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  • 1
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    Mutational robustness can facilitate adaptation (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-01-22
    Description: Robustness seems to be the opposite of evolvability. If phenotypes are robust against mutation, we might expect that a population will have difficulty adapting to an environmental change, as several studies have suggested. However, other studies contend that robust organisms are more adaptable. A quantitative understanding of the relationship between robustness and evolvability will help resolve these conflicting reports and will clarify outstanding problems in molecular and experimental evolution, evolutionary developmental biology and protein engineering. Here we demonstrate, using a general population genetics model, that mutational robustness can either impede or facilitate adaptation, depending on the population size, the mutation rate and the structure of the fitness landscape. In particular, neutral diversity in a robust population can accelerate adaptation as long as the number of phenotypes accessible to an individual by mutation is smaller than the total number of phenotypes in the fitness landscape. These results provide a quantitative resolution to a significant ambiguity in evolutionary theory.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3071712/" 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/PMC3071712/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Draghi, Jeremy A -- Parsons, Todd L -- Wagner, Gunter P -- Plotkin, Joshua B -- 2U54AI057168/AI/NIAID NIH HHS/ -- U54 AI057168/AI/NIAID NIH HHS/ -- U54 AI057168-06S1/AI/NIAID NIH HHS/ -- England -- Nature. 2010 Jan 21;463(7279):353-5. doi: 10.1038/nature08694.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20090752" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological/*genetics ; *Biological Evolution ; Genetic Fitness/genetics ; Genetic Variation/genetics ; Genetics, Population ; Genotype ; Models, Genetic ; Mutagenesis/*genetics ; Mutation/*genetics ; Phenotype ; Population Density ; 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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    Coding-sequence determinants of gene expression in Escherichia coli (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-04-11
    Description: Synonymous mutations do not alter the encoded protein, but they can influence gene expression. To investigate how, we engineered a synthetic library of 154 genes that varied randomly at synonymous sites, but all encoded the same green fluorescent protein (GFP). When expressed in Escherichia coli, GFP protein levels varied 250-fold across the library. GFP messenger RNA (mRNA) levels, mRNA degradation patterns, and bacterial growth rates also varied, but codon bias did not correlate with gene expression. Rather, the stability of mRNA folding near the ribosomal binding site explained more than half the variation in protein levels. In our analysis, mRNA folding and associated rates of translation initiation play a predominant role in shaping expression levels of individual genes, whereas codon bias influences global translation efficiency and cellular fitness.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3902468/" 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/PMC3902468/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kudla, Grzegorz -- Murray, Andrew W -- Tollervey, David -- Plotkin, Joshua B -- BB/D019621/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/DO19621/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/DO19621/1/Wellcome Trust/United Kingdom -- P50 GM068763/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2009 Apr 10;324(5924):255-8. doi: 10.1126/science.1170160.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology and Program in Applied Mathematics and Computational Science, University of Pennsylvania, Philadelphia, PA 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19359587" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Base Composition ; Cloning, Molecular ; *Codon ; Escherichia coli/*genetics/growth & development/metabolism ; *Gene Expression ; Gene Library ; Genes, Synthetic ; Green Fluorescent Proteins/*genetics/metabolism ; Mutation ; Nucleic Acid Conformation ; Protein Biosynthesis ; RNA Stability ; RNA, Bacterial/chemistry/genetics/metabolism ; RNA, Messenger/chemistry/*genetics/metabolism ; Spectrometry, Fluorescence
    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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    Molecular evolution: Hidden diversity sparks adaptation (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-06-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Draghi, Jeremy A -- Plotkin, Joshua B -- England -- Nature. 2011 Jun 2;474(7349):45-6. doi: 10.1038/474045a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21637251" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological/*genetics ; Animals ; *Biodiversity ; Epistasis, Genetic ; *Evolution, Molecular ; Genotype ; Humans ; RNA, Catalytic/genetics
    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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    The role of epistasis in protein evolution (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-05-31
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McCandlish, David M -- Rajon, Etienne -- Shah, Premal -- Ding, Yang -- Plotkin, Joshua B -- England -- Nature. 2013 May 30;497(7451):E1-2; discussion E2-3. doi: 10.1038/nature12219.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23719465" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Epistasis, Genetic/*genetics ; *Evolution, Molecular
