If you were asked what kinds of animals a whale most resembles, what would you say? Fishes? Sharks? Manatees? Perhaps even seals and sea lions? Whales live their whole lives in the water, and have a host of anatomical and physiological features that make them feel right at home there. So if DNA encodes these characteristics, you might think that whales should have DNA most similar to other aquatic animals.
Yet evolutionary biologists have long suspected that whales descended from land mammals. Whales are classified as mammals, having hair (albeit not much) and producing milk for their young, and nearly all other mammals are land dwelling. But is there any more evidence of this idea? Indeed, paleontologists have uncovered fossils that seem to document a transition from land dwelling whale-like mammals to fully aquatic whales. The distribution of these fossils further suggests that these mammals were geographically restricted until they made the plunge into water. Developing whale embryos even have tiny hindlimb buds that eventually disappear, implying that these beasts still retain some of the genetic machinery to produce four limbs.
So if fossils and developmental biology seem to be telling the same story, what does DNA say? To the initial surprise of paleontologists, whales have DNA that is extremely similar to even-toed hoofed mammals (artiodactyls), so-named because they always have an even number of toes. This group include animals like cows, deer, giraffes, hippos, pigs and camels.
In fact, whales aren’t just genetically similar to these mammals, they are genetically nested within them. By this I mean they are more genetically similar to some hoofed mammals than these hoofed mammals are to each other.
You can see this in the phylogeny below coming from a study [1] that compared 164 different species of mammals using 35,603 letters of DNA. Whales, indicated in part by paintings of a humpback and sperm whale near the middle of the figure, are most genetically similar to hippos (Hippopotamidae), a perhaps unsurprising finding given the semi-aquatic nature of the latter animals. The next closest group includes a batch of other hoofed mammals such as giraffes (Giraffidae; indicated by the okapi painting), deer (Cervidae; also associated with a painting), as well as cows (Bovidae), pronghorn antelope (Antilocapridae) and others. Outside of this whale + hippo + deer, cow, pronghorn, etc. grouping are the pigs and their relatives (Suidae + Tayassuidae) and camels (Camelidae).
It can be rather shocking when you first think about this given how completely different whales look from these animals, but there are distinct clues in the fossil record that point to this same conclusion. For example, some of the proto-whale fossils, such as Pakicetus, share some features that are unique to even-toed hoofed mammals, including a special indentation (trochlea) on the bottom of an ankle bone (astragalus).
When considering the evidence from DNA in conjunction with fossils, biogeography, development and now-defunct genes, a compelling picture is painted in which a group of hoofed mammals, against all odds, transitioned to a life in the oceans. Perhaps next time you go whale watching, think of it as viewing a herd of underwater giraffes or oceanic camels. You probably won’t look at whales the same way again.
Questions for Creationists
Why would the Creator design whales to have DNA so similar to hoofed mammals? With all of their adaptations for living in the water, shouldn’t their DNA be more similar to fish, sharks or other aquatic mammals such as manatees or seals? Is it possible that whales and hoofed mammals belong to the same kind, but whales evolved from these hoofed mammals over just a few thousand years? Wouldn’t this involve major evolutionary change at extraordinary speeds? Is it just a coincidence that whale DNA seems to tell the same story as the fossil record, geography and development?
References
Evolution For Skeptics 
hi christopher. what do you think about this paper?:
https://academic.oup.com/mbe/article/30/9/1999/1000991
Hi g!
I believed I addressed a similar topic in a previous discussion we had, but in case it wasn’t clear, I’ll try to elaborate on it here. This might sound a bit complicated, which may be even more difficult since English isn’t your native language, so please let me know if you need to be explain anything better!
So within the world of molecular phylogenetics research, the science of using DNA to reconstruct hereditary relationships among organisms, you basically have three types of results:
(1) some relationships amongst organisms are always or almost always recovered, no matter how much data you use. From my own experience, for instance, I believe every analysis I’ve ever performed results in tigers and domestic cats coming out more similar to each other than they are to other non-cat animals.
(2) some relationships are not apparent with small datasets (e.g., too few letters of DNA for comparison, not enough species for comparison) but become more and more robustly supported with larger datasets. One example of this might be the relationship of turtles to other reptiles. Initially they jumped all over the place (e.g., closer to lizards, closer to crocs, closer to crocs + birds, etc.) but with larger datasets, they seem to be consistently coming out as closest to birds + crocs. In other words, it appears to be a statistical power issue, namely that there isn’t enough information to infer the correct relationship.
