Recom bination y et inecien t selection along the Dr osophila melano gaster subgroup's fourth c hromosome Submission in tended as a Rese arc h Article

[1]  D. Petrov,et al.  X-Linked Genes Evolve Higher Codon Bias in Drosophila and Caenorhabditis , 2005, Genetics.

[2]  D. Presgraves,et al.  Recombination Enhances Protein Adaptation in Drosophila melanogaster , 2005, Current Biology.

[3]  Rodrigo Lopez,et al.  Clustal W and Clustal X version 2.0 , 2007, Bioinform..

[4]  F. Wright The 'effective number of codons' used in a gene. , 1990, Gene.

[5]  Hideki Innan,et al.  Statistical Tests of the Coalescent Model Based on the Haplotype Frequency Distribution and the Number of Segregating Sites , 2005, Genetics.

[6]  C. Ponting,et al.  Variable Strength of Translational Selection Among 12 Drosophila Species , 2007, Genetics.

[7]  J. Hey,et al.  Reduced natural selection associated with low recombination in Drosophila melanogaster. , 1993, Molecular biology and evolution.

[8]  Dmitri A Petrov,et al.  Genomic Heterogeneity of Background Substitutional Patterns in Drosophila melanogaster , 2005, Genetics.

[9]  E. Novitski,et al.  Evidence for Genetic Homology between Chromosomes I and IV in Drosophila Melanogaster, with a Proposed Explanation for the Crowding Effect in Triploids. , 1956, Genetics.

[10]  B. Charlesworth,et al.  Reduced efficacy of selection in regions of the Drosophila genome that lack crossing over , 2007, Genome Biology.

[11]  Yun S. Song,et al.  Joint estimation of gene conversion rates and mean conversion tract lengths from population SNP data , 2009, Bioinform..

[12]  J. Felsenstein The evolutionary advantage of recombination. , 1974, Genetics.

[13]  G. A. Watterson On the number of segregating sites in genetical models without recombination. , 1975, Theoretical population biology.

[14]  B. Charlesworth,et al.  The pattern of neutral molecular variation under the background selection model. , 1995, Genetics.

[15]  Colin N. Dewey,et al.  Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans , 2007, PLoS biology.

[16]  A. Eyre-Walker,et al.  The genomic rate of adaptive amino acid substitution in Drosophila. , 2004, Molecular biology and evolution.

[17]  G Harauz,et al.  Meiotic gene conversion tract length distribution within the rosy locus of Drosophila melanogaster. , 1994, Genetics.

[18]  Kevin Thornton,et al.  libsequence: a C++ class library for evolutionary genetic analysis , 2003, Bioinform..

[19]  S. Elgin,et al.  Position effect variegation in Drosophila is associated with an altered chromatin structure. , 1995, Genes & development.

[20]  S. Elgin,et al.  The fourth chromosome of Drosophila melanogaster: interspersed euchromatic and heterochromatic domains. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[21]  Paul Marjoram,et al.  Estimating the rate of gene conversion on human chromosome 21. , 2004, American journal of human genetics.

[22]  Jack W. Szostak,et al.  The double-strand-break repair model for recombination , 1983, Cell.

[23]  Anders Gorm Pedersen,et al.  RevTrans: multiple alignment of coding DNA from aligned amino acid sequences , 2003, Nucleic Acids Res..

[24]  Sarah C. R. Elgin,et al.  The dot chromosome of Drosophila: Insights into chromatin states and their change over evolutionary time , 2006, Chromosome Research.

[25]  A. Kondrashov Deleterious mutations and the evolution of sexual reproduction , 1988, Nature.

[26]  M. Nei,et al.  Mathematical model for studying genetic variation in terms of restriction endonucleases. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[27]  W. Li,et al.  Statistical tests of neutrality of mutations. , 1993, Genetics.

[28]  A. Betancourt,et al.  Linkage limits the power of natural selection in Drosophila , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[29]  J. Powell,et al.  Evolution of codon usage bias in Drosophila. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[30]  Adam Eyre-Walker,et al.  Adaptive protein evolution in Drosophila , 2002, Nature.

[31]  Richard R. Hudson,et al.  Generating samples under a Wright-Fisher neutral model of genetic variation , 2002, Bioinform..

[32]  M. Lynch,et al.  Transitions to Asexuality Result in Excess Amino Acid Substitutions , 2006, Science.

[33]  William D. Gilliland,et al.  Congression of achiasmate chromosomes to the metaphase plate in Drosophila melanogaster oocytes. , 2009, Developmental biology.

[34]  R. Hudson,et al.  Inferring the evolutionary histories of the Adh and Adh-dup loci in Drosophila melanogaster from patterns of polymorphism and divergence. , 1991, Genetics.

[35]  J. Wall,et al.  Gene conversion and different population histories may explain the contrast between polymorphism and linkage disequilibrium levels. , 2001, American journal of human genetics.

[36]  W. Stephan,et al.  Demography and natural selection have shaped genetic variation in Drosophila melanogaster: a multi-locus approach. , 2003, Genetics.

[37]  W. Rice,et al.  Sexual Recombination and the Power of Natural Selection , 2001, Science.

[38]  R. Hudson Two-locus sampling distributions and their application. , 2001, Genetics.

[39]  A. Jeffreys,et al.  Intense and highly localized gene conversion activity in human meiotic crossover hot spots , 2004, Nature Genetics.

