General Concepts in Evolutionary Genetics Views of EvolutionJames F Crow Evolution: Selectionist ViewAndreas Wagner Evolution: Neutralist ViewAndreas Wagner The Neo-selectionist Theory of Genome EvolutionGiorgio Bernardi Fitness and SelectionBrian Charlesworth Genetic Drift in Human PopulationsAndrew J Bohonak HeterozygosityWen-Hsiung Li Effective Population SizeMichael C Whitlock Population Differentiation: MeasuresStefano Mona, Giorgio Bertorelle Evolutionary DistanceWen-Hsiung Li Gene Trees and Species TreesWen-Hsiung Li Homologous, Orthologous and Paralogous GenesWen-Hsiung Li Evolution: Convergent and Parallel EvolutionCaro-Beth Stewart Mutation, Adaptation and Natural Selection Genetic Variation: Polymorphisms and MutationsAlan F Wright Polymorphisms: Origins and MaintenanceKenneth M Weiss Molecular Evolution: IntroductionDavid Penny Molecular Evolution: OverviewJan Klein Molecular Evolution: Genetics of AdaptationMichael Travisano Neutral Theory of Molecular EvolutionNaoyuki Takahata Molecular Evolution: Nearly Neutral TheoryTomoko Ohta Molecular Evolution: RatesLindell Bromham Molecular Evolution: Patterns and RatesLindell Bromham Nucleotide Substitution: Rate ofWen-Hsiung Li Synonymous and Nonsynonymous RatesSoojin Yi Mutational Change in EvolutionDan Graur Mutations and New Variation: OverviewMark O Johnston Single-base MutationDan Graur Mutation RateBertram Müller-Myhsok Mutation Rates: EvolutionDavid Metzgar Spectrum of Mutations in the Human Genome Inferred by Single Nucleotide PolymorphismsZhao Zhongming Mutational BiasesLev Y Yampolsky, Arlin Stoltzfus Mutations: DatingRoberto Colombo Diffusion TheoryGil McVean Molecular Clocks in MammalsWen-Hsiung Li, Kateryna D Makova Molecular ClocksAndrew Peter Martin Purifying Selection: Action on Silent SitesR Nielsen, H Akashi Selection against Amino Acid Replacements in Human ProteinsSankar Subramanian Identifying Regions of the Human Genome that Exhibit Evidence for Positive SelectionRyosuke Kimura, Jun Ohashi Positive Selection on Genes in Humans as Compared to ChimpanzeesMargaret A Bakewell, Jianzhi Zhang Selection Operating on Protein-coding Genes in the Human GenomeDiogo Meyer, Eugene E Harris Selective and Structural ConstraintsAustin L Hughes Substitution MatricesStephen F Altschul Fixation Probabilities and TimesSarah P Otto, Michael C Whitlock Genetic Code: EvolutionEdward N Trifonov Codon Usage in Molecular EvolutionRichard L Grantham Linkage DisequilibriumPeter JP Croucher Recombination and Human Genetic DiversityChris CA Spencer Comparison of Rates and Patterns of Meiotic Recombination between Human and ChimpanzeesJan Freudenberg Rapid Evolution of Genes on the Human X-chromosomeErika M Kvikstad, Kateryna D Makova Evolutionary and Population Genetics Gene Flow, Haplotype Patterns and Modern Human OriginsAlan R Templeton HapMap ProjectBryan J Traynor, Andrew Singleton MigrationGuido Barbujani Nonrandom MatingDennis H O'Neil Human Population Stratification and its Assessment by Microarray GenotypingMarc Bauchet Sequence AlignmentJulie D Thompson, Olivier Poch Sequence SimilarityJaap Heringa PhylogeneticsWen-Hsiung Li Phylogenetic FootprintingWyeth W Wasserman, Wynand Alkema Molecular Phylogeny ReconstructionSudhir Kumar, Alan