(3) some relationships, regardless of dataset size, give you different results depending on the precise methodology or precise sets of genes you use. The base of placental mammals, which the paper you provided a link to refers, is one of these examples. Two major groups of mammals always come out together: Laurasiatheria (carnivores, hoofed mammals, whales, pangolins, insectivores, bats) + Euarchontoglires (primates, flying lemurs, tree shrews, rodents, rabbits and pikas). Together, this large group is called Boreoeutheria. The rest of placental mammals include Afrotheria (elephants, manatees, hyraxes, African insectivores, aardvark, elephant shrews) and Xenarthra (sloths, armadillos, anteaters). The relative positioning of Boreoeutheria, Afrotheria and Xenarthra switches depending on the analysis.
So examples in category 3 would seem to imply evidence against evolutionary theory. Different dataset, different analysis, and you get different relationships means that these results can’t be trusted, right?
Well, it’s a little more complicated than that. First off, in my experience, the vast majority of examples fall into categories 1 and 2 described above, meaning there seems to be a consistent signal in the DNA pointing to hereditary relationships between organisms. You never get walruses being more genetically similar to flies than other mammals, or lemon trees being more genetically similar to penguins than other plants.
But how do we explain examples in category 3? First off, nearly all examples in category 3 result in the inference of what we call short branches in phylogenetic trees. What this means is that there are very few differences in DNA that seem to unite one group of organisms with another. Assuming evolutionary theory accurately describes reality, what would lead to such few shared DNA substitutions? First off, if the lineages split very quickly, then there may not have been enough time for DNA substitutions to be fixed in their common ancestor, or any shared substitutions may have been erased with reversals in the DNA over time.
Alternatively, perhaps ample time passed, but the organisms evolved very slowly. The speed of evolution depends on a number of things including the population size, whether natural selection is acting on the mutation, and how quickly does the organism reproduce. We think whales, for instance, are notoriously slowly evolving, in part because they typically only have a single baby and it takes a long time for them to become sexually active.
Assuming the evolution has not happened very quickly or the amount of time that has passed was minimal, then interbreeding may have a major effect. Normally the way we think new species form, corresponding to those branches in phylogenies, is that a population of organisms splits into two, and the two populations stay separate and evolve into different species. If they stay isolated or at least don’t recognize each other as potential mates, then they will eventually be very different from each other. Now imagine two populations evolving separately from one another, and they are each accumulating different DNA substitutions, but for some reason an individual from population A mates with an individual of population B. That hybrid will have a mix of DNA from each population. If that hybrid then mates back with population A, and the population B DNA is neutral or provides an advantage, then it can spread throughout the population. This is a phenomenon called introgression, which you may have read in the news in the context of some humans possessing Neanderthal DNA.
So going back to the base of placental mammals: if there was a rapid splitting between one population into three (the boreoeutherian, xenarthran and afrotherian lineages) and/or introgression between one or more of the populations, then there would be minimal signal in the DNA to separate the different lineages. In fact, because of the very nature of these phenomena, you can get different results depending on the sets of genes you use.
thanks for the explanation christopher. i think i understand what you mean (more or less).
Hey,
Please pardon my ignorant or childish questions. I myself see evidence for micro evolution but Not macro evolution. I also do not see traditional darminian evolution happening at the micro biological level, I am more of the thinking of Michael Behe the bio chemist, but at the end of the day I’m just a college drop out with a vocational certificate. Either way, it is Not a Salvidic Issue. But because I am for Truth always, I try to stay open minded. A couple of questions and please use simple layman’s terms for me, lol.
1. If the fossil that they found for what they call the ancestor of whales, the paciketus? I hope I spelled it right, the one they found in 1983? Several hundred of them I believe, dates at 50 million years….how is that possible when carbon dating only goes back some 50,000 years? Am I missing or not understanding something here? And again, my apologies if it is a stupid question.
2. Also, is there even surviving DNA on those 50 million year old fossils? How would they know if that is in fact a common ancestor that later became aquatic, without being able to compare it’s DNA to modern whales and dolphins?
3. Also, are we sure that the tests are not biased. Meaning they looked for the pairs in DNA that would match, instead of all other variables?
