223 Works

In Their Own Words

Patricia Nola Eugene Roberson, Gina Cortez, Laura H. Trull & Katherine Allison Lenger
Introduction: The opioid epidemic is ravaging people, families, and communities in Appalachia. However, limited research has examined how “everyday” people (e.g., not chronic pain patients, not medical professionals) living in these communities how opioids have impacted their lives. Objective: Identify the perception of the opioid epidemic on individuals, families, and communities from people living in region most impacted regions. Methods: Patients were recruited at Remote Area Medical clinics throughout Central and Southern Appalachia to complete...

The Critical Need for Peer Clinical Supervision Among School Counselors

Pamelia E. Brott, Lorraine DeKruyf, Jung Hyun, Christopher LaFever, Sarah Patterson-Mills, Mariama Sandifer & Victoria Stone

Data from: Data sharing, management, use, and reuse: practices and perceptions of scientists worldwide

Carol Tenopir, Natalie M. Rice, Suzie Allard, Lynn Baird, Josh Borycz, Lisa Christian, Mike Frame, Bruce Grant, Robert Olendorf, Robert Sandusky & Lisa Zolly
Background: With data becoming a centerpiece of modern scientific discovery, data sharing by scientists is now a crucial element of scientific progress. This article aims to provide an in-depth examination of the practices and perceptions of data management, including data storage, data sharing, and data use and reuse by scientists around the world. Methods: The Usability and Assessment Working Group of DataONE, an NSF-funded environmental cyberinfrastructure project, distributed a survey to a multinational and multidisciplinary...

Chloroplast genome of the invasive Pyrus calleryana

Marcin Nowicki, Matthew Huff, Margaret Staton & Robert Trigiano
The complete chloroplast genome of Pyrus calleryana (BioSample SAMC013142) was developed by de novo assembly from whole-genome sequencing data. Reference-guided (P. phaeocarpa) read mapping and assembly were followed by annotation and phylogenetic comparisons. The Pyrus calleryana chloroplast genome of 159,965 bp in length (36,56% of GC content) represents a classical quadripartite architecture, with two inverted repeats regions (IRs; each 26,392 bp in length) separating the large single-copy region (LSC; 87,942 bp) and the small single-copy...

Altitude-mediated soil properties, not geography or climatic distance, explain the distribution of a tropical endemic herb

Jacob Moutouama & Orou Gaoue
Understanding the ecological processes that govern species’ range margins is a fundamental question in ecology with practical implications in conservation biology. The centre-periphery hypothesis (CPH) predicts that organisms have higher abundance at the centre of their geographic range. However, most tests of the CPH often used raster data, assuming that climatic conditions are consistent across one square km. This assumption is not always justified, particularly for species that live in mountainous regions where climatic conditions...

Valenzuela phylogenomic dataset from: Illumina whole genome sequencing indicates ploidy level differences within the Valenzuela flavidus (Psocodea: Psocomorpha: Caeciliusidae) species complex

Robert De Moya
This contains data for the manuscript: "Illumina Whole Genome Sequencing indicates Ploidy Level Differences within the Valenzuela flavidus (Psocodea: Psocomorpha: Caeciliusidae) Species Complex". Valenzuela flavidus is a species of bark louse which is known to have asexual parthenogenetic populations in Europe but is believed to have sexual and asexual populations in North America as well. Historically, Valenzuela aurantiacus was the species epithet recognized for North American members until reports of asexual reproduction surfaced in certain...

Evolution and development at the origin of a phylum

Bradley Deline, Jeffery Thompson, Nicholas Smith, Samuel Zamora, Imran Rahman, Sarah Sheffield, William Ausich, Thomas Kammer & Colin Sumrall
Quantifying morphological evolution is key to determining the patterns and processes underlying the origin of phyla. We constructed a hierarchical morphological character matrix to characterize the radiation and establishment of echinoderm body plans during the early Paleozoic. This showed that subphylum-level clades diverged gradually through the Cambrian, and the distinctiveness of the resulting body plans was amplified by the extinction of transitional forms and obscured by convergent evolution during the Ordovician. Higher-order characters that define...

