Sun, 27 Jul 2008 08:04:02 BST CiteULike: emptyhb's natural_selection http://www.citeulike.org/user/emptyhb/tag/natural_selection CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/emptyhb/article/2982754 <i>Genetics, Vol. 155, No. 2. (June 2000), pp. 909-919.</i><br /><br />Selected substitutions at one locus can induce stochastic dynamics that resemble genetic drift at a closely linked neutral locus. The pseudohitchhiking model is a one-locus model that approximates these effects and can be used to describe the major consequences of linked selection. As the changes in neutral allele frequencies when hitchhiking are rapid, diffusion theory is not appropriate for studying neutral dynamics. A stationary distribution and some results on substitution processes are presented that use the theory of continuous-time Markov processes with discontinuous sample paths. The coalescent of the pseudohitchhiking model is shown to have a random number of branches at each node, which leads to a frequency spectrum that is different from that of the equilibrium neutral model. If genetic draft, the name given to these induced stochastic effects, is a more important stochastic force than genetic drift, then a number of paradoxes that have plagued population genetics disappear. Genetic drift in an infinite population. The pseudohitchhiking model. JH Gillespie Genetics, Vol. 155, No. 2. (June 2000), pp. 909-919. 2008-07-09T18:37:43-00:00 2000 Genetics 0016-6731 155 2 909 919 natural_selection population_genetics_modeling http://www.citeulike.org/user/emptyhb/article/2910110 <i>Science, Vol. 320, No. 5883. (20 June 2008), pp. 1629-1631.</i><br /><br />The role that natural selection plays in governing the locations and early evolution of copy-number mutations remains largely unexplored. We used high-density full-genome tiling arrays to create a fine-scale genomic map of copy-number polymorphisms (CNPs) in Drosophila melanogaster. We inferred a total of 2658 independent CNPs, 56% of which overlap genes. These include CNPs that are likely to be under positive selection, most notably high-frequency duplications encompassing toxin-response genes. The locations and frequencies of CNPs are strongly shaped by purifying selection, with deletions under stronger purifying selection than duplications. Among duplications, those overlapping exons or introns, as well as those falling on the X chromosome, seem to be subject to stronger purifying selection. 10.1126/science.1158078 Natural Selection Shapes Genome-Wide Patterns of Copy-Number Polymorphism in Drosophila melanogaster JJ Emerson Margarida Cardoso-Moreira Justin Borevitz Manyuan Long doi:10.1126/science.1158078 Science, Vol. 320, No. 5883. (20 June 2008), pp. 1629-1631. 2008-06-20T11:15:27-00:00 2008 Science 320 5883 1629 1631 copy_number_variation drosophila natural_selection http://www.citeulike.org/user/emptyhb/article/2680023 <i>Nature (16 April 2008)</i> The genomic and epidemiological dynamics of human influenza A virus Andrew Rambaut Oliver Pybus Martha Nelson Cecile Viboud Jeffery Taubenberger Edward Holmes doi:10.1038/nature06945 Nature (16 April 2008) 2008-04-17T05:20:03-00:00 2008 Nature 0028-0836 Nature Publishing Group natural_selection http://www.citeulike.org/user/emptyhb/article/172861 <i>Nature Genetics, Vol. 37, No. 5. (24 April 2005), pp. 544-548.</i> The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans Dee Denver Krystalynne Morris Todd Streelman Stuart Kim Michael Lynch Kelley Thomas doi:10.1038/ng1554 Nature Genetics, Vol. 37, No. 5. (24 April 2005), pp. 544-548. 2005-04-27T18:51:48-00:00 2005 Nature Genetics 1061-4036 37 5 544 548 Nature Publishing Group cis_regulatory_evolution natural_selection transcriptional_regulation http://www.citeulike.org/user/emptyhb/article/1089034 <i>Evolution Int J Org Evolution, Vol. 54, No. 4. (August 2000), pp. 1079-1091.