Johnson, Norman A. Darwinian detectives

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mysteries that only evolutionary biologists have the hubris to try to solve.

Like the cosmologists of physics or the theorists of quantum mechanics,

evolutionary biologists delight in paradoxes and puzzles, organisms that

shouldn’t exist, and genes that seem to defy reason. Though it doesn’t figure

in this slim book, I have devoted much of my life to the mystery of aging. The

fact of aging has been known for millennia. The difficult questions have

revolved around its origins, and whether there is any prospect of slowing its

onslaught. To my great pleasure, the culprits behind this crime turn out to be

both quite Darwinian and quite guilty. I am hot on their tail, and relishing

the chase.

Norman Johnson is now going to entice you to learn about evolutionary

detective work, its twists and turns, surprises and satisfactions. I know you’ll

enjoy it, too.

Michael R. Rose

California, July 

Forewordx

Preface

As a child of the s with dim memories of the Apollo space program, I

have sometimes felt that my childhood expectations of the future have not

been fulfilled. Where are the jetpacks? Where are the lunar colonies? Why

haven’t we been to Mars or even back to the Moon?

Two major technological transformations of the s, however, have

clearly exceeded my expectations. The first transformation is an obvious one:

the Internet. The year  saw the development of the hypertext transfer

protocol (HTTP) by Tim Berners-Lee, a technique that made the rapid explo-

sion of the World Wide Web possible.

By the end of the decade, the Web

contained billions of pages; indeed, the search engine Google claimed in the

year  that it had indexed . billion of them.

In the years since the turn

of the millennium, the growth of the Internet has accelerated and expanded

into new areas of multimedia, such as podcasting and videoconferencing.

Today, the Internet and other, associated computer technologies have

dramatically changed how we work and how we approach many other aspects

of our daily lives.

Less heralded is another revolution: a boon in genetics and biotechnology

that has changed the landscape of biology and medicine. In large part, this

revolution has come from great dramatic leaps in the ability of scientists to

ascertain the genetic information present in the sequences of DNA molecules.

Although we have understood that DNA is the genetic material since the

s and have known DNA’s biochemical structure since , scientists

had not had the ability to rapidly determine the sequences of DNA until

much more recently. Moreover, much as computational speed and power has

exploded, so also has the ability to sequence DNA.

Our sequencing capacity is such that we no longer just sequence individual

genes one at a time; now we can sequence the totality of DNA information

present in individual organisms, an entity that geneticists call the genome.

Coinciding with the fiftieth anniversary of Watson and Crick’s unraveling of

the structure of DNA, the DNA information contained in the human genome

was fully ascertained in April . This was no small feat, given the size of

the human genome (just over three billion of the basic units of DNA,

which biologists call nucleotides or base pairs). Yet the human genome was

sequenced—sooner than expected, and under budget.

In addition to the

human genome, we now also possess knowledge of the complete sequences

from the genomes of over five hundred organisms. Hundreds more will be

completed within the next decade.

The pace of discovery is also accelerating due to advances in the tech-

nologies used to sequence genes, as well as the development of new and more

powerful computers and computational tools. These advances led to the

emergence of the interconnected fields of genomics (study of genomes),

bioinformatics (the intersection of biology and computational sciences), and

proteomics (the study of the proteins that are produced from the genes in

genomes and their interactions). Many biologists now perform most of their

research not at the lab bench or in the field but at the computer, analyzing

the information of genes and genomes already contained in ever-expanding

databases.

Yet tension exists among different communities of biologists. In contrast

with the rapidly accelerating pace of research in genomics and other new

high-tech fields, older, more-established disciplines such as conservation

biology, ecology, and evolution receive far less attention and funding for

research. Geneticists and molecular biologists often dismiss these older fields

with the pejorative label “natural history.” When challenged, those studying

ecology and evolution often counter with statements that the lab-bound

scientists aren’t really studying nature. Such tensions are not new; indeed,

they predate the rise of molecular genetics, starting in the middle decades of

the last century.

Natural history should not be a pejorative label. Usually defined as the

study of entities (including organisms) in their natural environments, natural

history includes studies of their origins, evolution, interrelationships, and

behavior. Genes and genomes—the provinces of the molecular biologists—

also have natural histories. In fact, a great deal of molecular biology over the

past half century is about characterizing the genomes of organisms, a topic

that might be considered descriptive natural history. And researchers found

quite a few surprises! It is striking that only  to  of the genomes of

animals actually codes for genes. Although vertebrates (animals with back-

bones) generally have larger genomes than do insects and other invertebrates,

the vertebrate genome is less gene rich. In fact, although the human genome

Prefacexii

contains about ten times as much DNA as the genomes of roundworms and

fruit flies, the number of genes in humans is only about twice the number of

genes in these supposedly “simpler” organisms. Why is this? And what does

the  to  of the genome that does not encode for genes do? These

questions have been only somewhat answered, and will require a deep under-

standing of molecular genetics as well as evolutionary biology to be fully

addressed.

