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Missing Links

Evolutionary Concepts & Transitions through Time


Robert A. Martin

The McDonald & Woodward Publishing Company

Granville, Ohio

Missing Links


The McDonald & Woodward Publishing Company

Granville, Ohio

Missing Links

Evolutionary Concepts & Transitions through Time

Text © 2014 by Robert A. Martin

All images not credited to other sources © Robert A. Martin

All rights reserved; first printing February 2015

Printed in the United States of America

by McNaughton & Gunn, Inc., Saline, Michigan,

on paper that meets the minimum requirements of permanence

for printed library materials.

10  9  8  7  6  5  4  3  2  1

21  20  19  18  17  16  15

Library of Congress Cataloging-in-Publication Data

Martin, Robert A. (Robert Allen), author.

    Missing links : evolutionary concepts & transitions through time / by Robert

A. Martin. — Second edition.

        pages cm

    Includes bibliographical references and index.

    ISBN 978-1-935778-28-8 (pbk. : alk. paper)

    1. Vertebrates—Evolution. 2. Vertebrates, Fossil. 3. Evolution (Biology)

I. Title.

    QL607.5.M36 2014



Reproduction or translation of any part of this work, except for

short extracts used in reviews, without the written permission of

the copyright owner is unlawful. Requests for permission to

reproduce parts of this work, or for additional information, should

be addressed to the publisher.


Table of Contents

Preface: Preface to the Second Edition


Introduction: What Is a Missing Link?


Section I

A Primer of Evolutionary Science

Chapter 1: Sources of Knowledge and Earth History


1.1  There Are No False Clues; Science As a Way of Knowing


1.2   An Ancient and Dynamic Earth


1.3  Time Enough Indeed


Chapter 2: Classification and Ecology: Making Sense of Nature 35

2.1   Classification and Phylogeny


2.2  The Ecological Context


Chapter 3: The Origin and Evolution of Species


3.1  Microevolutionary Patterns and Processes


3.2  Macroevolutionary Patterns and Processes


Section II

Case Histories

Chapter 4: Origins


4.1  The Origin of Life


4.2  The Fossil Record of Early Life


Chapter 5: Fishes with Fingers?


5.1  What Is a Fish?


5.2  What Is a Tetrapod?


5.3  EusthenopteronPanderichthys, and Tiktaalik: Links to



5.4  Experiments with Limbs


Missing Links


Chapter 6: Eye of the Flounder


6.1  Flatfish Biology


6.2  Development


6.3  Fossil Record


6.4  Interpretation and Phylogeny


Chapter 7: The Thanksgiving Day Dinosaur


7.1 Characteristics of Modern Birds


7.2 Genealogy of Dinosaurs and Birds


7.3 The Amazing Archaeopteryx


7.4 Reptiles, Specifically Dinosaurs,  As Avian Ancestors


7.5 Origin of Flight


7.6 Frauds and Feathered Dinosaurs


7.7 Beyond Archaeopteryx


Chapter 8: Snakes with Limbs


8.1 Fossil Snakes with Limbs


8.2 How Snakes Lost Their Feet


Chapter 9: On Hearing and Hinges



.1   The Reptile–Mammal Transition


9.2   Evolution of the Hearing Apparatus and the Earliest



Chapter 10:  Pedestrian Whales


10.1   Characteristics of Modern Whales


10.2   Early Whales: Transition from Land


10.3   Whales Take to the Sea


Chapter 11: The Kentucky Derby in Deep Time: The

Cenozoic Evolution of Horses


11.1   What Are Horses?


11.2   Orthogenesis and the Bushy History of Horses


Chapter 12: Evolving Voles and Muskrats


12.1   North American Voles


12.2    Anatomy of a Speciation Event: European Water Voles 296

12.3   The Muskrat Ramble


Chapter 13: History of the Caddyshack Rodent in

Southwestern Kansas


13.1   The Replacement Pattern


13.2   Size and Morphological Change, and the Discovery

of an Intermediate



Chapter 14: A History of Upstanding Primates


14.1  Before Adam: Living and Fossil Monkeys and Apes


14.2  Earliest Hominids


14.3   Australopithecus africanus (2.8-2.5 Ma),

Australopithecus garhi (2.7 Ma), and

Australopithecus sediba (1.98 Ma)


