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Evidences for Evolution, Part 2b: The Whales’ Tale

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November 28, 2011 Tags: History of Life
Evidences for Evolution, Part 2b: The Whales’ Tale

Today's entry was written by David Kerk. You can read more about what we believe here.

This blog (first posted on June 28, 2010) is the third piece in a series by Darrel Falk and David Kerk. The previous entry is found here.

In our previous essay, we learned that a tree summarizing species relationships can be built using DNA information, and how we can use DNA as a “molecular clock” to date ancient events. Both of these methods have made specific predictions about the origin of whales. If evolution is true: whales are related to the even-toed hoofed mammals and should share common ancestors with them; transitional fossil forms dating from about 45 to 50 million years ago should be found which can be shown to be related to both the even-toed hoofed mammals and modern whales; whales are most closely related to modern hippos, and should share a common ancestor with them.

What other types of information might we be able to use to construct a phylogenetic tree (i.e. a family tree) of species relationships? It turns out that characteristics of body structure also can be used – for example, the presence or absence of certain bones, or the specific shapes of those bones. An advantage of using bony features is that they can be recovered from fossils, whereas DNA (with only certain limited exceptions) must come from living organisms.

We can also derive functional information from an examination of bony features. The various protrusions, bumps and knobs found on bones usually have important implications. For example, smooth rounded areas at the ends of bones allow them to fit together and move easily. The shapes of such surfaces determine which bone motions are “allowed” or “disallowed”. Consider, for example, the motion of the forearm against the upper arm at the elbow. This is a “hinge” joint, whose normal motion is defined by the shapes of the upper arm bone and one of the forearm bones, where they meet each other. You might normally exercise the action of this hinge joint when you pick up a cup of coffee, bring it to your mouth, then set it back down again. Let’s try to imagine another motion. For this exercise we first need to get our arm into the proper starting position. Place your arm at your side, bent at the elbow at a ninety degree angle, with your palm up. Now, while keeping your palm up, let’s attempt to move your arm only at the elbow (no shoulder motion – that’s cheating!). Now swing your forearm out to the side and attempt to end up with your fingers pointed directly away from your side. Most of you will not be able to do this. If you can, it’s because your shoulder is rotating in spite of yourself. This motion at the elbow is normally not allowed. Hence a careful analysis of bone shapes can allow us to infer how the bones were used. This in turn can assist us in the task of phylogenetic (evolutionary) classification of organisms. That is, we will have more confidence in the grouping together of animals in our tree diagram if corresponding bones are used functionally in the same way.

Therefore we would expect that we could use various bony features to help us examine the predictions generated by our previous look at different types of DNA data. Are there any bony features that are particularly relevant to the even-toed hoofed mammals? Well, it turns out that there are. These are mainly running animals, and there are several features of their ankle bones, which taken together define the “allowed” motions which make them efficient runners. If one takes the various ankle bones of a large group of mammals, examines them carefully to note their shapes, scores that information into a table, then uses a computer program to build a phylogenetic tree, it turns out that all the even-toed hoofed mammals are placed together. So far, so good. But what about whales? Well, now we have an obvious problem. Modern whales are very specialized, - they have flippers which correspond to the forelimbs, and they have almost no hind limbs! I say “almost” because they do have small pelvic bones, which are not attached to the rest of their skeletons. But they certainly have no ankles. This is where the fossils should come in – if evolution is true, we should expect to be able to identify transitional fossils which are ancestral to whales which contain the characteristic ankle bony features of the even-toed hoofed mammals.

Now let’s look at bony features from the whale perspective. We have already mentioned the almost complete loss of hind limbs, and the presence of forelimbs modified into flippers. In addition, as air breathers, whales have a blowhole at the top of their skull. And as powerful swimmers, which use a large tail fluke in vertical motions, whales have enormous sets of muscles which attach to enlarged projections from their vertebral column. So if evolution is true, we should begin to see fossil forms which manifest changes in bony features which correspond to the gradual accumulation of these whale-like characteristics. However, we still need more, because these various bony features all would be expected to occur in largely or exclusively aquatic forms. We might expect this to correspond to the later stages of a transition from terrestrial even-toed hoofed mammals. But what about the earlier stages? It would be very helpful if we had some “defining” characteristic of whales, similar to the ankle structure of even-toed hoofed mammals.

