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Evidence of Evolutionary Transitions

Michael Benton


All living organisms share the same family tree. This fact is backed by evidence such as:

  • Archaeopteryx, a missing link between reptiles and birds
  • mammalian hearing structure, which evolved from reptilian jawbones
  • the animals of the Galapagos, isolated from the rest of the world
  • DNA profiles of life forms, present and past

March 2001

Note: Because some of the information in this article may be outdated, it has been archived.

All life is related on the tree of life.

Fossil of Archaeopteryx bavarica from the Jurassic period. Paläontologisches Museum, München. Photograph: Luidger

One of the most startling discoveries of the past two centuries has been that all living organisms — all the millions of species of microbes, plants and animals alive on Earth today — share a common ancestry. However different an elephant, a dung beetle, an oak tree, and an AIDS virus may look, they can all be tracked back to common ancestors in the depths of geologic time. This insight was first articulated by Charles Darwin in 1859, and new lines of evidence have confirmed his discovery time and time again since then. There are two key lines of evidence:

  • missing links
  • shared characteristics
Fossils provide evidence of missing links.

The role of missing links is most difficult to understand. Surely, argue the creationists and other religious fundamentalists, if evolutionists claim that all of life is related through a single huge family tree extending from the present day back millions of years to a single point of origin, we should find fossils that are midway between established groups. ‘Where are the missing links?’ they cry. Palaeontologists have them!

Archaeopteryx- half reptile, half bird

Archaeopteryx was half reptile, half bird.

The first dramatic missing link came to light in 1861, only a couple of years after Darwin’s Origin of Species had been published. The first specimen of Archaeopteryx was discovered in a limestone quarry in southern Germany, and it was studied avidly by scientists throughout Europe. Early writers, such as Thomas Henry Huxley, immediately noticed that Archaeopteryx was an intermediate form.


Model of Archaeopteryx lithographica in the Oxford University Museum of Natural History. Photo: Michael Reeve

  • It had bird characters, feathers and wings.
  • It also had reptilian characters, the skeleton of a small theropod (flesh-eating) dinosaur, with a long bony tail, fingers with claws on the leading edge of the wing, and teeth in the jaws.

The role of Archaeopteryx has been debated ever since 1861. Is it really a missing link between reptiles and birds, or is it just a bird and not a missing link at all?

Fossils show how some reptiles became more bird-like.
  • A further seven skeletons have come to light, and all of them confirm that Huxley was correct.

  • In addition, fantastic new specimens of birds have been found in Spain and China, which are some 30 or 40 million years younger than Archaeopteryx, and they are more bird-like, exactly as an evolutionist predicts.

  • The new Spanish and Chinese birds have short bony tails, and their hand claws are reduced - they are becoming more bird-like.

  • The Chinese localities have not only produced amazing new birds, but also new dinosaur specimens with feathers!

It is now known that birds evolved from reptiles.

These new specimens clinch the argument. Archaeopteryx is no longer on its own, a single species that attests to the reality of an evolutionary transition from reptiles to birds. Below it, on the evolutionary tree, stretch countless theropod dinosaurs that become ever more birdlike through time, and above it stretch numerous bird species that bridge every step of the way from Archaeopteryx to fully-fledged birds. A long series of fossils through the Jurassic and Cretaceous periods, a span of 140 million years, document the evolutionary transition from reptile to bird.

Jaws to ears: An example of tracking missing links

Mammals can be traced back to reptilian origins.

The evolutionary route from reptile to mammal is known in just as much detail. Between the Permian and Triassic periods, mammal-like reptiles evolved from basal forms that were fully reptilian. Through dozens of intermediate steps they evolved into mammals by the Late Triassic, some 225 million years ago. All the steps are evident in fossils:

Jaws tell the story of reptile to mammal transition.
  • Step-by-step, palaeontologists can see the switch from peg-like reptilian teeth to the differentiated teeth of mammals (incisors, canines, molars).
  • Step-by-step the complex reptilian jaw, with five separate bones, changes to the mammalian jaw, with only one bone, the dentary.
  • In reptiles, both today and in the past, the jaw joint lies between the articular bone at the back of the lower jaw, and the quadrate bone in the skull.
  • In mammals, on the other hand, the jaw joint is between the dentary and the squamosal element of the skull.