14.4  The Robust Australopithecines (2.7-1.3 Ma)


14.5  The Earliest Humans (2.4-1.6 Ma): Homo habilis and

Homo rudolfensis


14.6   Advanced Fossil Hominins and the Origin of

Modern Humans


14.7   Putting It All Together: A Summary of the Fossil

Evidence for Human Evolution


Chapter 15: Yesterday, Today, and Tomorrow


15.1   A Snail’s Pace Is Not Necessarily Slow


15.2   Evolutionary Change among Living Animals


Epilogue: Charles Darwin and the Fossil “Problem”






Missing Links




Preface to the Second Edition

Missing Links has a new publisher, McDonald & Woodward,

specialty publishers in natural and cultural history. My original

intent for Missing Links was for it to be as readily available to the

general public as to college students, and I feel comfortable that in its

new home its first audience will now be as well served as the second.

Some things change a lot, some a little. Since the first edition

of Missing Links was published in 2004, the stories of life’s ori-

gins, early tetrapods, dinosaurs, and hominids has changed signifi-

cantly, sometimes with fascinating new discoveries such as the

ancient tetrapod Tiktaalik, a bevy of feathered dinosaurs, and the

enigmatic hominin Australopithecus sediba, and sometimes with

new interpretations, such as the modern focus on deep sea hydro-

thermal vents as the likely spawning ground for early life. The

terrestrial origin of whales is more firmly documented by skel-

etons of a new Eocene protocetid with a pregnant female showing

a near-term fetus in head-down position, as in terrestrial mammals

but not aquatic whales. Although the fossil history of voles has not

been wracked with new discoveries that shake its foundations, the

very density of fossils in this rapidly evolving group provides us

with novel insights into the timing of anatomical change and the

possibility of multiple origins of modern groups from separate an-

cestors. A new chapter documents the complex history of pocket

gophers, burrowing rodents from the Meade Basin of southwest-

ern Kansas, and another chapter considers the origin of snakes from

both evidence in the fossil record and our new understanding of

the role of Hox genes in limb formation. Finally, as additional in-

formation from long-term studies of extant animals continues to

Missing Links


accumulate, the more we realize the potential for rapid change

within species during the lifetime of a single observer, as with the

potential speciation of mosquitoes in the London underground rail-

way system since the 1940s.

The reader will notice the absence of a chapter on plants. In

the original manuscript I made the “executive decision” to limit

the example chapters to animals, in part to maintain the contents

within certain page limits and partly because the fossil history of

plants is not as dense as that for animals. Besides, plants seem to

hybridize so easily that determining fossil histories at the species

level is almost impossible. The absence of a chapter on fossil in-

vertebrates is for a similar reason; they are so developmentally and

anatomically flexible that identification of fossil species and inter-

pretation of morphological changes are problematic. The remain-

der of the Preface is similar to that in the first edition, with the

obvious addition of the new gopher and snake chapters and a vari-

ety of comments that refine the original chapter descriptions to

reflect new information and fossil material. I have also rearranged

the case histories in roughly phylogenetic order.

When Darwin published his Origin of the Species in 1859

very little fossil material was known. Darwin himself collected

many fossil specimens on his voyage around the world on H.M.S.

Beagle, but they were primarily described by Richard Owen, an

English paleontologist who rejected Darwin’s mechanism of natu-

ral selection for evolutionary change. Owen was a pretty active

fellow; he also named the Dinosauria. In the United States, the

first fossils were gathered from a marsh somewhere along the Ohio

River in 1739 by a French Canadian officer, Baron Charles de

Longueuil. It is a strange and sometimes ironic aspect of evolu-

tionary science that some of those influential in the development

of the modern synthesis of evolutionary theory themselves did not

embrace evolution or its primary mechanisms, either because they

were unaware of it or simply rejected it. A few of these include:

Carolus Linnaeus, a Swedish physician and father of animal and

plant classification, who believed he was cataloguing examples of

God’s omnipotence; Baron Georges Cuvier, the father of comparative


anatomy and paleontology, who was convinced that God initiated

“catastrophes” to erase entire communities of organisms; Alfred

Wallace, who developed the theory of natural selection at the same

time as Darwin and later rejected the idea that humans could have

resulted from this process; and the afore-mentioned Richard Owen,

England’s premiere paleontologist. But the one-two-three punch

provided by James Hutton’s Theory of the Earth, Charles Lyell’s

Principles of Geology, and Darwin’s Origin of Species sent

shockwaves through the scientific community and began a mod-

ern exploration for fossils and their meaning that continues to this

day. Hutton’s work, published in 1785 and popularized by Lyell in

his 1830-33 three volume tome, was particularly influential for

Darwin, as Hutton’s principle of uniformitarianism, the concept

that the same slow and methodical forces at work on the planet

today shaped the planet in the past, provided circumstantial evi-

dence for an ancient Earth. Fundamentalist Christians of Darwin’s

time fought Darwin very strongly, for a literal reading of the Chris-

tian Bible is incompatible with both an ancient Earth and the con-

cept of evolution. It is an amazing testimony to the power of reli-

gious influence that millions of Americans today still follow this

basic credo. And one of the tenets of those who support a “cre-

ationist” model for humans and the universe is that there are no

true “missing links,” extinct organisms that connect modern and

ancient life in an unbroken chain through long periods of time,

measured in the millions and billions of years. But we have come

a long way since Darwin’s day. Thousands of expeditions have

unearthed literally millions of fossils, today housed in many muse-

ums and academic institutions worldwide. Paleontologists have

described fossils 3.5 billion years old, and organisms are known

continuously from that point onward. Many “missing links” are

recognized (though, as we shall see, a fossil “missing link” is not

exactly what most creationists have in mind), and it is the primary

purpose of this book to provide a compendium of this information

for the general reader in the context of modern scientific inquiry.

Missing Links is designed to satisfy two needs. First, as repre-

sented by the case histories, it can be read purely as a compilation


Missing Links


of fossil histories in support of evolutionary theory. It is my hope

and intention that this anthology be used in every conceivable cir-

cumstance where such information is needed, from a student class-

room presentation to an intellectual religious discussion. The sec-

ond usage, represented by Section I, is as a primer on evolutionary

science, particularly as it applies to fossil materials. Evolution can

no longer be expressed by the simple phrase “survival of the fit-

test.” Hundreds of scientists have worked carefully for 150 years

to establish evolution as a theory that is profound in scope and

universally supported, and more scientists are likely at work today

on evolutionary problems than were active in the first 125 years

combined. This section should also be of interest to professionals,

as I present new perspectives on concepts such as punctuated equi-

librium and species selection.

Evolutionary science encompasses many fields and can be

extremely complicated to the novice. Consequently, I have pre-

pared a synthesis in Chapters 1-3 of the major concepts, processes,

and vocabulary necessary for a reasonable understanding of evolu-

tion, particularly as it applies to interpretation of the fossil record.

Because the focus of this treatment is on transitions in the fossil

record, there is little here on evolutionary genetics as practiced

with extant organisms. For those interested in this area, I recom-

mend the sections on that topic in the texts Evolutionary Analysis

by Scott Freeman and Jon C. Herron (2007; Prentice Hall) and

Evolution (2009; Sinauer) by Douglas Futuyma. Although it is not

necessary to be familiar with the contents of Section I to consult

the case histories, it will be of considerable benefit. This section

begins with a chapter on how science operates as a method of know-

ing. Most people fail to understand that science is not limited to

chemistry, biology, physics, etc., the so-called “hard” sciences.

Everything we do as an adult is based on a series of experiments

we performed as we were growing up. We could not function if

this were not so. Hopefully, as this universal aspect of science be-

comes more widely known and appreciated perhaps science will

not seem so mysterious. Chapter 1 also documents the ancient age

of the Earth and its dynamic nature. One of the greatest and most


powerful discoveries of our time, the theory of continental drift, is

reviewed. This is followed by a more specific examination of meth-

ods for dating rocks and fossils, called chronometry.

The publication of German systematist Willi Hennig’s book

Phylogenetic Systematics in 1966 led to a major revolution in the

way classification is accomplished. Today, with the help of power-

ful computer programs such as MacClade and PAUP, we methodi-

cally examine and analyze character variation in modern and fos-

sil organisms in order to identify relations among them. The un-

derlying philosophy of phylogenetic systematics, or cladistics as it

is sometimes known, is that classification should represent phy-

logeny, or the revealed genealogy of organic life. Because evolu-

tionary processes seem to work primarily at the population level

within species, and also because species seem to have morpho-

logical boundaries (albeit sometimes fuzzy ones) and are therefore

recognizable units, I have provided in Chapter 2 a brief examina-

tion of the species concept, concluding that species are dynamic

units, full of variation in time and space. Chapter 2 also considers

the myriad influences that lead to the creation of a fossil locality

and the way scientists learn about past environments. What forces

affect the burial, preservation and distribution of fossils? In what

ways can fossils be used to interpret past climates? In addition to

these applications, fossils also can lead to an understanding about

how ecological communities change through time.

