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- Herausgeber: John Wiley & Sons
- Kategorie: Wissenschaft und neue Technologien
- Sprache: Englisch
A freshly updated discussion of the foundations of—and latest developments in—molecular anthropology
In the newly revised second edition of An Introduction to Molecular Anthropology, retired researcher Dr. Mark Stoneking delivers an essential primer on genetics and molecular anthropology. The book is an accessible resource that covers key recent developments in the production and analysis of genome-wide data that highlights advances in methods and technologies, as well as the latest findings from ancient DNA.
The updated chapters build on basic genetics and evolutionary concepts to demonstrate how to make inferences about human population history and human evolution in the genomics age. It explores how evolution influences genes, how genes evolve, the different kinds of genetic variation in humans and how they are analyzed, and the latest technologies and ethical issues that arise from the sampling of modern populations.
Readers will also find:
- A thorough introduction to the genetic evidence of human origins and the spread of humans around the world
- Comprehensive explorations of the role of selection and adaptation in human evolution
- Practical discussions of the impact of culture on human genetic variation
- Complete treatments of likely future developments within molecular anthropology in the genomics era
Perfect for anthropology students and others studying introductory human evolution, An Introduction to Molecular Anthropology will also benefit practicing anthropologists and researchers in a variety of fields that touch on this topic.
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Veröffentlichungsjahr: 2025
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Table of Contents
Cover
Table of Contents
Title Page
Copyright
Dedication
Disclaimer
Preface to the Second Edition
Preface to the First Edition
About the Companion Website
Chapter 1: Genes: How They Are Inherited
Blood and ABO Blood Groups
Inheritance of ABO Blood Groups
Inheritance of More than One Gene: ABO and Rhesus Blood Groups
Sex Chromosomes
Determining How Traits Are Inherited: Pedigree Analysis
What Is – and Isn’t – Inherited
Concluding Remarks
References
Chapter 2: What Genes Are, What They Do, and How They Do It
Chromosomes, Proteins, and Nucleic Acids: Figuring Out What Genes Are
The Structure of Genes and What They Do: The Central Dogma and the Flow of Information
How Genes Do What They Do: Transcription and Translation
The Genetic Code
DNA Replication
The Consequences of Mutations
What Causes Mutations?
A Final Cautionary Note
References
Chapter 3: Genes in Populations
What Is a Population?
The Concept of “Effective Population Size”
The Sex Ratio and
N
e
Inbreeding and
N
e
Variation in Population Size over Time and
N
e
Differential Fertility and
N
e
N
e
for Humans
The Gene Pool with No Evolution: The Hardy–Weinberg Principle
Exceptions
A Real-life Example
Some Practical Uses for Hardy–Weinberg
References
Chapter 4: Evolutionary Forces
Nonrandom Mating
Small Population Size
Mutation
Migration
Selection
Evolutionary Forces: Summary
References
Chapter 5: Molecular Evolution
Functionally Less Important Molecules (or Parts of Molecules) Evolve Faster than More Important Ones
Conservative Substitutions Occur More Frequently than Disruptive Ones
The Rate of Molecular Evolution Is Approximately Constant
Contrasting Phenotypic and Molecular Evolution
How Do New Gene Functions Arise?
