369 Works

Data from: Loss of sexual recombination and segregation is associated with increased diversification in evening primroses

Marc T. J. Johnson, Richard Gareth FitzJohn, Stacey D. Smith, Mark D. Rausher & Sarah P. Otto
The loss of sexual recombination and segregation in asexual organisms has been portrayed as an irreversible process that commits asexually-reproducing lineages to reduced diversification. We test this hypothesis by estimating rates of speciation, extinction, and transition between sexuality and functional asexuality in the evening primroses. Specifically, we estimate these rates using the recently developed BiSSE (Binary State Speciation and Extinction) phylogenetic comparative method, which employs maximum likelihood and Bayesian techniques. We infer that net diversification...

Data from: Extensive sex-specific nonadditivity of gene expression in Drosophila melanogaster

Greg Gibson, Rebecca Riley-Berger, Larry Harshman, Artyom Kopp, Scott Vacha, Sergey Nuzhdin & Marta Wayne
Assessment of the degree to which gene expression is additive and heritable has important implications for understanding the maintenance of variation, adaptation, phenotypic divergence, and the mapping of genotype onto phenotype. We used whole-genome transcript profiling using Agilent long-oligonucleotide microarrays representing 12,017 genes to demonstrate that gene transcription is pervasively nonadditive in Drosophila melanogaster. Comparison of adults of two isogenic lines and their reciprocal F1 hybrids revealed 5820 genes as significantly different between at least...

Data from: Ecological effects on metabolic scaling amphipod responses to fish predators in freshwater springs

Douglas S. Glazier, Eric M. Butler, Sara A. Lombardi, Travis J. Deptola, Andrew J. Reese & Erin V. Satterthwaite
Metabolic rate is commonly thought to scale with body mass to the 3/4-power as a result of universal body-design constraints. However, recent comparative work has shown that the metabolic scaling slope may vary significantly among species and higher taxa, apparently in response to different lifestyles and ecological conditions, though the precise mechanisms involved are not well understood. To better understand these under-appreciated ecological effects and their causes, it is important to control for extraneous phylogenetic...

Data from: Gene expression profiles associated with the transition to parasitism in Ancylostoma caninum larvae

Jennifer M. Moser, Tori Freitas, Prema Arasu & Greg Gibson
Ancylostoma caninum is a common canine parasite responsible for anemia and death in infected dogs. Gene expression profiling was used to investigate molecular differences between two different forms of the third larval stage (L3s): infective free-living larvae and in vitro serum-stimulated larvae that mimic the initial stages of parasitism of a host. We developed an A. caninum cDNA microarray consisting of 4191 EST clones, and used it to identify a set of 113 genes that...

Data from: Phenotypic plasticity in sexual communication signal of a noctuid moth

Astrid Groot, Alice Classen, Heike Staudacher, Coby Schal & David Heckel
Variability within sex pheromone signalling systems is generally believed to be low because of strong stabilizing selection; yet the noctuid moth Heliothis subflexa (Hs) shows significant intraspecific variation. One possible explanation is that females may alter their sex pheromone blend depending on prevailing olfactory cues in the habitat, which we termed the "experience hypothesis". This could be adaptive if Hs females experiencing the pheromone of another species, Heliothis virescens (Hv), responded to reduce the frequency...

Data from: Comparing the genetic architecture and potential response to selection of native and invasive populations of reed canary grass

Brittny Calsbeek, Manisha Patel, Sebastien Lavergne & Jane Molofsky
Evolutionary processes such as migration, genetic drift, and natural selection are thought to play a prominent role in species invasions into novel environments. However, few empirical studies have explored the mechanistic basis of invasion in an evolutionary framework. One promising tool for inferring evolutionarily important changes in introduced populations is the genetic variance-covariance matrix (G matrix). G matrix comparisons allow for the inference of changes in the genetic architecture of introduced populations relative to their...