Chapter 3 has been completely rewritten to incorporate more

detail on almost every aspect of the evolutionary process. A revo-

lution is underway in our understanding of evolutionary change,

originating from the discovery of Hox gene complexes, conserved

gene groups shared by all metazoans (complex organisms), and

how these genes are responsible for basic body symmetry and shape.

Complex changes in body form may be the result of disproportion-

ate influence of only a few regulatory genes. Observations and pro-

cesses in the lifetime of single species (variation, natural selection,

genetic drift) are considered separately from patterns and processes

involved in the origin of new species and subsequent radiation within

clades. Can small-scale mutation in populations and intraspecific


Missing Links


natural selection explain life’s full panorama of diversity, or are

other processes, perhaps involving a selection mechanism at the

species level, necessary? How do we explain long-term morpho-

logical (anatomical) trends in species? Can trends arise by random

processes? Extinction, the flip side of origination, is also exam-

ined at different temporal and mechanistic scales. As the late

Stephen Jay Gould often noted, contingency (chance) can have a

powerful influence on the overall direction of life’s history.

The case histories begin, in Chapter 4, with a scenario for the

appearance of life on Earth (with contributions from Mars, if that

turns out to be the case). We see how Stanley Miller and others have

generated all the building blocks of complex cellular molecules, such

as DNA and ATP, in the laboratory. The mixture used by Miller may

not have been exactly appropriate, however, as other scientists con-

clude that life arose in deep sea hydrothermal vent ecosystems;

strange associations of organisms that exist without sunlight.

In Chapter 5 we examine one of the great changes in the his-

tory of vertebrate animals; namely, the transition from water to

land, or terrestrialization. Traditional ideas on the origin of limbs

in land animals, such as possessed by the modern amphibians, pro-

posed that hands and feet evolved to support the body on land. Not

so, says Jennifer Clack of Cambridge University. Her work indi-

cates that tetrapod (four-footed animal) limbs appeared first in fully

aquatic animals! If limbs are not present for support on land, then

what was their original purpose?

I almost retitled this book Eye of the Flounder, so excited

was I over recent discoveries regarding the origin of one of Earth’s

most amazing groups of animals, the “flatfish,” best represented

by flounders, halibut, sole, and the like. During development one

eye of these fishes migrates to the other side, and the adult ends up

swimming on its side, with its mouth still pointing sideways. I won’t

spoil the story by disclosing more information here, but new fossil

finds show that this condition in modern species evolved gradually

from Eocene ancestors.

Archaeopteryx needs little introduction, but again, as in

whales, there have been many new discoveries linking early birds


to their modern relatives. Chapter 7 examines these new finds in the

context of a raging debate about bird ancestry. Some paleontologists,

such as Robert Bakker, Louis Chiappe, and Kevin Padian, are con-

vinced that birds arose from dinosaurs; in fact are dinosaurs, whereas

another camp, led by Alan Feduccia and the late Larry Martin, think

that birds originated from an earlier reptilian ancestor that may have

given rise to both dinosaurs and birds. Whatever the outcome, new

fossils have cemented the links between reptiles and birds. Lots of

early “toothy” and feathered relatives are now known. New discover-

ies of fossil snakes with well-preserved partial hindlimbs prompted

me to include Chapter 8 on the fossils and work by developmental

biologists that help explain how limbs were lost in serpents.

Chapter 9 reviews the fossil evidence for the transition from

reptiles to mammals. It is an interesting segue, involving not only

modifications in thermoregulation, but also in hearing and food

acquisition and processing. Were the last mammal-like reptiles

endothermic? Did they possess fur? How does one define and rec-

ognize a mammal? Examination of the fossil record will show how

this question is answered with the fossil material available.

Chapter 10 tells the magnificent story of whale evolution that

has unfolded only in the last 20 years, complete with aquatic inter-

mediates sporting tiny hooves on their feet! In Chapter 11 we look

at the vast Cenozoic panorama of horse evolution, showing the

eventual progression of changes leading from tiny forest dwelling

ancestors to the large and speedy descendants of today. Thanks

largely to the modern work of Bruce MacFadden and Richard

Hulbert, we now can see that horses were a diverse lot, with many

experiments in both size and morphology that did not survive.