Gene Regulation and Phenotypic Evolution
References
Chapter 6: Genetic Markers
The First DNA Markers: Restriction Fragment Length Polymorphisms
Polymerase Chain Reaction
DNA Sequencing: The Sanger Method
Next-generation Sequencing
Targeting Single DNA Bases: SNPS
Variation in Length
Other Structural Variation
Concluding Remarks
References
Chapter 7: Ancient DNA
Properties of Ancient DNA: Degradation
Properties of Ancient DNA: Damage
Properties of Ancient DNA: Contamination
History of Ancient DNA Studies
References
Chapter 8: Sampling Issues
Sampling Populations: General Issues
Sampling Populations: Ethical Issues
Archival Samples
Ancient Remains
Sampling DNA Regions
Mitochondrial DNA
Y Chromosomal DNA
Autosomal DNA
X Chromosome
Public Databases
References
Chapter 9: Analysis of Genetic Data from Populations
Genetic Diversity Within Populations
Genetic Distances Between Populations
Analysis of Molecular Variance (AMOVA) and Mantel Tests
Displaying Genetic Distance Data: Trees
Displaying Genetic Data: Multidimensional Scaling, Principal Components, and Correspondence Analysis
References
Chapter 10: Analysis of Genetic Data from Individuals
Genetic Distances for DNA Sequences
Trees for DNA Sequences
Rooting Trees
Assessing the Confidence of a Tree
Network Analyses
Genome-wide Data: Unsupervised Analyses
References
Chapter 11: Inferences About Demographic History (Part 1)
Dating Events
Population Size and Population Size Change
References
Chapter 12: Inferences About Demographic History (Part 2)
Migration and Admixture
Putting It All Together: Simulations
References
Chapter 13: Human Origins
Our Closest Living Relatives
Resolving the Trichotomy
Complications
Ape Genetics and Genomics
The Origins of Our Species: Insights from Modern Populations
The Genetic Evidence: mtDNA
The Genetic Evidence: Y Chromosome
The Genetic Evidence: Autosomes
References
Chapter 14: The Origins of Our Species: Insights from Archaic Genomes
Enter the Denisovans
The Plot Thickens: Multiple Contributions of Ancestry from Archaic to Modern Humans…
… And Multiple Contributions of Ancestry from Modern to Archaic Humans!
Some Concluding Remarks
References
Chapter 15: Migration and Dispersal: The Colonization of the Americas
Into Remote Lands: The Colonization of the Americas
References
Chapter 16: Into Even More Remote Lands: The Colonization of Polynesia
What About Micronesia?
Contact Between Polynesia and the Americas?
Some Concluding Remarks
References
Chapter 17: Species-wide Selection
Species-wide Selection
Nonsynonymous Substitutions and the dN/dS Ratio
Tests Based on the Allele Frequency Distribution
Selection Tests Based on Comparing Divergence to Polymorphism
Archaic Genomes
References
Chapter 18: Local Selection
Example: Lactase Persistence
Example: EDAR
Using Admixture to Detect Selection
Concluding Remarks
References
Chapter 19: The Genetic Basis of Phenotypic Variation
Skin Pigmentation Variation
Hair and Eye Color Variation
Other Traits
Predicting Ancient Phenotypes
References
Chapter 20: Genes and Culture
Are Humans Still Evolving?
Genetic Variation Can Be Directly Influenced by Cultural Practices
Genetic Variation Can Be Indirectly Influenced by Cultural Practices
Using Genetic Analyses to Learn More About Cultural Practices: Farming/Language Family Expansions
Using Genetic Analyses to Learn More About Cultural Practices: Dating the Origin of Clothing
Concluding Remarks
References
Chapter 21: Ongoing and Future Developments in Molecular Anthropology
More Modern and Ancient DNA Genomic Studies
The Other “OMICS”
Beyond “YOU”: The Microbiome
More Analyses
Figuring Out What Mutations Do: Functional Genomics
Personal Ancestry Testing and Genomics
References
Index
End User License Agreement
List of Tables
Chapter 1
Table 1.1 Antigens and antibodies for the ABO blood groups.
Table 1.2 ABO blood group genotypes and corresponding phenotypes.
Table 1.3 Observed number of offspring who are Rh+ or Rh− and either afflicted with ellipt...
Chapter 3
Table 3.1 Values of and for different values of and .
Table 3.2 Estimates of the census and effective population sizes for great apes.
Table 3.3 MN blood group data for 16,000 Germans.
Table 3.4 ABO blood group genotypes under the 2-locus and 1-locus models.
a
Table 3.5 ABO blood types observed in an African Pygmy population and the expected numbers...
Table 3.6 Blood types observed among the offspring of families where one parent is type AB...
