1,370 Works

Data from: Concordance analysis in mitogenomic phylogenetics

David W. Weisrock
Here I advocate the utility of Bayesian concordance analysis as a mechanism for exploring the magnitude and source of phylogenetic signal in concatenated mitogenomic phylogenetic studies. While typically applied to the study of independently evolving gene trees, Bayesian concordance analysis can also be applied to linked, but individually analyzed, gene regions using a prior probability that reflects the expectation of similar phylogenetic reconstructions. For true branches in the mitogenomic tree, concordance factors should represent the...

Data from: Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma tigrinum) species complex

Eric M. O'Neill, Rachel Schwartz, C. Thomas Bullock, Joshua S. Williams, H. B. Shaffer, X. Aguilar-Miguel, Gabriela Parra-Olea & David W. Weisrock
Modern analytical methods for population genetics and phylogenetics are expected to provide more accurate results when data from multiple genome-wide loci are analyzed. We present the results of an initial application of parallel tagged sequencing (PTS) on a next generation platform to sequence thousands of barcoded PCR amplicons generated from 95 nuclear loci and 93 individuals sampled across the range of the tiger salamander (Ambystoma tigrinum) species complex. To manage the bioinformatic processing of this...

Data from: The role of inbreeding depression and mating system in the evolution of heterostyly

Jennifer J. Weber, Stephen G. Weller, Ann K. Sakai, Olga V. Tsyusko, Travis C. Glenn, Cesar A. Dominguez, Francisco E. Molina-Freaner, Juan Fornoni, Mike Tran, Nhu Nguyen, Karen Nguyen, Lien-Khuong Tran, Greg Joice & Ellen Harding
We investigated the role of morph-based differences in the expression of inbreeding depression in loss of the mid-styled morph from populations of tristylous Oxalis alpina as proposed by theoretical analyses. The extent of self-compatibility of reproductive morphs, the degree of self-fertilization, and the magnitude of inbreeding depression were investigated in three populations of O. alpina differing in their tristylous incompatibility relationships. All three populations exhibited significant inbreeding depression. In two populations with highly modified tristylous...

Data from: Species tree reconstruction of a poorly resolved clade of salamanders (Ambystomatidae) using multiple nuclear loci

Joshua S. Williams, John H. Niedzwiecki & David W. Weisrock
The analysis of diverse data sets can yield different phylogenetic estimates that challenge systematists to explain the source of discordance. The mole salamanders (family Ambystomatidae) are a classic example of this phylogenetic conflict. Previous attempts to resolve the ambystomatid species tree using allozymic, morphological, and mitochondrial sequence data have yielded different estimates, making it unclear which data source best approximates ambystomatid phylogeny and which ones yield phylogenetically inaccurate reconstructions. To shed light on this conflict,...

Data from: Gender differences in patterns of authorship do not affect peer review outcomes at an ecology journal

Charles W. Fox, C. Sean Burns, Anna D. Muncy & Jennifer A. Meyer
There is a widespread perception in the academic community that peer review is subject to many biases and can be influenced by the identity and biographic features (such as gender) of manuscript authors. We examined how patterns of authorship differ between men and women, and whether author gender influences editorial and peer review outcomes and/or the peer review process for papers submitted to the journal Functional Ecology between 2010 and 2014. Women represented approximately a...

Data from: Mechanical conflict system: a novel operant method for the assessment of nociceptive behavior

Steven Harte, Jessica B. Meyers, Renee R. Donahue, Bradley K. Taylor, Thomas J. Morrow & Steven E. Harte
A new operant test for preclinical pain research, termed the Mechanical Conflict System (MCS), is presented. Rats were given a choice either to remain in a brightly lit compartment or to escape to a dark compartment by crossing an array of height-adjustable nociceptive probes. Latency to escape the light compartment was evaluated with varying probe heights (0, .5, 1, 2, 3, and 4 mm above compartment floor) in rats with neuropathic pain induced by constriction...

