How the whale lost its genes « Why Evolution Is True

The evolution of whales, porpoises, and dolphins—the “cetaceans”—is well understood thanks to a plethora of fossils, mostly found in recent years (for a good general summary of the data, go here). Starting from a small, deerlike artiodactyl living around 48 million years ago (Indohyus may be related to the common ancestor of whales), this evolution proceeded rapidly, with the two groups of modern whales—Odontocetes (toothed whales, including dolphins) and Mysticetes (baleen whales), diverging only about 12 million years later. In other words, in a mere 12 million years—only about twice the time since we diverged from the lineage that led to modern chimps—evolution went from a terrestrial artiodactyl to a fully marine whale. That’s surely macroevolution, however you define it, and gives the lie to the creationist claim that major transitions aren’t seen to have occurred over time. (I discuss much of the fossil evidence in Why Evolution Is True).

Here’s a diagram of the evolutionary sequence of some of the forms, and the times they appear in the fossil record, taken from the UC Berkeley site Understanding Evolution. 

During this brief period, cetacean ancestors lost their hind legs and developed a fluke, the body became streamlined for swimming, body hair was lost (not needed in a fully marine whale), the nostrils evolved backward into a single blowhole, a lot of adaptations for diving evolved, as well as the ability of the species to collapse their lungs when diving, a layer of blubber evolved, and there were many other physiological and anatomical changes. These are described in a new paper in Science Advances (click on screenshot below, pdf here, reference at bottom of the post).

But the authors are not so concerned with the well-documented morphological changes, for they wanted to see what genes had changed, in particular, which genes in the ancestors of whales had been inactivated during whale evolution—inactivated because they were of no use to fully marine mammals.

To find these genes, the authors looked at whole genomes of cetaceans (bottlenose dolphins, killer whales, minke whales, and sperm whales) and compared them to the genomes of 62 placental mammals. They found 2472 genes in cetaceans that were broken: genes having deletions, stop codons, splice-site mutations, “frame-shift” mutations, and other changes that kept these genes from being expressed. They then carved out a subset of these genes that were not inactivated in 95% of the terrestrial mammals they used for comparison, so the broken genes were largely unique to all cetaceans. That took the sample of broken cetacean genes down to 350.

They then excluded genes already known to be broken in the cetacean lineage, including olfactory receptor genes (I discuss the loss of “smelling genes” in whales in WEIT) and keratin-associated genes, most involved in hair formation.

Finally, they excluded genes known to be intact in the closest living relative of whales—the hippopotamus. This left the authors with a sample of 85 genes that were inactivated in all sampled whales (mysticetes and odontocetes) but not in their living relatives; these were presumably genes that got broken in the common ancestor of the two groups of whales, and whose broken state was passed on to all living cetaceans.

Why would a gene become inactivated in a group? Well, presumably because it’s not needed. But there are then two ways that a non-useful gene could become broken via the accumulation of inactivating mutations. First, an inactivation could be “neutral”: a gene that’s not needed and becomes nonfunctional may not have a selective advantage or disadvantage over the active form, and could eventually become “fixed” (present in all individuals in a population) via random genetic drift.

Alternatively, a broken gene could increase in frequency because it has a selective advantage over its functional competitors. That is, the non-production of a gene product could save energy that could be diverted to other functions, or it could reduce an unneeded organ or feature that could be damaged (both of these arguments have been used to explain why eyes largely disappear in cave animals who don’t “need” them). The authors posit that most of the broken genes in cetaceans accumulated by neutral processes, but it’s very hard to distinguish that scenario from an increase-by-selection argument, as this involves comparing DNA sequences and looking for a “signature of selection”: nearly impossible in such data.

But this is a side question. What’s important are two things. The first one I emphasized in WEIT:

1). The presence of nonfunctional genes in whale genomes—genes that are functional in their living relatives—is strong evidence for common ancestry of whales from terrestrial organisms and against any creationist scenario. It’s also evidence for macroevolution. You’d be hard pressed indeed to give reasons why an intelligent designer or a god would install useless genes in a genome that remain useful in the “outgroup” relatives. But this is exactly what is expected if whales evolved from terrestrial species in whose descendants those genes remain useful. But we’ve known about broken genes for a long time (e.g., olfactory genes), and IDers and creationists still can’t explain them.

