50 Works

Data from: Interaction among ploidy, breeding system, and lineage diversification

Rosana Zenil-Ferguson, J. Gordon Burleigh, William A. Freyman, Boris Igic, Itay Mayrose & Emma E. Goldberg
If particular traits consistently affect rates of speciation and extinction, broad macroevolutionary patterns can be interpreted as consequences of selection at high levels of the biological hierarchy. Identifying traits associated with diversification rates is difficult because of the wide variety of characters under consideration and the statistical challenges of testing for associations from comparative phylogenetic data. Ploidy (diploid vs. polyploid states) and breeding system (self-incompatible vs. self-compatible states) are both thought to be drivers of...

Yards, block groups, and vegetation cover measures

Dexter Locke, Alessandro Ossola, Emily Minor & Brenda Lin
Residential yards are a significant component of urban socio-ecological systems; residential land covers 11% of the United States and is often the dominant land use within urban areas. Residential yards also play an important role in the sustainability of urban socio-ecological systems, affecting biogeochemical cycles, water, and the climate via individual- and household-level behaviors. Vegetation, such as trees and grasses, are unevenly distributed across front and back yards, and we sought to understand how similar...

Data from: Field evaluation of the safety, acceptability, and feasibility of early infant male circumcision using the AccuCirc device

Robert C. Bailey, Irene Nyaboke, Mary Ellen Mackesy-Amiti, Erick Okello, Valentine Pengo, Betha Ochomo, Mary Emmaculate Ouma, Simon Were, Stella Ojuok, Evelyne Adoyo, Mildred Adhiambo, Marisa R. Young, Rebeca M. Plank & Fredrick O. Otieno
Background: As countries scale up adult voluntary medical male circumcision (VMMC) for HIV prevention, they are looking ahead to long term sustainable strategies, including introduction of early infant male circumcision (EIMC). Although a number of devices for EIMC are prequalified by the World Health Organization, evaluation of additional devices can provide policy-makers and clinicians the information required to make informed decisions. We undertook a field evaluation of the safety and acceptability of the AccuCirc device...

Data from: Phylogenetic inference in section Archerythroxylum informs taxonomy, biogeography, and the domestication of coca (Erythroxylum species)

Dawson M. White, Melissa B. Islam & Roberta J. Mason-Gamer
This investigation establishes the first sequence-based phylogenetic hypothesis of species relationships in the Coca family (Erythroxylaceae). We focused our phylogenomic inference on the largest taxonomic section in the genus Erythroxylum (Archerythroxylum O. E. Schulz) using concatenation and gene tree reconciliation methods from hybridization-based target capture of 427 genes. We show that Neotropical Erythroxylum are monophyletic within the Paleotropical lineages, yet Archerythroxylum and all of the other taxonomic sections from which we sampled multiple species lack...

Data from: Symposium article: Which line to follow? the utility of different line-fitting methods to capture the mechanism of morphological scaling

Alexander W Shingleton
Bivariate morphological scaling relationships describe how the sizes of two traits co-vary among adults in a population. In as much as body shape is reflected by the relative size of various traits within the body, morphological scaling relationships capture how body shape varies with size, and therefore have been used widely as descriptors of morphological variation within and among species. Despite their extensive use, there is continuing discussion over which line-fitting method should be used...

Data from: Phylogenetic inference of reciprocal effects between geographic range evolution and diversification

Emma E. Goldberg, Lesley T. Lancaster & Richard H. Ree
Geographic characters---traits relating to the spatial distribution of a species---may both affect and be affected by processes associated with lineage birth and death. This is potentially confounding to comparative analyses of species distributions because current models do not allow reciprocal interactions between the evolution of traits and the growth of phylogenetic trees. Here we introduce a likelihood-based approach to estimating region-dependent rates of speciation, extinction, and range evolution from a phylogeny, using a new model...

