381 Works

AAV gene therapy encoding equine IL10

Brian Gilger
Equine recurrent uveitis (ERU) is a spontaneous, painful, and vision threatening disease affecting up to 25% of equine populations worldwide. Current treatments of ERU are non-specific and have many side effects which limits them to short-term use. In order to develop an effective therapy for ERU, we investigated the use of adeno-associated virus (AAV) gene therapy, exploiting a natural immune tolerance mechanism induced by equine interleukin-10 (Equine-IL10). The purpose of this study was to evaluate...

Data from: Quantifying historical trends in the completeness of the fossil record and the contributing factors: an example using Aves

Daniel T. Ksepka & Clint A. Boyd
Improvements in the perceived completeness of the fossil record may be driven both by new discoveries and by reinterpretation of known fossils, but disentangling the relative effects of these processes can be difficult. Here, we propose a new methodology for evaluating historical trends in the perceived completeness of the fossil record, demonstrate its implementation using the freely available software ASCC (version 4.0.0), and present an example using crown-group birds (Aves). Dates of discovery and recognition...

Data from: Do males matter? Testing the effects of male genetic background on female meiotic crossover rates in Drosophila melanogaster

Chad M. Hunter & Nadia D. Singh
Meiotic recombination is a critical genetic process as well as a pivotal evolutionary force. Rates of crossing-over are highly variable within and between species, due to both genetic and environmental factors. Early studies in Drosophila implicated female genetic background as a major determinant of crossover rate and recent work has highlighted male genetic background as a possible mediator as well. Our study employed classical genetics to address how female and male genetic backgrounds individually and...

Data from: Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement

Shan Wu, Kin H. Lau, Qinghe Cao, John P. Hamilton, Honghe Sun, Chenxi Zhou, Lauren Eserman, Dorcus Gemenet, Bode Olukolu, Haiyan Wang, Emily Crisovan, Grant T. Godden, Chen Jiao, Xin Wang, Mercy Kitavi, Norma Manrique-Carpintero, Brieanne Vaillancourt, Krystle Wiegert-Rininger, Xinsun Yang, Kan Bao, Yi Zheng, Jennifer Schaff, Jan Kreuze, Wolfgang Gruneberg, Awais Khan … & Zhangjun Fei
I_triloba_NSP323_stress_FPKM_expression_matrix_v3_anno.xlsxFPKM values of v3 high confidence gene models for 15 I. triloba abiotic and biotic stress RNA-seq libraries. The libraries are described in the 'Library Key' worksheet.I_triloba_NSP323_FPKM_expression_matrix_v3_anno.xlsxFPKM values of v3 high confidence gene models for 6 I. triloba RNA-seq libraries (flower, flowerbud, leaf, root1, root2, stem).NSP323_triloba_v3.hc.func_anno.txtPutative functional annotation of high confidence gene models.NSP323_triloba_v3.hc.gene_models.cdna.faNucleotide sequences of the high confidence gene model transcript sequences (cDNA).NSP323_triloba_v3.hc.gene_models.cds.faNucleotide sequences of the high confidence gene model coding sequences (CDS).NSP323_triloba_v3.hc.gene_models.gff3High confidence gene...

Data from: One QTL for intra- and interspecific variation in a sex pheromone

Astrid T. Groot, Heike Staudacher, Andrea Barthel, Olive Inglis, Richard G. Santangelo, Steffi Gebauer-Jung, Heiko Vogel, Jennifer Emerson, Coby Schal, David G. Heckel, Fred Gould & Gerhard Schoefl
Even though premating isolation is hypothesized to be a major driving force in speciation, its genetic basis is poorly known. In the noctuid moth Heliothis subflexa, one group of sex pheromone components, the acetates, emitted by the female, plays a crucial isolating role in preventing interspecific matings to males of the closely related Heliothis virescens, in which females do not produce acetates and males are repelled by them. We previously found intraspecific variation in acetates...

Data from: Enhanced diversity and aflatoxigenicity in interspecific hybrids of Aspergillus flavus and Aspergillus parasiticus

Rodrigo A. Olarte, Carolyn J. Worthington, Bruce W. Horn, Geromy G. Moore, Rakhi Singh, James T. Monacell, Joe W. Dorner, Eric A. Stone, De-Yu Xie & Ignazio Carbone
Aspergillus flavus and A. parasiticus are the two most important aflatoxin-producing fungi responsible for the contamination of agricultural commodities worldwide. Both species are heterothallic and undergo sexual reproduction in laboratory crosses. Here we examine the possibility of interspecific matings between A. flavus and A. parasiticus. These species can be distinguished morphologically and genetically, as well as by their mycotoxin profiles. Aspergillus flavus produces both B aflatoxins and cyclopiazonic acid (CPA), B aflatoxins or CPA alone,...

