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