Research Data Services in Academic Libraries: A Survey of North American Academic Libraries in 2019

Carol Tenopir, Jordan Kaufman, Robert J. Sandusky & Danielle Pollock
To determine the extent to which research data services (RDS) are supported in academic libraries and how that has changed over a decade, in 2019 a research team led by Carol Tenopir at the University of Tennessee Center for Information and Communication Studies, in collaboration with ACRL-Choice, surveyed academic library directors in the United States and Canada. This survey allowed us to compare results with a similar survey conducted in 2012. The goal of both...

Return of forest structure and diversity in tropical restoration plantings

Luis Carlos Beltrán, Henry F. Howe & Cristina Martínez-Garza
Stepping-stone restoration plantings can reconcile conservation goals and local land use needs in highly fragmented ecosystems. We explored how initial planting composition influences recruiting plant species density, diversity, abundance, and forest structure in a 13-year-old restoration experiment in Los Tuxtlas, Veracruz, Mexico. Treatments included 8 fenced plantings with animal-dispersed species, 8 plantings with wind-dispersed species, 8 unplanted plots to favor natural succession, and 8 plots in the primary forest as reference sites. We predicted that...

A web-based tool for automatically linking clinical trials to their publications - example calculation

Neil Smalheiser & Arthur Holt
Objective: Evidence synthesis teams, physicians, policy makers, and patients and their families all have an interest in following the outcomes of clinical trials and would benefit from being able to evaluate both the results posted in trial registries and in the publications that arise from them. Manual searching for publications arising from a given trial is a laborious and uncertain process. We sought to create a statistical model to automatically identify PubMed articles likely to...

Effects of enhanced productivity of resources shared by predators in a food-web module: Comparing results of a field experiment to predictions of mathematical models of intra-guild predation

David Wise & Monica Farfan
This dataset contains data from a field experiment described in the publication “Wise, D. H. & Farfan, M.A. (2021) Effects of enhanced productivity of resources shared by predators in a food-web module: Comparing results of a field experiment to predictions of mathematical models of intra-guild predation. Ecology and Evolution, 00: 1-11. https://doi.org/10.1002/ece3.8375”. The field experiment compared the response to increased input of nutrients and energy (artificial detritus) to an empirical model of intra-guild predation (IGP)...

Shallow population structure and shared phylogeographic and demographic patterns in seven Amazonian White-Sand ecosystems birds

João Marcos Guimarães Capurucho, Mary Ashley, Cintia Cornelius, Sérgio Borges, Camila Ribas & John Bates
White-sand ecosystems (WSE) have a patchy distribution throughout Amazonia and harbor a specialized community of birds. The patchiness of WSE lead to the expectation of highly fragmented and isolated populations across Amazonia. Additionally, the sandy substrate could render these ecosystems vulnerable climatic changes. We performed a comparative phylogeographic study of seven WSE birds using Ultra-conserved elements to evaluate their relation to Amazonian environmental and landscape history and the occurrence of shared patterns. Genetic structure varied...

Data from: Seed to seedling transitions in successional habitats across a tropical landscape

Marinés De La Peña-Domene, Henry F. Howe, Emiliano Cruz-León, Rita Jiménez-Rolland, Cesar Lozano-Huerta & Cristina Martínez-Garza
Recognition that tree recruitment depends on the balance between seed arrival and seedling survival has led to a surge of interest in seed-dispersal limitation and seedling-establishment limitation in primary forests. Virtually unaddressed are comparisons of this balance in mature and early successional habitats. We assessed seed rain and seedling recruitment dynamics of tree species in primary forest, secondary forest and pasture released from grazing in a tropical agricultural landscape. Seed to seedling ratios (seed effectiveness;...

Data from: The greatest hits of all time: the histories of dominant genera in the fossil record

Roy E. Plotnick & Peter Wagner
Certain taxa are noticeably common within collections, widely distributed, and frequently long-lived. We have examined these dominant genera as compared to rarer genera, with a focus on their temporal histories. Using occurrence data from the Paleobiology Database, we determined which genera belonging to six target groups ranked among the most common within each of 49 temporal bins based on occurrences. The turnover among these dominant taxa from bin-to-bin was then determined for each of these...