Data from: Utilizing descriptive statements from the Biodiversity Heritage Library to expand the Hymenoptera Anatomy Ontology

Katja C. Seltmann, Zsolt Pénzes, Matthew J. Yoder, Matthew A. Bertone & Andrew R. Deans
Hymenoptera, the insect order that includes sawflies, bees, wasps, and ants, exhibits an incredible diversity of phenotypes, with over 145,000 species described in a corpus of textual knowledge since Carolus Linnaeus. In the absence of specialized training, often spanning decades, however, these articles can be challenging to decipher. Much of the vocabulary is domain-specific (e.g., Hymenoptera biology), historically without a comprehensive glossary, and contains much homonymous and synonymous terminology. The Hymenoptera Anatomy Ontology was developed...

Data from: Genetic structure and post-glacial expansion of Cornus florida L. (Cornaceae): integrative evidence from phylogeography, population demographic history, and species distribution modeling

Ashley Call, Yan-Xia Sun, Yan Yu, Peter B. Pearman, David T. Thomas, Robert Trigiano, Ignazio Carbone, Qiu-Yun Xiang, Robert N. Trigiano, Yan-Xia Sun & Qiu-Yun Jenny Xiang
Repeated global climatic cooling and warming cycles during the Pleistocene played a major role in the distribution and evolution of the Earth biota. Here, we integrate phylogeography, coalescent-based Bayesian estimation of demographic history, and species distribution modeling (SDM) to understand the genetic patterns and biogeography of the flowering dogwood, Cornus florida subsp. florida L., since the Last Glacial Maximum (LGM). Natural populations of the species are severely threatened by dogwood anthracnose. We genotyped 306 plants...

Data from: Conservation implications of the evolutionary history and genetic diversity hotspots of the snowshoe hare

Ellen Cheng, Karen E. Hodges, José Melo-Ferreira, Paulo C. Alves & L. Scott Mills
With climate warming, the ranges of many boreal species are expected to shift northward and to fragment in southern peripheral ranges. To understand the conservation implications of losing southern populations, we examined range-wide genetic diversity of the snowshoe hare (Lepus americanus), an important prey species that drives boreal ecosystem dynamics. We analysed microsatellite (8 loci) and mitochondrial DNA sequence (cytochrome b and control region) variation in almost 1000 snowshoe hares. A hierarchical structure analysis of...

Data from: Adaptive geographical clines in the growth and defense of a native plant

Ellen Woods, Amy P. Hastings, Nash E. Turley, Stephen B. Heard, Anurag A. Agrawal & Ellen C. Woods
Broad-scale geographical gradients in the abiotic environment and interspecific interactions should select for clinal adaptation. How trait clines evolve has recently received increased attention because of anticipated climate change and the importance of rapid evolution in invasive species. This issue is particularly relevant for clines in growth and defense of plants, because both sets of traits are closely tied to fitness and because such sessile organisms experience strong local selection. Yet, despite widespread recognition that...

Data from: Phenotypic selection on floral traits in an urban landscape

Rebecca E. Irwin, Paige S. Warren & Lynn S. Adler
Native species are increasingly living in urban landscapes associated with abiotic and biotic changes that may influence patterns of phenotypic selection. However, measures of selection in urban and non-urban environments, and exploration of the mechanisms associated with such changes, are uncommon. Plant-animal interactions have played a central role in the evolution of flowering plants and are sensitive to changes in the urban landscape, and thus provide opportunities to explore how urban environments modify selection. We...

Data from: Describing a developing hybrid zone between red wolves and coyotes in eastern North Carolina, USA

Justin H. Bohling, Justin Dellinger, Justin N. McVey, David T. Cobb, Christopher E. Moorman, Lisette P. Waits & Justin M. McVey
When hybridizing species come into contact, understanding the processes that regulate their interactions can help predict the future outcome of the system. This is especially relevant in conservation situations where human activities can influence hybridization dynamics. We investigated a developing hybrid zone between red wolves and coyotes in North Carolina, USA to elucidate patterns of hybridization in a system heavily managed for preservation of the red wolf genome. Using noninvasive genetic sampling of scat, we...

