmann, Diane K. Brockman, Marina Cords, Linda M. Fedigan, Anne Pusey, Tara S. Stoinski, Karen B. Strier, William F. Morris & Anne M. Bronikowski
Women rarely give birth after approximately 45 years of age, and they experience the cessation of reproductive cycles – menopause – at approximately 50 years of age, after a fertility decline lasting almost two decades. Such reproductive senescence in mid-lifespan is an evolutionary puzzle of enduring interest because it should be inherently disadvantageous. Further, comparative data on reproductive senescence from other primates, or indeed other mammals, remains relatively rare. Here we carried out the first...

Data from: Association of orthostatic hypotension with incident dementia, stroke, and cognitive decline

Andreea M. Rawlings, Stephen P. Juraschek, Gerardo Heiss, Tim Hughes, Michelle L. Meyer, Elizabeth Selvin, A. Richey Sharrett, B. Gwen Windham & Rebecca F. Gottesman
Objective: To examine associations between orthostatic hypotension (OH) with dementia and long-term cognitive decline, and update previously published results in the same cohort for stroke with an additional 16 years of follow-up. Methods: We analyzed data from 11709 participants without a history of coronary heart disease or stroke who attended the baseline exam (1987-1989) of the prospective Atherosclerosis Risk in Communities (ARIC) study. OH was defined as a drop in systolic blood pressure (BP) of...

Data from: Population structure and connectivity of the mountainous star coral, Orbicella faveolata, throughout the wider Caribbean region

John P. Rippe, Mikhail V. Matz, Elizabeth A. Green, Mónica Medina, Nida Z. Khawaja, Thanapat Pongwarin, Jorge H. Pinzón C., Karl D. Castillo & Sarah W. Davies
As coral reefs continue to decline worldwide, it becomes ever more necessary to understand the connectivity between coral populations to develop efficient management strategies facilitating survival and adaptation of coral reefs in the future. Orbicella faveolata is one of the most important reef-building corals in the Caribbean and has recently experienced severe population reductions. Here, we utilize a panel of nine microsatellite loci to evaluate the genetic structure of O. faveolata and to infer connectivity...

Data from: Efficient and accurate extraction of in vivo calcium signals from microendoscopic video data

Pengcheng Zhou, Shanna L. Resendez, Jose Rodriguez-Romaguera, Jessica C. Jimenez, Shay Q. Neufeld, Andrea Giovannucci, Johannes Friedrich, Eftychios A Pnevmatikakis, Garret D. Stuber, Rene Hen, Mazen A. Kheirbek, Bernardo L. Sabatini, Robert E. Kass & Liam Paninski
In vivo calcium imaging through microendoscopic lenses enables imaging of previously inaccessible neuronal populations deep within the brains of freely moving animals. However, it is computationally challenging to extract single-neuronal activity from microendoscopic data, because of the very large background fluctuations and high spatial overlaps intrinsic to this recording modality. Here, we describe a new constrained matrix factorization approach to accurately separate the background and then demix and denoise the neuronal signals of interest. We...

Data from: Investigating behavioral drivers of seasonal Shiga-Toxigenic Escherichia Coli (STEC) patterns in grazing cattle using an agent-based model

Daniel E. Dawson, Jocelyn H. Keung, Monica G. Napoles, Michael R. Vella, Shi Chen, Mike Sanderson, Cristina Lanzas & Michael W. Sanderson
The causes of seasonal variability in pathogen transmission are not well understood, and have not been comprehensively investigated. In an example for enteric pathogens, incidence of Escherichia coli O157 (STEC) colonization in cattle is consistently higher during warmer months compared to cooler months in various cattle production systems. However, actual mechanisms for this seasonality remain elusive. In addition, the influence of host (cattle) behavior on this pattern has not been thoroughly considered. To that end,...

Data from: Using museum specimens to track morphological shifts through climate change

Heidi J. MacLean, Matthew E. Nielsen, Joel G. Kingsolver & Lauren B. Buckley
Museum specimens offer a largely untapped resource for detecting morphological shifts in response to climate change. However, morphological shifts can be obscured by shifts in phenology or distribution or sampling biases. Additionally, interpreting phenotypic shifts requires distinguishing whether they result from plastic or genetic changes. Previous studies using collections have documented consistent historical size changes, but the limited studies of other morphological traits have often failed to support, or even test, hypotheses. We explore the...

Data from: Application of benchmark concentration (BMC) analysis on zebrafish data – a new perspective for quantifying toxicity in alternative animal models

Jui-Hua Hsieh, Kristen Ryan, Alexander Sedykh, Ja-An Lin, Andrew J. Shapiro, Frederick Parham & Mamta Behl
Over the past decade, the zebrafish is increasingly being used as a model to screen for chemical-mediated toxicities including developmental toxicity (DT) and neurotoxicity (NT). One of the major challenges is lack of harmonization in data analysis approaches, thereby posing difficulty in comparing findings across laboratories. To address this, we sought to establish a unified data analysis strategy for both DT and NT data, by adopting the benchmark concentration (BMC) analysis. There are two critical...

Data from: Variation across mitochondrial gene trees provides evidence for systematic error: how much gene tree variation is biological?

Emilie J. Richards, Jeremy M. Brown, Anthony J. Barley, Rebecca A. Chong & Robert C. Thomson
The use of large genomic datasets in phylogenetics has highlighted extensive topological variation across genes. Much of this discordance is assumed to result from biological processes. However, variation among gene trees can also be a consequence of systematic error driven by poor model fit, and the relative importance of biological versus methodological factors in explaining gene tree variation is a major unresolved question. Using mitochondrial genomes to control for biological causes of gene tree variation,...