Using naturalistic incubation temperatures to demonstrate how variation in the timing and continuity of heat wave exposure influences phenotype

Anthony Breitenbach, Amanda Carter, Ryan Paitz & Rachel Bowden
Most organisms are exposed to bouts of warm temperatures during development, yet we know little about how variation in the timing and continuity of heat exposure influences biological processes. If heat waves increase in frequency and duration as predicted, it is necessary to understand how these bouts could affect thermally sensitive species, including reptiles with temperature-dependent sex determination (TSD). In a multi-year study using fluctuating temperatures, we exposed Trachemys scripta embryos to cooler, male-producing temperatures...

Panmixia across elevation in thermally sensitive Andean dung beetles

Ethan Linck, Jorge Celi & Kimberly Sheldon
Janzen’s seasonality hypothesis predicts that organisms inhabiting environments with limited climatic variability will evolve a reduced thermal tolerance breadth compared with organisms experiencing greater climatic variability. In turn, narrow tolerance breadth may select against dispersal across strong temperature gradients, such as those found across elevation. This can result in narrow elevational ranges and generate a pattern of isolation-by-environment, or neutral genetic differentiation correlated with environmental variables that is independent of geographic distance. We tested for...

Recent hybrids recapitulate ancient hybrid outcomes

Zachariah Gompert, Samridhi Chaturvedi, Lauren Lucas, C. Alex Buerkle, James Fordyce, Matthew Forister & Chris Nice
Genomic outcomes of hybridization depend on selection and recombination in hybrids. Whether these processes have similar effects on hybrid genome composition in contemporary hybrid zones versus ancient hybrid lineages is unknown. Here we show that patterns of introgression in a contemporary hybrid zone in Lycaeides butterflies predict patterns of ancestry in geographically adjacent, older hybrid populations. We find a particularly striking lack of ancestry from one of the hybridizing taxa, Lycaeides melissa, on the Z...

Changes in taxonomic and phylogenetic diversity in the Anthropocene

Daijiang Li, Julian Olden, Julie Lockwood, Sydne Record, Michael McKinney & Benjamin Baiser
To better understand how ecosystems are changing, a multifaceted approach to measuring biodiversity that considers species richness and evolutionary history across spatial scales is needed. Here we compiled 162 datasets for fish, bird, and plant assemblages across the globe and measured how taxonomic and phylogenetic diversity changed at different spatial scales (within site α diversity and between sites spatial β diversity). Biodiversity change is measured from these datasets in three ways: across land use gradients,...

Data from: Habitat suitability and connectivity modeling reveal priority areas for Indiana bat (Myotis sodalis) conservation in a complex habitat mosaic

Ashleigh Cable, Joy O'Keefe, Jill Deppe, Tara Hohoff, Steven Taylor & Mark Davis
Context Conservation for the Indiana bat (Myotis sodalis), a federally endangered species in the United States of America, is typically focused on local maternity sites; however, the species is a regional migrant, interacting with the environment at multiple spatial scales. Hierarchical levels of management may be necessary, but we have limited knowledge of landscape-level ecology, distribution, and connectivity of suitable areas in complex landscapes. Objectives We sought to 1) identify factors influencing M. sodalis maternity...

Do selfing species have greater niche breadth? Support from ecological niche modeling

Alannie-Grace Gabrielle Grant
We explore the relationship between plant mating system (selfing or outcrossing) and niche breadth to gain new insights into processes that drive species distributions. Using a comparative approach with highly selfing versus highly outcrossing sister species, we test the extent to which: (1) species pairs have evolved significant niche divergence and less niche overlap, (2) selfers have wider niche breadths than outcrossers or vice versa, and (3) niches of selfers and outcrossers are defined by...

