295 Works

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: 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: 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: 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: 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: 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: Rapid evolution and the genomic consequences of selection against interspecific mating

Martha O. Burford Reiskind, Paul Labadie, Irka Bargielowski, L. Philip Lounibos & Michael H. Reiskind
While few species introduced into a new environment become invasive, those that do provide critical information on ecological mechanisms that determine invasions success and the evolutionary responses that follow invasion. Aedes albopictus (the Asian tiger mosquito) was introduced into the naturalized range of Aedes aegypti (the yellow fever mosquito) in the USA in the mid-1980s, resulting in the displacement of A. aegypti in much of the southeastern USA. The rapid displacement was likely due to...

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: Mammal communities are larger and more diverse in moderately developed areas

Arielle Waldstein Parsons, Tavis Forrester, Megan C. Baker-Whatton, William J. McShea, Christopher T. Rota, Stephanie G. Schuttler, Joshua J. Millspaugh & Roland Kays
Developed areas are thought to have low species diversity, low animal abundance, few native predators, and thus low resilience and ecological function. Working with citizen scientist volunteers to survey mammals at 1427 sites across two development gradients (wild-rural-exurban-suburban-urban) and four plot types (large forests, small forest fragments, open areas and residential yards) in the eastern US, we show that developed areas actually had significantly higher or statistically similar mammalian occupancy, relative abundance, richness and diversity...

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: 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: 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: 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: Urbanization drives unique latitudinal patterns of insect herbivory and tree condition

Michael G. Just, Adam G. Dale, Lawrence C. Long & Steven D. Frank
Urban landscapes are characterized by high proportions of impervious surface resulting in higher temperatures than adjacent natural landscapes. In some cities, like those at cooler latitudes, trees may benefit from warmer urban temperatures, but trees in many cities are beset with problems like drought stress and increased herbivory. What drives patterns of urban tree health across urbanization and latitudinal temperature gradients? In natural systems, latitude-herbivory relationships are well-studied, and recent temperate studies have shown that...

Data from: A genome-wide gene expression signature of environmental geography in leukocytes of Moroccan Amazighs

Youssef Idaghdour, John D. Storey, Sami J. Jadallah & Greg Gibson
The different environments that humans experience are likely to impact physiology and disease susceptibility. In order to estimate the magnitude of the impact of environment on transcript abundance, we examined gene expression in peripheral blood leukocyte samples from 46 desert nomadic, mountain agrarian and coastal urban Moroccan Amazigh individuals. Despite great expression heterogeneity in humans, as much as one third of the leukocyte transcriptome was found to be associated with differences among regions. Genome-wide polymorphism...

Data from: Effects of population structure and sex on association between serotonin receptors and Drosophila heart rate

Naruo Nikoh, April Duty & Greg Gibson
As a first step toward population and quantitative genetic analysis of neurotransmitter receptors in Drosophila melanogaster, we describe the parameters of nucleotide variation in three serotonin receptors and their association with pupal heart rate. Thirteen kilobases of DNA including the complete coding regions of 5-HT1A, 5-HT1B, and 5-HT2 were sequenced in 216 highly inbred lines extracted from two North American populations in California and North Carolina. Nucleotide and amino acid polymorphism is in the normal...

Data from: Association between nucleotide variation in Efgr and wing shape in Drosophila melanogaster

Arnar Palsson & Greg Gibson
As part of an effort to dissect quantitative trait locus effects to the nucleotide level, association was assessed between 238 single-nucleotide and 20 indel polymorphisms spread over 11 kb of the Drosophila melanogaster Egfr locus and nine relative warp measures of wing shape. One SNP in a conserved potential regulatory site for a GAGA factor in the promoter of alternate first exon 2 approaches conservative experimentwise significance (P < 0.00003) in the sample of 207...

Data from: Nucleotide variation in the Egfr locus of Drosophila melanogaster

Arnar Palsson, Ann Rouse, Rebecca Riley-Berger, Ian Dworkin & Greg Gibson
The Epidermal growth factor receptor is an essential gene with diverse pleiotropic roles in development throughout the animal kingdom. Analysis of sequence diversity in 10.9 kb covering the complete coding region and 6.4 kb of potential regulatory regions in a sample of 250 alleles from three populations of Drosophila melanogaster suggests that the intensity of different population genetic forces varies along the locus. A total of 238 independent common SNPs and 20 indel polymorphisms were...

Data from: The effects of weak genetic perturbations on the transcriptome of the wing imaginal disc, and its association with wing shape in Drosophila melanogaster

Ian Dworkin, Julie A. Brown Anderson, Youssef Idaghdour, Erin Kennerly Parker, Eric A. Stone, Greg Gibson & Julie A. Anderson
A major objective of genomics is to elucidate the mapping between genotypic and phenotypic space as a step toward understanding how small changes in gene function can lead to elaborate phenotypic changes. One approach that has been utilized is to examine overall patterns of co-variation between phenotypic variables of interest, such as morphology, physiology and behavior, and underlying aspects of gene activity, in particular transcript abundance on a genome wide scale. Numerous studies have demonstrated...

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: 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: Episodic radiations in the fly tree of life

Brian M. Wiegmann, Michelle D. Trautwein, Isaac S. Winkler, Norman B. Barr, Jung-Wook Kim, Christine Lambkin, Matthew A. Bertone, Brian K. Cassel, Keith M. Bayless, Alysha M. Heimberg, Benjamin M. Wheeler, Kevin J. Peterson, Thomas Pape, Bradley J. Sinclair, Jeffrey H. Skevington, Vladimir Blagoderov, Jason Caravas, Sujatha Narayanan Kutty, Urs Schmidt-Ott, Gail E. Kampmeier, F. Christian Thompson, David A. Grimaldi, Andrew T. Beckenbach, Gregory W. Courtney, Markus Friedrich … & J.-W. Kim
Flies are one of four superradiations of insects (along with beetles, wasps, and moths) that account for the majority of animal life on Earth. Diptera includes species known for their ubiquity (Musca domestica house fly), their role as pests (Anopheles gambiae malaria mosquito), and their value as model organisms across the biological sciences (Drosophila melanogaster). A resolved phylogeny for flies provides a framework for genomic, developmental, and evolutionary studies by facilitating comparisons across model organisms,...

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: 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...

Environmental decomposition of olefinic cuticular hydrocarbons of Periplaneta americana generates a volatile pheromone that guides social behaviour

Eduardo Hatano, Ayako Wada-Katsumata & Coby Schal
Once emitted, semiochemicals are exposed to reactive environmental factors that may alter them, thus disrupting chemical communication. Some species, however, might have adapted to detect environmentally mediated breakdown products of their natural chemicals as semiochemicals. We demonstrate that air, water vapour and ultraviolet (UV) radiation break down unsaturated cuticular hydrocarbons (CHCs) of Periplaneta americana (American cockroach), resulting in the emission of volatile organic compounds (VOCs). In behavioural assays, nymphs strongly avoided aggregating in shelters exposed...

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