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  • 1
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    Evidence for DNA loss as a determinant of genome size (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-02-11
    Description: Eukaryotic genome sizes range over five orders of magnitude. This variation cannot be explained by differences in organismic complexity (the C value paradox). To test the hypothesis that some variation in genome size can be attributed to differences in the patterns of insertion and deletion (indel) mutations among organisms, this study examines the indel spectrum in Laupala crickets, which have a genome size 11 times larger than that of Drosophila. Consistent with the hypothesis, DNA loss is more than 40 times slower in Laupala than in Drosophila.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Petrov, D A -- Sangster, T A -- Johnston, J S -- Hartl, D L -- Shaw, K L -- New York, N.Y. -- Science. 2000 Feb 11;287(5455):1060-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Harvard University Society of Fellows, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. dpetrov@oeb.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10669421" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; DNA/genetics ; Drosophila/*genetics ; *Evolution, Molecular ; *Genome ; Gryllidae/*genetics ; Likelihood Functions ; Multigene Family ; *Mutation ; Phylogeny ; Polymerase Chain Reaction ; Pseudogenes ; *Retroelements ; Sequence Deletion ; Species Specificity
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
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    Recent origin of Plasmodium falciparum from a single progenitor (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-07-21
    Description: Genetic variability of Plasmodium falciparum underlies its transmission success and thwarts efforts to control disease caused by this parasite. Genetic variation in antigenic, drug resistance, and pathogenesis determinants is abundant, consistent with an ancient origin of P. falciparum, whereas DNA variation at silent (synonymous) sites in coding sequences appears virtually absent, consistent with a recent origin of the parasite. To resolve this paradox, we analyzed introns and demonstrated that these are deficient in single-nucleotide polymorphisms, as are synonymous sites in coding regions. These data establish the recent origin of P. falciparum and further provide an explanation for the abundant diversity observed in antigen and other selected genes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Volkman, S K -- Barry, A E -- Lyons, E J -- Nielsen, K M -- Thomas, S M -- Choi, M -- Thakore, S S -- Day, K P -- Wirth, D F -- Hartl, D L -- New York, N.Y. -- Science. 2001 Jul 20;293(5529):482-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Harvard-Oxford Malaria Genome Diversity Project, Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11463913" target="_blank"〉PubMed〈/a〉
    Keywords: Africa ; Agriculture ; Alternative Splicing ; Animals ; Base Sequence ; *Biological Evolution ; Genes, Protozoan ; *Genetic Variation ; Humans ; *Introns ; Malaria, Falciparum/epidemiology/parasitology/transmission ; *Microsatellite Repeats ; Molecular Sequence Data ; Mutation ; Plasmodium/genetics ; Plasmodium falciparum/*genetics ; *Polymorphism, Single Nucleotide
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
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    Population genetics in forensic DNA typing (1991)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1991-12-20
    Description: Variable number of tandem repeat (VNTR) sequences are used to link defendants with crimes by matching DNA patterns. The probative value of a match is often calculated by multiplying together the estimated frequencies with which each particular VNTR pattern occurs in a reference database. However, this method is liable to potentially serious errors because ethnic subgroups within major racial categories exhibit genetic differences that are maintained by endogamy. The multiplication procedure currently in use can be made scientifically valid only by extensive sampling of VNTR frequency distributions in a variety of ethnic groups, similar to the ethnic studies of various blood groups done in the past. Alternative approaches for dealing with subpopulation heterogeneity are discussed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lewontin, R C -- Hartl, D L -- New York, N.Y. -- Science. 1991 Dec 20;254(5039):1745-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1845040" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Blood Group Antigens/genetics ; *DNA Fingerprinting ; DNA Probes ; Ethnic Groups/genetics ; European Continental Ancestry Group/genetics ; Gene Frequency ; *Genetics, Medical ; *Genetics, Population ; Humans ; Repetitive Sequences, Nucleic Acid ; United States
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    Genetic properties influencing the evolvability of gene expression (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-05-26
    Description: Identifying the properties of gene networks that influence their evolution is a fundamental research goal. However, modes of evolution cannot be inferred solely from the distribution of natural variation, because selection interacts with demography and mutation rates to shape polymorphism and divergence. We estimated the effects of naturally occurring mutations on gene expression while minimizing the effect of natural selection. We demonstrate that sensitivity of gene expression to mutations increases with both increasing trans-mutational target size and the presence of a TATA box. Genes with greater sensitivity to mutations are also more sensitive to systematic environmental perturbations and stochastic noise. These results provide a mechanistic basis for gene expression evolvability that can serve as a foundation for realistic models of regulatory evolution.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Landry, Christian R -- Lemos, Bernardo -- Rifkin, Scott A -- Dickinson, W J -- Hartl, Daniel L -- New York, N.Y. -- Science. 2007 Jul 6;317(5834):118-21. Epub 2007 May 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA. clandry@post.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17525304" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; *Evolution, Molecular ; *Gene Expression ; Gene Expression Regulation, Fungal ; *Gene Regulatory Networks ; *Genes, Fungal ; Genetic Variation ; Linear Models ; Models, Genetic ; *Mutation ; Oligonucleotide Array Sequence Analysis ; Phenotype ; Promoter Regions, Genetic ; Saccharomyces cerevisiae/*genetics ; Selection, Genetic ; TATA Box ; Transcription Factors/metabolism ; Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