Data from: If you build it, they may not come: modifiable barriers to patient portal use among pre- and post-kidney transplant patients

Mark Lockwood, Karen Dunn-Lopez, Heather Pauls, Larisa Burke, Sachin D. Shah, Milda A. Saunders & Mark B Lockwood
Background: Patient access to health information using electronic patient portals is increasingly common. Portal use has the potential to improve patients' engagement with their health and is particularly important for patients with chronic illness; however, patients’ abilities, attitudes, and use of portals is poorly understood. Methods: A single-center, cross-sectional survey was conducted of 240 consecutive pre- and post-kidney transplant patients of all levels of technological proficiency who presented to an urban transplant center in the...

Data from: Combined effects of seed and soil quality drive seedling performance of a late-successional canopy tree in a tropical forest

Jenny Zambrano, Henry F. Howe & Miquel Gonzalez-Meler
Habitat loss and fragmentation affect the structure and functioning of forested ecosystems worldwide, yet we lack an understanding of how species respond to environmental changes. Here, we examined reproductive success and seedling performance of Poulsenia armata (Moraceae) in continuous and fragmented forests of Los Tuxtlas, southern Mexico. We further investigated how maternal habitat and soil conditions manifested in the seedling stage. We determined seed quality and seedling performance by combining isotopic analyses in seed quality...

Data from: A quantitative electrophysiological biomarker of duplication 15q11.2-q13.1 syndrome

Joel Frohlich, Damla Senturk, Vidya Saravanapandian, Peyman Golshani, Lawrence T. Reiter, Raman Sankar, Ronald Thibert, Charlotte Distefano, Scott Huberty, Edwin H. Cook & Shafali S. Jeste
Background: Duplications of 15q11.2-q13.1 (Dup15q syndrome) are highly penetrant for autism spectrum disorder (ASD). A distinct electrophysiological (EEG) pattern characterized by excessive activity in the beta band has been noted in clinical reports. We asked whether EEG power in the beta band, as well as in other frequency bands, distinguished children with Dup15q syndrome from those with non-syndromic ASD and then examined the clinical correlates of this electrophysiological biomarker in Dup15q syndrome. Methods: In the...

Data from: Examining the effects of the histone methyltransferase inhibitor BIX-01294 on histone modifications and gene expression in both a clinical population and mouse models

K.A. Chase, B. Feiner, M.J. Ramaker, E. Hu, C. Rosen & R.P. Sharma
Schizophrenia has been consistently characterized by abnormal patterns of gene down-regulation, increased restrictive chromatin assemblies, and reduced transcriptional activity. Histone methyltransferase (HMT) mRNA and H3K9me2 levels are elevated in postmortem brain and peripheral blood cells of persons with schizophrenia. Moreover, this epigenomic state likely contributes to the disease, as HMT levels correlate with clinical symptomatology. This manuscript sought to establish the potential therapeutic value of the HMT inhibitor BIX-01294 (BIX). Human peripheral mononuclear cells (PBMC)...

Data from: Both flowering time and distance to conspecific plants affect reproduction in Echinacea angustifolia, a common prairie perennial

Jennifer L. Ison & Stuart Wagenius
1. In small fragmented plant populations, reproductive failure due to pollen limitation is often attributed to spatial isolation of individuals. While flowering time has been shown to affect seed set, its role in pollen limited fragmented populations is less understood. 2. In this study, we quantified near-neighbour distances, flowering phenology, and how they interact to affect seed set in individual plants. We followed the daily flowering phenology of over 2,400 heads on over 500 Echinacea...

Data from: Bushmeat hunting changes regeneration of African rainforests

Edu O. Effiom, Gabriela Nuñez-Iturri, Henrik G. Smith, Ulf Ottosson, Ola Olsson & G. Nunez-Iturri
To assess ecological consequences of bushmeat hunting in African lowland rainforests, we compared paired sites, with high and low hunting pressure, in three areas of southeastern Nigeria. In hunted sites, populations of important seed dispersers—both small and large primates (including the Cross River gorilla, Gorilla gorilla diehli)—were drastically reduced. Large rodents were more abundant in hunted sites, even though they are hunted. Hunted and protected sites had similar mature tree communities dominated by primate-dispersed species....

