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Mark Stoneking AN INTRODUCTION TO MOLECULAR ANTHROPOLOGY MARK STONEKING AN INTRODUCTION TO MOLECULAR ANTHROPOLOGY AN INTRODUCTION TO MOLECULAR ANTHROPOLOGY Mark Stoneking Department of Evolutionary Genetics Max Planck Institute for Evolutionary Anthropology Leipzig, Germany Copyright © 2017 by John Wiley & Sons, Inc. All rights reserved. Published by John Wiley & Sons, Inc., Hoboken, New Jersey. Published simultaneously in Canada. No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, scanning, or otherwise, except as permitted under Section 107 or 108 of the 1976 United States Copyright Act, without either the prior written permission of the Publisher, or authorization through payment of the appropriate per-copy fee to the Copyright Clearance Center, Inc., 222 Rosewood Drive, Danvers, MA 01923, (978) 750-8400, fax (978) 750-4470, or on the web at www.copyright.com. Requests to the Publisher for permission should be addressed to the Permissions Department, John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030, (201) 748-6011, fax (201) 748-6008, or online at http://www.wiley.com/go/permission. Limit of Liability/Disclaimer of Warranty: While the publisher and author have used their best efforts in preparing this book, they make no representations or warranties with respect to the accuracy or completeness of the contents of this book and specifically disclaim any implied warranties of merchantability or fitness for a particular purpose. No warranty may be created or extended by sales representatives or written sales materials. The advice and strategies contained herein may not be suitable for your situation. You should consult with a professional where appropriate. Neither the publisher nor author shall be liable for any loss of profit or any other commercial damages, including but not limited to special, incidental, consequential, or other damages. For general information on our other products and services or for technical support, please contact our Customer Care Department within the United States at (800) 762-2974, outside the United States at (317) 572-3993 or fax (317) 572-4002. Wiley also publishes its books in a variety of electronic formats. Some content that appears in print may not be available in electronic formats. For more information about Wiley products, visit our web site at www.wiley.com. Library of Congress Cataloging-in-Publication Data: Stoneking, Mark. An introduction to molecular anthropology / Mark Stoneking. pages cm Includes bibliographical references and index. ISBN 978-1-118-06162-6 (pbk. : alk. paper) 1. Human genetics–Variation. 2. Human molecular genetics. 3. Molecular evolution. 4. Human evolution. I. Title. QH431.S784 2015 572.8–dc23 2014039320 10987654321 For my students, who I hope have learned as much from me as I have from them. “A study of the blood of individual nations enables us to decode their distant past” —Ludwik Hirszfeld, A Story of One Life, 1946 “Whether or not it is true that the proper study of mankind is man, it is certain that he finds great difficulty in studying anything else.” —John William Navin Sullivan, Aspects of Science, 1923 CONTENTS Preface xi Chapter 4 A simple model: Hardy–Weinberg equilibrium 35 Chapter 1 Genes: How they are The gene pool with no evolution: The inherited 1 Hardy–Weinberg principle 35 Blood and ABO blood groups 1 Exceptions 38 Inheritance of ABO blood groups 3 A real-life example 39 Inheritance of more than one gene: ABO Some practical uses for Hardy–Weinberg 41 and rhesus blood groups 4 Sex chromosomes 9 Chapter 5 Evolutionary forces 45 Determining how traits are inherited: Non–random mating 45 Pedigree analysis 10 Small population size 48 What is—and isn’t—inherited 12 Mutation 53 Concluding remarks 14 Migration 56 Selection 60 Chapter 2 What genes are, what Evolutionary forces: Summary 68 they do, and how they do it 15 Chromosomes, proteins, and nucleic acids: Chapter 6 Molecular evolution 69 Figuring out what genes are 15 Functionally less important molecules (or The structure of genes and what they do: parts of molecules) evolve faster than more The central dogma and the flow of important ones 70 information 18 Conservative substitutions occur more How genes do what they do: Transcription frequently than disruptive ones 71 and translation 19 The rate of molecular evolution is The genetic code 22 approximately constant 72 DNA replication 23 Contrasting phenotypic and The consequences of mutations 23 molecular evolution 73 What causes mutations? 25 How do new gene functions arise? 74 A final cautionary note 26 Gene regulation and phenotypic evolution 77 Chapter 3 Genes in populations 27 What is a population? 