Data from: Thermal regime drives a latitudinal gradient in morphology and life history in a livebearing fish

Rüdiger Riesch, Ryan A. Martin, Sarah E. Diamond, Jonas Jourdan, Martin Plath & R. Brian Langerhans
Within-species diversity is often driven by changing selective regimes along environmental gradients. Here, we provide a direct test of the environmental factors underlying phenotypic diversity across the wide native distribution of eastern mosquitofish (Gambusia holbrooki). We investigated life-history and body-shape divergence (including multiple measures of body size) across more than 14 degrees of latitude in North America, and used Akaike’s information criterion-based model selection to determine the relative contributions of thermal regime, population densities and...

Data from: Challenges in analysis and interpretation of microsatellite data for population genetic studies

Alexander I. Putman & Ignazio Carbone
Advancing technologies have facilitated the ever-widening application of genetic markers such as microsatellites into new systems and research questions in biology. In light of the data and experience accumulated from several years of using microsatellites, we present here a literature review that synthesizes the limitations of microsatellites in population genetic studies. With a focus on population structure, we review the widely used fixation (FST) statistics and Bayesian clustering algorithms and find that the former can...

Data from: Macronutrient intake regulates sexual conflict in decorated crickets

James Rapkin, Kim Jensen, Sarah M. Lane, Clarissa M. House, Scott K. Sakaluk & John Hunt
Sexual conflict results in a diversity of sex-specific adaptations, including chemical additions to ejaculates. Male decorated crickets (Gryllodes sigillatus) produce a gelatinous nuptial gift (the spermatophylax) that varies in size and free amino acid composition, which influences a female's willingness to fully consume this gift. Complete consumption of this gift maximizes sperm transfer through increased retention of the sperm-containing ampulla, but hinders post-copulatory mate choice. Here, we examine the effects of protein (P) and carbohydrate...

Data from: Reproductive interference explains persistence of aggression between species

Jonathan P. Drury, Kenichi W. Okamoto, Christopher N. Anderson & Gregory F. Grether
Interspecific territoriality occurs when individuals of different species fight over space, and may arise spontaneously when populations of closely related territorial species first come into contact. But defence of space is costly, and unless the benefits of excluding heterospecifics exceed the costs, natural selection should favour divergence in competitor recognition until the species no longer interact aggressively. Ordinarily males of different species do not compete for mates, but when males cannot distinguish females of sympatric...

Data from: Winter coat color polymorphisms identify global hotspots for evolutionary rescue from climate change

L. Scott Mills, Eugenia V. Bragina, Alexander V. Kumar, Marketa Zimova, Diana J.R. Lafferty, Jennifer Feltner, Brandon M. Davis, Klaus Hacklander, Paulo C. Alves, Jeffrey M. Good, Jose Melo-Ferreira, Andreas Dietz, Alexei V. Abramov, Natalia Lopatina & Kairsten Fay
Maintenance of biodiversity in a rapidly changing climate will depend on the efficacy of evolutionary rescue, whereby population declines due to abrupt environmental change are reversed by shifts in genetically-driven adaptive traits. However, a lack of traits known to be under direct selection by anthropogenic climate change has limited the incorporation of evolutionary processes into global conservation efforts. In 22 vertebrate species, some individuals undergo a seasonal color molt from summer brown to winter white...

Data from: Large birds travel farther in homogeneous environments

Marlee A. Tucker, Olga Alexandrou, , Keith L. Bildstein, Katrin Böhning-Gaese, Chloe Bracis, John N. Brzorad, Evan R. Buechley, David Cabot, Justin M. Calabrese, Carlos Carrapato, André Chiaradia, Lisa C. Davenport, Sarah C. Davidson, Mark Desholm, Christopher R. DeSorbo, Robert Domenech, Peter Enggist, William F. Fagan, Nina Farwig, Wolfgang Fiedler, Christen H. Fleming, Alastair Franke, John M. Fryxell, Clara García-Ripollés … & João Paulo Silva
Aim: Animal movement is an important determinant of individual survival, population dynamics, and ecosystem structure and function. Yet it is still unclear how local movements are related to resource availability and the spatial arrangement of resources. Using resident bird species and migratory bird species outside of the migratory period, we examined how the distribution of resources affect the movement patterns of both large terrestrial birds (e.g., raptors, bustards, hornbills) and waterbirds (e.g., cranes, storks, ducks,...