Not all genes within the same genome have the same evolutionary histories;

different regions of genome can experience considerably dissimilar environ-

ments. The way we inherit our genomes facilitates dissimilar evolutionary

histories for various parts of the genome. When gametes are made, the

genome—even including genes that are on the same chromosome—is

scrambled in a process known as genetic recombination. As we will see in

chapter , the time and place identified for the most recent common ancestor

for all humanity depend upon which gene is chosen for study.

This book explores how evolutionary biologists use the tools of molecular

genetics to unravel the secrets of the natural histories of genes and genomes.

Much like detectives looking to ascertain the circumstances behind a crime,

evolutionary biologists can make and test inferences about the nature of the

evolutionary pressures that have shaped the organisms that harbor such

genes. The clues they obtain come from examination of patterns in the infor-

mation contained in genes. By immersing themselves in the natural histories

of genes and genomes and by using the tools of mathematical evolutionary

theory, such Darwinian detectives can and are asking questions such as these:

Why do some organisms have a much lower genome size than their

close relatives?

Has natural selection, and if so what kind of natural selection, oper-

ated on a particular gene?

What were the genetic changes that were associated with our becom-

ing human?

In addition to telling stories about genes and the organisms that harbor

them, I also aim to give a sense of the thought processes scientists use to

unravel these puzzles of the natural world. Although science is based on facts,

it is much more than just facts. Ultimately, science is about making sense of

the universe and its parts. Science involves forming explanations for the pat-

terns we observe; in this regard, it is a creative activity. These explanations,

formally known as hypotheses, are tentative at first. In addition to formulating

hypotheses, science requires the rigorous testing of those hypotheses with

experimentation and further observation. Unfortunately, most nonscientists

(even those with a strong interest in science) lack a clear understanding of

exactly how science is practiced today. A major goal of this book is to facili-

tate the public’s understanding of the professional science of evolutionary

biology, and in doing so, maintain clarity but with as little dilution of rigor

as possible.

Preface xiii

The general public’s lack of understanding of science, and of evolution in

particular, has enabled the rise of a most pernicious political movement: a

new faith-based creationism that presents itself as if it were actually science.

Between  and , school boards and legislatures in several American

states have attempted to either minimize the teaching of evolution or to

introduce a form of creationism called “Intelligent Design” as an alternative

to the teaching of Darwinian evolution in public schools. Countering these

efforts—which are entirely political and religious, and not scientific—will

require more education of the general public about what evolution is and how

science is practiced.

The book begins with a chapter demonstrating why evolution not only is

the central organizing principle of biology but also is worthy of study for very

practical, real-world reasons. In the second chapter, we will also examine why

Intelligent Design creationism is not science, and why it is not an alternative

to evolution for explaining the natural world. Here we will also encounter the

Discovery Institute, the Seattle-based think-tank that has been supporting

and funding the Intelligent Design movement. The mission of the Discovery

Institute extends beyond promotion of Intelligent Design; indeed, its aims

include undermining and overturning the principles of the Enlightenment

on which the United States was founded and replacing these principles with

theistic ones.

Next we’ll turn to Darwin’s prime explainer of evolutionary patterns:

natural selection. Consider the honeybees; they have evolved elaborate

“dance” behaviors that allow them to communicate to others in their nest the

location of food sources that may be hundreds of yards away. Natural selection

is a requirement for the evolution of these dance behaviors and other intri-

cate adaptations to the environment. The process of evolution, however, is

more complicated than just adaptation via natural selection. First, natural

selection is not the only evolutionary force; random processes such as the

sampling error known as genetic drift also influence evolution. Moreover,

natural selection comes in several forms. The type of selection that increases

the frequencies of advantageous genetic variants and ultimately allows for the

bee dance and other adaptations is often called positive selection. In contrast,

selection against recurrent deleterious mutations is called negative selection.

Selection can also actively maintain different variants of genes; this is called

balancing selection.

In chapters  through , we’ll explore how evolutionary geneticists go

about their detective work of finding the footprints of selection on genes.

Chapter  begins with a discussion of the importance of negative selection in

the evolution of DNA and protein sequences; at the molecular level, the

weeding out of deleterious mutations by negative selection is usually more

frequent than the actions of either positive or balancing selection. After

discussing a negative selection, we turn to a conceptual framework that

explains the patterns of molecular evolution that would be expected if the

fates of genetic variants were determined primarily by mutation, genetic drift,

Prefacexiv

and negative selection alone. This conceptual framework, by the Japanese

geneticist Motoo Kimura, is called the neutral theory of molecular evolution,

and it forms the foundation of many of the studies that are explored in the

remainder of the book.

Evolutionary geneticists now use Kimura’s neutral theory of molecular

evolution to establish tests for positive and balancing selection. These

Darwinian detectives start with figuring out what would happen if no positive

or balancing selection operated. They then look for deviations from those

expected patterns, and these deviations (if found) can provide support for

claims of positive or balancing selection. Chapter  introduces some of the

basic tests used to detect positive natural selection, and presents biological

examples in which positive selection has been detected. Next, chapter 

describes the tests used for detecting balancing selection. Many of the best-

known cases of balancing selection involve human diseases such as malaria.