Filipski Evolutionary Distance: EstimationMasatoshi Nei, Jianzhi Zhang Coalescent TheorySimon Tavaré Stationary Allele Frequency DistributionsBruce Rannala Developmental EvolutionSusan Lindsay Morphological Diversity: EvolutionGraham Budd Male-driven EvolutionHans Ellegren Coevolution: MolecularRonald M Adkins Concerted EvolutionDaiqing Liao Sociobiology, Evolutionary Psychology and GeneticsPatrick Bateson Are Humans Still Evolving?Floyd A Reed Human Evolution Hominids: Molecular PhylogeneticsUlfur Arnason, Morgan Kullberg Human Evolution: OverviewBernard A Wood Molecular Clocks: Determining the Age of the Human--Chimpanzee DivergenceMichael I Jensen-Seaman, Kathryn A Hooper-Boyd On the Number of Ancestral Human SpeciesDarren Curnoe Human Evolution: Early RadiationsBernard A Wood Human Evolution: Radiations in the Last 300000 YearsOsbjorn M Pearson Modern Humans: Origin and EvolutionTodd R Disotell Modern Human Origins: The `Out of Africa' DebateJohn H Relethford Origin of Modern Humans: Interpreting the Molecular EvidenceHenry C Harpending Human Populations: EvolutionRebecca L Cann Human Populations: Origins and EvolutionRosalind M Harding, John H Relethford Humans: Demographic HistoryHenry Harpending DNA Markers and Human EvolutionRebecca L Cann Reconstructing Human History Using Autosomal, Y-Chromosomal and Mitochondrial MarkersBryndis Yngvadottir, Denise R Carvalho-Silva Population History and Linkage DisequilibriumSebastian Zollner Human Population Genetics: Drift and MigrationRanajit Chakraborty Human Genetics and LanguagesDavid Comas, Elena Bosch, Francesc Calafell Surnames and GeneticsMark A Jobling Population History of Europe: GeneticsGuido Barbujani Genetic Diversity in AfricaAlicia Sanchez-Mazas, Estella S. Poloni Genetic Diversity in the German PopulationMichael Krawczak, Timothy T Lu, Sascha Willuweit, Lutz Roewer Genetics and the History of the Basque PeopleSantos Alonso Genetics and the Origins of the British PopulationMartin Richards, Cristian Capelli, James F Wilson Genetics and the Origins of the ChineseQing-Peng Kong, Hui Pan, Ya-Ping Zhang Genetics and the Origins of the FinnsReijo Norio Genetics and the Origins of the IrishBrian McEvoy, Daniel G Bradley Genetics and the Origins of the PolynesiansGeoffrey K Chambers Origins of the Australian and New Guinean AboriginesSheila M van Holst Pellekaan Origins of the Austro-Asiatic PopulationsB Mohan Reddy, Vikrant Kumar Peopling of India: Insights from GeneticsPartha P Majumder Population Genetics of the AshkenazimMarina Faerman Roma (Gypsies): Genetic StudiesBharti Morar, Luba Kalaydjieva The Peopling of the Americas as Revealed by Molecular Genetic StudiesTheodore G Schurr Primates and the Origin of CultureWC McGrew Human Genome Evolution Evolution of Genome OrganizationWolfgang Stephan Genome Organization of VertebratesGiorgio Bernardi Evolutionary History of the Human GenomeGiorgio Bernardi Sequencing the Human Genome: Novel Insights into its Structure and FunctionHildegard Kehrer-Sawatzki, David N Cooper Single Nucleotide Polymorphism (SNP)Anthony J Brookes Human Genetic DiversityLynn B Jorde Human and Chimpanzee Nucleotide DiversityHenrik Kaessmann Divergence between the Human and Chimpanzee Genomes and its Impact