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  • 1
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    Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-07-23
    Description: The dynamics of adaptation determine which mutations fix in a population, and hence how reproducible evolution will be. This is central to understanding the spectra of mutations recovered in the evolution of antibiotic resistance, the response of pathogens to immune selection, and the dynamics of cancer progression. In laboratory evolution experiments, demonstrably beneficial mutations are found repeatedly, but are often accompanied by other mutations with no obvious benefit. Here we use whole-genome whole-population sequencing to examine the dynamics of genome sequence evolution at high temporal resolution in 40 replicate Saccharomyces cerevisiae populations growing in rich medium for 1,000 generations. We find pervasive genetic hitchhiking: multiple mutations arise and move synchronously through the population as mutational 'cohorts'. Multiple clonal cohorts are often present simultaneously, competing with each other in the same population. Our results show that patterns of sequence evolution are driven by a balance between these chance effects of hitchhiking and interference, which increase stochastic variation in evolutionary outcomes, and the deterministic action of selection on individual mutations, which favours parallel evolutionary solutions in replicate populations.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3758440/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3758440/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lang, Gregory I -- Rice, Daniel P -- Hickman, Mark J -- Sodergren, Erica -- Weinstock, George M -- Botstein, David -- Desai, Michael M -- GM046406/GM/NIGMS NIH HHS/ -- GM071508/GM/NIGMS NIH HHS/ -- P50 GM071508/GM/NIGMS NIH HHS/ -- R01 GM046406/GM/NIGMS NIH HHS/ -- R37 GM046406/GM/NIGMS NIH HHS/ -- England -- Nature. 2013 Aug 29;500(7464):571-4. doi: 10.1038/nature12344. Epub 2013 Jul 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Lewis-Sigler Institute for Integrative Genomics and Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA. glang@lehigh.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23873039" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological/genetics ; Cell Nucleus/genetics ; Clone Cells/*cytology/metabolism ; *Evolution, Molecular ; Genes, Fungal/genetics ; Mutation/genetics ; Saccharomyces cerevisiae/classification/cytology/*genetics/*growth & development ; Stochastic Processes ; Time Factors
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Microbial evolution. Global epistasis makes adaptation predictable despite sequence-level stochasticity (2014)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2014-06-28
    Description: Epistatic interactions between mutations can make evolutionary trajectories contingent on the chance occurrence of initial mutations. We used experimental evolution in Saccharomyces cerevisiae to quantify this contingency, finding differences in adaptability among 64 closely related genotypes. Despite these differences, sequencing of 104 evolved clones showed that initial genotype did not constrain future mutational trajectories. Instead, reconstructed combinations of mutations revealed a pattern of diminishing-returns epistasis: Beneficial mutations have consistently smaller effects in fitter backgrounds. Taken together, these results show that beneficial mutations affecting a variety of biological processes are globally coupled; they interact strongly, but only through their combined effect on fitness. As a consequence, fitness evolution follows a predictable trajectory even though sequence-level adaptation is stochastic.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4314286/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4314286/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kryazhimskiy, Sergey -- Rice, Daniel P -- Jerison, Elizabeth R -- Desai, Michael M -- GM104239/GM/NIGMS NIH HHS/ -- R01 GM104239/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2014 Jun 27;344(6191):1519-22. doi: 10.1126/science.1250939.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. skryazhi@oeb.harvard.edu mdesai@oeb.harvard.edu. ; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. ; Department of Physics, Harvard University, Cambridge, MA 02138, USA. FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. ; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. Department of Physics, Harvard University, Cambridge, MA 02138, USA. FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. skryazhi@oeb.harvard.edu mdesai@oeb.harvard.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24970088" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptation, Physiological ; Base Sequence ; Directed Molecular Evolution ; *Epistasis, Genetic ; *Evolution, Molecular ; Genes, Fungal ; *Genetic Fitness ; Genome, Fungal ; Genotype ; Models, Genetic ; Molecular Sequence Annotation ; Mutation ; Saccharomyces cerevisiae/*genetics/*physiology ; Sequence Analysis, DNA ; Stochastic Processes
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Sex speeds adaptation by altering the dynamics of molecular evolution (2016)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2016-02-26
    Description: Sex and recombination are pervasive throughout nature despite their substantial costs. Understanding the evolutionary forces that maintain these phenomena is a central challenge in biology. One longstanding hypothesis argues that sex is beneficial because recombination speeds adaptation. Theory has proposed several distinct population genetic mechanisms that could underlie this advantage. For example, sex can promote the fixation of beneficial mutations either by alleviating interference competition (the Fisher-Muller effect) or by separating them from deleterious load (the ruby in the rubbish effect). Previous experiments confirm that sex can increase the rate of adaptation, but these studies did not observe the evolutionary dynamics that drive this effect at the genomic level. Here we present the first, to our knowledge, comparison between the sequence-level dynamics of adaptation in experimental sexual and asexual Saccharomyces cerevisiae populations, which allows us to identify the specific mechanisms by which sex speeds adaptation. We find that sex alters the molecular signatures of evolution by changing the spectrum of mutations that fix, and confirm theoretical predictions that it does so by alleviating clonal interference. We also show that substantially deleterious mutations hitchhike to fixation in adapting asexual populations. In contrast, recombination prevents such mutations from fixing. Our results demonstrate that sex both speeds adaptation and alters its molecular signature by allowing natural selection to more efficiently sort beneficial from deleterious mutations.