4. Do we even know what DNA really is? Is it not more than saying what and who we are related too?
Sorry if these are dumb or ignorant questions. GOD BLESS YOU.
Hi Ingrid, thank you for your comment! And I do not feel that these are dumb questions by any means! Evolution is a tricky subject and you are doing your best to understand 🙂
Question 1: yes, you are correct in saying that scientists believe that carbon-14 dating generally ceases to be accurate beyond 50,000 years. However, there are other times of radiometric dating methods. As you may know, the general idea is that carbon 14 “decays” into carbon 12 at a clock-like rate, and the relative proportion of these two types of carbon gives an estimate of the age of the material. Similarly, there is potassium-argon dating in which potassium-40 decays to argon-40 at a clock lite rate, and is used to date things in a range of 4.3 billion to 100,000 years old. Another common radiometric dating method is uranium-lead dating, in which uranium-238 decays to lead-206, and is used to date rocks 4.5 billion to 1 million years old.
In fact, there are a bunch of other isotopes used that I’ve never heard of (but I’m not a geologist!): https://en.wikipedia.org/wiki/Radiometric_dating#Potassium–argon_dating_method
But beyond these, there are other forms of dating that exist. Paleomagnetism, for instance, helps with dating rocks (and the fossils contained within) by looking at how certain metals (iron I believe) are oriented relative to the poles of the earth. Scientists believe that earth’s poles have flipped quite a few times in earth’s history, such that north becomes south and south becomes north, and then flip again. When this happens, newly formed metallic rocks will orient towards the north pole, just like in a compass. So if you have an idea of when the earth’s poles flipped, you can use that to help date the rocks.
More on rock dating here if interested! https://en.wikipedia.org/wiki/Geochronology
In short, the dating of Pakicetus doesn’t rely on carbon dating, but rather other methodologies to help bring precision. To understand what methods they used, one would have to read the actual paper for the rationale.
Question 2: quick answer is no, we don’t believe DNA can last that long intact. Though there is evidently some ongoing work to clarify if this is indeed the case, that’s the general consensus.
So without DNA, you are absolutely right to wonder how we can be sure. The truth is, we can’t be 100% sure, with this or anything in science (even whether gravity really works the way we think it does!). However, we do have anatomy to compare Pakicetus and these other probable early whales with. Whales and the putative proto-whales have certain anatomical features in common which you don’t find in any other aquatic animals. It can range from the number and shapes of bones in the skull, the location of the external nares (think nostrils), the ankle bones, etc. Scientists don’t just point out the features in common though, they also develop methods that allow for computational and statistical analyses of the features to test whether Pakicetus and others really do group with whales in terms of similarity, as opposed to the scientists performing an exercise in confirmation bias!
Question 3: even though there is no DNA in Pakicetus, I do think this is worth addressing! There’s a great quote by a scientist that goes something like this: “Science is a set of rules that keep scientists from lying to each other.” I would amend to this: “…and lying to themselves.” Bias are always a possibility in any sort of scientific analysis, and this is why scientists come up with tools to try to minimize this. Furthermore, it’s why we have things like peer review, where we evaluate the legitimacy of other scientists. In other words, we’re trying to prevent others from making stuff up, tricking themselves, looking at the bigger picture, etc. We are Truth seekers, just like you 🙂 I, for instance, find it frustrating that in my little subbranch of science there are certain kinds of analyses of DNA that come off as exaggerated claims, and whenever i review these papers, I make sure to make my point known. They may disagree with me, but my opinion must be respected in the peer review process.
Question 4: well, I’d like to say “yes we do know what it is”, but there are always new things that we don’t understand 🙂 A very brief answer is that DNA is much like a “code” that provides instructions for making proteins, molecules that (as I tell my students) so almost everything in our bodies and the bodies of all other organisms. For instance, antibodies which you’ve probably heard about a lot with COVID and vaccines are proteins, you use proteins to carry oxygen in your body, proteins to stop you from bleeding, proteins to absorb light in the back of your eye, proteins to send electrical signals down your nerves, proteins to contract your muscles, etc. DNA tells your cells how to make those, where to make them, how much to make of them and how often. This is why it’s passed down from parents to children, and that, therefore, is why we use it for paternity tests, family tree purpose, and determining relationships among different species.
I hope that all made sense! If you have further questions or comments though, please let me know! 🙂