Yours truly and others have chosen to work with the fossil

history of the innocuous but ubiquitous rodents, in the hope that

the dense fossil record of these animals will reveal the secrets of

evolution, if for no other reason than that there are so many fossils

available for study. Chapter 12 provides examples of short-term

change in species, or microevolution, as well as a likely record of an

arvicolid speciation event. In the rodents we have good fossil evi-

dence for considerable morphological and size change at different


Missing Links


chronological scales. Here we can get a close-up look at how links

operate, and we see that it is often a blurry mess of related popula-

tions originating in an almost helter-skelter fashion, each with its

own set of characteristics and evolutionary trajectories. There is a ben-

efit to working with a group that has a dense fossil record.

Chapter 13 continues the stories provided by the rodent record,

this time with subterranean rodents from southwestern Kansas

known as pocket gophers, those furry animals that made life mis-

erable for Bill Murray in the movie Caddyshack. The Meade Basin

record of these rodents is unparalleled for any vertebrate animal

group in the late Cenozoic (last 5 million years), and here we see

that despite their success today, their history is replete with species

extinctions and replacements. The Kansas record also demonstrates

a significant anatomical transition, from animals with rooted to

unrooted cheek teeth (premolars and molars), the latter which char-

acterizes all living pocket gophers.

Our own heritage is taken up in Chapter 14. As with the whales

and birds, new hominids are being reported regularly. As I began

outlining this chapter for the first time, Australopithecus

bahrelhghazali was described from three to four million year old

deposits in Chad. Soon after, the amazing, diminutive Homo

floresiensis was discovered in southeast Asia, and in 2010

Australopithecus sediba was described from South Africa. It is an

exciting time in paleoanthropology, and as one might expect, there are

probably as many theories of human relationships as there are investi-

gators. There was an old joke that suggested there are likely as many

anthropologists studying hominids as there are fossils, a past testa-

ment to a lousy fossil record, but that isn’t true any more. There are

now hundreds of specimens of Australopithecus afarensis alone.

The final chapter is one that may seem unusual in a book

on missing links, but hopefully by the time the reader has made it

this far its purpose will be obvious. In this chapter I consider the

“smoking gun” of evolution; evolution in action during the life-

time of the reader as an observer. Missing links on a generational

scale, complete with the sudden appearance of new forms, ana-

tomical change, and the potential for new species.



I must first acknowledge evolutionary scientists worldwide,

whose diligent research provided the source of most of the infor-

mation in this book. I could not cite even a small part of the tre-

mendous written database supporting Darwin’s grand theory of

evolution, and I apologize to the hundreds of scientists, past and

present, whose names do not appear here.

Many of my colleagues contributed in one way or another to the

writing of this treatment. Pablo Peláez-Campomanes and the late Jim

Honey taught me everything I know about field paleontology, from

identifying likely fossiliferous sites, to stratigraphy, to field procedures

to reclaim and preserve the fossils. Ted Daeschler, Robert Carroll, J.

W. Schopf, Jim Hopson, Michael Bell, Richard Hulbert, Jr., Hans

Thewissen, Ian Tattersall, Larry Martin, Howard Whiteman, Jennifer

Clack, Alan Feduccia, Frances James, Kevin Padian, Dave Canning,

and Ed Zimmerer either reviewed chapters or provided useful infor-

mation and opinions for both editions. Thanks are also due Ian Tatter-

sall for granting permission to use some of the many outstanding illus-

trations in his book The Fossil Trail. I tried out early versions of Miss-

ing Links in my undergraduate Evolution classes at Murray State Uni-

versity, and I appreciate the help provided by Tom Timmons in mak-

ing the various accommodations necessary for this process.

Judy Hauck, a former editor at Jones & Bartlett, was the first

individual in the publishing business to get excited about Missing Links,

and I thank her and the staff at Jones & Bartlett for publishing the first

edition. The second edition owes its existence to publication by

McDonald & Woodward, and I want to thank Jerry McDonald, whose

work in paleontology I have known about for many years, for recog-

nizing the value of Missing Links and giving me the opportunity to

produce a second edition. My extended family, Marsha, Rachel, Jer-

emy, and Alice, provide constant encouragement and support, and

I also want to acknowledge my second wife, the late Linda L. Mar-

tin, for her many kindnesses and help in myriad ways.


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