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4855304/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4855304/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McDonald, Michael J -- Rice, Daniel P -- Desai, Michael M -- GM104239/GM/NIGMS NIH HHS/ -- R01 GM104239/GM/NIGMS NIH HHS/ -- England -- Nature. 2016 Mar 10;531(7593):233-6. doi: 10.1038/nature17143. Epub 2016 Feb 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA. ; FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA. ; Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26909573" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological/*genetics ; Clone Cells/cytology/metabolism ; *Evolution, Molecular ; Genetic Fitness/genetics ; Genetics, Population ; Models, Genetic ; Mutation/*genetics ; Recombination, Genetic/genetics ; Reproduction, Asexual/genetics/*physiology ; Saccharomyces cerevisiae/cytology/*genetics/*physiology ; Selection, Genetic/*genetics ; *Sex ; Time Factors
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 4
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    Gene Expression Evolves under a House-of-Cards Model of Stabilizing Selection (2015)
    Oxford University Press
    Details
    Publication Date: 2015-07-18
    Description: Divergence in gene regulation is hypothesized to underlie much of phenotypic evolution, but the role of natural selection in shaping the molecular phenotype of gene expression continues to be debated. To resolve the mode of gene expression, evolution requires accessible theoretical predictions for the effect of selection over long timescales. Evolutionary quantitative genetic models of phenotypic evolution can provide such predictions, yet those predictions depend on the underlying hypotheses about the distributions of mutational and selective effects that are notoriously difficult to disentangle. Here, we draw on diverse genomic data sets including expression profiles of natural genetic variation and mutation accumulation lines, empirical estimates of genomic mutation rates, and inferences of genetic architecture to differentiate contrasting hypotheses for the roles of stabilizing selection and mutation in shaping natural expression variation. Our analysis suggests that gene expression evolves in a domain of phenotype space well fit by the House-of-Cards (HC) model. Although the strength of selection inferred is sensitive to the number of loci controlling gene expression, the model is not. The consistency of these results across evolutionary time from budding yeast through fruit fly implies that this model is general and that mutational effects on gene expression are relatively large. Empirical estimates of the genetic architecture of gene expression traits imply that selection provides modest constraints on gene expression levels for most genes, but that the potential for regulatory evolution is high. Our prediction using data from laboratory environments should encourage the collection of additional data sets allowing for more nuanced parameterizations of HC models for gene expression.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    Resampling QTL Effects in the QTL Sign Test Leads to Incongruous Sensitivity to Variance in Effect Size (2012)
    Genetics Society of America (GSA)
    Details
    Publication Date: 2012-08-04
    Description: Allelic effects at quantitative trait loci (QTL) between lineages are potentially informative for indicating the action of natural selection. The QTL Sign Test uses the number of + and – alleles observed in a QTL study to infer a history of selection. This test has been constructed to condition on the phenotypic difference between the two lines in question. By applying the test to QTL data simulated under selection, we demonstrate that conditioning on the phenotypic difference results in a loss of power to reject the neutral hypothesis and marked sensitivity to variation in locus effect magnitude.
    Electronic ISSN: 2160-1836
    Topics: Biology
    Published by Genetics Society of America (GSA)
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  • 6
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    Does the Permeability of Gravel River Beds Affect Near-bed Hydrodynamics? (2017)
    Wiley
    Details
    Publication Date: 2017-09-19
    Description: The permeability of river beds is an important control on hyporheic flow and the movement of fine sediment and solutes into and out of the bed. However, relatively little is known about the effect of bed permeability on overlying near-bed flow dynamics, and thus on fluid advection at the sediment-water interface. This study provides the first quantification of this effect for water-worked gravel-beds. Laboratory experiments in a recirculating flume revealed that flows over permeable beds exhibit fundamental differences compared with flows over impermeable beds of the same topography. The turbulence over permeable beds is less intense, more organised and more efficient at momentum transfer because eddies are more coherent. Furthermore, turbulent kinetic energy is lower, meaning that less energy is extracted from the mean flow by this turbulence. Consequently, the double-averaged velocity is higher and the bulk flow resistance is lower over permeable beds, and there is a difference in how momentum is conveyed from the overlying flow to the bed surface. The main implications of these results are three-fold. First, local pressure gradients, and therefore rates of material transport, across the sediment-water interface are likely to differ between impermeable and permeable beds. Second, near-bed and hyporheic flows are unlikely to be adequately predicted by numerical models that represent the bed as an impermeable boundary. Third, more sophisticated flow resistance models are required for coarse-grained rivers that consider not only the bed surface but also the underlying permeable structure. Overall, our results suggest that the effects of bed permeability have critical implications for hyporheic exchange, fluvial sediment dynamics and benthic habitat availability.