on Protein and Transcriptome EvolutionHildegard Kehrer-Sawatzki, David N Cooper Indels in the Evolution of the Human and Chimpanzee GenomesAnna Wetterbom, Lucia Cavelier, Tomas F Bergström Inferring the Process of Human--Chimpanzee SpeciationK Ryo Takahasi, Hideki Innan Human Genome Diversity Project (HGDP)Morris W Foster Blocks of Limited Haplotype DiversityNewton E Morton Gene Conversion during Primate EvolutionYoko Satta Biased Gene Conversion and its Impact on Human Genome EvolutionNicolas Galtier, Laurent Duret Repetitive DNA: EvolutionWolfgang Stephan, J Bruce Walsh Simple Sequence Repeats in the Human Genome: EvolutionDonald E Riley, John N Krieger Evolution of Microsatellite DNAIris M Vargas Jentzsch, Andrew Bagshaw, Emmanuel Buschiazzo, Angelika Merkel, Neil J Gemmell Evolution of Alpha Satellite DNADuroica Ugarkovic Comparative Genetics of Trinucleotide Repeats in the Human and Ape GenomesLoris Mularoni, Macarena Toll-Riera, M Mar Albà Endogenous Retroviral Sequences; their Evolutionary Contribution to the Human GenomeJens Mayer Human Endogenous Retroviruses; Evolutionary Dynamics, Chromosomal Location and Host BenefitPaul Nelson, Graham Freimanis, Denise Roden Evolutionary History and Impact of Human DNA TransposonsCédric Feschotte Evolution of Human Retrosequences: AluAstrid M Roy-Engel, Mark A Batzer, Prescott L Deininger Long Interspersed Nuclear Elements (LINEs): EvolutionAnthony V Furano, Stéphane Boissinot Bacterial DNA in the Human GenomeJan O Andersson Chromosome-specific Repeats (Low-copy Repeats)M-C Potier, G Golfier, EE Eichler TelomereChrista Lese Martin, David H Ledbetter Telomeric and Subtelomeric Repeat SequencesDmitri Churikov, Carolyn M Price Subtelomeres: Evolution in the Human GenomeM Katharine Rudd The Evolution of Centromeric DNA SequencesJoshua J Bayes, Harmit S Malik Segmental Duplications and Their Role in the Evolution of the Human GenomeYali Xue, Chris Tyler-Smith Copy Number Variation in the Human GenomeHildegard Kehrer-Sawatzki Gene Duplication: EvolutionWen-Hsiung Li Gene Families: Formation and EvolutionTomoko Ohta Gene Families: Multigene Families and SuperfamiliesTomoko Ohta Gene Clustering in EukaryotesJeffrey G Lawrence, Thomas Blumenthal Clustering of Highly Expressed Genes in the Human GenomeHinco J Gierman, Rogier Versteeg Gene Distribution in Human ChromosomesGiorgio Bernardi, Salvatore Saccone Evolution of Gene Deserts in the Human GenomeJames Taylor The Impact of Gene Duplication on Human Genome EvolutionJames A Cotton Genetic RedundancyDavid C Krakauer DNA Methylation: EvolutionAharon Razin, Ruth Shemer Evolution of Imprinting: Imprinted Gene Function in Human DiseaseBenjamin JA Dickins, Gavin Kelsey Imprinting: EvolutionHamish G Spencer Epigenetic Variation in HumansJon F Wilkins Dosage Compensation Mechanisms: EvolutionIgnacio Marín Evolution of X-chromosome InactivationAlexander I Shevchenko, Suren M Zakian Ultraconserved DNA Sequence Elements in the Human GenomeAlison P Lee, B Venkatesh The Biological Significance of Conserved Non-Generic DNAEmmanouil T Dermitzakis Evolutionarily Conserved Noncoding DNAAnil G Jegga, Bruce J Aronow Human-specific Accelerated Evolution of Noncoding SequencesMatthew T Webster Rapidly Evolving Regions