Progress and prospects in mapping recent selection in the genome

[1]  Kevin R. Thornton,et al.  Controlling the False-Positive Rate in Multilocus Genome Scans for Selection , 2007, Genetics.

[2]  John Maynard Smith,et al.  The hitch-hiking effect of a favourable gene. , 1974, Genetical research.

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

[4]  W. Stephan,et al.  Evidence of gene conversion associated with a selective sweep in Drosophila melanogaster. , 2006, Molecular biology and evolution.

[5]  D. Tautz,et al.  A change of expression in the conserved signaling gene MKK7 is associated with a selective sweep in the western house mouse Mus musculus domesticus , 2006, Journal of evolutionary biology.

[6]  W. Stephan,et al.  Inferring the Demographic History and Rate of Adaptive Substitution in Drosophila , 2006, PLoS genetics.

[7]  Molly Przeworski,et al.  How reliable are empirical genomic scans for selective sweeps? , 2006, Genome research.

[8]  D. Tautz,et al.  An analysis of signatures of selective sweeps in natural populations of the house mouse. , 2006, Molecular biology and evolution.

[9]  J. Pritchard,et al.  A Map of Recent Positive Selection in the Human Genome , 2006, PLoS biology.

[10]  Kevin R. Thornton,et al.  Approximate Bayesian Inference Reveals Evidence for a Recent, Severe Bottleneck in a Netherlands Population of Drosophila melanogaster , 2006, Genetics.

[11]  Yuseob Kim Allele Frequency Distribution Under Recurrent Selective Sweeps , 2006, Genetics.

[12]  J. Pool,et al.  A Scan of Molecular Variation Leads to the Narrow Localization of a Selective Sweep Affecting Both Afrotropical and Cosmopolitan Populations of Drosophila melanogaster , 2006, Genetics.

[13]  W. Stephan,et al.  Evidence for a Selective Sweep in the wapl Region of Drosophila melanogaster , 2006, Genetics.

[14]  Kosuke M. Teshima,et al.  Directional Positive Selection on an Allele of Arbitrary Dominance , 2006, Genetics.

[15]  T. Ishida,et al.  Evidence for recent positive selection at the human AIM1 locus in a European population. , 2006, Molecular biology and evolution.

[16]  C. Bustamante,et al.  Selective sweep mapping of genes with large phenotypic effects. , 2005, Genome research.

[17]  R. Nielsen Molecular signatures of natural selection. , 2005, Annual review of genetics.

[18]  Carlos Bustamante,et al.  Genomic scans for selective sweeps using SNP data. , 2005, Genome research.

[19]  G. Coop,et al.  THE SIGNATURE OF POSITIVE SELECTION ON STANDING GENETIC VARIATION , 2005, Evolution; international journal of organic evolution.

[20]  P. Andolfatto Adaptive evolution of non-coding DNA in Drosophila , 2005, Nature.

[21]  W. Stephan,et al.  Inferring the effects of demography and selection on Drosophila melanogaster populations from a chromosome-wide scan of DNA variation. , 2005, Molecular biology and evolution.

[22]  C. Aquadro,et al.  Multiple Signatures of Positive Selection Downstream of Notch on the X Chromosome in Drosophila melanogaster , 2005, Genetics.

[23]  Shamil Sunyaev,et al.  Evolutionary constraints in conserved nongenic sequences of mammals. , 2005, Genome research.

[24]  Brian Charlesworth,et al.  Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content , 2005, Genome Biology.

[25]  C. Bustamante,et al.  Distinguishing Between Selective Sweeps and Demography Using DNA Polymorphism Data , 2005, Genetics.

[26]  C. Bustamante,et al.  A Composite-Likelihood Approach for Detecting Directional Selection From DNA Sequence Data , 2005, Genetics.

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

[28]  Steven G. Schroeder,et al.  The Effects of Artificial Selection on the Maize Genome , 2005, Science.

[29]  Ryan D. Hernandez,et al.  Simultaneous inference of selection and population growth from patterns of variation in the human genome , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[30]  Jason E Stajich,et al.  Disentangling the effects of demography and selection in human history. , 2004, Molecular biology and evolution.

[31]  J. Doebley The genetics of maize evolution. , 2004, Annual review of genetics.

[32]  Deborah A Nickerson,et al.  Population History and Natural Selection Shape Patterns of Genetic Variation in 132 Genes , 2004, PLoS biology.

[33]  D. Hartl,et al.  Identification of a Locus Under Complex Positive Selection in Drosophila simulans by Haplotype Mapping and Composite-Likelihood Estimation , 2004, Genetics.

[34]  H. Innan,et al.  Pattern of polymorphism after strong artificial selection in a domestication event. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[35]  R. Nielsen,et al.  Linkage Disequilibrium as a Signature of Selective Sweeps , 2004, Genetics.

[36]  D. Schluter,et al.  The Genetic Architecture of Parallel Armor Plate Reduction in Threespine Sticklebacks , 2004, PLoS biology.

[37]  Chung-I Wu,et al.  Inference of positive and negative selection on the 5' regulatory regions of Drosophila genes. , 2004, Molecular biology and evolution.