2.) The broken genes give evidence about what the genes were used for in the ancestors, and why they weren’t needed in cetaceans. Thus, the authors looked at what the genes do when they’re functional, which helps tell us why they might not be needed in cetaceans. The broken genes fall into several classes; I’ll highlight just three:

a. Genes involved in blood coagulation.  When cetaceans dive, peripheral blood flow is reduced, making it more likely that damaging blood clots could form, especially when nitrogen microbubbles form in the blood (this is what causes “the bends” in divers). The authors found two genes involved in blood coagulation that were broken in whales. Like all of the broken genes, this scenario for why genes are inactivated is speculative, but can still prompt further research.

b. Genes involved in DNA repair. When tissues become short of oxygen, as when cetaceans are diving and then get a surge of oxygen later, forms of “reactive” oxygen accumulate that can damage DNA. Cetaceans have lost an enzyme, POLM, that repairs DNA, but does so by inducing many errors in the repaired DNA. Since there are other less error-prone ways of repairing DNA, the authors speculate that the loss of POLM is a way to avoid a “mutagenic risk factor” in cetaceans.  The idea is that it’s better, if you’re prone to damaged DNA from diving, to get rid of a system that repairs with errors, and rely instead on another system that repairs more slowly but with fewer errors.

c. Genes involved in melatonin biosynthesis. Whales, like ducks, sleep with only half of their brain at a time, with the other half active and awake to watch for danger and, in whales, to keep the animal swimming, surfacing, and breathing, maintaining body heat. The sides alternate over time so that the entire brain eventually gets a rest. (This shows how important sleep is, though we don’t yet know why.) Melatonin is a hormone synthesized by the pineal gland that helps keep animals entrained to daily (circadian) rhythms. The authors found that four genes involved in melatonin synthesis (AANAT, MTNR1A, MTNR1B, and ASMT) were inactive in cetaceans but not in their relatives.

The authors speculate that the loss of melatonin synthesis “helps decouple sleep-wake patterns from daytime,” as whales sleep with half their brains during both day and night. Further, since melatonin synthesis inhibits body-temperature regulation, its absence may help whales maintain their high body temperature in a chilly environment.

There were other pathways in which cetaceans showed broken genes, including those involved in transporting amino acids to the kidneys and genes expressed in the lungs, which may facilitate non-damaging lung collapse  that occurs in diving cetaceans. You can read about these in the paper; again, the reasons for their loss are plausible but speculative.

Finally, the authors looked at two other groups of aquatic mammals whose ancestors independently invaded the sea: manatees (sirenians, related to elephants and hyraxes) and pinnipeds like seals and sea lions (descended from terrestrial carnivores). Their goal was to see if there was independent “convergent” loss of similar genes between these groups and cetaceans. They found two genes, including AANAT, that were inactivated in manatees or pinnipeds, but not in their terrestrial relatives.

What does it all mean? As I said above, this paper gives further evidence for evolution in the form of dead genes, genes not needed in some groups of animals but needed (and “alive”) in their terrestrial relatives and presumably ancestors. This gives further evidence for evolution and especially common ancestry, though the evidence (even in the form of dead genes) is at this point somewhat superfluous.

More important, the work tells us what genes may have been useless—and therefore inactivated—in the ancestors of all cetaceans: genes that would be a hindrance to adapting to a fully marine way of life. Now we don’t know that the genes mentioned above were definitely inactivated because of new way of life, but the authors at least provide a suggestive but useful list for further investigation. Are these genes inactivated in all cetaceans? Do they do what they’re said to do when they’re active, and is their inactivation useful in cetaceans? This is all grist for further research.

Finally, what mechanism led to the gene inactivation? The authors posit mutation followed by the generation of “neutral” gene forms, with the inactive forms fixed in cetaceans by genetic drift:

Many of these gene losses were likely neutral, and their loss happened because of relaxed selection to maintain their function.

Well, that might be true, but such fixations of broken genes take a long time, and if they’re neutral they’re likely to keep both active and inactive forms of a gene around for a long time, especially in large populations. And why would the broken gene always be “fixed” in cetaceans rather than coexisting with the active form?

Given that the authors speculate that the loss of gene function might be adaptive in cetaceans, it seems more likely that natural selection swept the broken genes to fixation because they were adaptively superior to active genes (see above for reasons why). It’s a challenge for future work to try to determine, through DNA-sequence analysis, whether broken genes come to be fixed by positive selection or by random genetic drift due to “relaxed selection” (i.e., no selection either way on broken versus non-broken genes).


Huelsmann, M., N. Hecker, M. S. Springer, J. Gatesy, V. Sharma, and M. Hiller. 2019. Genes lost during the transition from land to water in cetaceans highlight genomic changes associated with aquatic adaptations. Science Advances 5:eaaw6671.


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