Most amazing of all is the evolutionary transition to the mammalian middle ear.

  • In reptiles, as in amphibians and fishes, there is a single hearing bone, the stapes, which is simply a straight rod that links the eardrum to the hearing structures of the inner ear and the brain.
  • Mammals, including humans, have three ear ossicles (small bones), the malleus, incus and stapes (or hammer, anvil, and stirrup).

The evolutionary steps were worked out first in Victorian times by the study of mammal embryos and then the fossils confirmed it:

You hear yourself chewing because parts of your hearing structure evolved from reptilian jawbones.
  • The mammalian stapes is the same as that of their ancestors. But the malleus and incus have moved into the middle ear from their former function as the reptilian jaw joint.

  • Life is stranger than fiction: the reptilian lower jaw has been subsumed into the mammalian middle ear to enhance the hearing function.

  • And the fossils show how some Triassic mammal-like reptiles had effectively two jaw joints: the reptilian joint was reduced, and the new dentary-squamosal joint came into play.

  • At a certain point, in the Late Triassic, the reptilian jaw joint had shifted function.

  • We can still detect the legacy of this astonishing transition: when you chew a hamburger, you can hear your jaw movements deep inside your ears.

Evolutionary transitions are highly predictable.

Every day, new fossil finds are reported — the first insect, the oldest hominid, the first sauropod dinosaur, an Eocene whale with legs — and so it goes on. The new fossil finds that hit the headlines are all concrete evidence of evolutionary transitions. The fossils are rarely bizarre or unexpected; they fit into the predictions of evolutionary trees. Dinosaurs with feathers and whales with legs are pretty startling discoveries, but biologists were convinced they existed from the predictions of their evolutionary trees. But is this the sole evidence of evolutionary transitions?

The great tree of life

The single great tree of life is profound evidence for evolutionary transitions. Darwin, as he toured South America and the Galapagos Islands in the 1830s, became increasingly puzzled about the distributions of plants and animals, both geographically and geologically. He went out on the expedition as a traditional creationist. Instead, this is what he discovered:

Darwin’s observations of species relationships provided major clues to speciation.
  • He saw that the strange and wonderful plants and animals of South America were related to each other. Why should that be if they had simply been created?
  • He also saw some of the relatively recent fossils of South American mammals — the giant ground sloths and glyptodonts. Why were these fossils so obviously relatives of the modern sloths and anteaters that are unique to South America?
  • Famously, he saw that the singular animals of the Galapagos Islands were all close relatives of animals from the mainland of Ecuador, and they varied from island to island. Why?
Darwin’s answer to similarities in species: evolution.

The solution then hit Darwin like a hammer blow. The similarities in time and space were easy to explain: life had evolved. It had not been created, species by species. The Galapagos finches, tortoises, and iguanas had diverged from single ancestors that arrived by chance on the islands a few thousand or million years ago. South America had been isolated from the rest of the world, and its own unique birds and mammals had evolved through long spans of time from single ancestors. Tracking back to the very origin of life, he suggested, daringly, that all of life came from a single ancestor.

Molecular confirmation

Since 1859, that great tree has been built up painstakingly by close study of fossils and modern organisms. And then, Darwin’s speculation, and all that careful work, was confirmed from an unpredicted source — the molecules.

DNA differences among species is relative to the time they diverged on the tree of life.
  • Proteins in the bodies of all organisms, and indeed DNA and RNA, the fundamental molecules of life, carry records of evolutionary transitions.
  • Simply put, the degree of difference between the same proteins (or the DNA or RNA) in different species is proportional to the time since they split apart. So, humans have molecules that are nearly identical to those of chimpanzees, rather more different from those of cows, and very different from those of slime molds. The amount of difference is proportional to the time of divergence on the evolutionary tree.
Molecular biology confirms evolutionary transitions.