Data from: Species discovery and validation in a cryptic radiation of endangered primates: coalescent-based species delimitation in Madagascar's mouse lemurs

Scott Hotaling, Mary Foley, Nicolette Lawrence, Jose Bocanegra, Marina B. Blanco, Rodin Rasoloarison, Peter M. Kappeler, Meredith A. Barrett, Anne D. Yoder, David W. Weisrock, Mary E. Foley & Nicolette M. Lawrence
Implementation of the coalescent model in a Bayesian framework is an emerging strength in genetically based species delimitation studies. By providing an objective measure of species diagnosis, these methods represent a quantitative enhancement to the analysis of multilocus data, and complement more traditional methods based on phenotypic and ecological characteristics. Recognized as two species 20 years ago, mouse lemurs (genus Microcebus) now comprise more than 20 species, largely diagnosed from mtDNA sequence data. With each...

Data from: Recruitment of reviewers is becoming harder at some journals: a test of the influence of reviewer fatigue at six journals in ecology and evolution

Charles W. Fox, Arianne Y. K. Albert & Timothy H. Vines
Background: It is commonly reported by editors that it has become harder to recruit reviewers for peer review and that this is because individuals are being asked to review too often and are experiencing reviewer fatigue. However, evidence supporting these arguments is largely anecdotal. Main body: We examine responses of individuals to review invitations for six journals in ecology and evolution. The proportion of invitations that lead to a submitted review has been decreasing steadily...

Data from: The influence of locus number and information content on species delimitation: an empirical test case in an endangered Mexican salamander

Paul M. Hime, Scott Hotaling, Richard E. Grewelle, Eric M. O'Neill, S. Randal Voss, H. Bradley Shaffer & David W. Weisrock
Perhaps the most important recent advance in species delimitation has been the development of model-based approaches to objectively diagnose species diversity from genetic data. Additionally, the growing accessibility of next-generation sequence datasets provides powerful insights into genome-wide patterns of divergence during speciation. However, applying complex models to large datasets is time consuming and computationally costly, requiring careful consideration of the influence of both individual and population sampling, as well as the number and informativeness of...

Data from: Two complete mitochondrial genomes from Praticolella mexicana Perez, 2011 (Polygyridae) and gene order evolution in Helicoidea (Mollusca, Gastropoda)

Russell L. Minton, Marco A. Martinez Cruz, Mark L. Farman & Kathryn E. Perez
Helicoidea is a diverse group of globally distributed land snails. While much is known regardingthe relationships of helicoid taxa, comparatively little is known about the evolution of themitochondrial genome in the superfamily. We sequenced two complete mitochondrial genomesfrom Praticolella mexicana Perez, 2011 representing the first such data from the helicoid familyPolygyridae, and used them in an evolutionary analysis of mitogenomic gene order. We foundthe mitochondrial genome of P. mexicana to be 14,008 bp in size,...

Data from: Natatanuran frogs used the Indian Plate to step-stone disperse and radiate across the Indian Ocean

Zhi-Yong Yuan, Bao-Lin Zhang, Christopher J. Raxworthy, David W. Weisrock, Paul M. Hime, Jie-Qiong Jin, Emily M. Lemmon, Alan R. Lemmon, Sean D. Holland, Michelle L. Kortyna, Wei-Wei Zhou, Min-Sheng Peng, Jing Che & Elizabeth Prendini
Natatanura raw assembled sequencesNatatanura_seqs.zip

Data from: Insecticides promote viral outbreaks by altering herbivore competition

Huipeng Pan, Evan L. Preisser, Dong Chu, Shaoli Wang, Qingjun Wu, Yves Carrière, Xuguo Zhou & Youjun Zhang
While the management of biological invasions is often characterized by a series of single-species decisions, invasive species exist within larger food webs. These biotic interactions can alter the impact of control/eradication programs and may cause suppression efforts to inadvertently facilitate invasion spread and impact. We document the rapid replacement of the invasive Bemisia MEAM1 cryptic species by the cryptic MED species throughout China, and demonstrate that MED is more tolerant of insecticides and a better...