[38]  Adam Eyre-Walker,et al.  Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila. , 2004, Genome research.

[39]  Toshihiro Tanaka The International HapMap Project , 2003, Nature.

[40]  Jennifer R. Moran,et al.  Ecological Adaptation During Incipient Speciation Revealed by Precise Gene Replacement , 2003, Science.

[41]  Sarah A Tishkoff,et al.  Patterns of human genetic diversity: implications for human evolutionary history and disease. , 2003, Annual review of genomics and human genetics.

[42]  C. Schlötterer,et al.  A microsatellite variability screen for positive selection associated with the "out of Africa" habitat expansion of Drosophila melanogaster. , 2003, Genetics.

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

[44]  Leif Andersson,et al.  A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig , 2003, Nature.

[45]  A. Clark,et al.  Molecular population genetics of inducible antibacterial peptide genes in Drosophila melanogaster. , 2003, Molecular biology and evolution.

[46]  D. Hartl,et al.  Maximum likelihood and Bayesian methods for estimating the distribution of selective effects among classes of mutations using DNA polymorphism data. , 2003, Theoretical population biology.

[47]  P. Tam The International HapMap Consortium. The International HapMap Project (Co-PI of Hong Kong Centre which responsible for 2.5% of genome) , 2003 .

[48]  C. Schlötterer Hitchhiking mapping--functional genomics from the population genetics perspective. , 2003, Trends in genetics : TIG.

[49]  M. Shriver,et al.  Interrogating a high-density SNP map for signatures of natural selection. , 2002, Genome research.

[50]  G. McVean,et al.  A genealogical interpretation of linkage disequilibrium. , 2002, Genetics.

[51]  Pardis C Sabeti,et al.  Detecting recent positive selection in the human genome from haplotype structure , 2002, Nature.

[52]  C. Schlötterer,et al.  Hitchhiking mapping: A population-based fine-mapping strategy for adaptive mutations in Drosophila melanogaster , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[53]  M. Long,et al.  Intron presence–absence polymorphism in Drosophila driven by positive Darwinian selection , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[54]  Noah A. Rosenberg,et al.  Genealogical trees, coalescent theory and the analysis of genetic polymorphisms , 2002, Nature Reviews Genetics.

[55]  Molly Przeworski,et al.  The signature of positive selection at randomly chosen loci. , 2002, Genetics.

[56]  M. Nachman,et al.  Gene density and human nucleotide polymorphism. , 2002, Molecular biology and evolution.

[57]  W. Stephan,et al.  Detecting a local signature of genetic hitchhiking along a recombining chromosome. , 2002, Genetics.

[58]  Christian Schlötterer,et al.  A microsatellite-based multilocus screen for the identification of local selective sweeps. , 2002, Genetics.

[59]  A. Di Rienzo,et al.  Complex signatures of natural selection at the Duffy blood group locus. , 2002, American journal of human genetics.

[60]  K. M. Wegner,et al.  Rapid genetic divergence in postglacial populations of threespine stickleback (Gasterosteus aculeatus): the role of habitat type, drainage and geographical proximity , 2001, Molecular ecology.

[61]  D. Hartl,et al.  Patterns of DNA sequence variation suggest the recent action of positive selection in the janus-ocnus region of Drosophila simulans. , 2001, Genetics.

[62]  M. Kreitman,et al.  Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences. , 2001, Genome research.

[63]  A. Ogurtsov,et al.  Selective constraint in intergenic regions of human and mouse genomes. , 2001, Trends in genetics : TIG.

[64]  J. Wall,et al.  Recombination and the frequency spectrum in Drosophila melanogaster and Drosophila simulans. , 2001, Molecular biology and evolution.

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

[66]  Nicholas H. Barton,et al.  The effect of hitch-hiking on neutral genealogies , 1998 .

[67]  A. Eyre-Walker,et al.  Investigation of the bottleneck leading to the domestication of maize. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[68]  G. Churchill,et al.  Properties of statistical tests of neutrality for DNA polymorphism data. , 1995, Genetics.

[69]  W Stephan,et al.  The hitchhiking effect on the site frequency spectrum of DNA polymorphisms. , 1995, Genetics.

[70]  M. Aguadé,et al.  Polymorphism and divergence in the Mst26A male accessory gland gene region in Drosophila. , 1992, Genetics.

[71]  C. Aquadro,et al.  Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster , 1992, Nature.

[72]  Thomas Wiehe,et al.  The Effect of Strongly Selected Substitutions on Neutral Polymorphism: Analytical Results Based on Diffusion Theory , 1992 .

[73]  B. Cowart Let them eat soap , 1991, Nature.

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

[75]  N L Kaplan,et al.  The "hitchhiking effect" revisited. , 1989, Genetics.

[76]  F. Tajima The effect of change in population size on DNA polymorphism. , 1989, Genetics.

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

[78]  J. David,et al.  Genetic variation of Drosophila melanogaster natural populations. , 1988, Trends in genetics : TIG.

[79]  M. Ashburner,et al.  Historical Biogeography of the Drosophila melanogaster Species Subgroup , 1988 .

[80]  R. Hudson,et al.  A test of neutral molecular evolution based on nucleotide data. , 1987, Genetics.

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