Data from: Mixture modeling of transcript abundance classes in natural populations

Wen-Ping Hsieh, Gisele Passador-Gurgel, Eric A. Stone & Greg Gibson
BACKGROUND: Populations diverge in genotype and phenotype under the influence of such evolutionary processes as genetic drift, mutation accumulation, and natural selection. Because genotype maps onto phenotype by way of transcription, it is of interest to evaluate how these evolutionary factors influence the structure of variation at the level of transcription. Here, we explore the distributions of cis-acting and trans-acting factors and their relative contributions to expression of transcripts that exhibit two or more classes...

Data from: Quantitative trait transcripts for nicotine resistance in Drosophila melanogaster

Gisele Passador-Gurgel, Wen-Ping Hsieh, Priscilla Hunt, Nigel Deighton & Greg Gibson
Although most genetic association studies are performed with the intention of detecting nucleotide polymorphisms that are correlated with a complex trait, transcript abundance should also be expected to associate with diseases or phenotypes. We performed a scan for such quantitative trait transcripts in adult female heads of the fruit fly (Drosophila melanogaster) that might explain variation for nicotine resistance. The strongest association was seen for abundance of ornithine aminotransferase transcripts, implicating detoxification and neurotransmitter biosynthesis...

Data from: Impact of population structure on genetic diversity of a potential vaccine target in the canine hookworm (Ancylostoma caninum)

Jennifer M. Moser, Ignazio Carbone, Prema Arasu & Greg Gibson
Ancylostoma caninum is a globally distributed canine parasitic nematode. To test whether positive selection, population structure, or both affect genetic variation at the candidate vaccine target Ancylostoma secreted protein 1 (asp-1), we have quantified the genetic variation in A. caninum at asp-1 and a mitochondrial gene, cytochrome oxidase subunit 1 (cox-1), using the statistical population analysis tools found in the SNAP Workbench. The mitochondrial gene cox-1 exhibits moderate diversity within 2 North American samples, comparable...

Data from: Exploring variation in fitness surfaces over time or space

Brittny Calsbeek
As the number of studies estimating selection on multiple traits has increased in recent years, fitness surfaces have become a fundamental tool for understanding multivariate selection and evolution. However, rigorous statistical comparisons of multivariate selection surfaces over time or space have been limited to parametric analyses of selection coefficients estimated using a quadratic regression model. Although parametric comparisons are useful when selection is approximately linear or quadratic in nature, they are limited when confronting the...

Data from: Epidermal growth factor receptor and transforming growth factor-beta signaling contributes to variation for wing shape in Drosophila melanogaster

Ian Dworkin & Greg Gibson
Wing development in Drosophila is a common model system for the dissection of genetic networks and their roles during development. In particular, the RTK and TGF-beta regulatory networks appear to be involved with numerous aspects of wing development, including patterning, cell determination, growth, proliferation, and survival in the developing imaginal wing disc. However, little is known as to how subtle changes in the function of these genes may contribute to quantitative variation for wing shape,...

Data from: Contrasting selection pressures on components of the Ras-mediated signal transduction pathway in Drosophila

Greg Gibson, Rebecca M. Riley & Wei Jin
The molecular genetics of several signal transduction pathways is well characterized, providing an opportunity to address the nature of the population genetic forces acting on functionally related suites of pleiotropic regulatory genes. Signal transduction is the process by which signals are transmitted from the cell surface to the nucleus or other cellular structures. It plays a fundamental role in regulating a wide range of developmental and physiological processes, many of which are likely to be...

Data from: The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster

Wei Jin, Rebecca M. Riley, Russell D. Wolfinger, Kevin P. White, Gisele Passador-Gurgel & Greg Gibson
Here we present a statistically rigorous approach to quantifying microarray expression data that allows the relative effects of multiple classes of treatment to be compared and incorporates analytical methods that are common to quantitative genetics. From the magnitude of gene effects and contributions of variance components, we find that gene expression in adult flies is affected most strongly by sex, less so by genotype and only weakly by age (for 1- and 6-wk flies); in...

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: 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: 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...

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