Ancestors in Our Genome: The New Science of Human Evolution

263 Pages·2014·5.47 MB·English

by  Eugene E. Harris

Ancestors in Our Genome
A O G
NCESTORS IN UR ENOME
The New Science of Human Evolution
Eugene E. Harris
Oxford University Press is a department of the University of Oxford.
It furthers the University’s objective of excellence in research, scholarship and education by publishing
worldwide.
Oxford New York
Auckland Cape Town Dar es Salaam Hong Kong Karachi
Kuala Lumpur Madrid Melbourne Mexico City Nairobi
New Delhi Shanghai Taipei Toronto
With offices in
Argentina Austria Brazil Chile Czech Republic France Greece
Guatemala Hungary Italy Japan Poland Portugal Singapore
South Korea Switzerland Thailand Turkey Ukraine Vietnam
Oxford is a registered trademark of Oxford University Press in the UK and certain other countries.
Published in the United States of America by
Oxford University Press
198 Madison Avenue, New York, NY 10016
© Eugene Harris 2015
All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or
transmitted, in any form or by any means, without the prior permission in writing of Oxford University
Press, or as expressly permitted by law, by license, or under terms agreed with the appropriate reproduction
rights organization. Inquiries concerning reproduction outside the scope of the above should be sent to the
Rights Department, Oxford University Press, at the address above.
You must not circulate this work in any other form and you must impose this same condition on any
acquirer.
Library of Congress Cataloging-in-Publication Data
Harris, Eugene E. (Professor), author. Ancestors in our genome : the new science of human evolution /
Eugene E. Harris.
p. ; cm.
Includes bibliographical references and index.
ISBN 978–0–19–997803–8 (alk. paper)
I. Title. [DNLM: 1. Genome, Human. 2. Biological Evolution. 3. Hominidae—genetics. QU 460] QP624
611’.018166—dc23
2014010296
eISBN 978–0–19–997820–5
To my parents, Joan and Whitney, and my son, Bryan
CONTENTS
List of Figures and Tables
Acknowledgments
Prologue
1. Looks Can Be Deceiving
2. Many Trees in the Forest: The DNA Quest to Find Our Closest Ape Relative
3. The Great Divorce: How and When Did Humans and Chimpanzees Part
Ways?
4. A Population Crash in the Past
5. What Can the Genome Tell Us about Being Human?
6. The Genomic Origins of Modern Humans
7. The Ongoing Evolutionary Journey
8. Kissing Cousins—Clues in Ancient Genomes
Epilogue
Glossary
Notes
Index
List of Figures and Tables
FIGURES
1.1 Species tree depicting morphological relationship of the papionin
African monkeys
1.2 The nuclear genome and the mitochondrial genome
1.3 Mitochondrial DNA tree of the papionin African monkeys
2.1 Evolutionary tree of great apes and humans
2.2 DNA sequences for the alpha 1, 3 GT gene from the three great apes
compared with humans
2.3 Speciation in a species tree
2.4 Gene tree branches in two gene trees
2.5 Crossover between chromosomes during the formation of sperm and
eggs
2.6 Differences in gene trees and the species tree for apes and humans
2.7 Comparing species trees with smaller or larger ancestral populations
and longer or shorter internodes
2.8 The mosaic pattern of ancestry of human chromosomes
3.1 How species and gene trees can differ
3.2 How internodes and effective population size affect gene trees
3.3 Number of DNA differences between the great apes and humans
3.4 Genetic relationships of apes and humans at different DNA sites
3.5 Different coalescence times for two different genes
3.6 Different coalescence times for human and chimpanzee genes
3.7 Allopatric or parapatric speciation of humans and chimpanzees
3.8 Pre-and post-speciation human-specific DNA changes
3.9 Unique human features in an extinct ape
4.1 The seesaw of genetic drift vs. natural selection
4.2 The effect of population size on natural selection
4.3 Amino acid-altering vs. silent DNA sites
4.4 Of mice, primates, and different evolutionary forces
5.1 Detecting positive selection in human genes
5.2 Comparing our genome to those of other species
6.1 SNP variation among three different people
6.2 Human migration and loss of DNA variation
6.3 Microarray plate (or DNA-chip)
6.4 Early modern human fossils from different geographic regions in
Africa and Southwest Asia
6.5 Possible metapopulation model for evolution of the modern humans
6.6 Nuclear and mitochondrial gene models for the evolution of humans
in Africa
6.7 Genetic “surfing” in geographically expanding populations
7.1 An evolutionary “selective sweep”
7.2 Testing Maasai in Tanzania for the genetic basis for lactose tolerance
7.3 Scan to identify regions of the genome shaped by natural selection
7.4 Distribution curve for variation in people’s height
7.5 The effects of a “soft selective sweep” on a polygenetic trait such as
height
7.6 Interaction between a genetic variant and different populations’ diets
8.1 Marcellin Boule and his interpretation of Neandertals
8.2 A human evolutionary tree
8.3 The cave where the Denisovan hominin was discovered
8.4 The ABBA-BABA test reveals potential interbreeding of archaic and
modern humans
8.5 Distribution of archaic and modern human fossil sites and areas of
possible interbreeding
8.6 Caves in Israel where adjacent Neandertal and human fossils were
discovered
8.7 Evolutionary relationships among modern humans, Neandertals, and
Denisovans
TABLE
3.1 Planet of the apes: fossil apes in Africa, Southwest Asia, and
southern Europe
ACKNOWLEDGMENTS
I thank the following colleagues for their generous time in commenting on
chapters: Drs. Günter Bräuer, Henry Harpending, Jody Hey, Carles Lalueza-Fox,
Diogo Meyer, Maryellen Ruvolo, Caro-Beth Stewart, as well as two anonymous
reviewers. Rebecca Ham deserves very special thanks for her extremely
thorough editorial advice, organization suggestions, and encouragement. All
illustrations were rendered with the expert and very gracious help of Kei
Hayashi. Drs. Sarah Tishkoff, Hopi Hoekstra, Günter Bräuer, Michael Day, and
John Fleagle kindly allowed me to use research photos of theirs. Tim White and
David Brill allowed me to use photos of fossil skulls. Stephen Nash generously
allowed me to use his original illustrations of papionin monkeys. I thank Jeremy
Lewis, Erik Hane and Michael Stein at Oxford University Press for their
generous editorial advice. An extra special thanks goes to my agent Deirdre
Mullane for her sound editorial advice and her steadfast and generous support in
guiding this project along. I also owe a debt of gratitude to my previous mentors
Terry Harrison, Clifford Jolly, Todd Disotell and Jody Hey. I also thank Dean
Falk for her helpful advice and support, Lisa Schlotterhausen for her editorial
suggestions, as well as my colleagues Avelin Malyango, Varsha Pilbrow, and
Scott Sherman. Any inaccuracies or mistakes in interpretation of other people’s
work are my own.