    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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  • 5
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    Evolution. In evolution, the sum is less than its parts (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-06-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kryazhimskiy, Sergey -- Draghi, Jeremy A -- Plotkin, Joshua B -- New York, N.Y. -- Science. 2011 Jun 3;332(6034):1160-1. doi: 10.1126/science.1208072.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of Pennsylvania, Philadelphia, PA 19103, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21636764" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; *Biological Evolution ; *Epistasis, Genetic ; Escherichia coli/*genetics/physiology ; Evolution, Molecular ; *Genetic Fitness ; Genome, Bacterial ; Methylobacterium extorquens/*genetics/physiology ; *Mutation
    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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  • 6
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    Cell biology. The lives of proteins (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-02-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Plotkin, Joshua B -- New York, N.Y. -- Science. 2011 Feb 11;331(6018):683-4. doi: 10.1126/science.1202010.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology and Program in Applied Mathematics and Computational Science, University of Pennsylvania, Philadelphia, PA 19104, USA. jplotkin@sas.upenn.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21310990" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Cycle Proteins/*metabolism ; *Cell Division ; Cell Line, Tumor ; Fluorescence ; Half-Life ; Humans ; Proteins/*metabolism
    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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  • 7
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    Evolution, safety, and highly pathogenic influenza viruses (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-06-23
    Description: Experience with influenza has shown that predictions of virus phenotype or fitness from nucleotide sequence are imperfect and that predicting the timing and course of evolution is extremely difficult. Such uncertainty means that the risk of experiments with mammalian-transmissible, possibly highly virulent influenza viruses remains high even if some aspects of their laboratory biology are reassuring; it also implies limitations on the ability of laboratory observations to guide interpretation of surveillance of strains in the field. Thus, we propose that future experiments with virulent pathogens whose accidental or deliberate release could lead to extensive spread in human populations should be limited by explicit risk-benefit considerations.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3467308/" 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/PMC3467308/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lipsitch, Marc -- Plotkin, Joshua B -- Simonsen, Lone -- Bloom, Barry -- U54 GM088558/GM/NIGMS NIH HHS/ -- U54GM088558/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 Jun 22;336(6088):1529-31. doi: 10.1126/science.1223204.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Communicable Disease Dynamics and Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA. mlipsitc@hsph.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22723411" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigenic Variation ; Antigens, Viral ; Antiviral Agents/pharmacology/therapeutic use ; Biohazard Release ; *Containment of Biohazards ; Drug Resistance, Viral ; *Evolution, Molecular ; Ferrets ; Humans ; Influenza A Virus, H5N1 Subtype/genetics/*pathogenicity ; Influenza A virus/drug effects/genetics/immunology/*pathogenicity ; Influenza, Human/drug therapy/transmission/*virology ; Laboratory Infection/epidemiology ; Mutation ; Orthomyxoviridae Infections/transmission/*virology ; Public Policy ; Risk Assessment ; *Safety ; Security Measures ; United States/epidemiology
    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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  • 8
    Electronic Resource
    Electronic Resource
    Evolutionary genomics Codon volatility does not detect selection (reply) (2005)
    [s.l.] : Nature Publishing Group
    Nature 433.2005, 7023, E7-, (2 S.) 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Plotkin et al. reply - The criticisms of our results by Hahn et al., Nielsen and Hubisz, and Chen, Emerson and Martin fall into three categories: the formal justification for our method, the potential for confounding factors, and the interpretation of our empirical ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/nature03224
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    Paper (German National Licenses)
    Fulltext
  • 9
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    Predicting species diversity in tropical forests (2000)
    National Academy of Sciences
    Details
    Publication Date: 2000-09-26
    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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  • 10
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    Reconciling molecular phylogenies with the fossil record (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-09-19
    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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