Whale Evolution: Theory, Prediction and Converging Lines of Evidence

| By on Letters to the Duchess

This article was originally posted as a short series in March of 2012. 

Evolution: just a theory

One game that my (young) children like to play is a guessing game where both players select a character from among many choices, and by process of elimination, tries to guess the character the other has selected. Questions like “does your character have red hair? glasses?” etc., are used to narrow down the possibilities. Once you have guessed correctly which character your opponent has selected, you can perfectly predict the answer to every question thereafter (and a good many parents likely prolong the questioning to keep the hopes of victory alive for their children). When considered separately, the individual features of each character—glasses, brown hair, purple hat, and so on—mean almost nothing, since they could be features shared with other characters in the game. Only the convergence of multiple features is indicative of a good guess, and the accuracy of that guess is put to the test every time a new question is asked.

A good theory is something like this: an educated guess, based on and consistent with all past work on the topic to date. It allows you to predict how future tests should pan out. In the guessing game, there are limited options to choose from (so the analogy, like all analogies, eventually breaks down). In science, we don’t really know the true way things actually work. What we have are theories—broad explanatory frameworks supported by experimentation, that make sense of our current collection of facts—that we can use to make testable predictions about the natural world. All theories in science are provisional in that they are not complete descriptions of how the world actually works and are subject to future revision; but at the same time they are robust frameworks that can be used to predict how experiments should behave with almost boring regularity. So, far from the colloquial usage of “theory” as speculation, “just a theory” is high praise in science.

The current understanding of evolutionary theory in all its scope and diversity is far more complex than Darwin himself could have ever envisaged. (As a geneticist, I’ve often wished I could have a cup of tea with him to show him how far his theory has grown, especially given his confusion about how heredity worked.) Our understanding of how evolution works has grown by leaps and bounds since the 1850s. What is remarkable is just how much Darwin got “right” given his time and place. His main hypotheses—that species descend from ancestral forms through descent with modification, that and natural selection acting on heritable variation is a significant force in that process—remains the core of modern evolutionary theory. We’ve added a lot of detail since then (population genetics, kin selection, neutral evolution/genetic drift, symbiosis, horizontal gene transfer, molecular exaptation, and so on), but Darwin’s core ideas have produced a wealth of successful predictions. They were a very good “guess” that continues to pay rich scientific dividends.

Whale evolution: an example of converging lines of evidence

One of the things I personally find quite enjoyable about evolutionary theory is the counter-intuitiveness of some of the predictions it makes. One example that is a personal favorite, and one I often use to illustrate how evolution makes sense of converging lines of evidence, is cetacean (whale) evolution. Let’s set up the “problem” that evolutionary biology forces upon us:

  • Modern cetaceans are mammals – they nourish their young in utero through a placenta, give birth to live young, and feed newborns with milk – all features of standard mammalian biology.
  • Mammals are tetrapods – organisms with four limbs. Mammalian life shows up in the fossil record as an innovation within tetrapods, so mammals are “nested within the set” of tetrapod forms. Not all tetrapods are mammals (amphibians, for example) but all mammals are tetrapods.
  • Tetrapods are by and large terrestrial creatures. Having four limbs for locomotion is a distinctly land-based adaptation.

The “problem”, of course, is that modern whales are emphatically not terrestrial, nor do they have four limbs – they have two front flippers and a tail, with no hind limbs in sight. Yet they are mammals, which forces evolution’s hand as it were. Evolution thus is dragged, under protest, to the prediction that modern whales, as mammals, are descended, with modification, from ancestral terrestrial, tetrapod ancestors. Instantly this prediction raises a host of uncomfortable questions: where did their hind limbs go? How did they acquire a blowhole on the top of their heads when other mammals have two nostrils on the front of their faces? How did they transition to giving birth in the water? What happened to the teeth of the baleen whales? What happened to the hair characteristic of mammals? And so on. In some ways, evolutionary thinking about whales creates more difficulties than it appears to solve.

And yet, these difficulties are the stuff of science. If indeed our “educated guess” of terrestrial, tetrapod ancestry for whales is correct, the evidence will show that these transitions, challenging though they may seem, did indeed occur on the road to becoming “truly cetacean.”