Protected area, easement, and rental contract data reveal five communities of land protection in the United States

Heather Bird Jackson, Kailin Kroetz, James Sanchirico, Alexandra Thompson & Paul Armsworth
Land protection efforts represent large societal investments and are critical to biodiversity conservation. Land protection involves a complex mosaic of areas managed by multiple organizations, using a variety of mechanisms to achieve different levels of protection. We develop an approach to synthesize, describe, and map this land protection diversity over large spatial scales. We use cluster analysis to find distinct “communities” of land protection based on the organizations involved, the strictness of land protection, and...

Data for: Phylogenomic analyses reveal non-monophyly of the antbird genera Herpsilochmus and Sakesphorus (Thamnophilidae), with description of a new genus for Herpsilochmus sellowi

Gustavo Bravo, Bret Whitney, Ricardo Belmonte-Lopes, Marcos Bornschein, Natalia Aristizabal, Renata Beco, Jaqueline Battilana, Luciano Naka, Alexandre Aleixo, Marcio Pie, Luis Silveira, Elizabeth Derryberry & Robb Brumfield
The family Thamnophilidae is a species-rich Neotropical radiation of passerine birds. Current classification of its 235 species is mostly based on morphological similarities, but recent studies integrating comprehensive phenotypic and phylogenetic data have redefined taxonomic limits of several taxa. Here, we assess generic relationships of Herpsilochmus, Sakesphorus, Thamnophilus, Biatas, and Dysithamnus using DNA sequences from the mitochondrion, nuclear exons, and ultraconserved elements (UCEs), with further attention to interspecific relationships within Herpsilochmus. We show that Herpsilochmus...

Methodological advances for hypothesis‐driven ethnobiology

Orou G. Gaoue, Jacob Moutouama, Michael Coe, Matthew Bond, Elizabeth Green, Nadejda Sero, Bezeng Simmy & Kowiyou Yessoufou
Ethnobiology as a discipline has evolved recently to increasingly embrace theory-inspired and hypothesis driven approaches to study why and how local people choose plants and animals they interact with and use for their livelihood. However, testing complex hypotheses or a network of ethnobiological hypotheses is challenging, particularly for datasets with non-independent observations due to species phylogenetic relatedness or socio-relational links between participants. Further, to fully account for the dynamics of local ecological knowledge, it is...

Data from: Fish functional traits correlated with environmental variables in a temperate biodiversity hotspot

Benjamin P. Keck, Zachary H. Marion, Derek J. Martin, Jason C. Kaufman, Carol P. Harden, John S. Schwartz & Richard J. Strange
The global biodiversity crisis has invigorated the search for generalized patterns in most disciplines within the natural sciences. Studies based on organismal functional traits attempt to broaden implications of results by identifying the response of functional traits, instead of taxonomic units, to environmental variables. Determining the functional trait responses enables more direct comparisons with, or predictions for, communities of different taxonomic composition. The North American freshwater fish fauna is both diverse and increasingly imperiled through...

Data from: Hybridization between two gartersnake species (Thamnophis) of conservation concern: A threat or an important natural interaction?

John S. Placyk, Benjamin M. Fitzpatrick, Gary S. Casper, Randall L. Small, R. Graham Reynolds, Daniel W. A. Noble, Ronald J. Brooks & Gordon M. Burghardt
Distinguishing between hybrid zones formed by secondary contact versus parapatric divergence-with-gene-flow is an important challenge for understanding the interplay of geographic isolation and local adaptation in the origin of species. Similarly, distinguishing between natural hybrid zones and those that formed as a consequence of recent human activities has important conservation implications. Recent work has demonstrated the existence of a narrow hybrid zone between the plains gartersnake (Thamnophis radix) and Butler’s gartersnake (T. butleri) in the...

Data from: Replicated divergence in cichlid radiations mirrors a major vertebrate innovation

Matthew D. McGee, Brant C. Faircloth, Samuel R. Borstein, Jimmy Zheng, Christopher Darrin Hulsey, Peter C. Wainwright & Michael E. Alfaro
Decoupling of the upper jaw bones—jaw kinesis—is a distinctive feature of the ray-finned fishes, but it is not clear how the innovation is related to the extraordinary diversity of feeding behaviours and feeding ecology in this group. We address this issue in a lineage of ray-finned fishes that is well known for its ecological and functional diversity—African rift lake cichlids. We sequenced ultraconserved elements to generate a phylogenomic tree of the Lake Tanganyika and Lake...

