Note: Intro -- Preface -- Contents -- Part I: Non-neutral Evolution on Human Genes -- Chapter 1: Anthropogeny -- 1.1 Getting at the Origins of the Human Phenomenon -- 1.2 Our Evolutionary Roots -- 1.2.1 Homo Sapiens: The Paradoxical Ape -- 1.2.2 Measuring Genetic Distance -- 1.2.3 Ancient Genome Data -- 1.2.4 Limits to Detecting Ancient Selection -- 1.2.5 Phenotypes Are More Than Nucleic Acids and Proteins -- 1.3 Phenotypes: From Fossils to Past Behavior, Current Physiology, and Cognition -- 1.3.1 Fossil Data -- 1.3.2 Archeological Data: Fossilized Behavior -- 1.3.3 Stable Isotopes, Paleoclimate, and Paleonutrition -- 1.3.4 Learning from Living Foragers -- 1.3.5 The Holocene Trap -- 1.3.6 Biological Proxies for Past Behavior -- 1.3.7 The Crying Need for Phenotypic Data of Non-human Hominids -- 1.3.8 Niche Construction and Top-Down Effects -- 1.3.9 The Physical Niche -- 1.3.10 The Socio-Cognitive Niche -- 1.4 The Cultural Niche -- 1.5 Language and Theory of Mind -- 1.5.1 The Brain Needs the Body and the Group -- 1.6 Opportunities and Limitations -- 1.7 Open Minds, Closed Umbrellas -- 1.7.1 The Need for Transdisciplinarity -- 1.8 Why Anthropogeny? -- 1.9 Note of Caution -- References -- Chapter 2: Positive Selection in Human Populations: Practical Aspects and Current Knowledge -- 2.1 Statistical Approaches to Identify Signals of Positive Selection -- 2.1.1 Using Polymorphism Data -- 2.1.1.1 Tests Based on Long Haplotypes -- 2.1.1.2 Tests Based on Site Frequency Spectrum -- 2.1.1.3 Tests Based on Genetic Differentiation -- 2.2 Practical Challenges in Detecting Positive Selection Using Polymorphism Data -- 2.2.1 Distortions Due to Ascertainment Bias -- 2.2.2 The Confounding Factor of Background Selection -- 2.2.3 Demography Can Mimic Positive Selection -- 2.2.3.1 Migration and Structure -- 2.2.3.2 Population Expansion -- 2.2.3.3 Population Bottleneck. , 2.2.3.4 Founder Effect -- 2.2.4 Has a Region of Interest Evolved Under Positive Selection? -- 2.2.4.1 Using Simulations Accounting for Demography -- 2.2.4.2 Outlier Approach -- 2.2.4.3 Combination of Different Tests -- 2.2.5 Selection Not Only by Hard Sweep -- 2.2.5.1 Soft Sweep -- 2.2.5.2 Polygenic Adaptation -- 2.2.5.3 Recent Methodological Advances in Detecting Alternative Sweep Scenarios -- 2.2.6 From Putative Advantageous Mutation to Increased Fitness -- 2.3 Current Knowledge on Positive Selection in the Human Genome -- 2.3.1 Candidate Gene Studies of Positive Selection -- 2.3.2 Genome-Wide Scans for Positive Selection -- 2.3.3 Insights from Published Studies of Positive Selection in Humans -- 2.3.3.1 Functional Categories for the Selected Protein-Coding Genes -- 2.3.3.2 Complex Adaptive Traits -- 2.3.3.3 The Importance of Regulatory Elements -- 2.4 Concluding Remarks -- References -- Chapter 3: Population Genomics of High-Altitude Adaptation -- 3.1 Background -- 3.2 High-Altitude Human Populations -- 3.2.1 Tibet -- 3.2.2 Andes -- 3.2.3 Ethiopia -- 3.3 Physiological Clues of High-Altitude Adaptation -- 3.4 Genetic Basis of High-Altitude Adaptation -- 3.4.1 Two Well-Recognized Genes (EPAS1 and EGLN1) and a Core Pathway (HIF) -- 3.4.2 A Broader Perspective from Multi-omics Resources -- 3.4.3 ``Borrowed Fitness´´ from Archaic Hominins -- 3.4.4 Convergent Adaptation -- 3.5 Current Limitations and Future Directions -- References -- Part II: Evolution of Modern Human Populations -- Chapter 4: Mitochondrial DNA -- 4.1 Outline of This Chapter -- 4.2 Characters of mtDNA and Its Merits for Studying Human Populations -- 4.3 Emergence of Modern Humans and Establish of Genetic Diversity of Current Human Populations -- 4.3.1 Neanderthals and Modern Humans -- 4.4 Controversy Between Pedigree Based Estimation and Divergence Based Estimation -- 4.5 Haplogroups. , 4.5.1 Phylogeny of Haplogroups -- 4.6 Demographic History Estimation Based on mtDNA -- 4.6.1 mtDNA Research Example Using BSP: Peopling to America -- 4.7 Disease -- 4.7.1 Missing Heritability and mtDNA Variation -- References -- Chapter 5: The Y Chromosome -- 5.1 The Odd Chromosome and Its History -- 5.2 Not All Y Chromosomes Are Created Equal: Polymorphisms in the Y Chromosome -- 5.3 Climbing Down the Y Tree -- 5.4 La Donna è Mobile Ma Non Troppo -- 5.5 Male Lines -- 5.6 A Royal Mystery in Three Acts -- 5.7 Hacking the Y Chromosome -- References -- Chapter 6: Africa -- 6.1 The African Landscape -- 6.2 African Genetic Diversity in a Global Scale -- 6.3 Genetic Diversity Within Africa -- 6.4 Local Genetic Diversity Within Africa -- 6.4.1 North Africans, the Misfit Within the Continent -- 6.4.2 Khoisan-Speakers, the Deepest Branch in the Humankind Tree -- 6.4.3 The Pygmies, the Hunter-Gatherers of the African Equatorial Forest -- 6.4.4 East African Groups, Source and Sink of Genetic Diversity -- 6.4.5 Western and Bantu-Speakers, the Major Component in Africa -- 6.4.6 Madagascar, an Island Between Two Distant Continents -- 6.5 Some Adaptive Variants in African Groups -- References -- Chapter 7: Peopling and Population Structure of West and South Asia -- 7.1 Introduction -- 7.2 Inferences from Uniparental Markers -- 7.3 Inferences from the Nuclear Genome -- References -- Chapter 8: Europe -- 8.1 Introduction: Genes and the Neolithic -- 8.2 The Making of the European Paleolithic Populations -- 8.3 The Genetic Legacy of Paleolithic Europe -- 8.4 The Genetic Legacy of Neolithic Europe -- 8.5 More Complex Models, More Complex Facts -- 8.6 Post-Neolithic Events in the European Gene Pool -- 8.7 Comparing Models -- 8.8 Conclusion -- References -- Chapter 9: Southeast Asia -- 9.1 Introduction -- 9.2 Contact with Archaic Humans in Southeast Asia. , 9.3 Ancient Migrants and Hunter Gatherers -- 9.4 Human Diversity in Mainland Southeast Asia -- 9.5 Impact of Human Expansions Driven by Agriculture -- 9.6 Concluding Remarks and Perspectives -- References -- Chapter 10: Australia and Oceania -- 10.1 Geography and Ecology of Australia and Oceania -- 10.2 Australia -- 10.3 Oceania -- 10.3.1 Near Oceania in the Pleistocene -- 10.3.2 The Austronesian Expansion and the Colonisation of Remote Oceania -- 10.3.3 Duality of Oceanian Heritage -- 10.3.4 Evidence for Contact Between South America and Polynesia -- 10.3.5 The Unique History of Santa Cruz -- 10.4 Archaic Admixture in Australia and Oceania -- 10.5 Conclusions -- References -- Chapter 11: America -- 11.1 Introduction -- 11.2 Peopling of the American Continents During the Prehistoric Age -- 11.2.1 Environment -- 11.2.2 First Humans of the American Continents -- 11.3 Genetic Analysis of Contemporary Native Americans -- 11.3.1 Genome Analysis with mtDNA and the Y Chromosome -- 11.3.2 Genome Analysis