Going out on a limb

Anyone who has seen a modern whale skeleton in a museum and noted it carefully may have noticed that though whales lack hind limbs, they do have a bit of bone back there where the hind limbs ought to be. While this is suggestive of a vestigial characteristic (a feature in a modern organism that has a reduced role relative to the role the structure played in an ancestral species), it’s hardly a smoking gun for evolution. Still, it’s consistent with the idea.

When we look at the cetacean fossil record, we also see forms suggestive of a progressive loss of hind limb function and structure over time, as David Kerk and Darrel Falk have elegantly explained before. Again, if one were resistant to evolutionary explanations, it would be possible (if a bit strained) to interpret these creatures as having been created directly as we find them in the fossil record. The facts that we do not see these forms in the present day, and that they seem to blur the distinctions between terrestrial tetrapods and whales might make one a bit uncomfortable, however.

Recent work on cetacean embryogenesis (how whales and their relatives develop from fertilized eggs into fully-formed baby whales) has shed even more light on the issue for modern species, however. Dolphin embryos actually have four limbs early in their development, as well as a few facial hairs, just as any good mammal should have. The hind limbs and hairs are lost later in development, and work on the molecular signaling events that halt hind limb growth and cause the limb bud to regress into the body wall have now been worked out in some detail. Moreover, early in dolphin development the nostrils are distinct and on the front of the face, and only fuse into a blowhole and migrate to the top of the head later in development. Early dolphin embryogenesis is distinctly mammalian and uncannily tetrapod-like.

… and passing the test

Taken in isolation, these facts about whales are interesting trivia. Taken together, however, they begin to form a picture entirely consistent with the prediction that modern whales are derived from terrestrial ancestors. The true strength of evolution as a scientific theory for the origin of whales is this: not that we can prove it (for no theory is ever proven in science due to its permanently provisional nature), nor that we have full access to every bit of data we would like (consider how fragmentary the fossil record is, for example), but rather that we haven’t been able to disprove it yet, despite our best efforts. Descent with modification remains a productive educated guess that grows stronger with each investigation.

Evolution: A Theory with Bite

If indeed modern whales are descended from ancestral, four-limbed, terrestrial ancestors, then those ancestors, like mammals in general, had teeth. Modern toothed whales (order Odontoceti) have retained those teeth to the present day, but baleen whales have adopted a new way of life as filter-feeders. Researchers were curious to see if traces of a “toothed past” could be found in the genomes of modern baleen whales, so they went hunting for remnants of genes devoted to making teeth. Such defective gene remnants would be examples of pseudogenes, and we have discussed pseudogenes previously in this series. While pseudogenes in and of themselves are powerful evidence for evolution, pseudogenes that are “out of place” are especially so. One such example we have seen before is the human vitellogenin pseudogene, the remains of a gene used for yolk production in egg-laying organisms found in the exact location in the genome that evolution would predict for it. As mammals that receive embryonic nourishment through a placenta, we have no need of egg-yolk genes. Similarly, baleen whales have no need for genes responsible for making teeth, and finding the remnants of such genes would make a strong case for an evolutionary origin of baleen whales as the modified descendents of toothed whale ancestors.

Independent Lines of Evidence, but Contradictory Stories?

Some of the genes known to be used in all mammals for tooth formation were the obvious candidate genes to start with: the products of the ameloblastin, amelogenin, and enamelin genes are all used in the formation of tooth enamel, the hardest structure in the vertebrate skeleton. Researchers went looking for these genes in several Mysticete (i.e. toothless whale) species. The results showed that all the species studied did indeed have these three genes present as pseudogenes (and more specifically, as unitary pseudogenes, a special class of pseudogene we have discussed in detail previously). Finding these genes as pseudogenes in toothless whales was exactly what evolution predicted, but there was a catch: none of the mutations that removed the functions of these three genes were shared between different species, suggesting that these genes lost their function independently in the species studied. This finding was at odds with data from the fossil record, which suggested that teeth were lost only once, and early in the lineage leading to all modern toothless whales. So, the researchers seemed to have two lines of evidence that at face value contradicted each other. The fossil record suggested that tooth loss occurred once in the common ancestor of all toothless whales, but these three genes seemed to have been inactivated independently, several times over, suggesting that loss of teeth should be happening later in Mysticete evolution, and more than once.