Data from: Facultative endosymbionts mediate dietary breadth in a polyphagous herbivore

Steven M. Wagner, Adam J. Martinez, Yong-Ming Ruan, Kyungsun L. Kim, Paul A. Lenhart, Allison C. Dehnel, Kerry M. Oliver & Jennifer A. White
1. Intraspecific variation in dietary breadth can influence important ecological and evolutionary processes, yet the mechanisms generating this variation are usually unknown. Maternally-transmitted bacterial symbionts frequently infect insect herbivores, and many have been shown to mediate key ecological interactions. For polyphagous herbivores, infection with particular symbionts is often strongly correlated with feeding on particular plant species, suggesting that facultative symbionts might directly determine herbivore food plant specificity. However, previous tests of this hypothesis have returned...

Data from: Mutualism effectiveness of a fungal endophyte in an annual grass is impaired by ozone

Andrea C. Ueno, Pedro E. Gundel, Marina Omacini, Claudio M. Ghersa, Lowell P. Bush & María Alejandra Martínez-Ghersa
1. Ozone is an increasing tropospheric contaminant of climate change. Exposure to ozone may affect the symbiotic relationship between plants and beneficial microorganisms. In particular, the herbivore resistance mechanism conferred by fungal endophytes (defensive mutualism) may be affected, as any of the ozone-triggered effects (such as elicitation of defence mechanisms against biotrophic fungi or oxidative stress in the apoplastic space) may target the symbiont. 2. Symbiotic and non-symbiotic Lolium multiflorum plants were exposed to ozone...

Data from: Multigenerational exposure to silver ions and silver nanoparticles reveals heightened sensitivity and epigenetic memory in Caenorhabditis elegans

Carolin L. Schultz, Anye Wamucho, Olga V. Tsyusko, Jason M. Unrine, Alison Crossley, Claus Svendsen & David J. Spurgeon
The effects from multigenerational exposures to engineered nanoparticles (ENPs) in their pristine and transformed states are currently unknown despite such exposures being an increasingly common scenario in natural environments. Here, we examine how exposure over 10 generations affects the sensitivity of the nematode Caenorhabditis elegans to pristine and sulfidized Ag ENPs and AgNO3. We also include populations that were initially exposed over six generations but kept unexposed for subsequent four generations to allow recovery from...

Data from: A method to generate multi-locus barcodes of pinned insect specimens using MiSeq

Trace Akankunda, Hien To, Carlos R Lopez, Remko Leijs & Katja Hogendoorn
For molecular insect identification, amplicon sequencing methods are recommended because they offer a cost effective approach for targeting small sets of informative genes from multiple samples. In this context, high-throughput multilocus amplicon sequencing has been achieved using the MiSeq Illumina sequencing platform. However, this approach generates short gene fragments of less than 500 bp, which then have to be overlapped using bioinformatics to achieve longer sequence lengths. This increases the risk of generating chimeric sequences...

Phylogenetic relatedness mediates persistence and density of soil seed banks

Margherita Gioria, Petr Pyšek, Carol Baskin & Angelino Carta
Soil seed banks can strongly affect survival and expansion of plant populations by spreading mortality risks and distributing genetic diversity through time. Knowledge of the main factors regulating the ability of seeds to persist in the soil beyond the first growing season is however limited. While morphological and physiological seed traits, and the degree of environmental uncertainty are considered important in shaping the seed-banking strategies of plants, global assessments that explicitly account for phylogenetic relatedness...