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    Parasitology. A game of cat and mouth (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-01-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Volkman, Sarah K -- Hartl, Daniel L -- New York, N.Y. -- Science. 2003 Jan 17;299(5605):353-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12532003" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Cat Diseases/parasitology/transmission ; Cats ; Female ; Food Parasitology ; Genes, Protozoan ; Genetic Variation ; Humans ; Life Cycle Stages ; Mice ; Mouth ; Mutation ; Polymorphism, Genetic ; Pregnancy ; Pregnancy Complications, Parasitic/parasitology ; Recombination, Genetic ; Reproduction ; Toxoplasma/*genetics/pathogenicity/*physiology ; Toxoplasmosis/*parasitology/transmission ; Toxoplasmosis, Animal/*parasitology/transmission ; Toxoplasmosis, Congenital/epidemiology/parasitology ; Virulence
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
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    Compensated deleterious mutations in insect genomes (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-10-23
    Description: Relatively little is known about the importance of amino acid interactions in protein and phenotypic evolution. Here we examine whether mutations that are pathogenic in Drosophila melanogaster become fixed via epistasis in other Dipteran genomes. Overall divergence at pathogenic amino acid sites is reduced. However, approximately 10% of the substitutions at these sites carry the exact same pathogenic amino acid found in D. melanogaster mutants. Hence compensatory mutation(s) must have evolved. Surprisingly, the fraction 10% is not affected by phylogenetic distance. These results support a selection-driven process that allows compensated amino acid substitutions to become rapidly fixed in taxa with large populations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kulathinal, Rob J -- Bettencourt, Brian R -- Hartl, Daniel L -- GM068465/GM/NIGMS NIH HHS/ -- P41-HG00739/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2004 Nov 26;306(5701):1553-4. Epub 2004 Oct 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15498973" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Anopheles gambiae/*genetics ; Codon, Nonsense ; Drosophila/*genetics ; Drosophila melanogaster/*genetics ; Epistasis, Genetic ; *Evolution, Molecular ; Genes, Insect ; *Genome ; Insect Proteins/chemistry/*genetics ; Molecular Sequence Data ; *Mutation ; Mutation, Missense ; Phenotype ; Phylogeny ; Selection, Genetic ; Sequence Alignment
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
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    DNA fingerprinting (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-10-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hartl, D L -- Lewontin, R C -- New York, N.Y. -- Science. 1994 Oct 14;266(5183):201; author reply 202-3.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7802835" target="_blank"〉PubMed〈/a〉
    Keywords: *DNA Fingerprinting/standards ; Genetics, Population ; Humans ; Jurisprudence
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
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    DNA fingerprinting report (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-04-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hartl, D L -- Lewontin, R C -- New York, N.Y. -- Science. 1993 Apr 23;260(5107):473-4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8475378" target="_blank"〉PubMed〈/a〉
    Keywords: Continental Population Groups ; *DNA Fingerprinting ; Ethnic Groups ; Genetics, Population ; Humans ; Probability
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
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    Darwinian evolution can follow only very few mutational paths to fitter proteins (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-04-08
    Description: Five point mutations in a particular beta-lactamase allele jointly increase bacterial resistance to a clinically important antibiotic by a factor of approximately 100,000. In principle, evolution to this high-resistance beta-lactamase might follow any of the 120 mutational trajectories linking these alleles. However, we demonstrate that 102 trajectories are inaccessible to Darwinian selection and that many of the remaining trajectories have negligible probabilities of realization, because four of these five mutations fail to increase drug resistance in some combinations. Pervasive biophysical pleiotropy within the beta-lactamase seems to be responsible, and because such pleiotropy appears to be a general property of missense mutations, we conclude that much protein evolution will be similarly constrained. This implies that the protein tape of life may be largely reproducible and even predictable.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weinreich, Daniel M -- Delaney, Nigel F -- Depristo, Mark A -- Hartl, Daniel L -- New York, N.Y. -- Science. 2006 Apr 7;312(5770):111-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA. dmw@post.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16601193" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Anti-Bacterial Agents/pharmacology ; Cefotaxime/metabolism/*pharmacology ; *Drug Resistance, Bacterial ; Enzyme Stability ; Epistasis, Genetic ; Escherichia coli/*drug effects/enzymology/genetics ; *Evolution, Molecular ; Models, Genetic ; *Mutation ; Mutation, Missense ; Point Mutation ; Probability ; Selection, Genetic ; beta-Lactamases/*genetics/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 10
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    T-cell receptor beta-chain expression: dependence on relatively few variable region genes (1985)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1985-08-09
    Description: Fifteen independently isolated complementary DNA clones that contain T-cell receptor (TCR) V beta genes were sequenced and found to represent 11 different V beta genes. When compared with known sequences, 14 different V beta genes could be defined from a total of 25 complementary DNA's; 11 clones therefore involved repeated usage of previously identified V beta's. Based on these data, we calculate a maximum likelihood estimate of the number of expressed germline V beta genes to be 18 with an upper 95 percent confidence bound of 30 genes. Southern blot analysis has shown that most of these genes belong to single element subfamilies which show very limited interstrain polymorphism. The TCR beta-chain diversity appears to be generated from a limited V beta gene pool primarily by extensive variability at the variable-diversity-joining (V-D-J) junctional site, with no evidence for the involvement of somatic hypermutation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Behlke, M A -- Spinella, D G -- Chou, H S -- Sha, W -- Hartl, D L -- Loh, D Y -- GM07200/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1985 Aug 9;229(4713):566-70.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3875151" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; Base Sequence ; Chromosome Mapping ; Cloning, Molecular ; Dna ; Gene Pool ; *Genetic Variation ; Humans ; Hybridomas ; Immunoglobulin Variable Region/genetics ; Mice ; Mice, Inbred BALB C/genetics ; Mice, Inbred C57BL/genetics ; Mice, Inbred Strains/genetics ; Receptors, Antigen, T-Cell/*genetics ; Species Specificity ; Spleen ; T-Lymphocytes ; Thymus Gland
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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