Chapter 4
Table 4.1 Summary of the influence of each evolutionary force on genetic variation within ...
Chapter 5
Table 5.1 Substitution rates based on comparisons between human and rodent genes.
Chapter 9
Table 9.1 Diversity values for different markers and populations.
a
Table 9.2 values for worldwide populations, based on different types of genetic marker...
Chapter 10
Table 10.1 Observed number of substitutions per site, based on parsimony analysis of 20 hum...
Chapter 13
Table 13.1 Genetic diversity (number of polymorphic sites per 1000 base pairs, based on com...
Chapter 18
Table 18.1 Frequency of the LP trait and the −13910T allele in various populations
Chapter 20
Table 20.1 Apportionment of variation for autosomal DNA, mtDNA, and Y chromosomal DNA in hu...
Guide
Cover
Table of Contents
Title Page
Copyright
Dedication
Disclaimer
Preface to the Second Edition
Preface to the First Edition
About the Companion Website
Begin Reading
Index
End User License Agreement
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An Introduction to Molecular Anthropology
Mark Stoneking
Université Claude Bernard Lyon 1 and LBBE
Villeurbanne, France
Second Edition
Copyright © 2025 by John Wiley & Sons, Inc.,
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Published by John Wiley & Sons, Inc., Hoboken, New Jersey.
Published simultaneously in Canada.
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Library of Congress Cataloging-in-Publication Data:
Names: Stoneking, Mark author | John Wiley & Sons publisher
Title: An introduction to molecular anthropology / Mark Stoneking.
Description: Second edition. | Hoboken, New Jersey : Wiley, [2025] | Includes bibliographical references and index.
Identifiers: LCCN 2025025535 | ISBN 9781394262595 hardback | ISBN 9781394262618 adobe pdf | ISBN 9781394262601 epub
Subjects: LCSH: Human genetics—Variation | Human molecular genetics | Molecular evolution | Human evolution
Classification: LCC QH431 .S784 2025 | DDC 599.93/5—dc23/eng/20250812
LC record available at https://lccn.loc.gov/2025025535
Cover Design: Wiley
Cover Images: Maps depicting human dispersals during the Holocene inferred from genomic data, modified with permission from Stoneking, M., et al., “Genomic perspectives on human dispersals during the Holocene,” Proceedings of the National Academy of Sciences USA 120: e2209475119, 2023, Author explaining the results to Khwe community in Namibia, photo courtesy of Brigitte Pakendorf, Max Planck Institute for Evolutionary Anthropology
This one is for Brigitte.
“A study of the blood of individual nations enables us to decode their distant past.”
—Ludwik Hirszfeld, A Story of One Life, 1946
“The proper study of Mankind is Man”
—Alexander Pope, Essay on Man, 1734
“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
Disclaimer: No artificial intelligence was used in the writing of this book (only natural stupidity).
Preface to the Second Edition
As it is more than 10 years now since I started working on the first edition of Introduction to Molecular Anthropology, an updated version is sorely needed. It is amazing indeed to contemplate how much has changed; developments that seemed so new and wondrous at that time, such as getting genome sequences from archaic humans and all that they have told us about human evolution, are now considered part of mainstream science – if you need further proof, look no further than the awarding of the 2022 Nobel Prize in Physiology or Medicine to paleogenomicist extraordinaire Svante Pääbo for “… discoveries concerning the genomes of extinct hominins and human evolution.” There have been enormous advances in our ability to obtain and analyze ancient DNA; who would have thought back then that we would now have genome-wide data from more than 10,000 ancient modern human remains, dating to as much as 40,000 years ago or so, or that it would be possible to reconstruct entire genealogies of ancient communities? We also have much more in the way of genome-wide data from contemporary human populations, including whole-genome sequences from tens of thousands of individuals, and there have been similarly incredible advances in our ability to analyze and interpret such massive amounts of data. And there have also been major advances in other aspects of molecular anthropology, such as determining the important genetic changes that made humans human and what those genetic changes actually do. So, there is a lot of new stuff in this book and it is well worth reading, in case you’ve seen the first edition and were wondering how much is new!