Data from: Data sharing by scientists: practices and perceptions

Carol Tenopir, Suzie Allard, Kimberly Douglass, Arsev Umur Aydinoglu, Lei Wu, Eleanor Read, Maribeth Manoff & Mike Frame
Background: Scientific research in the 21st century is more data intensive and collaborative than in the past. It is important to study the data practices of researchers –data accessibility, discovery, re-use, preservation and, particularly, data sharing. Data sharing is a valuable part of the scientific method allowing for verification of results and extending research from prior results. Methodology/Principal Findings: A total of 1329 scientists participated in this survey exploring current data sharing practices and perceptions...

Data from: Comparative limb bone loading in the humerus and femur of the tiger salamander: testing the ‘mixed-chain’ hypothesis for skeletal safety factors

Sandy M. Kawano, D. Ross Economy, Marian S. Kennedy, Delphine Dean & Richard W. Blob
Locomotion imposes some of the highest loads upon the skeleton, and diverse bone designs have evolved to withstand these demands. Excessive loads can fatally injure organisms; however, bones have a margin of extra protection, called a ‘safety factor’ (SF), to accommodate loads that are higher than normal. The extent to which SFs might vary amongst an animal's limb bones is unclear. If the limbs are likened to a chain composed of bones as ‘links’, then...

Data from: Feeding ecology underlies the evolution of cichlid jaw mobility

Christopher M. Martinez, Matthew David McGee, Samuel Robert Borstein & Peter C. Wainwright
The fish feeding apparatus is among the most diverse functional systems in vertebrates. While morphological and mechanical variation of feeding systems are well studied, we know far less about the diversity of the motions that they produce. We explored patterns of feeding movements in African cichlids from Lakes Malawi and Tanganyika, asking whether the degree of kinesis is associated with dietary habits of species. We used geometric morphometrics to measure feeding kinesis as trajectories of...

DateLife: leveraging databases and analytical tools to reveal the dated Tree of Life

Luna Luisa Sanchez Reyes, Emily Jane McTavish & Brian O'Meara
Achieving a high-quality reconstruction of a phylogenetic tree with branch lengths proportional to absolute time (chronogram) is a difficult and time-consuming task. But the increased availability of fossil and molecular data, and time-efficient analytical techniques has resulted in many recent publications of large chronograms for a large number and wide diversity of organisms. Knowledge of the evolutionary time frame of organisms is key for research in the natural sciences. It also represent valuable information for...

Data from: Evidence for repeated loss of selective constraint in rhodopsin of amblyopsid cavefishes (Teleostei: Amblyopsidae)

Matthew Lance Niemiller, Benjamin Minault Fitzpatrick, Premal Shah, Lars Schmitz & Thomas J. Near
The genetic mechanisms underlying regressive evolution—the degeneration or loss of a derived trait—are largely unknown, particularly for complex structures such as eyes in cave organisms. In several eyeless animals, the visual photoreceptor rhodopsin appeared to retain functional amino-acid sequences. Hypotheses to explain apparent maintenance of function include weak selection for retention of light-sensing abilities and its pleiotropic roles in circadian rhythms and thermotaxis. In contrast, we show that there has been repeated loss of functional...

Data from: Genetic analyses reveal cryptic diversity in the native North American fire ants (Hymenoptera: Formicidae: Solenopsis)

Pablo Chialvo, Dietrich A. Gotzek, D. DeWayne Shoemaker, Kenneth G. Ross & DEWAYNE SHOEMAKER
The native North American fire ants (Solenopsis) comprise a difficult group taxonomically that has undergone multiple revisions in the past century yet remains in a state of taxonomic uncertainty. In this study, we utilized a large set of microsatellite markers to conduct the first robust genetic analysis of the nominal species. Our approach used a variety of methods to test operational criteria commonly employed in species delimitation, including genotypic clustering, reproductive isolation/cohesion, and monophyly. We...

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