</i><br /><br />One of the oldest problems in evolutionary biology remains largely unsolved. Which mutations generate evolutionarily relevant phenotypic variation? What kinds of molecular changes do they entail? What are the phenotypic magnitudes, frequencies of origin, and pleiotropic effects of such mutations? How is the genome constructed to allow the observed abundance of phenotypic diversity? Historically, the neo-Darwinian synthesizers stressed the predominance of micromutations in evolution, whereas others noted the similarities between some dramatic mutations and evolutionary transitions to argue for macromutationism. Arguments on both sides have been biased by misconceptions of the developmental effects of mutations. For example, the traditional view that mutations of important developmental genes always have large pleiotropic effects can now be seen to be a conclusion drawn from observations of a small class of mutations with dramatic effects. It is possible that some mutations, for example, those in cis-regulatory DNA, have few or no pleiotropic effects and may be the predominant source of morphological evolution. In contrast, mutations causing dramatic phenotypic effects, although superficially similar to hypothesized evolutionary transitions, are unlikely to fairly represent the true path of evolution. Recent developmental studies of gene function provide a new way of conceptualizing and studying variation that contrasts with the traditional genetic view that was incorporated into neo-Darwinian theory and population genetics. This new approach in developmental biology is as important for microevolutionary studies as the actual results from recent evolutionary developmental studies. In particular, this approach will assist in the task of identifying the specific mutations generating phenotypic variation and elucidating how they alter gene function. These data will provide the current missing link between molecular and phenotypic variation in natural populations. Evolutionary developmental biology and the problem of variation. DL Stern Evolution Int J Org Evolution, Vol. 54, No. 4. (August 2000), pp. 1079-1091. 2007-02-05T18:26:44-00:00 2000 Evolution Int J Org Evolution 0014-3820 54 4 1079 1091 cis_regulatory_evolution natural_selection phenotype review http://www.citeulike.org/user/emptyhb/article/966355 <i>Nature Genetics, Vol. 38, No. 12. (05 November 2006), pp. 1406-1412.</i> Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale Christopher Herring Anu Raghunathan Christiane Honisch Trina Patel Kenyon Applebee Andrew Joyce Thomas Albert Frederick Blattner Dirk van den Boom Charles Cantor Bernhard doi:10.1038/ng1906 Nature Genetics, Vol. 38, No. 12. (05 November 2006), pp. 1406-1412. 2006-11-29T09:46:32-00:00 2006 Nature Genetics 1061-4036 38 12 1406 1412 Nature Publishing Group natural_selection http://www.citeulike.org/user/emptyhb/article/2746015 <i>Nature, Vol. 299, No. 5879. (1982), pp. 111-117.</i> Molecular drive: a cohesive mode of species evolution Gabriel Dover doi:10.1038/299111a0 Nature, Vol. 299, No. 5879. (1982), pp. 111-117. 2008-05-02T14:40:35-00:00 1982 Nature 299 5879 111 117 molecular_evolution natural_selection http://www.citeulike.org/user/emptyhb/article/595410 <i>Nature, Vol. 403, No. 6769. (3 February 2000), pp. 564-567.</i> Evidence for stabilizing selection in a eukaryotic enhancer element Michael Ludwig Casey Bergman Nipam Patel Martin Kreitman doi:10.1038/35000615 Nature, Vol. 403, No. 6769. (3 February 2000), pp. 564-567. 2006-04-22T18:30:45-00:00 2000 Nature 403 6769 564 567 cis_regulatory_evolution drosophila even-skipped_enhancer function_study natural_selection http://www.citeulike.org/user/emptyhb/article/759438 <i>Science, Vol. 313, No. 5784. (14 July 2006), pp. 224-226.</i><br /><br />Competitor species can have evolutionary effects on each other that result in ecological character displacement; that is, divergence in resource-exploiting traits such as jaws and beaks. Nevertheless, the process of character displacement occurring in nature, from the initial encounter of competitors to the evolutionary change in one or more of them, has not previously been investigated. Here we report that a Darwin's finch species (Geospiza fortis) on an undisturbed Galapagos island diverged in beak size from a competitor species (G. magnirostris) 22 years after the competitor's arrival, when they jointly and severely depleted the food supply. The observed evolutionary response to natural selection was the strongest recorded in 33 years of study, and close to the value predicted from the high heritability of beak size. These findings support the role of competition in models of community assembly, speciation, and adaptive radiations. 10.1126/science.1128374 Evolution of Character Displacement in Darwin's Finches Peter Grant Rosemary Grant doi:10.1126/science.1128374 Science, Vol. 313, No. 5784. (14 July 2006), pp. 224-226. 2006-07-14T19:36:14-00:00 2006 Science 313 5784 224 226 natural_selection