The overall philosophy and raison d’être (pardon my French, but now that I’ve retired and moved to France I need to practice!) of this edition remain the same as that of the first edition, so the interested reader should consult the preface to the first edition (included after this preface) for that information. The structure of the book, however, has changed somewhat. Chapters 1–5 include background material on basic aspects of genetics, molecular genetics, evolutionary and population genetics, and molecular evolution; not much has changed here. Chapter 6 deals with properties of the various kinds of genetic markers that are used in molecular anthropological studies; here I have decided, with great reluctance, to remove the discussion of classical markers (blood groups, serum proteins, red cell enzymes, and so forth) in order to keep the length of the book manageable, as these are hardly studied anymore – and if they are, it is at the DNA level, and not at the marker level. The interested reader can still find this information in the first edition, as well as in Luca Cavalli-Sforza’s magnum opus, The History and Geography of Human Genes, which is a magnificent summary of everything we learned from classical markers (which turns out to be quite a lot!). Chapter 8 covers ancient DNA and is moved up in prominence in the book (in accordance with the prominence ancient DNA now occupies in molecular anthropology!) and considerably updated, to reflect that fact that ancient DNA is now a mature science. Chapter 8 covers issues concerned with sampling individuals, populations, and genomic regions for molecular anthropological studies, as these can all have profound effects on the outcome and interpretation of such studies. This is followed by four chapters (up from three in the previous edition) on methods for analyzing genetic/genomic data from populations (Chapter 9), from individuals (Chapter 10), and on making inferences about demographic history – the latter split into two chapters (Chapters 11 and 12), to reflect both the enormous increase in methods devoted to various aspects of demographic history, and because I’ve tried to respond to requests to include more examples in these chapters. Be forewarned, though, it is still not easy going through these chapters!
Beginning with chapter 13, the book now turns to what we’ve actually learned about ourselves from molecular anthropological studies. Chapter 13 covers human origins, and includes what are arguably two of the most important contributions of the molecular approach to anthropology, namely the answers to the following questions: who are our closest living relatives, and what model best explains the origin of modern humans? For the latter, it turns out that genome sequences from archaic humans were the key to the answer, and that is the subject of Chapter 14. The next subject is dispersal and migration, and the next two chapters cover in some detail what we’ve learned about two of the more remarkable accomplishments of humans, namely the colonization of the New World (Chapter 15) and the colonization of Oceania (Chapter 16). This is followed by two chapters on identifying and evaluating the impact of natural selection on humans – Chapter 17 deals with species-wide selection (i.e., selection that influenced all humans and led to the genetic changes that were important in making humans human), and Chapter 18 with local selection (i.e., selection that has influenced only some human populations, and led to the genetic changes that were important for humans to be able to colonize more of this planet than any other organism – with the exception of our parasites, of course!). Chapter 19 is then a brand-new chapter on the genetic basis of phenotypic variation (although some of this material was scattered in different chapters in the first edition); before molecular genetics, biological anthropology was mostly concerned with trying to understand phenotypic variation, so it is useful to consider what more we’ve learned from molecular anthropology. Chapter 20 considers the relationship between genes and culture, with an emphasis on how culture may influence genetic variation, as well as how we can use genetic studies to learn more about our cultural practices (including a genetic approach to dating the origin of clothing – I kid you not!). Finally, the book ends with Chapter 21 on ongoing and (likely) future developments in molecular anthropology, covering such topics as other “omics” (transcriptomics, proteomics, etc.), the microbiome, functional genomics, and personal ancestry testing (among others). Molecular anthropology is such a vibrant, fast-moving field, and it is hard to keep up – I don’t know how many times I’ve had to go back and rewrite sections that I thought were finished, because of new studies that appeared (I even considered issuing a plea for people to stop publishing anything new, just for a couple of months until I finished writing!).
