An Introduction to Molecular Anthropology

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 Ne 30

Differential fertility and Ne 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

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