Data from: Direct detection of male quality can facilitate the evolution of female choosiness and indicators of good genes: evolution across a continuum of indicator mechanisms

Sumit Dhole, Caitlin A. Stern & Maria R. Servedio
The evolution of mating displays as indicators of male quality has been the subject of extensive theoretical and empirical research for over four decades. Research has also addressed the evolution of female mate choice favoring such indicators. Yet, much debate still exists about whether displays can evolve through the indirect benefits of female mate choice. Here, we use a population genetic model to investigate how the extent to which females can directly detect male quality...

Data from: Compensatory evolution in RNA secondary structures increases substitution rate variation among sites

Jennifer L. Knies, Kristen K. Dang, Todd J. Vision, Noah G. Hoffman, Ronald Swanstrom & Christina L. Burch
There is growing evidence that interactions between biological molecules (e.g., RNA-RNA, protein-protein, RNA-protein) place limits on the rate and trajectory of molecular evolution. Here, by extending Kimura's model of compensatory evolution at interacting sites, we show that the ratio of transition to transversion substitutions (κ) at interacting sites should be equal to the square of the ratio at independent sites. Because transition mutations generally occur at a higher rate than transversions, the model predicts that...

Data from: Female preference for male courtship effort can drive the evolution of male mate choice

Sandra Helen South, Göran Arnqvist & Maria R. Servedio
The evolution of male mate choice is constrained by costs of choice in species with a male-biased operational sex ratio. Previous theoretical studies have shown that significant benefits of male choice are required, e.g., by mating with more fecund females, in order for these costs to be offset and a male preference to spread. In a series of population genetic models we show the novel effect that male mating preference, expressed as a bias in...

Data from: Phenotype uniformity in combined-stress environments has a different genetic architecture than in single-stress treatments

G. Buddhika Makumburage & Ann E. Stapleton
For crop production it is desirable for the mapping between genotype and phenotype to be consistent, such that an optimized genotype produces uniform sets of individual plants. Uniformity is strongly selected in breeding programs, usually automatically, as harvest equipment eliminates severely non-uniform individuals. Uniformity is genetically controlled, is known to be increased by interplant competition, and is predicted to increase upon abiotic stress. We mapped maize loci controlling genotype by environment interaction in plant height...

Data from: Gene exchange between two divergent species of the fungal human pathogen, Coccidioides

Colin Scott Maxwell, Kathleen Mattox, David A. Turissini, Marcus M. Teixeira, Bridget M. Barker & Daniel Ricardo Matute
The fungal genus Coccidioides is composed of two species, Coccidioides immitis and C. posadasii. These two species are the causal agents of coccidioidomycosis, a pulmonary disease also known as valley fever. The two species are thought to have shared genetic material due to gene exchange in spite of their long divergence. To quantify the magnitude of shared ancestry between them, we analyzed the genomes of a population sample from each species. Next, we inferred what...

Data from: The behavioral origins of novelty: did increased aggression lead to scale-eating in pupfishes?

Michelle E. St. John, Joseph A. McGirr & Christopher H. Martin
Behavioral changes in a new environment are often assumed to precede the origins of evolutionary novelties. Here, we examined whether an increase in aggression is associated with a novel scale-eating trophic niche within a recent radiation of Cyprinodon pupfishes endemic to San Salvador Island, Bahamas. We measured aggression using multiple behavioral assays and used transcriptomic analyses to identify differentially expressed genes in aggression and other behavioral pathways across three sympatric species in the San Salvador...

UNC-Chapel Hill Coronavirus Research

On the Books

Assessing the impact of product inhibition in a chromogenic assay

Michael Stobb, Karin Leiderman, Suzanne Sindi & Dougald Monroe
Chromogenic substrates (CS) are synthetic substrates used to monitor the activity of a target enzyme. It has been reported that some CSs display competitive product inhibition with their target enzyme. Thus, in assays where enzyme activity is continuously monitored over long periods of time, the product inhibition may significantly interfere with the reactions being monitored. Despite this knowledge, it is rare for CSs to be directly incorporated into mathematical models that simulate these assays. This...

Social context, but not individual personality, alters immigrant viability in a spider with mixed social structure

Jessica Purcell, Spencer Ingley, Jonathan Pruitt & Inon Scharf
Immigrant viability is a major determinant of the realized rate of gene flow across populations. For social organisms, the social context in which immigrants disperse across contrasting environments may have important implications for their viability post dispersal. Here, we use social spiders whose individual personalities as well as group personality compositions vary across sites to test whether the strength of selection against immigrants (i.e. mortality rates) differs depending on whether spiders are transplanted (1) as...

United States National Lynching Data, 1883-1941

Charles Seguin & David Rigby
These data extend existing data on lynching victims to cover the 48 contiguous United States from 1883 to 1941. The data here cover 38 states not included in Tolney and Beck's (1995) original data, as well as 3 additional victims in the 10 states covered by Tolney and Beck. The authors confirmed 1,319 victims from previous data and found 15 additional victims not recorded in any prior data set.

On Portfolio Separation Theorems with Heterogeneous Beliefs and Attitudes towards Risk

Fousseni Chabi-Yo, Eric Ghysels & Eric Renault
The early work of Tobin (1958) showed that portfolio allocation decisions can be reduced to a two stage process: first decide the relative allocation of assets across the risky assets, and second decide how to divide total wealth between the risky assets and the safe asset. This so called twofund separation relies on special assumptions on either returns or preferences. Tobin (1958) analyzed portfolio demand in a mean-variance setting. We revisit the fund separation in...

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