Data from: Dynamic occupancy modeling reveals a hierarchy of competition among fishers, grey foxes, and ringtails

David S. Green, Sean M. Matthews, Robert C. Swiers, Richard L. Callas, J. Scott Yaeger, Stuart L. Farber, Michael K. Schwartz & Roger A. Powell
1. Determining how species coexist is critical for understanding functional diversity, niche partitioning and interspecific interactions. Identifying the direct and indirect interactions among sympatric carnivores that enable their coexistence are particularly important to elucidate because they are integral for maintaining ecosystem function. 2. We studied the effects of removing 9 fishers (Pekania pennanti) on their population dynamics and used this perturbation to elucidate the interspecific interactions among fishers, grey foxes (Urocyon cinereoargenteus), and ringtails (Bassariscus...

Data from: Peptide sequences from the first Castoroides ohioensis skull and the utility of old museum collections for paleoproteomics

Timothy Cleland, Elena Schroeter, Robert Feranec, Deepak Vashishth, Elena R. Schroeter, Timothy P. Cleland & Robert S. Feranec
Vertebrate fossils have been collected for hundreds years and are stored in museum collections around the world. These remains provide a readily available resource to search for preserved proteins; however, the vast majority of paleoproteomic studies have focused on relatively recently collected bones with a well-known handling history. Here, we characterize proteins from the nasal turbinates of the first Castoroides ohioensis skull ever discovered. Collected in 1845, this is the oldest museum curated specimen characterized...

Data from: Tracking transcription factor mobility and interaction in Arabidopsis roots with fluorescence correlation spectroscopy

Natalie M Clark, Elizabeth Hinde, Cara M Winter, Adam P Fisher, Giuseppe Crosti, Ikram Blilou, Enrico Gratton, Philip N Benfey & Rosangela Sozzani
To understand complex regulatory processes in multicellular organisms, it is critical to be able to quantitatively analyze protein movement and protein-protein interactions in time and space. During Arabidopsis development, the intercellular movement of SHORTROOT (SHR) and subsequent interaction with its downstream target SCARECROW (SCR) control root patterning and cell fate specification. However, quantitative information about the spatio-temporal dynamics of SHR movement and SHR-SCR interaction is currently unavailable. Here, we quantify parameters including SHR mobility, oligomeric...

Data from: Biologically and diagenetically derived peptide modifications in Moa collagens

Timothy P. Cleland, Elena R. Schroeter & Mary Higby Schweitzer
The modifications that occur on proteins in natural environments over time are not well studied, yet characterizing them is vital to correctly interpret sequence data recovered from fossils. The recently extinct moa (Dinornithidae) is an excellent candidate for investigating the preservation of proteins, their post-translational modifications (PTMs) and diagenetic alterations during degradation. Moa protein extracts were analysed using mass spectrometry, and peptides from collagen I, collagen II and collagen V were identified. We also identified...

Data from: Diversity and evolution of the primate skin microbiome

Sarah E. Council, Amy M. Savage, Julie M. Urban, Megan E. Ehlers, J. H. Pate Skene, Michael L. Platt, Robert R. Dunn & Julie E. Horvath
Skin microbes play a role in human body odour, health and disease. Compared to gut microbes we know comparatively little about the changes in the composition of skin microbes in response to evolutionary changes in hosts, or more recent behavioral and cultural changes in humans. No studies have used sequence-based approaches to consider the skin microbe communities of gorillas and chimpanzees, for example. Comparison of the microbial associates of non-human primates with those of humans...

Data from: Paleotropical diversification dominates the evolution of the hyperdiverse ant tribe Crematogastrini (Hymenoptera: Formicidae)

Bonnie B. Blaimer, Philip S. Ward, Ted R. Schultz, Brian L. Fisher & Seán G. Brady
Levels of diversity vary strikingly among different phylogenetic lineages of ants. Rapid radiations in early ant evolution have often proven difficult to resolve with traditional Sanger-sequencing data sets of modest size. We provide a phylogenomic perspective on the evolution of the hyperdiverse ant tribe Crematogastrini by analyzing sequence data for nearly 1800 ultraconserved element (UCE) loci from 153 species comprising 56 genera. We reconstruct a next-to-complete genus-level phylogeny using concatenated maximum-likelihood and species-tree approaches, estimate...

Data from: Muscle–spring dynamics in time-limited, elastic movements

Michael V. Rosario, Gregory P. Sutton, Sheila N. Patek & Gregory S. Sawicki
Muscle contractions that load in-series springs with slow speed over a long duration do maximal work and store the most elastic energy. However, time constraints, such as those experienced during escape and predation behaviours, may prevent animals from achieving maximal force capacity from their muscles during spring-loading. Here, we ask whether animals that have limited time for elastic energy storage operate with springs that are tuned to submaximal force production. To answer this question, we...

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