    Print ISSN: 0197-9337
    Electronic ISSN: 1096-9837
    Topics: Geography , Geosciences
    Published by Wiley
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  • 7
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    Investigation of radiometric properties of LANDSAT-4 MSS (1983)
    In:  Other Sources
    Details
    Publication Date: 2011-08-18
    Description: Two full frames of radiometrically corrected (Type A) LANDSAT-4 MSS data were analyzed digitally and visually for evidence of residual calibration differences between detectors, quantization effects, and other sensor-related artifacts. Both standard statistical and Fourier analysis techniques were employed. Opportunities for coincident coverage by LANDSATS 3 and 4 were identified in the contiguous 48 states. Paired acquisitions for two scenes were obtained and analyzed to establish relationships between signal values from common areas imaged by the two MSS Systems. Initial findings on detector-to-detector differences, coherent noise, and LANDSAT 4 to LANDSAT 3 calibration are summarized. Results show that LANDSAT 4 MSS produces data of generally good quality with dynamic ranges and target responses similar to those of previous sensors.
    Keywords: EARTH RESOURCES AND REMOTE SENSING
    Type: NASA. Goddard Space Flight Center LANDSAT-4 Sci. Characterization; 3 p
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    NASA TECHNICAL REPORTS
  • 8
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    Characterization of LANDSAT-4 MSS and TM digital image data (1985)
    In:  Other Sources
    Details
    Publication Date: 2019-06-28
    Description: The launch of LANDSAT-4 in July 1982 represents a continuation in the remote sensing of earth resources. The 80-m spatial resolution provided by the Multispectral Scanner (MSS) on board the satellite is fine enough to resolve many natural features and land-use details in both rural and urban settings. The second sensor of the spacecraft, the Thematic Mapper (TM), introduce a new era of sensing with refined spatial resolution (30 m) and expanded spectral coverage (7 bands). This paper describes results from engineering studies of the characteristics of digital image data from the two LANDSAT-4 sensors are described. These studies form a part of the LANDSAT-4 Image Data Quality Analysis program (LIDQA). The image data were generally found to be of high quality and the TM provided several improvements over the MSS, in its spatial and spectral characteristics.
    Keywords: EARTH RESOURCES AND REMOTE SENSING
    Type: Study on Spectral(Radiometric Characteristics of the Thematic Mapper for Land Use Applications; p 5-20
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    NASA TECHNICAL REPORTS
  • 9
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    Wheat yield forecasts using LANDSAT data (1977)
    In:  CASI
    Details
    Publication Date: 2019-06-27
    Description: Several considerations of winter wheat yield prediction using LANDSAT data were discussed. In addition, a simple technique which permits direct early season forecasts of wheat production was described.
    Keywords: EARTH RESOURCES AND REMOTE SENSING
    Type: Proc. of the 11th Intern. Symp. on Remote Sensing of Environment, Vol. 2; p 1245-1254
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    NASA TECHNICAL REPORTS
  • 10
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    Crop identification technology assessment for remote sensing (CITARS). Volume 10: Interpretation of results (1975)
    In:  CASI
    Details
    Publication Date: 2019-06-27
    Description: The CITARS was an experiment designed to quantitatively evaluate crop identification performance for corn and soybeans in various environments using a well-defined set of automatic data processing (ADP) techniques. Each technique was applied to data acquired to recognize and estimate proportions of corn and soybeans. The CITARS documentation summarizes, interprets, and discusses the crop identification performances obtained using (1) different ADP procedures; (2) a linear versus a quadratic classifier; (3) prior probability information derived from historic data; (4) local versus nonlocal recognition training statistics and the associated use of preprocessing; (5) multitemporal data; (6) classification bias and mixed pixels in proportion estimation; and (7) data with differnt site characteristics, including crop, soil, atmospheric effects, and stages of crop maturity.
    Keywords: EARTH RESOURCES AND REMOTE SENSING
    Type: NASA-CR-147718 , LEC-4326H-VOL-10 , JSC-09393-VOL-10
    Format: application/pdf
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    NASA TECHNICAL REPORTS
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