of the Human GenomeSubhash Mohan Agarwal GC-Rich Isochores in the Interphase NucleusSalvatore Saccone, Giorgio Bernardi Evolution of Human Gene Structure and Function Gene Structure: EvolutionTomoko Ohta Gene Evolution and Human AdaptationEugene E Harris The Evolution of Introns in Human GenesElodie Gazave, Olga Fernando, Arcadi Navarro Intron Evolution in Duplicated Human GenesKamel Jabbari, Edda Rayko Intron Loss and GainTobias Mourier, Daniel C Jeffares Introns: MovementsManyuan Long, Rüdiger Cerff Introns: Phase CompatibilityLászló Patthy Evolutionarily Conserved Intronic Splicing Regulatory Elements in the Human GenomeEric L Van Nostrand, Gene W Yeo Evolutionary Conservation of Splice SitesMichelle L. Hastings, Ravi Sachidanandam Alternative Splicing: EvolutionLászló Patthy Alternative Splicing in the Human Genome and its Evolutionary ConsequencesLiliana Florea Dual-coding Regions in Alternatively Spliced Human GenesHan Liang, Laura F Landweber Birth and Evolution of Human ExonsMaria Dulcetti Vibranovski, Noboru Jo Sakabe, Manyuan Long Exons and Protein ModulesLászló Patthy Insertion and Deletion of Exons During Human Gene EvolutionDavid N Cooper Exons: ShufflingLászló Patthy PseudoexonsManyuan Long Domain Duplication and Gene Elongation Wen-Hsiung LiKateryna D Makova The Contribution of Frameshift Translation to the Generation of Novel Human ProteinsKohji Okamura, Stephen W Scherer Transposable Element-driven Duplications during Hominoid Genome EvolutionBud Mishra The Contribution of Transposable Elements to Human ProteinsJean-Nicolas Volff Evolutionary Emergence of Genes Through RetrotranspositionRichard Cordaux, Mark A Batzer Multigene Families: EvolutionJ Bruce Walsh, Wolfgang Stephan Paralogous Genes and Chromosomal RegionsLars-Gustav Lundin, Dan Larhammar, Finn Hallböök Bi-directional Gene Pairs in the Human GenomeKanako O Koyanagi, Tadashi Imanishi, Takashi Gojobori Gene FusionEsther Betrán Protein Families: EvolutionRichard R Copley Fibroblast Growth Factors: EvolutionDavid M Ornitz Globin Genes: EvolutionRoss C Hardison Hox Genes and Body Plan: EvolutionElla Tour, William McGinnis Pax Genes: Evolution and FunctionMaxime Bouchard, Alexander Schleiffer, Frank Eisenhaber, Meinrad Busslinger Low-density Lipoprotein Receptor (LDLR) Family: Genetics and EvolutionWolfgang Johann Schneider Major Histocompatibility Complex (MHC) Genes: EvolutionAustin L Hughes Major Histocompatibility Complex (MHC) Genes: Polymorphism Diogo MeyerSteven J Mack Vertebrate Immune System: EvolutionAustin L Hughes Evolution of the Human Immune SystemNadia Danilova Complement System: EvolutionMasaru Nonaka Somatic Hypermutation of Antigen Receptor Genes: EvolutionMarilyn Diaz, Laurent K Verkoczy Neuropeptides and their Receptors: EvolutionCharles HV Hoyle Nuclear Receptor Genes: EvolutionGareth I Owen Olfactory Receptor Genes: EvolutionYoshihito Niimura Visual Pigment Genes: EvolutionShozo Yokoyama Bitter Taste Sensitivity in Humans and ChimpanzeesMaik Behrens, Wolfgang Meyerhof Evolution of Skin Pigmentation Differences in HumansHeather Norton Population Genetics of Lactase Persistence and Lactose IntoleranceCatherine Janet Ellen Ingram, Dallas Mary Swallow Defensins: EvolutionAustin L Hughes Cystic Fibrosis