Data from: Distinct cold tolerance traits independently vary across genotypes in Drosophila melanogaster

Mark Joseph Garcia, Aerianna S. Littler, Aditya Sriram & Nicholas Teets
The ability to cope with low temperature is a critical adaptation in thermally variable environments. Cold hardiness is comprised of several traits, including minimum temperatures for growth and activity, ability to survive severe cold, and ability to recover normal function after cold subsides. Across species, these traits are correlated and share physiological mechanisms, suggesting they were shaped by shared evolutionary processes. However, the extent cold hardiness traits and their associated mechanisms covary within populations has...

Data from: Mountaintop removal mining alters stream salamander population dynamics

Steven J. Price, Sara Beth Freytag, Simon J. Bonner, Andrea N. Drayer, Brenee' L. Muncy, Jacob M. Hutton & Christopher D. Barton
Aim: Population dynamics are often tightly linked to the condition of the landscape. Focusing on a landscape impacted by mountaintop removal coal mining (MTR), we ask the following questions: (1) How does MTR influence vital rates including occupancy, colonization and persistence probabilities, and conditional abundance of stream salamander species and life stages? (2) Do species and life stages respond similar to MTR mining or is there significant variation among species and life stages? Location: Freshwater...

Genotyping validates the efficacy of photographic identification in a capture-mark-recapture study based on the head scale patterns of the prairie lizard (Sceloporus consobrinus)

Sarah Tomke & Chris Kellner
Population studies often incorporate capture-mark-recapture (CMR) techniques to gather information on long-term biological and demographic characteristics. A fundamental requirement for CMR studies is that an individual must be uniquely and permanently marked to ensure reliable reidentification throughout its lifespan. Photographic identification involving automated photographic identification software has become a popular and efficient non-invasive method for identifying individuals based on natural markings. However, few studies have a) robustly assessed the performance of automated programs by using...


Vinod K Srivastava
Children experiencing trauma and entering child protective services have been continuously increasing. Problems associated with childhood trauma, such as neurodevelopmental disorder, trauma and stress-related disorders, personality disorders, substance use disorder, externalizing and internalizing disorders, academic problems, relational difficulties, and delinquent behaviors, have been found increasing despite advances in trauma and translational research. Children’s trauma is mostly interpersonal in nature and nested in their immediate environment. There is a need for a change in focus from...


Alyssa Jones
Shame is a predominant emotion for some trauma-exposed individuals—particularly survivors of interpersonal violence (IPV)—that is associated with more severe symptoms of posttraumatic stress disorder (PTSD; see Saraiya & Lopez-Castro, 2016). Despite growing evidence of shame’s importance in recovery from trauma and PTSD, measurement challenges have played a large role in difficulties understanding and comparing the impact of shame across studies. These challenges include: 1) the use of measures that assess trait shame as opposed to...


Vertebrate limb is an ideal model to study growth, patterning and morphogenesis and the interplay between these processes. The developing limb bud is a three-dimensional structure and its outgrowth depends on the interaction between 2 important signaling centers: the Apical Ectodermal Ridge (AER) at the junction of the dorsal and ventral halves of the limb bud and the Zone of Polarizing activity (ZPA) in the posterior mesenchyme. These centers produce their respective key molecules and...

Experimental Rapid Renewal Project (Bridge Construction)

Bobby W. Meade, Sudhir Palle & Theodore, II Hopwood
The objectives of this study were to develop specifications and contract language and to monitor the implementation them to effectively use rapid reconstruction and extended service life concepts in new bridge construction. Through the use of A + B bidding, a duplex protective coating system using Hot Dipped Galvanizing (HDG) and paint, and preservation techniques such as concrete sealers and stains the Kentucky Transportation Cabinet attained those goals.


Don Offutt
This descriptive case study of a historical period in education in the Commonwealth of Kentucky identifies the resiliency factors utilized by the first class to desegregate the Bowling Green, Kentucky, public school system. The participants in the study were members of the first African-American class to integrate the Bowling Green school system in 1965. Critical Race Theory provided the tenets undergirding the research study. The qualitative research methods included conducting semi-structured interviews with participants; studying...

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