It turns out that the structure of the bones of the skull and ear apparatus of whales are highly modified to allow efficient hearing underwater. The mechanical aspects of efficiently receiving sound through water are somewhat different than receiving sound travelling through air. If evolution is true, we should expect to be able to find key transitional fossil forms with a progressive series of modifications of the skull and ear bones, features which would not be found in any other mammals.

Now that we know what we should expect to see, if evolution is true, let’s look at what has actually been found in the fossil record. Over the last fifteen years or so, a series of fossils, many of them discovered in the Indian subcontinent, have fulfilled nearly all of our predictions.1,2 Let’s look at the figure below (Figure 1), reproduced from a recent popular book on evolution.3 This shows a series of fossils, arranged in approximate chronological order, with a modern whale at the top. How old are these fossil forms? The entire fossil progression illustrated occurs from a little over 50 million years ago to about 40 million years ago. So a remarkable alteration in general body form occurred in a little over 10 million years. This time frame agrees well with the previous prediction from the DNA “clock” that we discussed in our previous essay. Second, the general change in body shape corresponds to what we predicted in our discussion of whale bony features above. That is, there is a gradual elongation and streamlining, there is a modification of the forelimb into flippers and progressive reduction of the hindlimb, the nostrils for breathing move toward the top of the skull to form a blowhole (not obvious from the diagram), and the vertebrae develop enlarged projections to support the attachment of swimming muscles.

Figure 1: Skeletons and Body Forms of Modern Whales and Fossil Ancestors
The reconstructed skeletons (black) from modern whales (top) and various ancestral skeletal forms (series below) are in chronological order (from Pakicetus up). Indohyus is an extinct whale “cousin”. Relative body size, to scale, is indicated by the gray shapes at the right of each animal.

There is probably little question that the last fossil species in the figure (Durodon) is well on the way to becoming a modern whale. However, it might be argued by a skeptic that the earlier species (like Rhodocetus, Ambulocetus, or Pakicetus), despite the “cetus” (whale) part of their names, are not so obviously “whale-like” that they deserve to be considered as fossil whale ancestors. However, remember the characteristic whale skull modifications for hearing? It has been shown very clearly that throughout this series of fossil species, the various bony changes necessary to support efficient hearing in water were being acquired in a stepwise fashion. Organisms earlier in the sequence had skeletal characteristics consistent with them being able to hear well in both air (using the “classic” mammalian hearing apparatus), and newly acquired changes to also allow better hearing in water. Later organisms in the sequence become increasingly specialized for hearing in water only.4

What of the earliest fossil shown in this diagram –Pakicetus? Careful examination shows that it has the features we would predict for an early whale ancestor. It has the ankle bone characteristics of the even-toed hoofed mammals (in fact these features are also found in several of the later fossil forms as well, ensuring their continuity). This confirms one of the predictions made by the DNA evidence we discussed earlier. Furthermore, it has some of the modifications of the skull bones necessary for more efficient underwater hearing, which were previously documented only for modern whales and their later (more obvious) ancestors.4 These features are also shared with the “whale cousin” Indohyus.5 Preservation of more of the skeleton of this latter species has allowed detailed analysis indicating characteristics likely shared with whale ancestors. Indohyus was probably a wading animal, which spent much of its time in the water. It appears to have fed mostly on land, so it is suggested that resort to the water was made to escape predators.5

Finally, we need to look back at the last prediction from our previous DNA evidence, namely that modern whales are most closely related to hippos. If evolution is true, we should expect to find fossil forms linking these two modern groups. This has proven to be a tougher nut to crack, mainly because the ancestral whales first appear about 50 million years ago in what is now south Asia, and the hippo family first appears about 15 million years ago, in Africa. The most recent tree diagram, produced by using a combination of skeletal features and DNA data, still supports this family connection, as shown by the following figure (Figure 2).6

Figure 2: Phylogenetic Tree Showing the Relationship of Modern Whales to Living and Extinct Even-Toed Hoofed Mammals
This tree is based on both bony features and DNA data. The organisms presented in blue are semi-aquatic or aquatic forms. Organisms shown in green are terrestrial even-toed hoofed mammals (Artiodactyls). In black is shown a member of the odd-toed hoofed mammals. In red is an extinct fossil ancestor group. (This figure is adapted from Fig 1a in Reference 6).