Transmembrane Conductance Regulator Sequences: Comparative AnalysisJian-Min Chen, Guillaume Lecointre, Erick Denamur, Claude Férec ATP-binding Cassette (ABC) Transporter Supergene Family: Genetics and EvolutionMichael Dean Proteases: EvolutionChristopher Southan Serpins: EvolutionGary A Silverman, David J Askew, James A Irving, Cliff J Luke, Dion Kaiserman, Phillip I Bird, James C Whisstock Adaptive Evolution of Primate Sperm ProteinsNathaniel L Clark Drug Metabolism: EvolutionDaniel W Nebert rRNA Genes: EvolutionIris L Gonzalez, James E Sylvester MicroRNA Evolution in the Human GenomeBing Su, Rui Zhang Pseudogene Evolution in the Human GenomeZhaolei Zhang, Deyou Zheng Human Lineage-specific Gene InactivationWendy E Grus, Jianzhi Zhang Pseudogenes: AgeAllen R Rhoads, Felix Friedberg Pseudogenes: Patterns of MutationRosa Martínez-Arias, Francesc Calafell, Jaume Bertranpetit Processed Pseudogenes and Their Functional Resurrection in the Human and Mouse GenomesHiroaki Sakai, Takeshi Itoh, Takashi Gojobori Evolution of Gene Expression Transcriptional Regulation: EvolutionGregory A Wray Promoters: EvolutionDeborah L Gumucio Evolution of Human Gene Expression ControlCourtney C Babbitt, Gregory A Wray Positive Selection and the Evolution of ProdynorphinMatthew V Rockman Human Transcriptome EvolutionXun Gu, Yong Huang Evolution of Gene Expression in Human and Chimpanzee BrainsNaoki Osada, Sugano Sumio, Yutaka Suzuki Human and Chimpanzee Transcriptomes: Comparative EvolutionPhilipp Khaitovich, David Cooper, Hildegard Kehrer-Sawatzki Human and Macaque Transcriptiomes: A comparisonStephen J Walker Transcription Factor-binding Sites: Recent Evolution in the Human LineageBerthold Göttgens Alternative Polyadenylation in the Human Genome: EvolutionBin Tian Mitochondrial Genome Evolution Mitochondrial Genome: EvolutionMark Stoneking Mitochondrial Non-Mendelian Inheritance: Evolutionary Origin and ConsequencesC William Birky Jr Mitochondrial Genome Sequences and Their Phylogeographic InterpretationVincent Macaulay, Martin Richards Mitochondrial Origins of Human Nuclear Genes and DNA SequencesWilliam F Martin Chromosomal Evolution Chromosomes in Mammals: Diversity and EvolutionJohannes Wienberg, Stefan Müller Chromosome Numbers in MammalsHarry Scherthan Chromosome Rearrangement Patterns in Mammalian EvolutionJohannes Wienberg, Stefan Müller Hotspots of Mammalian Chromosome EvolutionLutz Froenicke, Leslie A Lyons Chromosomal Rearrangements in PrimatesRoscoe Stanyon, Francesca Bigoni Chromosomal Rearrangements in the Human and Chimpanzee LineagesHildegard Kehrer-Sawatzki, David N Cooper Human Chromosome EvolutionGerald P Holmquist, Johannes Wienberg Polyploid Origin of the Human GenomeMasanori Kasahara Chromatin Structure and Human Genome EvolutionColin AM Semple Mammalian Sex Chromosome EvolutionGerald J Wyckoff, Christine M Malcom Evolution of the Mammalian X ChromosomePaul D Waters, Terence J Robinson Y Chromosome EvolutionVladimir A Gvozdev X and Y Chromosomes: Homologous RegionsNisrine El-Moghabel, Jennifer A M Graves Evolution of Common Fragile SitesAnne Helmrich Comparative Genomics Comparative CytogeneticsMatthew Breen, Cordelia Langford Comparative Cytogenetics TechnologiesStefan Müller, Johannes