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  • 1
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    The ecoresponsive genome of Daphnia pulex (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-02-05
    Description: We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia's genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3529199/" 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/PMC3529199/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Colbourne, John K -- Pfrender, Michael E -- Gilbert, Donald -- Thomas, W Kelley -- Tucker, Abraham -- Oakley, Todd H -- Tokishita, Shinichi -- Aerts, Andrea -- Arnold, Georg J -- Basu, Malay Kumar -- Bauer, Darren J -- Caceres, Carla E -- Carmel, Liran -- Casola, Claudio -- Choi, Jeong-Hyeon -- Detter, John C -- Dong, Qunfeng -- Dusheyko, Serge -- Eads, Brian D -- Frohlich, Thomas -- Geiler-Samerotte, Kerry A -- Gerlach, Daniel -- Hatcher, Phil -- Jogdeo, Sanjuro -- Krijgsveld, Jeroen -- Kriventseva, Evgenia V -- Kultz, Dietmar -- Laforsch, Christian -- Lindquist, Erika -- Lopez, Jacqueline -- Manak, J Robert -- Muller, Jean -- Pangilinan, Jasmyn -- Patwardhan, Rupali P -- Pitluck, Samuel -- Pritham, Ellen J -- Rechtsteiner, Andreas -- Rho, Mina -- Rogozin, Igor B -- Sakarya, Onur -- Salamov, Asaf -- Schaack, Sarah -- Shapiro, Harris -- Shiga, Yasuhiro -- Skalitzky, Courtney -- Smith, Zachary -- Souvorov, Alexander -- Sung, Way -- Tang, Zuojian -- Tsuchiya, Dai -- Tu, Hank -- Vos, Harmjan -- Wang, Mei -- Wolf, Yuri I -- Yamagata, Hideo -- Yamada, Takuji -- Ye, Yuzhen -- Shaw, Joseph R -- Andrews, Justen -- Crease, Teresa J -- Tang, Haixu -- Lucas, Susan M -- Robertson, Hugh M -- Bork, Peer -- Koonin, Eugene V -- Zdobnov, Evgeny M -- Grigoriev, Igor V -- Lynch, Michael -- Boore, Jeffrey L -- P42 ES004699/ES/NIEHS NIH HHS/ -- P42 ES004699-25/ES/NIEHS NIH HHS/ -- P42ES004699/ES/NIEHS NIH HHS/ -- R01 ES019324/ES/NIEHS NIH HHS/ -- R24 GM078274/GM/NIGMS NIH HHS/ -- R24 GM078274-01A1/GM/NIGMS NIH HHS/ -- R24GM07827401/GM/NIGMS NIH HHS/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2011 Feb 4;331(6017):555-61. doi: 10.1126/science.1197761.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Genomics and Bioinformatics, Indiana University, 915 East Third Street, Bloomington, IN 47405, USA. jcolbour@indiana.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21292972" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Amino Acid Sequence ; Animals ; Base Sequence ; Chromosome Mapping ; Daphnia/*genetics/physiology ; *Ecosystem ; Environment ; Evolution, Molecular ; Gene Conversion ; Gene Duplication ; Gene Expression ; Gene Expression Profiling ; Gene Expression Regulation ; Genes ; Genes, Duplicate ; *Genome ; Metabolic Networks and Pathways/genetics ; Molecular Sequence Annotation ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Sequence Analysis, DNA
    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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  • 2
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    Temporal variation, dormancy, and coexistence: A field test of the storage effect (1997)
    National Academy of Sciences
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    Publication Date: 1997-08-19
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 3
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    Timing variations in the secondary eclipse of NN Ser (2014)
    Oxford University Press
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    Publication Date: 2014-01-18
    Description: The eclipsing white dwarf plus main-sequence binary NN Serpentis provides one of the most convincing cases for the existence of circumbinary planets around evolved binaries. The exquisite timing precision provided by the deep eclipse of the white dwarf has revealed complex variations in the eclipse arrival times over the last few decades. These variations have been interpreted as the influence of two planets in orbit around the binary. Recent studies have proved that such a system is dynamically stable over the current lifetime of the binary. However, the existence of such planets is by no means proven and several alternative mechanisms have been proposed that could drive similar variations. One of these is apsidal precession, which causes the eclipse times of eccentric binaries to vary sinusoidally on many year time-scales. In this Letter, we present timing data for the secondary eclipse of NN Ser and show that they follow the same trend seen in the primary eclipse times, ruling out apsidal precession as a possible cause for the variations. This result leaves no alternatives to the planetary interpretation for the observed period variations, although we still do not consider their existence as proven. Our data limit the eccentricity of NN Ser to e  〈 10 –3 . We also detect a 3.3 ± 1.0 s delay in the arrival times of the secondary eclipses relative to the best planetary model. This delay is consistent with the expected 2.84 ± 0.04 s Rømer delay of the binary, and is the first time this effect has been detected in a white dwarf plus M dwarf system.