27 Chapter 7 Genetic markers 79 The concept of “effective population size” 28 Classical markers: Immunogenetic markers 79 The sex ratio and Ne 29 Classical markers: Biochemical Inbreeding and Ne 30 polymorphisms 81 Variation in population size over time The first DNA markers: Restriction fragment and Ne 30 length polymorphisms 84 Differential fertility and Ne 31 Polymerase chain reaction 86 Ne for humans 33 DNA sequencing: The sanger method 89 vii viii Contents Next-generation sequencing 90 The genetic evidence: mtDNA 222 Targeting single DNA bases: SNPs 92 The genetic evidence: Y chromosome 224 Variation in length 94 The genetic evidence: Autosomes 225 Other structural variation 99 Concluding remarks 100 Chapter 15 Ancient DNA 229 Properties of ancient DNA: Degradation 229 Chapter 8 Sampling populations Properties of ancient DNA: Damage 229 and individuals 103 Properties of ancient DNA: Contamination 232 Sampling populations: General issues 103 History of ancient DNA studies 236 Sampling populations: Ethical issues 105 Ancient DNA: Archaic humans 237 Archival samples 108 Other uses for ancient DNA 244 Chapter 9 Sampling DNA Chapter 16 Dispersal and regions 111 migration 247 Mitochondrial DNA 111 Out of Africa—how many times, when, and Y chromosomal DNA 116 which way did they go? 251 Autosomal DNA 119 Into remote lands: The colonization of the X chromosome DNA 121 Americas 259 Public databases 122 Into even more remote lands: The colonization of Polynesia 267 Chapter 10 Analysis of genetic Some concluding remarks 281 data from populations 125 Genetic diversity within populations 125 Chapter 17 Species-wide Genetic distances between populations 128 selection 283 Displaying genetic distance data: Trees 135 Species-wide selection 284 Displaying genetic data: Multidimensional Nonsynonymous mutations and the dN/dS scaling, principal components, and ratio 284 correspondence analysis 139 Tests based on the allele frequency distribution 288 Chapter 11 Analysis of genetic Selection tests based on comparing data from individuals 147 divergence to polymorphism 293 Genetic distances for DNA sequences 147 Archaic genomes 297 Trees for DNA sequences 153 Rooting trees 156 Chapter 18 Local selection 299 Assessing the confidence of a tree 157 Example: Lactase persistence 304 Network analyses 160 Example: EDAR 309 Genome-wide data: Unsupervised analyses 161 Ancient DNA 318 Concluding remarks 318 Chapter 12 Inferences about demographic history 175 Chapter 19 Genes and culture 321 Dating events 175 Are humans still evolving? 321 Population size and population size change 187 Genetic variation can be directly influenced Migration and admixture 194 by cultural practices 322 Putting it all together 197 Genetic variation can be indirectly influenced by cultural practices 322 Chapter 13 Our closest living Using genetic analyses to learn more relatives 201 about cultural practices: Agricultural Resolving the trichotomy 205 expansions 326 Complications 206 Using genetic analyses to learn more Ape genetics and genomics 208 about cultural practices: Language replacements 332 Chapter 14 The origins of our Using genetic analyses to learn more species 211 about cultural practices: Dating the origin of Human origins: The fossil record 215 clothing 333 Models for human origins 218 Concluding remarks 339 Contents ix Chapter 20 Ongoing and future Relating phenotypes to genotypes 351 developments in molecular Personal ancestry testing and genomics 360 anthropology 341 More—and different kinds of—data: The References 363 other “omics” 341 Suggestions for additional reading 373 Beyond “you”: The microbiome 344 Index 375 More analyses 347 PREFACE When most people think about anthropology, the anthropology in most undergraduate textbooks in bio- image that usually comes to mind is that of intrepid, logical anthropology or human evolution is often quite Indiana Jones-like characters, traveling to remote and superficial and generally leaves a lot to be desired— exotic locations; living and working under arduous while there are some good advanced books, there is conditions; digging up fossils, stone tools, or other nothing really comparable for the beginning student, evidence of our past; and making headlines by pro- who may have little in the way of any previous back- claiming that what they have found overturns every- ground in science. The present book is an attempt to thing we thought we knew about human evolution. remedy this situation by assuming no prior knowledge However, there is another type of anthropology that of genetics and by trying to focus on understanding the is becoming an increasingly important source of infor- logic and reasoning behind various methods and find- mation about our past, rivaling the study of fossils or ings, while omitting (or at least, placing less emphasis artifacts, and that is molecular anthropology,which on) the technical details. can be defined as the use of molecular genetic methods In addition to beginning students, it is hoped that to address questions and issues of anthropological this book will be useful to professionals from other interest. More specifically, molecular anthropology fields (such as linguists or archaeologists) who wantto uses genetic evidence to obtain insights into human know more about molecular anthropology and how it origins, migrations, and population history, as well as might inform their own work, as well as the interested the role of natural selection during human evolution, layperson.
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