The blue lines in the diagram show species in which the skeleton is specially thickened, and the bone structure more dense. This is an adaptation which allows wading animals (like modern hippos and the fossil Indohyus) to be good “bottom-walkers” (it prevents them from floating due to lighter body tissues), and allows fully marine organisms (like modern whales) to have “neutral buoyancy” (so they don’t always tend to pop up to the water surface, like a cork). There has also been progress in clarifying the relationships between fossil ancestors of hippos and those of modern whales. A recent study of hippo evolution, based only on skeletal characteristics, has conclusively shown that the hippo family are descended from an extinct group of fossil Artiodactyls, known to go back more than 40 million years, and whose fossils are from southern Asia. Furthermore, this study produced a phylogenetic tree predicting that this extinct hippo ancestor group also shared a common ancestor with the fossil whales.7 Thus the investigation of hippo origins is independently leading us back toward the origin of whales. However, in this study the statistical support for predicted common ancestor of the ancient hippo group and the ancient whale group is not as strong as scientists would like to consider this “case closed”. What is necessary is more fossils, of the appropriate age in order to complete the story of hippo evolution. We still need that to fill in the details of the predicted relationship of hippos to modern whales.

Thus the “Whales’ Tale” is not yet complete. It is a story of scientific discovery in progress. As we finish, let’s briefly summarize what we have found out. Different types of DNA evidence agree that modern whales are most closely related to the even-toed hoofed mammals, despite the obvious great changes in limb anatomy of the modern whales. This prediction has been amply confirmed by the fossil record. The DNA sequence evidence predicted a time frame during which critical early events in evolution of whale ancestors should occur. This prediction has also been amply confirmed. Finally, DNA evidence predicts that modern whales are most closely related to hippos. There is some fossil evidence supporting a predicted common ancestor, but more data is needed. A final caution to possible sceptics – this state of “unfinished business” is precisely how the scientific process works. There is no “crisis”. There is no indication that evolution is not true. There is simply the ongoing work of mapping out of various lines of evidence. A scientific conclusion is considered well supported if “all roads lead to Rome”. In the case of whale evolution it might be prudent to say that the evidence has not quite converged in Rome yet, but that we are now in the suburbs. That is precisely what makes science interesting and fun. Stay tuned!

The next blog in this series can be found here.


1: Thewissen J.G.M., Williams E.M., Roe L.J. and Hussain S.T. 2001. Skeletons of terrestrial cetaceans and the relationship of whales to artiodactyls. Nature. 413: 277-281.

2: Gingerich P.D., ul Haq M., Zalmout I.S., Khan I.H., Malkani M.S. 2001. Origin of Whales from Early Artiodactyls: Hands and Feet of Eocene Protocetidae from Pakistan. Science. 293:2239-2242.

3: Coyne, J.A. 2009. Why Evolution is True. Viking Penguin, New York. Pg 50.

4: Numella S., Thewissen J.G.M., Bajpai S.,Hussain T., Kumar K. 2007. Sound Transmission in Archaic and Modern Whales: Anatomical Adaptations for Underwater Hearing. The Anatomical Record. 290:716-733.

5: Thewissen J.G.M., Cooper L.N., Clementz M.T., Bajpai S., Tiwari B.N. 2007. Whales originated from aquatic artiodactyls in the Eocene epoch of India. Nature. 450:1190-1194.

6: Geisler J.H. and Theodor J.M. 2009. Hippopotamus and whale phylogeny. Nature. 458:E1-E4.

7: Boisserie J.-R., Lihoreau F., Brunet M. 2005. The position of Hippopotamidae within Cetartiodactyla. Proceedings of the National Academy of Sciences U.S.A. 102(5):1537-1541.