[40]  P. Fearnhead,et al.  A Comparison of Three Estimators of the Population-Scaled Recombination Rate: Accuracy and Robustness , 2005, Genetics.

[41]  Ziheng Yang PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.

[42]  R. Hudson,et al.  Statistical properties of the number of recombination events in the history of a sample of DNA sequences. , 1985, Genetics.

[43]  J. Ajioka,et al.  Lack of polymorphism on the Drosophila fourth chromosome resulting from selection. , 1991, Genetics.

[44]  B. Charlesworth,et al.  Reduced Effectiveness of Selection Caused by a Lack of Recombination , 2009, Current Biology.

[45]  J. Huelsenbeck,et al.  Inference of Population Structure Under a Dirichlet Process Model , 2007, Genetics.

[46]  G. McVean,et al.  Estimating Meiotic Gene Conversion Rates From Population Genetic Data , 2007, Genetics.

[47]  V. Pirrotta,et al.  Painting of fourth, a chromosome-specific protein in Drosophila , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[48]  Brian Charlesworth,et al.  Genetic linkage and molecular evolution , 2001, Current Biology.

[49]  Kevin R. Thornton,et al.  Nucleotide variation and recombination along the fourth chromosome in Drosophila simulans. , 2004, Genetics.

[50]  William D. Gilliland,et al.  Heterochromatic Threads Connect Oscillating Chromosomes during Prometaphase I in Drosophila Oocytes , 2009, PLoS genetics.

[51]  H. Akashi,et al.  Inferring weak selection from patterns of polymorphism and divergence at "silent" sites in Drosophila DNA. , 1995, Genetics.

[52]  P. Andolfatto,et al.  Selection, Recombination and Demographic History in Drosophila miranda , 2006, Genetics.

[53]  J. McCarter,et al.  The population genetics of the origin and divergence of the Drosophila simulans complex species. , 2000, Genetics.

[54]  F J Ayala,et al.  Evidence for positive selection in the superoxide dismutase (Sod) region of Drosophila melanogaster. , 1994, Genetics.

[55]  Paul Marjoram,et al.  Estimating Recombination Rates From Single-Nucleotide Polymorphisms Using Summary Statistics , 2006, Genetics.

[56]  O. L. Mohr Genetical and Cytological Proof of Somatic Elimination of the Fourth Chromosome in DROSOPHILA MELANOGASTER. , 1932, Genetics.

[57]  M. Kreitman,et al.  Adaptive protein evolution at the Adh locus in Drosophila , 1991, Nature.

[58]  Kevin R. Thornton,et al.  Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations. , 2005, Genome research.

[59]  P. Andolfatto,et al.  Positive and negative selection on noncoding DNA in Drosophila simulans. , 2008, Molecular biology and evolution.

[60]  R. Griffiths,et al.  Bounds on the minimum number of recombination events in a sample history. , 2003, Genetics.

[61]  Justin C. Fay,et al.  Positive and negative selection on the human genome. , 2001, Genetics.

[62]  R. Hudson Gene genealogies and the coalescent process. , 1990 .

[63]  Justin C. Fay,et al.  Hitchhiking under positive Darwinian selection. , 2000, Genetics.

[64]  J. Hey,et al.  USING HITCHHIKING GENES TO STUDY ADAPTATION AND DIVERGENCE DURING SPECIATION WITHIN THE DROSOPHILA MELANOGASTER SPECIES COMPLEX , 1994, Evolution; international journal of organic evolution.

[65]  Malin J. Svensson,et al.  Painting of fourth in genus Drosophila suggests autosome-specific gene regulation. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[66]  A. Sturtevant Preferential Segregation of the Fourth Chromosomes in Drosophila melanogaster. , 1934, Proceedings of the National Academy of Sciences of the United States of America.

[67]  Kevin R. Thornton,et al.  Nucleotide Variation Along the Drosophila melanogaster Fourth Chromosome , 2002, Science.

[68]  Chenhui Zhang,et al.  Adaptive genic evolution in the Drosophila genomes , 2007, Proceedings of the National Academy of Sciences.

[69]  Michael Ashburner,et al.  Drosophila: A laboratory handbook , 1990 .

[70]  B. Charlesworth,et al.  The effects of deleterious mutations on evolution in non-recombining genomes. , 2009, Trends in genetics : TIG.

[71]  B. Charlesworth,et al.  Patterns of genetic variation at a chromosome 4 locus of Drosophila melanogaster and D. simulans. , 2002, Genetics.

[72]  A. Sturtevant Preferential Segregation in Triplo-IV Females of Drosophila Melanogaster. , 1936, Genetics.

[73]  D. Petrov,et al.  Pervasive Natural Selection in the Drosophila Genome? , 2009, PLoS genetics.

[74]  B. S. Baker,et al.  The rox1 and rox2 RNAs are essential components of the compensasome, which mediates dosage compensation in Drosophila. , 1999, Molecular cell.

[75]  D. Bachtrog Adaptation shapes patterns of genome evolution on sexual and asexual chromosomes in Drosophila , 2003, Nature Genetics.

[76]  F. Tajima Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. , 1989, Genetics.

[77]  John J Welch,et al.  Estimating the Genomewide Rate of Adaptive Protein Evolution in Drosophila , 2006, Genetics.

[78]  R. Lewontin The Interaction of Selection and Linkage. I. General Considerations; Heterotic Models. , 1964, Genetics.