An Introduction to Molecular Anthropology

Molecular anthropology uses molecular genetic methods to address questions and issues of anthropological interest.  More specifically, molecular anthropology is concerned with genetic evidence concerning human origins, migrations, and population relationships, including related topics such as the role of recent natural selection in human population differentiation, or the impact of particular social systems on patterns of human genetic variation. Organized into three major sections, An Introduction to Molecular Anthropology first covers the basics of genetics – what genes are, what they do, and how they do it – as well as how genes behave in populations and how evolution influences them. The following section provides an overview of the different kinds of genetic variation in humans, and how this variation is analyzed and used to make evolutionary inferences. The third section concludes with a presentation of the current state of genetic evidence for human origins, the spread of humans around the world, the role of selection and adaptation in human evolution, and the impact of culture on human genetic variation.  A final, concluding chapter discusses various aspects of molecular anthropology in the genomics era, including personal ancestry testing and personal genomics. An Introduction to Molecular Anthropology is an invaluable resource for students studying human evolution, biological anthropology, or molecular anthropology, as well as a reference for anthropologists and anyone else interested in the genetic history of humans.

Table of Contents:
Preface xi Chapter 1 Genes: How they are inherited 1 Blood and ABO blood groups 1 Inheritance of ABO blood groups 3 Inheritance of more than one gene: ABO and rhesus blood groups 4 Sex chromosomes 9 Determining how traits are inherited: Pedigree analysis 10 What is—and isn’t—inherited 12 Concluding remarks 14 Chapter 2 What genes are, what they do, and how they do it 15 Chromosomes, proteins, and nucleic acids: Figuring out what genes are 15 The structure of genes and what they do: The central dogma and the flow of information 18 How genes do what they do: Transcription and translation 19 The genetic code 22 DNA replication 23 The consequences of mutations 23 What causes mutations? 25 A final cautionary note 26 Chapter 3 Genes in populations 27 What is a population? 27 The concept of “effective population size” 28 The sex ratio and Ne 29 Inbreeding and Ne 30 Variation in population size over time and Ne30 Differential fertility and N>e 31 Ne for humans 33 Chapter 4 A simple model: Hardy–Weinberg equilibrium 35 The gene pool with no evolution: The Hardy–Weinberg principle 35 Exceptions 38 A real-life example 39 Some practical uses for Hardy–Weinberg 41 Chapter 5 Evolutionary forces 45 Non–random mating 45 Small population size 48 Mutation 53 Migration 56 Selection 60 Evolutionary forces: Summary 68 Chapter 6 Molecular evolution 69 Functionally less important molecules (or parts of molecules) evolve faster than more important ones 70 Conservative substitutions occur more frequently than disruptive ones 71 The rate of molecular evolution is approximately constant 72 Contrasting phenotypic and molecular evolution 73 How do new gene functions arise? 74 Gene regulation and phenotypic evolution 77 Chapter 7 Genetic markers 79 Classical markers: Immunogenetic markers 79 Classical markers: Biochemical polymorphisms 81 The first DNA markers: Restriction fragment length polymorphisms 84 Polymerase chain reaction 86 DNA sequencing: The sanger method 89 Next-generation sequencing 90 Targeting single DNA bases: SNPs 92 Variation in length 94 Other structural variation 99 Concluding remarks 100 Chapter 8 Sampling populations and individuals 103 Sampling populations: General issues 103 Sampling populations: Ethical issues 105 Archival samples 108 Chapter 9 Sampling DNA regions 111 Mitochondrial DNA 111 Y chromosomal DNA 116 Autosomal DNA 119 X Chromosome DNA 121 Public databases 122 Chapter 10 Analysis of genetic data from populations 125 Genetic diversity within populations 125 Genetic distances between populations 128 Displaying genetic distance data: Trees 135 Displaying genetic data: Multidimensional scaling, principal components, and correspondence analysis 139 Chapter 11 Analysis of genetic data from individuals 147 Genetic distances for DNA sequences 147 Trees for DNA sequences 153 Rooting trees 156 Assessing the confidence of a tree 157 Network analyses 160 Genome-wide data: Unsupervised analyses 161 Chapter 12 Inferences about demographic history 175 Dating events 175 Population size and population size change 187 Migration and admixture 194 Putting it all together 197 Chapter 13 Our closest living relatives 201 Resolving the trichotomy 205 Complications 206 Ape genetics and genomics 208 Chapter 14 The origins of our species 211 Human origins: The fossil record 215 Models for human origins 218 The genetic evidence: mtDNA 222 The genetic evidence: Y chromosome 224 The genetic evidence: Autosomes 225 Chapter 15 Ancient DNA 229 Properties of ancient DNA: Degradation 229 Properties of ancient DNA: Damage 229 Properties of ancient DNA: Contamination 232 History of ancient DNA studies 236 Ancient DNA: Archaic humans 237 Other uses for ancient DNA 244 Chapter 16 Dispersal and migration 247 Out of Africa—how many times, when, and which way did they go? 251 Into remote lands: The colonization of the Americas 259 Into even more remote lands: The colonization of Polynesia 267 Some concluding remarks 281 Chapter 17 Species-wide selection 283 Species-wide selection 284 Nonsynonymous mutations and the dN/dS ratio 284 Tests based on the allele frequency distribution 288 Selection tests based on comparing divergence to polymorphism 293 Archaic genomes 297 Chapter 18 Local selection 299 Example: Lactase persistence 304 Example: EDAR 309 Ancient DNA 318 Concluding remarks 318 Chapter 19 Genes and culture 321 Are humans still evolving? 321 Genetic variation can be directly influenced by cultural practices 322 Genetic variation can be indirectly influenced by cultural practices 322 Using genetic analyses to learn more about cultural practices: Agricultural expansions 326 Using genetic analyses to learn more about cultural practices: Language replacements 332 Using genetic analyses to learn more about cultural practices: Dating the origin of clothing 333 Concluding remarks 339 Chapter 20 Ongoing and future developments in molecular anthropology 341 More—and different kinds of—data: The other “omics” 341 Beyond “you”: The microbiome 344 More analyses 347 Relating phenotypes to genotypes 351 Personal ancestry testing and genomics 360 References 363 Suggestions for additional reading 373 Index 375

About the Author :
Mark Stoneking directs the Human Population History group in the Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, and is Honorary Professor of Biological Anthropology at the University of Leipzig.