with Nuclear DNA -- 11.4 Genetic Complexities and Ethical Issues on Genome Analysis of Native Americans -- References -- Chapter 12: Simulations of Human Dispersal and Genetic Diversity -- 12.1 Introduction -- 12.2 Modelling and Simulating Human Dispersal -- 12.3 Realistic Simulation with Spatially Explicit Simulations -- 12.4 SPLATCHE: An Example of Spatially Explicit Simulation Program -- 12.4.1 Spatial Structure -- 12.5 Main Results and Discussion -- 12.5.1 Genes Surfing the Waves of Expansion -- 12.5.2 Hybridization During Expansion -- 12.5.3 Limitations and Future Developments -- 12.6 Conclusion -- References -- Index.

Note: Intro -- Preface -- Contents -- Part I: Overview of the Human Genome -- Chapter 1: Human Evolution and Human Genome at a Glance -- 1.1 Brief Description of Human Evolution -- 1.1.1 From Origin of Life to Emergence of Primates -- 1.1.2 Evolution of Primates and Classification of Hominidae Species -- 1.1.3 Divergence Patterns of Hominoids -- 1.1.4 Sequencing of Hominoid Genomes -- 1.2 Structure of the Human Genome -- 1.2.1 Human Chromosomes and Their Band Structure -- 1.2.2 Protein Genes of the Human Genome -- 1.3 RNA-Coding Genes and Gene Expression Control Regions in the Human Genome -- 1.4 Various Types of Mutations Which Accumulated During Evolution of the Human Genome -- References -- Chapter 2: Rubbish DNA: The Functionless Fraction of the Human Genome -- 2.1 Introduction -- 2.2 What Is Function? -- 2.3 An Evolutionary Classification of Genome Activity and Genome Function -- 2.4 Changes in Functional Affiliation -- 2.5 Genome Size Variation -- 2.6 The C-Value Paradox as Evidence for the Existence of Junk DNA Within the Human Genome -- 2.7 Genetic Mutational Load: Can the Human Genome Be 100% Functional? -- 2.8 Detecting Functionality at the Genome Level -- 2.9 What Proportion of the Human Genome Is Functional? -- 2.10 How Much Garbage DNA Exists in the Human Genome? -- 2.11 Mutational Origins of Junk DNA -- 2.12 Why So Much of the Genome Is Transcribed, or Is It? -- 2.13 Hypotheses Concerning the Maintenance of Junk DNA -- 2.14 Selectionist Hypotheses -- 2.15 Nucleotypic and Nucleoskeletal Hypotheses -- 2.16 The Neutralist Hypothesis -- 2.17 Selfish DNA -- 2.18 The Mutational Hazard Hypothesis: A Nearly Neutralist Hypothesis -- 2.19 Genome Size and Bottlenecks: The Simultaneous Accumulation of Alus, Pseudogenes, and Numts Within Primate Genomes -- 2.20 Is It Junk DNA or Is It Indifferent DNA? -- References. , Chapter 3: GC Content Heterogeneity -- 3.1 Brief History of the GC Content Studies -- 3.2 Three Hypotheses on the Isochore Evolution -- 3.2.1 The Thermodynamic Stability Hypothesis (The Selection Model) -- 3.2.2 The GC-Biased Gene Conversion Hypothesis -- 3.2.3 The Mutation Bias Hypothesis -- 3.3 Definition of Isochore: As a Framework for the Genomic Evolutions -- 3.4 Controversy Over the Isochore Evolution -- 3.5 A New Framework with Nonlinear Dynamics -- 3.6 General Discussion on an Evolutionary Study Based on Nonlinear Dynamics -- 3.7 An Impact of Big Data and Extensive Simulation -- References -- Chapter 4: Protein-Coding and Noncoding RNA Genes -- 4.1 Human Protein-Coding Genes -- 4.1.1 Concepts of Human Protein-Coding Genes -- 4.1.2 A Typical Human Protein-Coding Gene -- 4.1.3 Number of Protein-Coding Genes -- 4.1.4 