Genomes, Evolution, and Culture

Rene Herrera Emeritus, Department of Molecular and Human Genetics, College of Medicine, Florida International University, USA Ralph Bertrand Department of Biology, Colorado College, USA Francisco Salzano Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Brazil

Preface, ix

1 The history of human evolutionary genetics, 1

World views, 1

Science and philosophy, 1

The biology of mankind: anatomy and physiology in a historical context (up to the 16th century), 3

Beginnings of the present scientific model, 4

Biological evolution and genetic foundations: the brilliant quartet, 5

Nineteenth century: cytology, embryology, and reproduction, 9

Twentieth century, the century of genetics, 10

The synthetic theory of evolution, 11

Bacterial and molecular genetics, 11

Parallel developments: paleoanthropology, 12

Technical and methodological developments, 13

Conclusions, 14

Review questions and exercises, 14

References, 14

2 The human genome: structure, function, and variation, 16

Science, politics, and ethics, 16

Structural aspects, 17

Normal and abnormal phenotype distribution, 19

Function, 21

Sex chromosomes, 23

Paleogenomics, 25

Variability: mtDNA, 28

Nuclear variability, 28

Exomes and proteomes, 30

Selection or drift? History, 31

Selection or drift? Methods, 32

Selection or drift? Analyses, 34

Nervous system and culture, 37

Conclusions, 37

Review questions and exercises, 37

References, 38

3 Population structure, 42

DNA-based marker systems, 42

SNPs, STRs, and Indels as DNA markers, 45

Population genetic tools for analyzing population structure, 49

Forces affecting population dynamics, structure, and evolution, 55

Applications of population genetics, 60

From populations to races and species, 62

Review questions and exercises, 64

References, 65

4 Genetic variability, 68

On the nature of variability, 68

Mechanisms responsible for generating genetic variability, 69

Randomness of mutations, 71

Inheritance and environment, 75

Selection works on the phenotype, 76

The impact of selection, 77

Cultural expressions as markers of ancestry, 79

Congruency among marker systems, 80

Does junk DNA exist?, 80

How genetic diversity is studied?, 82

Epigenetic diversity, 84

Review questions and exercises, 85

References, 86

5 Gene and genomic dynamics, 87

Molecular evidence for punctuated equilibrium and gradualism, 88

Next-generation sequencing, 90

Genetic variation, 92

Variation, population structure, and effective population size, 94

Recombination and its effect on variation, 94

Linkage equilibrium and disequilibrium, 95

Forces leading to linkage disequilibrium, 98

Linkage disequilibrium and SNP haplotypes, 99

Linkage disequilibrium in humans, 100

Genome structural variations, 102

CNV classifications and formation mechanisms, 102

Methods used to detect CNVs, 103

CNVs associated with human phenotypes, 105

CNVs and evolution, 106

CNV in primates, 107

Chromosome rearrangements and selfish genetic elements, 108

Transposable elements, 109

Population dynamics of transposable elements, 110

Transposons in human evolution, 111

Selfish genetic elements in evolution, 113

Genome-wide association studies, 113

Concerns over the effective use of GWAS, 117

Conclusions, 117

Review questions and exercises, 118

References, 119

6 Human origins and early diasporas, 124

The on switch to humanity, 124

Early hominins, 128

Emerging themes and variations in hominin evolution, 130

The first hominin migrants, 134

The emergence of modern humans, 135

The Saharan pump, 135

Early migrations, 136

Neanderthals prevailed, 136

Review questions and exercises, 138

References, 139

7 Culture, 141

Concept, 141

Origin and development, 141

Factors that could condition cultural evolution, 142

Biology–culture interaction, 145

Language, 146

Domestication, 148

Art, 151

Free will, morality, and religion, 153

Conclusions, 155

Review questions and exercises, 155

References, 155

8 Health and disease, 158

Hopes and reality, 158

Concept of health and methods of study, 158

Darwinian medicine, 160

Parent–offspring conflict, 161

Pathogen history, 161

Evolution of infectious diseases, 162

DNA damage, mutagenesis, and teratogenesis, 163

What is better, more or less gene product?, 165

Genetic manipulation of animals to study health and disease, 166

Reproductive fitness and health, 167

Consanguinity, 168

Violence, 168

Cancer, 171

Degenerative diseases, 172

Ecogenetics, pharmacogenetics, and pharmacogenomics, 174

Detection of genetic diseases, 176

Genetic counseling, 176

Treatment, 178

Conclusions, 179

Review questions and exercises, 179

References, 180

9 Recent human evolution: an integrative approach, 182

Recent human evolution, 182

Out of Africa, 184

Back to Africa, 188

Beyond Arabia, 190

The Asian agricultural revolution and the Austronesian expansion, 194

Evidence from plants and animals, 198

Contacts between South America and Polynesia, 200

Review questions and exercises, 202

References, 203

10 Bioethics: consequences and implications of genetic technology on human evolution, 206

Social and biological evolution, 207

Overview of ethics and philosophical influences on Western ethics, 207

Evolution of ethics and morality, 212

The history and beginning of modern-day bioethics, 213

Reproductive technologies and the new eugenics: unnatural selection?, 216

Enhancement through IVF, PGD, and CRISPR, 219

Ethical issues associated with medical technology, 220

Gene therapy, 220

Stem cell therapy, 222

Biosimilars, 222

Genetic privacy, 222

Genetic testing, 223

DNA profiling, 224

Conclusions, 227

Review questions and exercises, 227

References, 228

11 Future of human evolution, 230

Gene and culture coevolution, 231

Life expectancy and population growth: past, present, and future, 231

Mutation rates and future evolution, 232

The evolution of new genes, 234

Climate change, 234

Diet, 235

Sex selection, 236

Artificial selection, 236

Transhumanism and artificial intelligence, 237

Conclusions, 238

Review questions and exercises, 239

References, 239

Appendix, 241

Index, 249