    Print ISSN: 1745-3925
    Electronic ISSN: 1745-3933
    Topics: Physics
    Published by Oxford University Press
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  • 4
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    The planets around NN Serpentis: still there (2013)
    Oxford University Press
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    Publication Date: 2013-12-06
    Description: We present 25 new eclipse times of the white dwarf binary NN Ser taken with the high-speed camera ULTRACAM on the William Herschel Telescope and New Technology Telescope, the RISE camera on the Liverpool Telescope and HAWK-I on the Very Large Telescope to test the two-planet model proposed to explain variations in its eclipse times measured over the last 25 yr. The planetary model survives the test with flying colours, correctly predicting a progressive lag in eclipse times of 36 s that has set in since 2010 compared to the previous 8 yr of precise times. Allowing both orbits to be eccentric, we find orbital periods of 7.9 ± 0.5 and 15.3 ± 0.3 yr, and masses of 2.3 ± 0.5 and 7.3 ± 0.3 M J . We also find dynamically long-lived orbits consistent with the data, associated with 2:1 and 5:2 period ratios. The data scatter by 0.07 s relative to the best-fitting model, by some margin the most precise of any of the proposed eclipsing compact object planet hosts. Despite the high precision, degeneracy in the orbit fits prevents a significant measurement of a period change of the binary and of N -body effects. Finally, we point out a major flaw with a previous dynamical stability analysis of NN Ser, and by extension, with a number of analyses of similar systems.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 5
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    Life-history evolution in a Daphnia ambigua population during community assembly (2015)
    Oxford University Press
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    Publication Date: 2015-03-25
    Description: Population and community dynamics influence, and are influenced by, among-individual variation in traits. However, studies examining rapid evolution during community assembly remain rare. We examined how four life-history traits in Daphnia ambigua have evolved during community assembly in a recently created lake. Microfossils, preserved in sediments, suggest that D. ambigua was one of the original zooplankton colonizers, followed by Daphnia dentifera and Daphnia pulicaria . We used water column collections and dormant eggs from sediment cores to isolate 45 isofemale lines into laboratory culture, representing four time periods of lake colonization. We measured size at birth, size and time to maturity, clutch size, and juvenile growth rate and found significant differences among time periods in two of the traits, size at maturity and first clutch size. Although isofemale lines from the founding and recent population are known to differ in their competitive ability, we found no evidence that these temporal populations differ in measured life-history traits, sensitivity to resources or population growth rate. Nevertheless, our experimental results note rapid and non-directional evolution of two life-history traits, closely tied to fitness, during the assembly of this community.
    Print ISSN: 0142-7873
    Electronic ISSN: 1464-3774
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    Disease in freshwater zooplankton: what have we learned and where are we going? (2014)
    Oxford University Press
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    Publication Date: 2014-03-08
    Description: In the last few decades, zooplankton (especially Daphnia ) have emerged as a model system for examining the ecological and evolutionary roles of parasites in populations, communities and ecosystems. We build on this foundation, moving towards continued integration of epidemiology and community ecology to understand the distribution and abundance of infectious diseases. Future studies should link processes that occur over multiple time scales: from deep-time phylogenetic patterns that have shaped and been shaped by host–parasite interactions, to the dynamics that play out over decades or within seasons, to the physiological time scales over which parasites operate to infect and kill their hosts. We also consider how the combination of processes across multiple time scales has shaped the biogeography and changing mosaic of host–parasite interactions in time and space. Finally, we consider a future where zooplankton–parasite interactions are influenced by global change. The Daphnia –parasite model system offers a powerful tool to link anthropogenic changes to infectious diseases, including zoonotic diseases of significance to human health.
    Print ISSN: 0142-7873
    Electronic ISSN: 1464-3774
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    PHYSICAL STRUCTURE OF LAKES CONSTRAINS EPIDEMICS INDAPHNIAPOPULATIONS (2006)
    Wiley
    Details
    Publication Date: 2006-06-01
    Print ISSN: 0012-9658
    Electronic ISSN: 1939-9170
    Topics: Biology
    Published by Wiley on behalf of Ecological Society of America.
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