Immunoglobulin and T-Cell Receptor Genes -- 4.1.5 Pseudogenes -- 4.2 Noncoding RNA Genes -- 4.2.1 Classification of Noncoding RNA Genes -- 4.2.2 Long Noncoding RNAs -- 4.2.3 miRNA and Other Small ncRNAs -- 4.3 Alternative Splicing -- 4.3.1 Mechanisms of AS -- 4.3.2 Patterns of AS -- 4.3.3 Examples of Human AS -- 4.3.4 Evolutionary Conservation of AS -- 4.4 Other Mechanisms for Proteome Diversification -- 4.4.1 Alternative ORFs -- 4.4.2 NAGNAG Introns -- 4.4.3 Selenoproteins -- 4.5 Human Gene Databases -- 4.5.1 HUGO Gene Nomenclature Committee (HGNC) -- 4.5.2 RefSeq -- 4.5.3 GENCODE -- 4.5.4 H-InvDB -- 4.5.5 lncRNAdb -- 4.5.6 Comparisons of Databases -- 4.6 Conclusion -- References -- Chapter 5: Duplicated Genes -- 5.1 Fate of Duplicated Genes: Pseudogenization or Gain of New Function -- 5.2 Short History of Gene Duplication Studies -- 5.3 Types of Gene Duplication -- 5.4 The Number of Tandemly Duplicated Genes in Humans -- References -- Chapter 6: Recombination. , 6.1 Recombination and Its Distribution Along the Genome, Linkage Disequilibrium -- 6.2 Linkage Disequilibrium and a Population View -- 6.3 The Role of Linkage Disequilibrium in Reconstructing Our Past and the Origins of Modern Humans -- References -- Chapter 7: CNVs and Microsatellite DNA Polymorphism -- 7.1 Microsatellite DNA in Human Genome -- 7.1.1 Genomic Distribution -- 7.1.2 Mutational Pattern -- 7.1.3 Microsatellite DNA as Genetic Markers -- 7.2 CNV on Human Genome -- 7.2.1 What Is CNV -- 7.2.2 Variation of CNVs in Human Population -- 7.2.3 CNVs and Chemosensory Receptor Genes -- 7.3 Microsatellite DNA and CNV -- 7.3.1 Variation in Human Populations of Microsatellite DNA -- 7.3.2 CNV and Genome Size -- References -- Part II: The Human Genome Viewed Through Genes -- Chapter 8: Genes on X and Y Chromosomes -- 8.1 The Origin of Sex Chromosomes -- 8.2 History of Human X-Y Chromosome Differentiation -- 8.3 Origins of Genes on Human Sex Chromosomes -- 8.4 Origins of Genes in PAR on Human X and Y Chromosome -- 8.5 Human-Specific Gene Gain and Loss -- 8.6 Conclusion -- References -- Chapter 9: Human Leukocyte Antigen (HLA) Region in Human Population Studies -- 9.1 Introduction -- 9.2 HLA Genotyping Methods -- 9.3 Nomenclature of HLA Alleles -- 9.4 Factors Affecting HLA Diversity -- 9.5 Application of HLA Genotyping -- References -- Chapter 10: Evolution of Genes for Color Vision and the Chemical Senses in Primates -- 10.1 Introduction to Vision and Chemosensory Genes in Primates -- 10.2 Primate Color Vision and Opsin Genes -- 10.2.1 A Basic Knowledge on Primate Color Vision -- 10.2.1.1 Vision Specialization of Primates -- 10.2.1.2 L/M and S Opsins and Trichromatic Color Vision in Primates -- 10.2.1.3 The ``Three-Sites´´ Rule and Variation of Primate L/M Opsins -- 10.2.2 Visual Opsins and the Evolutionary Origin of Primate Color Vision. , 10.2.2.1 S Opsin Loss and Monochromacy -- 10.2.2.2 Dichromacy and Nocturnality -- 10.2.2.3 Origin of Trichromacy Under Dim Light -- 10.2.3 2.3. Visual Opsin Variation in New World Monkeys and Evolutionary Significance of Primate Color Vision -- 10.2.3.1 Overview and General Implications -- 10.2.3.2 Unexpected Hybrid L/M Opsins in Howler Monkeys -- 10.2.3.3 Unequal Allele Frequencies of L/M Opsins -- 10.2.3.4 Behavioral Studies and Evaluation of Trichromacy Advantage -- Limited Support or Contradictive Observations for Trichromacy Advantage -- Dichromat Advantage -- Direct Evaluation of Fitness Effect of Trichromacy -- Revising Conditions of Trichromacy Advantage -- 10.2.4 Uniform and Normal Trichromacy in Catarrhine Primates and Exceptional Variation in Human Color Vision -- 10.2.4.1 Nonhuman Catarrhines Contrasting to Platyrrhines -- 10.2.4.2 Uniqueness of Human Color Vision -- 10.3 Primate Olfaction -- 10.3.1 Evolutionary Trends Among Olfactory Receptor Genes: Numbers, Diversity, and Preservation of Function -- 10.3.2 Genetic Diversity of OR Gene Repertoire in Modern Humans -- 10.3.3 Olfactory Sensitivity of Primates -- 10.3.4 Sensory Ecology and Cross-Modal Usage of Olfaction in Primates -- 10.3.4.1 Uses of Olfactory Behavior -- 10.3.4.2 Sensory Integration: Olfaction, Vision, and the Other Senses (Taste, Touch, Sound) -- 10.3.5 Heterologous Gene Expression Assay for Current and Ancestral ORs in Primates -- 10.3.6 Future Directions in Olfactory Research -- 10.4 Primate Bitter Taste Reception -- 10.4.1 Neutral vs Non-neutral Genetic Variation of Bitter Taste Receptors in Humans and Chimpanzees -- 10.4.2 TAS2R38 Nontaster Variations Independently Arising in Human, Chimpanzee, Macaques -- 10.5 Umami/Sweet Taste Reception -- 10.6 Ending Remarks -- References -- Chapter 11: Global Landscapes of Human Phenotypic Variation in Inherited Traits. , 11.1 Introduction -- 11.2 What Drives Phenotypic Differentiation Between Human Populations? -- 11.3 Identification of Signatures of Adaptive Evolution in the Human Genome -- 11.4 Genes Associated with Common Phenotypic Variations I: Visible Traits -- 11.4.1 Height -- 11.4.2 Obesity -- 11.4.3 Pigmentation -- 11.4.4 Morphology of Hair, Teeth, and Other Skin Appendages -- 11.4.5 Baldness -- 11.4.6 Facial Morphology -- 11.5 Genes Associated with Common Phenotypic Variations II: Physiological Traits -- 11.5.1 Lactase Persistence -- 11.5.2 Alcohol Intolerance -- 11.5.3 Apocrine Gland Secretion -- 11.5.4 Blood Types -- 11.6 Closing Remarks -- References -- Chapter 12: Transcription Factor Genes -- 12.1 General Features of Transcription Factor Genes -- 12.1.1 Structure -- 12.1.2 Transcription Regulation -- 12.2 DNA-Binding Domain -- 12.2.1 Zinc Finger -- 12.2.2 Homeodomain -- 12.2.3 Helix-Loop-Helix Domain -- 12.3 Evolution of TF Gene Families -- 12.3.1 Hox Cluster Genes -- 12.3.2 Forkhead Box Genes -- 12.3.3 T-Box Genes -- 12.4 Recent Studies Related to TF Binding Sites -- 12.5 Recent Studies Related to TF Networks -- References -- Chapter 13: Genetics of Diabetes: Are They Thrifty Genotype? -- 13.1 Introduction -- 13.2 Fundamental Problem of Insulin Regulation -- 13.3 Genetics of Diabetes: Is It Still Geneticist´s Nightmare? -- 13.3.1 Genome-Wide Association Studies of T2D -- 13.3.2 Complexity of MODY and MODY-Related Genes -- 13.3.3 Transcriptional Regulatory Pathways Disrupted by T2D-Associated Variants -- 13.4 How Do T2D Susceptibilities Survive in Human History? -- 13.5 Reevaluation of ``Thrifty´´ Genotype Hypothesis -- References -- Chapter 14: Disease-Related Genes from Population Genetic Aspect and Their Functional Significance -- 14.1 Introduction -- 14.2 Atopic Dermatitis -- 14.3 Atopic Dermatitis and Filaggrin Gene -- 14.4 Filaggrin Mutations. , 14.5 Natural Vaccination Hypothesis.