One proposed explanation for the apparent discrepancy (among several put forward) was to predict that a fourth gene required for enamel formation was lost early in Mysticete evolution. The loss of any one gene necessary for forming enamel would be enough to prevent the process altogether. In this case, the loss of this fourth gene would prevent tooth enamel from forming, even though the genetic sequences of the other three enamel genes would still be intact. Once enamel function was lost, random mutations in the remaining enamel genes could then accumulate later in Mysticete evolution after speciation in this group was already underway. To test this hypothesis, the research group went hunting for other enamel genes in toothless whales.

Signature in the SINE

The smoking gun for tooth loss in Mysticetes turned out to be exactly what was predicted: a fourth gene, necessary for enamel production, and mutated with the same inactivating mutation in all modern toothless whales. The gene in question, named enamelysin, was destroyed when a mobile genetic element called a SINE transposon inserted into it, breaking it into two halves and removing its function:


The fact that the same SINE insertion mutation at an identical location is found in all modern Mysticete species indicates that this mutation happened once in a common ancestor and then was inherited by the entire group. Since this must have occurred early in the evolution of toothless whales in order to happen in the common ancestor of the entire group, the picture from the genetics and the fossil record match. Once again, findings in one discipline (in this case, paleontology) can be used to make very detailed predictions about what another, unrelated discipline (comparative genomics) should reveal. These results are also entirely consistent with the observation, made in the 1920s, that toothless whales form tooth buds during embryogenesis that are later reabsorbed prior to the point when the deposition of enamel would begin. As with the hind limb story in whale evolution, lines of evidence from genetics, paleontology and embryology converge to support the hypothesis that modern toothless whales descend, through modification, from toothed ancestors.

From nostrils to blowhole, and other details

Numerous whale species in the fossil record support the notion that the nostril-to-blowhole transition arose slowly. Earlier whales in the fossil record have nostrils at the tip of their snouts, and several later species are known with nostrils progressively further back on the skull. Some of these species have been discussed here previously and provide some “snapshots” of the process over large spans of time.

In addition to these observations, embryology yields still more clues. During early embryogenesis, modern cetaceans look like a typical mammalian embryo: four limb buds (as we have discussed previously) with distinct digits visible, a tapering tail that extends past the anal opening (the characteristic mammalian “post-anal tail”), and two nares (the technical term for nostrils) on the front of the face. Indeed, one would be hard-pressed to distinguish whale embryos from other mammals at this point, even humans, unless one knew about small differences to look for. Later in development, however, things are markedly more whale-like: the digits are no longer discernible in what are now clearly flippers, the tail is no longer slender and tapered but is developing projections that will become flukes, and the nostrils have migrated to the top of the head to form a blowhole. Taken together, paleontology and embryology provide independent lines of evidence that these features arose over time as gradual modifications to a more typical mammalian body plan.

Dolphin embryos show hindlimb buds in early stages of development.


Giving birth: from land to water?

One area of whale evolution that remains less understood is the transition from birth on land (the ancestral state, since whale ancestors are terrestrial) to birth in the water. One key difference between cetaceans and land-dwelling mammals is giving birth tail first, instead of head first. The discovery of one early whale, Maicetus, has provided evidence that early amphibious whales retained land-based birthing, though this interpretation has be challenged by other experts in the field. The evidence comes from one fossil specimen that appears to have a near-term fetus positioned for head-first birth inside it. While the evidence is suggestive and intriguing, other interpretations have been put forward (such as the possibility that the second, smaller skeleton was actually a recent meal, and not a fetus). Future work, with additional specimens, will hopefully shed more light on this issue.

Et tu, Homo Sapiens?

While these posts have used whale evolution as an example to illustrate the predictive power of evolution and the converging lines of evidence that support it, human evolution stands on an equally strong footing. From genome comparisons, to shared pseudogenes, to embryology (did you know you once had a post-anal tail, for example?) to the abundant fossil record of transitional forms that blur the distinctions between humans and other primates, these and other converging lines of evidence continue to support human evolution—and cause consternation for anti-evolutionary approaches.