Data from: Similar but different: dynamic social network analysis highlights fundamental differences between the fission-fusion societies of two equid species, the onager and Grevy's zebra

Daniel I. Rubenstein, Siva R. Sundaresan, Ilya R. Fischhoff, Chayant Tantipathananandh & Tanya Y. Berger-Wolf
Understanding why animal societies take on the form that they do has benefited from insights gained by applying social network analysis to patterns of individual associations. Such analyses typically aggregate data over long time periods even though most selective forces that shape sociality have strong temporal elements. By explicitly incorporating the temporal signal in social interaction data we re-examine the network dynamics of the social systems of the evolutionarily closely-related Grevy’s zebras and wild asses...

Data from: Identifying ecological drivers of interspecific variation in song complexity in songbirds (Passeriformes, Passeri)

Nicholas M.A. Crouch, Roberta J. Mason-Gamer, Nicholas M. A. Crouch & Roberta J. Mason‐Gamer
A diversity of selective pressures and stochastic processes have likely created substantial variation in song structure, creating difficulties in quantifying the influence of specific ecological factors. This problem is further compounded by differences in study taxa and methods of data analysis between studies. Large comparative studies offer the potential to mitigate some of these methodological difficulties by maximizing the power of statistical analyses and minimizing the probability of misidentifying the magnitude and direction of relationships...

Birds suppress pests in corn but release them in soybean crops within a mixed prairie/agriculture system

Megan Garfinkel, Emily Minor & Christopher Whelan Whelan
Birds provide ecosystem services (pest control) in many agroecosystems and have neutral or negative ecological effects (disservices) in others. Large-scale, conventional row crop agriculture is extremely widespread globally, yet few studies of bird effects take place in these agroecosystems. We studied indirect effects of insectivorous birds on corn and soybean crops in fields adjacent to a prairie in Illinois (USA). We hypothesized that prairie birds would forage for arthropods in adjacent crop fields and that...

The origins of coca: museum genomics reveals multiple independent domestications from progenitor Erythroxylum gracilipes

Dawson White, Jen Pan Huang, Orlando Jara-Muñoz, Santiago Madriñan, Richard Ree & Roberta Mason-Gamer
Coca is the natural source of cocaine as well as a sacred and medicinal plant farmed by South American Amerindians and mestizos. The coca crop comprises four closely related varieties classified into two species (Amazonian and Huánuco varieties within Erythroxylum coca Lam., and Colombian and Trujillo varieties within E. novogranatense (D.Morris) Hieron.) but our understanding of their wild progenitor(s) and origins remains rudimentary. In this study we use genomic data from natural history collections to...

Aerosol formation due to a dental procedure: Insights leading to the transmission of diseases to the environments

Parisa Mirbod, Eileen Haffner, Maryam Bagheri & Jonathan Higham
As a result of the outbreak and diffusion of SARS-CoV-2, there has been a directive to advance medical working conditions. In dentistry, airborne particles are produced through aerosolization facilitated by dental instruments. To develop methods for reducing risks of infection in confined environments, understanding the nature and dynamics of these droplets is imperative and timely. This study provides the first evidence of aerosol droplet formation from an ultrasonic scalar under simulated oral conditions. State-of-the-art optical...

Data from: Amphibious mudskipper populations are genetically connected along coastlines, but differentiated across water

Joel Corush, Benjamin Fitzpatrick, Todd Pierson, Jen-Chieh Shiao, Yukitoshi Katayama & Jie Zhang
Aim: Many mudskippers in the family Gobiidae are obligately amphibious, requiring both aquatic and terrestrial portions of their life cycle. The terrestrial phase involves restrictions to mudflat habitats during breeding, when adults build burrows in the mud to lay eggs. The effects of this restricted out-of-water phase might be reflected in the population structure of the species. However, dispersal during the aquatic larval phase could connect distant populations. We examine one such mudskipper, Periophthalmus modestus,...

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Affiliations

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