David Kerk is Professor of Biology, Emeritus, at Point Loma Nazarene University. Dr. Kerk obtained his PhD in Anatomy at UCLA and is currently involved in bioinformatics research at the University of Calgary. He resides on Vancouver Island, in Parksville, B.C. Canada.

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Bilbo - #66290

November 28th 2011

I have no problem accepting the mainstream view of whale evolution, however, a recent video has raised doubts (for me, at least) about a good deal of the fossil evidence:


Ashe - #66301

November 29th 2011

Strange (or predictable) that they never mention the fossil evidence of the blow hole in transition:

Rodhocetus and Ambulocetus and Pakicetus appear to have been desman-like. The pelvis of Rodhocetus was similarly large to that of land mammals and earlier fossils, and  it was still connected to the sacral vertebrae, meaning that Rodhocetus could still support its weight on land. The ilium of the pelvis was short compared to that of the mesonychids, which is characteristic of mammals that use their hind limbs for swimming rather than walking, and the femur was about 1/3 shorter than Ambulocetus’s because the body size of Rodhocetus is smaller.

Bilbo - #66303

November 29th 2011

Hi Ashe,

You’re right, they don’t discuss the evidence of the blow hole, but they do discuss the fact that Ambulocetus is no longer considered an ancestor of whales, and that there is no evidence that Rodhocetus had a fluke or flippers.  Was it even aquatic?

Ashe - #66307

November 29th 2011

Unfortunately, the creationist video succeeded in persuading you that an off-hand comment by Gingrich expressing some doubts about Ambulocetus being on the “main line” of whale evolution means that it’s no longer considered an intermediate. That’s simply not true, Gingrich still considers it a protocetid. 

We have nearly the entire hind limb for Abmulocetus, pelvis, femur, parts, of tibia, and fibula, some of the tarsals, all four metatarsals, and a number of phalanges. It is quite clear that the animal could support its weight on land. The limbs are a compromise between land and water locomotion, they are suited for both, but not great at either. 

The fluke bit is a red herring, it’s clear from the post above (and my discussion)  that Ambulocetus and Rodhocetus are about 50% of the way to being fully aquatic. These are what is called “semiaquatic” mammals, but retained little ability to walk on land. 
Ashe - #66308

November 29th 2011

err not protocetid, but on the spectrum from fully terrestrial artiodactyl ancestors at 55 million years ago to fully aquatic archaeocete whales. 

Bilbo - #66332

November 30th 2011

Gingerich’s exact words about Ambulocetus:  “...may be on a slight sideline…maybe not on the mainline [of whale evolution].”

As far as Rodhocetus, is it well-known that it lacked flippers and fluke?  Or is it just as “predictable” that most evolutionists won’t be informed about this?

Ashe - #66336

November 30th 2011

Regarding the mainline/sideline issue here’s a link that explains what I was trying to say a bit more simply, even if it’s true that ambulocetus may be on a “slight sideline”:

Look at warning 2.

Regarding Rodhocetus, “evolutionists” have known that it lacks well preserved fluke for years:

“Terminal caudals are lacking in the type specimen  of Rodhocetus and we cannot assess the possible presence of a caudal  fluke, but it is reasonable to expect development of a fluke to coincide  with shortening of the neck, flexibility of the sacrum, and reduction of  hind limbs, first observed in Rodhocetus.  This idea can be tested when a more complete tail of Rodhocetus is found.”

Nature, Volume 368, 28 April 1994, pages 844-847:

Bilbo - #66405

December 3rd 2011

A recent find of a whale jawbone that seems to date to 49 million years ago reduces the time span for whale evolution from 15 million years to 4 million years.  I think the jawbone even predates Ambulocetus:


BTW, when did they stop drawing pictures of Rodhocetus with fluke and flippers?