The discussion of how evolutionary geneticists detect different forms of

natural selection prepares us well for the subject of the next section: what

genetic sequence information can tell us about human origins and evolution-

ary history. In chapters  and , we’ll look at the tracking of genetic changes

to unravel details about our recent evolutionary history. One surprising

finding is that the common ancestor of all human females lived substantially

earlier than did the common ancestor of all human males. Answers from

these studies allow us to address whether Neanderthals contributed to our

gene pool, and whether Neanderthals and modern humans should be con-

sidered two separate species or two subspecies of the same species. Chapter 

explores the data that show that our closest relatives are the common chim-

panzee and the bonobo (formerly known as the pygmy chimpanzee).

What were the genetic changes that made us human? Perhaps we will never

know the answer to that question, but we can address a related question:

which genetic changes that occurred along the human branch of the evolu-

tionary tree were also driven by positive selection? chapter  tackles this

question, building on the tests discussed in chapter  with new information

from the human and chimpanzee genomes. In chapters  and , we return

to more recent human evolutionary history, asking questions about correlations

between linguistic and genetic variation, and the genetic changes that occurred

in the plants and animals that humans domesticated.

In the final chapter, we turn to the properties of genomes and, in particular,

the variation in the size of genomes in different organisms. For example, why

do pufferfish have much smaller genomes than do their close relatives?

The chapter also explores a recent hypothesis that many general features of

the genomes of different organisms may be the result of a few key parameters

such as the population size and the mutation rate.

In writing this book I have tried to accurately present to a wide audience

a glimpse into how scientists solve complex problems. Although both evolu-

tionary biology and genetics rest upon a rich body of mathematical theory,

I have kept the mathematics to a bare minimum and have instead presented

Preface xv

concepts in verbal terms. In chapters  and , the more mathematical material

is set aside in boxes from the rest of the text. Occasionally, I have simplified

concepts and results; in some cases, I provide more information in the end-

notes, and in others, I provide references to those who wish to delve deeper

into the literature. I have also ventured into areas, such as anthropology and

linguistics, in which I am not an expert. To practitioners in these subject

areas, I apologize for any misrepresentations or oversimplifications. I have

minimized but not completely eliminated jargon. To assist with understanding

vocabulary that may be unfamiliar to the general reader, I have introduced

special terms upon first appearance and have provided a glossary at the back

of the book.

Prefacexvi

Acknowledgments

It is difficult to imagine publication of Darwinian Detectives coming to pass

without the enthusiastic guidance and assistance of Peter Prescott, my editor

at Oxford. Since the time I pitched the idea for such a project to him back in

summer of , Peter has been a steady champion. I am also grateful to

Alycia Somers, Keith Faivre, Suzanne Copenhagen, and the rest of the staff at

Oxford University Press for their excellent work.

To my family, friends, and colleagues: thank you for your support

and your continued attention. I thank my mentors and teachers, espe-

cially Bruce Grant. I am also grateful for the support given by the

Department of Plant, Soil, and Insect Sciences and the Graduate Program of

Organismic and Evolutionary Biology at the University of Massachusetts at

Amherst.

Alan Dickman at the University of Oregon read the entire first draft. His

insightful comments and suggestions improved the book substantially. I

thank the following for reading and commenting on one or more chapters

from the book: Carol Boggs, Julie Froehlig, Jay Hegde, Chad Hoefler, Olivia

Judson, Michael Lynch, John McDonald, Mohamed Noor, Ben Normarck,

Sarah Purvis, Lynnette Leidy Sievert, Michael Wade, and Sean Werle. Several

anonymous reviewers also read parts of the manuscript at various stages;

their assistance was very valuable. I thank Sylvia Purvis, research librarian at

Central Connecticut State University (and my aunt), for tracking down the

source of an obscure quote.

Sean Werle assisted with the construction of many of the figures. I am

deeply grateful for his help. I also thank Kara Belinsky, Ray Coppinger, Simon

Fisher, Laurie Godfrey, Chad Hoefler, Sarah Huber, Sharlene Santa, and

Frank Williams for assistance in providing illustrations.

Acknowledgmentsxviii

Contents

Foreword vii

 The Baby with the Baboon Heart: Why Evolution Still Matters 

 Why Intelligent Design Is Not Science 

INTERLUDE I: Natural Selection 

 Negative Selection and the Neutral Theory of Molecular Evolution 

 Detecting Positive Selection 

 Balancing Selection and Disease 

INTERLUDE II: Human Origins and Evolution 

 Finding Our Roots: Did “Eve” Know “Adam”? 

 Who Were the Neanderthals? 

 Are We the Third Chimpanzee? 

 What Are the Genetic Differences That Made Us Human? 

 Clicks, Genes, and Languages 

 Who Let the Dogs in? The Domestication

of Animals and Plants 

 Size Matters: Toward Understanding the Natural

History of Genomes 

Notes 

Glossary 

References 

Index 