The scope of the evidence and the challenge for Christian anti-evolutionism

As we have seen, the strength of evolution as a scientific theory does not rest in any one piece of evidence, but rather in the numerous pieces from multiple disciplines that fit together in a cohesive way, mutually reinforcing one another. One aspect of Christian anti-evolutionary materials that I find frustrating is that the broad sweep of evidence for evolution is avoided in favor of focusing in on specific, isolated details in an attempt to refute them individually. This approach fosters the misleading impression that evolution, as a theory, stands or falls on the interpretation of small experimental details. In reality, evolution as a theory is supported by a vast array of data from many independent fields, and any attempt to refute evolution will fail scientifically unless it addresses that vast array. As such, Christian anti-evolutionary approaches do not offer a significant scientific challenge to evolution. Rather, they merely create an impression of evolution that does not do justice to its true strength.

If Christian groups wish to supplant evolutionary theory with a different approach they feel is more consonant with their theistic convictions, the challenge is to offer an explanatory framework that is more useful to scientists than evolutionary theory. To date, all such models offer scientists less that is scientifically useful, not more. The reason Christian anti-evolutionary approaches are absent from the mainstream scientific literature is not because scientists are theologically or philosophically biased against them, but rather because they offer little in the way of useful tools for making accurate predictions about the natural world. Scientists are pragmatists, by and large: they go with what works. Evolution, as a theory, has worked, and worked exceptionally well, for over 150 years—a fact that even scholarly young-earth creationists concede. Any contender for its place as an explanatory framework in biology will have to work even better, while also accounting for everything evolution already explains so well. That’s a tall order for any model, and one that, to date, anti-evolutionary approaches have not come close to fulfilling.




Venema, Dennis. "Whale Evolution: Theory, Prediction and Converging Lines of Evidence"
https://biologos.org/. N.p., 26 Dec. 2017. Web. 19 January 2018.


Venema, D. (2017, December 26). Whale Evolution: Theory, Prediction and Converging Lines of Evidence
Retrieved January 19, 2018, from /blogs/dennis-venema-letters-to-the-duchess/understanding-evolution-theory-prediction-and-evidence-1

References & Credits

Further reading

J. G. M. Thewissen, M. J. Cohn, L. S. Stevens, S. Bajpai, J. Heyning, and W. E. Horton, Jr. (2006). Developmental basis for hind-limb loss in dolphins and origin of the cetacean bodyplan. Proceedings of the National Academy of Sciences 103 (22), 8414–8418. available freely online.

Meredith, R.W., Gatesy, J., Cjeng, J., and Springer, M.S. (2011). Pseudogenization of the tooth gene enamelysin (MMP20) in the common ancestor of extant baleen whales. Proceedings of the Royal Society B: 278 (1708); 993 – 1002. Available online: http://rspb.royalsocietypublishing.org/content/early/2010/09/16/rspb.2010.1280.full.pdf

Ridewood, W.G. (1923). Observations on the skull in foetal specimens of whales of the genera Megaptera and Balaenoptera. Philosophical Transactions of the Royal Society of London B: 211; 209 - 272. Available online: http://rstb.royalsocietypublishing.org/content/211/382-390/209.full.pdf

Gingerich PD, ul-Haq M, von Koenigswald W, Sanders WJ, Smith BH, et al. (2009) New Protocetid Whale from the Middle Eocene of Pakistan: Birth on Land, Precocial Development, and Sexual Dimorphism. PLoS ONE 4(2): e4366. Available online.

The Digital Library of Dolphin Development

Bajpai S, Thewissen, JGM, and Sahni, A (2010) The origin and early evolution of whales: macroevolution documented on the Indian Subcontinent. J. Biosci 34 (5); 673 -686.

About the Author

Dennis Venema

Dennis Venema is professor of biology at Trinity Western University in Langley, British Columbia and Fellow of Biology for BioLogos. He holds a B.Sc. (with Honors) from the University of British Columbia (1996), and received his Ph.D. from the University of British Columbia in 2003. His research is focused on the genetics of pattern formation and signaling using the common fruit fly Drosophila melanogaster as a model organism. Dennis is a gifted thinker and writer on matters of science and faith, but also an award-winning biology teacher—he won the 2008 College Biology Teaching Award from the National Association of Biology Teachers. He and his family enjoy numerous outdoor activities that the Canadian Pacific coast region has to offer. 

More posts by Dennis Venema