Bilbo - #66406

December 3rd 2011

According to this article, ambulocetus was 48 million years old:


Ed Babinski - #66761

December 23rd 2011

Hi Bilbo, Do you remember the days when Duane T. Gish used to lecture
for the Institute for Creation Research on the impossibility of whale
evolution by showing a slide of a cow turning into a caricature of a
cow-whale and saying, “Udderly ridiculous?” Those days were so much
simpler for creationists. The fossil record of early cetacea was nil or
practically nil back then. Then Gish denied the relevancy of some of the
earliest cetacean fossils with long spines and tiny rear feet by
claiming they were sea-reptile fossils until it was pointed out to him
that they were indeed mammalian fossils, cetacean fossils in fact, not
reptilian. Today there’s more early cetacean fossils known than ever
before. Do you know why? Because some geologists got curious and studied
the places in the world where the rock was exposed during the time when
early cetacean evolution supposedly took place, and where some
relatively shallow seas once existed—as evidenced by what was known of
such formations geologically and based on what other fossils were known
to be found there.  So the geologists got some funding and went to those
sties to look for early cetacean fossil remains. And lo, they found
them, as the previously gained geological and radiometric analysis had
directed them. They looked for the niche in geologic time and the
formations most likely to be examined, which were exposed. That’s also
how geologists found the first mammal-like reptiles, and the earliest
known amphibian-like fish. The geologic record led geologists to those
fossil discoveries.

Ed Babinski - #66762

December 23rd 2011

Besides such early cetacean fossils one may note photos showing hind
limb buds on cetacean embryos, along with documented cases of adult
cetacea with hind limb remnants. And there’s fossil evidence of nasal
drift from the tips of ancient cetacea to the middle to the top of their
heads over time. In fact some species of cetacea still have two blow
holes on the tops of their heads, reminiscent of the the two nostrils
their ancestors once had. Their two blowholes have not yet merged into a
single blowhole. Neither do the earliest cetacea fossils show evidence
of echolocation features in their skulls that are only found in some
branches of more recent species of cetacea. In other words that type of
specialization occurred over time, and only in some branches of cetacean

Also, is it really worth your time haggling over exactly which species
gave rise to which species of cetacean since no evolutionist nor
geologist believes that each individual cetacean laid down and died and
was fossilized directly on top of its immediate ancestor. To quote Carl
Zimmer, “Life doesn’t proceed from one point to another—it forks and
like the cladograms that represent it. Paleontologists have found many
other whale bones in Eocene rocks of Pakistan and India. Mostly they are
teeth—the rock surrenders a few skulls as well—but even teeth
clearly show that their owners were not clones of Pakicetus or the other
better-known whales. Ambulocetus kept to brackish deltas and coastal
water, but Thewissen has found whale teeth from about the same age in
what at the time was the open ocean. Gingerich has found at least three
contemporaries of Rodhocetus a few million years younger than
Ambulocetus: Takracetus, with a wide, flat head; Gavinocetus, with a
slender skull and loose hips; and Dalanistes, a whale with a head as
long and narrows as a heron’s set on a long neck, with hips cemented
firmly enough to its spine to walk on land. If this is a confusing
picture, it should be. As time passed, certain whale species emerged
that were more and more adapted to life in the water, but other species
simultaneoulsy branched away in many directions. Walking and swimming
whales lived side by side, or in some cases traded homes as the buckling
birth of the Himalayas shuffled their habitats. Some were only a minor
variation on a theme that would carry through to modern whales, but
others—heron-headed Dalamistes, for example—belonged to strange
branches unilke anything alive today.” Carl Zimmer, At the Water’s Edge

The point however is that there used to be species that walked on land
with four legs that had early cetacean-like skulls, and other species
more adapted to the water, and still others later on with smaller hind
limbs still intact that were adapted to living their whole lives in the
water, to today’s species that lack hind limbs entirely but who have
hind-limb buds that show up in their embryos briefly and sometimes such
hind-limb remnants show up in adults as well. The outline of whale
evolution has been filled in to a greater extent than Duane T. Gish
could have imagined, and instead of being an “impossible” evolutionary
progression its general outlines are more than visible. The “udderly
ridiculous” cow-whale is no longer a center piece exhibit for the
“impossibility” of evolution. Instead it’s the creationists and even the
I.D.ists on the defensive, attempting to deny the obvious outline by
quote-mining piccayune points.

