Anthropology : current and future development. v. 2, Genomics in biological anthropology : new challenges, new opportunities / edited by Manuela Lima, Amanda Ramos & Cristina Santos. -- Sharjah : Bentham Science Publishers, 2016. – (59.3/A628/v.2)

Contents

FOREWORD  i

PREFACE  ii

LIST OF CONTRIBUTORS    iv

CHAPTER 1  HUMAN GENOMIC PROJECTS: SETTING THE STAGE FOR GENOME-SCALE ANTHROPOLOGICAL STUDIES  3

1.1. THE FOUNDATION OF GENOMICS: OVERVIEW OF THE HUMAN GENOME PROJECT  4

1.2. HUMAN GENOMIC PROJECTS: GENERAL CHARACTERIZATION AND IMPACT ON BIOLOGICAL ANTHROPOLOGY  6

1.3. THE NEANDERTHAL GENOME PROJECT: AN IN-DEPTH JOURNEY INTO OUR PAST  13

1.4. GENOMICS OF OUR RELATIVES: THE NON-HUMAN PRIMATE GENOME PROJECTS  14

CONCLUDING REMARKS  18

CONFLICT OF INTEREST  19

ACKNOWLEDGEMENTS  19

REFERENCES  19

CHAPTER 2  COMPLETE MITOCHONDRIAL DNA THROUGH MASSIVELY PARALLEL SEQUENCING: METHODOLOGY AND APPLICATIONS  25

2.1. INTRODUCTION  26

2.2. MTDNA CHARACTERISTICS AND APPLICATIONS  26

2.3. AMPLIFICATION STRATEGIES  28

2.4. MPS PLATFORMS  33

2.5.  IMPLEMENTATION OF MPS IN THE ROUTINE RESEARCH AND DIAGNOSTIC LABORATORIES  43

CONCLUDING REMARKS  44

CONFLICT OF INTEREST  45

ACKNOWLEDGEMENTS  45

REFERENCES  45

CHAPTER 3  SOMATIC VS GERMINAL MUTATIONS IN MITOCHONDRIAL DNA: IS THERE ANY RELATION WITH HUMAN HEALTH AND AGING?  50

3.1. INTRODUCTION  51

3.2. MATERIAL AND METHODS  53

3.3. RESULTS  56

3.4. DISCUSSION  58

CONFLICT OF INTEREST    60

ACKNOWLEDGEMENTS  60

REFERENCES  61

CHAPTER 4  HUMAN Y CHROMOSOME MUTATION RATE'-PROBLEMS AND PERSPECTIVES

4.1. INTRODUCTION    66

4.2. THE Y CHROMOSOME    69

4.3. DATING THE TREE  73

4.4. MUTATION RATES  76

4.5. APPLICATION TO TWO PUBLIC DATABASES  81

CONCLUSIVE REMARKS  86

CONFLICT OF INTEREST  86

ACKNOWLEDGEMENTS  86

REFERENCES  86

CHAPTER 5  GENOMICS OF ISOLATED POPULATIONS: INFERENCES FOR GENE-FINDING STUDIES  92

5.1. GENETIC VARIATION AND DISEASE IN HUMAN POPULATIONS  93

5.2. HUMAN GENETIC ISOLATES:. GENERAL CHARACTERISTICS  94

5.3. THE USE OF POPULATION ISOLATES IN GENE FINDING STUDIES: ADVANTAGES AND LIMITATIONS

5.4. THE GENOMIC ERA AND THE USE OF ISOLATED POPULATIONS FOR GENE FINDING

CONCLUDING REMARKS  101

CONFLICT OF INTEREST  101

ACKNOWLEDGEMENTS  101

REFERENCES  102

CHAPTER 6  COMPLEX HUMAN PHENOTYPES: THE INTERPLAY BETWEEN GENES AND ENVIRONMENT  106

6.1. INTRODUCTION  107

6.2. TWIN STUDIES: DISENTANGLING THE INVOLVEMENT OF GENES AND ENVIRONMENT IN COMPLEX TRAITS  108

6.3. GENE-ENVIRONMENT INTERPLAY MECHANISMS  113

CONCLUDING REMARKS  128

CONFLICT OF INTEREST  129

ACKNOWLEDGEMENTS  129

REFERENCES  129

CHAPTER 7  ANCIENT DNA: FROM SINGLE WORDS TO FULL LIBRARIES IN 30 YEARS  138

7.1. HISTORY OF ANCIENT DNA ANALYSIS  138

7.2. ANCIENT DNA FEATURES AND ENVIRONMENTAL FACTORS  145

CONCLUDING REMARKS  152

CONFLICT OF INTEREST  152

ACKNOWLEDGEMENTS  152

REFERENCES  152

CHAPTER 8  TROUBLES AND EFFICIENCY OF aDNA  160

8.1. AUTHENTICITY CRITERIA  160

8.2. INHIBITION AND NATURE OF THE INHIBITORS  165

8.3. TISSUES FROM WHERE THE DNA CAN BE EXTRACTED  167

CONCLUDING REMARKS  173

CONFLICT OF INTEREST  173

ACKNOWLEDGEMENTS  174

REFERENCES  174

CHAPTER 9  ADNA METHODOLOGICAL REVOLUTION  183

9.1. EVOLUTION OF THE EXTRACTION METHODS  183

9.2. EVOLUTION OF THE SEQUENCING METHODS  185

9.3. RECONSIDERING AUTHENTICITY CRITERIA  193

CONCLUDING REMARKS AND FUTURE PERSPECTIVES  196

CONFLICT OF INTEREST  198

ACKNOWLEDGEMENTS  198

REFERENCES  198

CHAPTER 10  COMPLICITIES BETWEEN FORENSIC ANTHROPOLOGY AND FORENSIC GENETICS: NEW OPPORTUNITIES FOR GENOMICS?  206

10.1. INTRODUCTION: MAIN ATTRIBUTIONS OF FORENSIC ANTHROPOLOGY  207

10.2. WHEN DOES FORENSIC ANTHROPOLOGY NEEDS GENETICS?  208

10.3. AN EMERGENT ROLE FOR GENOMICS IN FORENSIC SCIENCES?  212

CONCLUDING REMARKS  215

CONFLICT OF INTEREST  216

ACKNOWLEDGEMENTS  216

REFERENCES  216

SUBJECT INDEX  219