In my haste to complete the first edition of this book, I inadvertently left out a few people who should have been thanked (mea culpa!), so the following includes people who helped make either (or both) editions a reality. Rolf Pakendorf provided useful advice on contracts and on the publishing business in general. At Wiley, Gillian Kay, Ellen McArthur, Natalie Misyak, Dhanapriya Velumurthy, and Neena Ganjoo ably steered this book through the production process. Brenda Bradley, Ana Duggan, Kevin Langergraber, and Lluis Quintana-Murci all gave valuable and/or encouraging comments, while Janet Kelso and David Meltzer kindly answered a few last-minute questions. Anett Pechstein and the staff at the MPI-EVA library helped track down arcane references, while Wikipedia has been a most helpful source of illustrations and information (the latter, I hasten to add, always verified with other sources!). I’d like to thank the various students in my courses over the years who were subjected to various forms of the material in this book, and whose questions have helped me in trying to clarify my explanations; in particular, the students in the Molecular Anthropology course that I taught at the Institute for Vertebrate Paleontology and Paleoanthropology in Beijing in November 2024 provided valuable feedback on some of the new material that ended up in this book. I am particularly grateful to Laurent Duret of the CNRS Laboratoire de Biométrie et Biologie évolutive in Lyon, France, for arranging a guest position and access to an office after my retirement from Germany, and to all the LBBE members for providing a congenial atmosphere in which to work (and for stimulating conversations over nice lunches – France does have its advantages!). I also want to reiterate that the ideas presented in this book have been shaped over the years by numerous discussions with numerous colleagues and students, too many to mention by name. I feel greatly privileged to have worked for 23 years at the best place in the world for this sort of research, namely the Max Planck Institute for Evolutionary Anthropology, and one of the best parts of working there was all the great people I’ve gotten to know as a result. Finally, I am especially grateful to Brigitte Pakendorf; she not only read and commented on various drafts with her usual eagle-eye for spotting discrepancies, but our shared field-trip experiences were some of the most rewarding times of my life, and the discussions we’ve had over the years have had the most influence on my thinking about many aspects of molecular anthropology. For these reasons (and more), this book is dedicated to her.
Preface to the First Edition
When most people think about anthropology, the image that usually comes to mind is that of intrepid, Indiana Jones-like characters, traveling to remote and exotic locations; living and working under arduous conditions; digging up fossils, stone tools, or other evidence of our past; and making headlines by proclaiming that what they have found overturns everything we thought we knew about human evolution. However, there is another type of anthropology that is becoming an increasingly important source of information about our past, rivaling the study of fossils or artifacts, and that is molecular anthropology, which can be defined as the use of molecular genetic methods to address questions and issues of anthropological interest. More specifically, molecular anthropology uses genetic evidence to obtain insights into human origins, migrations, and population history, as well as the role of natural selection during human evolution, and the impact of particular cultural practices on patterns of human genetic variation. And while working in a molecular genetics laboratory or sitting in front of a computer (which is where most of the work is done nowadays) may lack the glamour and excitement of paleoanthropological fieldwork (although a lucky few of us do all too rarely get to go out and collect samples), molecular anthropology has already had, and is continuing to have, a major impact on our understanding of our evolutionary past – from the first demonstration of a surprisingly close relationship between humans and chimpanzees in the 1960s, to the mtDNA evidence for a recent African origin that developed in the 1980s, to the current fascination with whole-genome sequences from Neandertals and other archaic humans.
Molecular anthropology can thus be considered a full-fledged, mature subfield of biological anthropology (alongside paleoanthropology, primatology, and demography), and therefore deserving of equal coverage in the curricula of university anthropology departments. However, the treatment of molecular anthropology in most undergraduate textbooks in biological anthropology or human evolution is often quite superficial and generally leaves a lot to be desired – while there are some good advanced books, there is nothing really comparable for the beginning student, who may have little in the way of any previous background in science. The present book is an attempt to remedy this situation by assuming no prior knowledge of genetics and by trying to focus on understanding the logic and reasoning behind various methods and findings, while omitting (or at least, placing less emphasis on) the technical details.