Ed Babinski - #66763

December 23rd 2011

And I haven’t even discussed the outline of sirenian evolution (sea
cows, dugongs, that still have toenails on their flippers and some of
their fossil ancestors having the same skulls but with complete hind
limbs). Or photos showing rudimentary pelvis and hind limb bones in the
embryos of snakes. Or species of feathered dinosaurs that existed prior
to the time of the earliest known bird fossils showing that feathers
preceded birds. Or the fact that even young-earth creationists now admit
that numerous genuine early hominid fossils such as homo erectus have
been discovered (such finds are not flukes); and the genetic evidence
for chimpanzees being our cousins is a genuine difficulty for those who
deny common ancestry (as a creationist biologist at Bryan College

James R - #66892

January 1st 2012

For those who are interested, here are links for some videos in which difficulties with the standard whale evolution scenario are discussed by a specialist in evolutionary biology:



melanogaster - #66900

January 2nd 2012

Does your specialist have a PhD from a top-flight university?

Does your specialist have a long record of highly-cited publications?

Does your specialist have a faculty position?

Or does your specialist just say things you wish were true?
James R - #66906

January 2nd 2012

Oh, he has two Ph.D.s in evolutionary biology, and quite a few peer-reviewed publications.  As for where he got his Ph.D., it seems to me that not very long ago, there was someone here named “John” who purported to be a top research scientist.  He was quite scornful of the idea that it mattered where one did one’s Ph.D., or who one worked under.  He said that all that mattered was the quality of the research published after the Ph.D. was finished.  I guess you disagree with “John,” since you seem so concerned about where or by whom a researcher was trained.

As for a faculty position, again, I think that you would have disagreed with “John,” who represented himself as not having a faculty position, but instead as being a researcher at a major biological/medical institute.  “John” certainly did not believe that having a faculty position was necessary to being a good scientific specialist.

So who should we believe about what is important, you or the illustrious “John”?

By the way, why did you change your pseudonym from S. cerevisiae to melanogaster?  A new look for the new year?  Or does the transformation from yeast to fruit fly symbolize an “evolution” of some kind? 

melanogaster - #66914

January 3rd 2012


Of course, you know why I specified a top-flight university. It’s because that was what you specified in the other page when promoting Wells as an authority in a subject in which he has zero training or experience. 

Of course, you know that von Sternberg’s degrees are from places no one has heard of, so it appears that the university from which one earned a degree is of no importance to you when you are promoting von Sternberg.

As for publications, my question specified highly-cited publications. He doesn’t have any.

So the question is not why I might disagree with someone else, but why you disagree with yourself.
James R - #66923

January 3rd 2012

melanogaster/S. cerevisiae:

I didn’t catch your reference to previous comments of mine, and was simply replying to what you wrote as if you meant it; but now I see you were trying to employ a dialogical trap.  Come to think of it, that’s the sort of thing “John” used to do.  Maybe you would get along with him fine after all.  Too bad for you he’s gone.  (I notice that he vanished just after expressing strong opinions in bioinformatics, which was not his self-described research field, and being more or less pummelled by a rising young scientist whose field was precisely that.  Whether there was a causal relationship between the pummelling and the departure, I leave for others to conjecture about.)

I don’t see why a publication has to be highly cited in order to be of high quality.  Far more is published than anyone has time to read, and many excellent articles and books go relatively uncelebrated.

I actually didn’t promote von Sternberg.  I simply indicated that one could find his opinions expressed in the linked media.  My indication that he was a specialist in evolutionary biology was probably due to the fact that most people who post strong opinions on evolutionary theory on the internet (including some columnists here) aren’t themselves specialists in evolutionary biology, but geneticists or cell biologists or something else (physicists, computer scientists, pastors, etc.) with a hobbyist’s interest in evolutionary biology.  I just wanted to let people know that at least one evolutionary biologist had expressed an alternate view to the one expressed in the column above.  People can listen to both sides and make up their own minds.  Do you object to that?  Or would you prefer that von Sternberg’s work be censored or hidden from view?

Ashe - #67481

February 1st 2012

I still haven’t seen anything but press releases about the new Antarctic whale, strange—it doesn’t seem to fit with everything else we know about early whale evolution so I am skeptical about its interpretation.  Normally people release information to the press timed with a formal publication describing the science behind the press release.  

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