Since 1960, molecular biologists have been drawing up their own evolutionary trees, and these match those based on fossils and museum specimens of living plants and animals. The final, and most startling, confirmation of Darwin’s insight also comes from the molecular biology. All living things, from viruses to humans, from bacteria to grasses, share complex molecular machinery — the whole DNA/ RNA code of life and protein synthesis machinery and the ATP system of energy transfer.


Conclusion: Shared ancestry of all living things has been proven by molecular biology.

Evolutionary transitions are demonstrated by so-called ‘missing links’, fossils like Archaeopteryx, and the whole array of intermediates between dinosaurs and modern birds that lie on either side of it. There are thousands of other fossils that plug the gaps between modern groups that are quite separate, and new finds every year plug yet more gaps. But, the evidence for evolutionary transitions can be seen also in geographic distributions: close relatives are often found close to each other at the base of the evolutionary branch. The shapes of evolutionary trees have now been confirmed from independent evidence of molecular structures. Indeed, the fact that all microbes, plants, and animals today possess certain complex molecular mechanisms proves conclusively that all of life arose ultimately from a single ancestor billions of years ago.

Michael Benton, Ph.D., is a vertebrate palaeontologist with interests in dinosaur origins and fossil history. He holds the Chair in Vertebrate Palaeontology at the University of Bristol, UK, in addition to chairing the Masters program in palaeobiology at the university. He has written some 30 books on dinosaurs and palaeobiology, ranging from professional tomes to popular kids’ books.

Evidence of Evolutionary Transitions


Understanding Evolution

Your one-stop source for information on evolution. Learn the facts in Evolution 101, browse the resource library, read about evolution in the news, or discover a wealth of materials to help educate others about evolution and related concepts—it’s all right here!

Some excellent web sites about Archaeopteryx

Fossils and dating methods

Michael Benton wrote another article, Accuracy of Fossils and Dating Methods, for which describes how fossils are dated.

2006 missing link discovery

Read about the recent fossil discovery of a 380-million-year-old fish considered to be the missing link between fish and land animals.

Transitional vertebrate fossils

“A summary of known vertebrate fossil history in those lineages that led to familiar modern forms, with the known transitions and with the known major gaps both clearly mentioned.”

The ‘tree of life’

Provides an overview of evolution and transitional forms.

Fossil evidence in 3D

This gallery contains five modern primate crania and five fossil crania which can be rotated 360°. Each cranium is accompanied by a short description of its relevance to human evolution.

Where to see dinosaurs

The Dinosaur Society site provides a listing of where to see dinosaur exhibits worldwide. You may want to check the list when planning a trip - click on the “Exhibitions” link on the site navigation menu for more information. original lesson

This lesson has been written by a science educator to specifically accompany the above article. It includes article content and extension questions, as well as activity handouts for different grade levels.

Lesson Title: Evolution: Are There Really Missing Links?
Levels: high school - undergraduate
Summary: This lesson focuses on applying evidence for evolutionary transitions to the general theory of evolution. Students can investigate how Darwin’s finches would adapt to simulated island environments, create an exhibit of “missing links” art, market a virtual natural history museum… and more!

Download/view lesson.
(To open the lesson’s PDF file, you need Adobe Acrobat Reader free software.)

Lessons for middle school

The following links will take you to middle school lessons available on other web sites:

Useful links for student research

In addition to the links in the “learn more” section above:


  • » Benton, M. J., 2000. Vertebrate Palaeontology. Blackwell Scientific, Oxford.
  • » Eldredge, N., 2000. The Triumph of Evolution — and the Failure of Creationism. W.H. Freeman.
  • » Eldredge, N., 1998. The Pattern of Evolution. W.H. Freeman.


Understanding Science