Wienberg Reconstruction of Ancestral GenomesRoscoe Stanyon, Fiorella Garofalo, Francesca Bigoni Comparative Human GenomicsI King Jordan, Eugene V Koonin Orthologues, Paralogues and Xenologues in Human and Other GenomesOlga Zhaxybayeva, J Peter Gogarten, Lorraine Olendzenski Comparing the Human and Sea Urchin GenomesR Andrew Cameron Comparing the Human and Fish GenomesYoichiro Nakatani, Shinichi Morishita Comparing the Human and Medaka GenomesTakashi Sasaki, Nobuyoshi Shimizu Fugu: The Pufferfish Model GenomeB Venkatesh The Mouse Genome as a Rodent Model in Evolutionary StudiesJessica Vamathevan, Joanna D Holbrook, Richard D Emes The Rat Genome as a Rodent Model in Evolutionary StudiesKim Fechtel Comparing the Human and Canine GenomesMarek Switonski, Izabela Szczerbal Primate PhylogeneticsTodd R Disotell The Sequencing of the Rhesus Macaque Genome and its Comparison with the Genome Sequences of Human and ChimpanzeeRichard A Gibbs, Kim C Worley, Hildegard Kehrer-Sawatzki, David N Cooper The Chimpanzee Genome ProjectDavid N Cooper, Hildegard Kehrer-Sawatzki Comparing the Human and Chimpanzee GenomesMonica Uddin, Derek E Wildman, Morris Goodman Nucleotide Sequence Divergence between Humans and ChimpanzeesFeng-Chi Chen, Trees-Juen Chuang Human-specific Changes of Genome StructureR Alan Harris, Aleksandar Milosavljevic Evolution and Disease Susceptibility Evolutionary Thinking in the Medical SciencesStephen C Stearns Darwinian MedicineGeorge C Williams Pathological Missense Mutations Provide New Insights into the Evolution of Trypsinogen GenesJian-Min Chen, David N Cooper, Claude Férec Balancing Selection in Human EvolutionEric J Vallender, Welkin E Johnson Selective Constraints on Human Disease Mutations and PolymorphismsHernán Dopazo Genetic of Large Populations and Association StudiesPauline Hélène Garnier-Géré, Lounès Chikhi Genetic Disease in the Ashkenazim: Role of a Founder Effect Inbal Kedar-Barnes, Paul Rozen, Mordechai ShohatHagit N Baris Single Nucleotide Polymorphisms in Human Disease and Evolution: Phylogenies and GenealogiesPaul D Thomas Structural Diversity of the Human Genome and Disease SusceptibilityRichard S Smith, María Gutiérrez-Arcelus, Charles W Tran, Stephanie Park, Cheryn J Couter, Charles Lee Segmental Duplications and Genetic DiseaseBeverly S Emanuel, Tamim H Shaikh Genetics of Susceptibility to Human Infectious DiseasesRichard A Kaslow, Sadeep Shrestha, Jianming 'James' Tang The Genetics of Malarial Resistance and SusceptibilityBrian C Verrelli The Evolution of Fatness and Susceptibility to ObesityJonathan CK Wells Thrifty Genotype Hyphothesis and Complex Genetic DiseasePnina Varidi, Konstantin Bloch An Evolutionary Framework for Common DiseaseFrancesca Luca, Anna Di Rienzo On Sequence Variants that Influence the Risk of Common DiseasesKári Stefánsson, Jeffrey R Gulcher An Evolutionary Genetic Framework for Heritable DisordersMatthew C Keller Analysis of Ancient DNA Ancient DNA: Recovery and AnalysisSusanne Hummel Ancient DNA: Phylogenetic ApplicationsMichael Knapp, Linda Vigilant, Michael Hofreiter Neanderthal Mitochondrial DNAWilliam Goodwin, Igor Ovchinnikov Reconstructing Ancient DNA Sequences in SilicoJian Ma
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