Supplemental Information Adaptive Evolution of Gene Expression in Drosophila

[1]  B. O’Meara,et al.  MODELING STABILIZING SELECTION: EXPANDING THE ORNSTEIN–UHLENBECK MODEL OF ADAPTIVE EVOLUTION , 2012, Evolution; international journal of organic evolution.

[2]  Páll Melsted,et al.  Comparative RNA sequencing reveals substantial genetic variation in endangered primates. , 2012, Genome research.

[3]  V. Le Corre,et al.  The genetic differentiation at quantitative trait loci under local adaptation , 2012, Molecular ecology.

[4]  Kevin R. Thornton,et al.  The Drosophila melanogaster Genetic Reference Panel , 2012, Nature.

[5]  D. Tautz,et al.  The evolutionary origin of orphan genes , 2011, Nature Reviews Genetics.

[6]  Matko Bosnjak,et al.  REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms , 2011, PloS one.

[7]  Michael Lässig,et al.  Formation of Regulatory Modules by Local Sequence Duplication , 2011, PLoS Comput. Biol..

[8]  Dave T. Gerrard,et al.  Gene expression divergence recapitulates the developmental hourglass model , 2010, Nature.

[9]  H. P. de Vladar,et al.  The statistical mechanics of a polygenic character under stabilizing selection, mutation and drift , 2010, Journal of The Royal Society Interface.

[10]  Aviv Regev,et al.  The Role of Nucleosome Positioning in the Evolution of Gene Regulation , 2010, PLoS biology.

[11]  V. Sheeba.  The Drosophila melanogaster circadian pacemaker circuit , 2008, Journal of Genetics.

[12]  T. F. Hansen,et al.  A Comparative Method for Studying Adaptation to a Randomly Evolving Environment , 2008, Evolution; international journal of organic evolution.

[13]  Martin Vingron,et al.  Ontologizer 2.0 - a multifunctional tool for GO term enrichment analysis and data exploration , 2008, Bioinform..

[14]  Scott A. Rifkin,et al.  Natural selection on gene expression. , 2006, Trends in genetics : TIG.

[15]  A. King,et al.  Phylogenetic Comparative Analysis: A Modeling Approach for Adaptive Evolution , 2004, The American Naturalist.

[16]  M. Lynch,et al.  The altered evolutionary trajectories of gene duplicates. , 2004, Trends in genetics : TIG.

[17]  Terence P. Speed,et al.  A comparison of normalization methods for high density oligonucleotide array data based on variance and bias , 2003, Bioinform..

[18]  Martin Vingron,et al.  Variance stabilization applied to microarray data calibration and to the quantification of differential expression , 2002, ISMB.

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

[20]  C. Aquadro,et al.  Genome-wide variation in the human and fruitfly: a comparison. , 2001, Current opinion in genetics & development.

[21]  S. Leal.  Genetics and Analysis of Quantitative Traits , 2001 .

[22]  K. Spitze.  Population structure in Daphnia obtusa: quantitative genetic and allozymic variation. , 1993, Genetics.

[23]  R. Lande.  NEUTRAL THEORY OF QUANTITATIVE GENETIC VARIANCE IN AN ISLAND MODEL WITH LOCAL EXTINCTION AND COLONIZATION , 1992, Evolution; international journal of organic evolution.

[24]  P. Sharp,et al.  The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications. , 1987, Nucleic acids research.

[25]  M. Nei,et al.  Genetic differentiation of quantitative characters between populations or species: I. Mutation and random genetic drift , 1982 .

[26]  S. Wright,et al.  Genetical Structure of Populations , 1950, Nature.

[27]  S. Wright,et al.  Isolation by Distance. , 1943, Genetics.

[28]  Rasmus Nielsen,et al.  Modeling gene expression evolution with an extended Ornstein-Uhlenbeck process accounting for within-species variation. , 2014, Molecular biology and evolution.

[29]  Wen-Hsiung Li.  Unbiased estimation of the rates of synonymous and nonsynonymous substitution , 2006, Journal of Molecular Evolution.

[30]  A. Force,et al.  The probability of duplicate gene preservation by subfunctionalization. , 2000, Genetics.