DNA points to reptilian ancestry of birds

As I discussed in the previous post, the fossil record tells a story that at first seems implausible: birds are descendants of dinosaurs. Part of what’s surprising about this idea is that dinosaurs typically appeared very reptilian, whereas birds do not.

Without providing a formal definition of “reptile”, you probably have a general image in your head. This is because reptiles possess a suite of characteristics that intuitively unite them into a group. For instance, reptiles are covered in scales, walk around on all fours, have tails, typically have simple conical teeth and warm up by basking in the sun.

Birds, by contrast, are covered in feathers, walk around on just their hind legs and/or fly, lack tails, have no teeth whatsoever, and are able to generate their own heat, similar to mammals.

Anybody that is at least vaguely aware of animal diversity probably would never mistake a bird for a reptile. So besides a pattern in the fossil record and remnants of tooth genes in their genomes, is there any other evidence that birds are descended from dinosaurs and, ultimately, other reptiles?

One line of evidence comes from comparisons of DNA. When researchers have compared the genes of birds, reptiles, and other animals, they find something that perfectly fits the conclusion of the fossil record: birds are genetically nested within reptiles. In fact, crocodilians are more genetically similar to birds than they are are to turtles or lizards. As just one example of a study that demonstrates this, Chiari et al. [1] compared 248 genes, with a total of 187,026 letters of DNA, among multiple species of reptiles, birds and other vertebrates and found this very pattern:

12915_2011_Article_592_Fig1_HTML

The green branches on this phylogenetic tree indicate lizards, red are turtles, blue are crocodilians and purple are birds.

The link between crocs and birds isn’t entirely surprising to anatomists, who have long remarked that modern and ancient crocodilians share a number of traits with dinosaurs, including teeth set in sockets (thecodonty), holes in the skull in front of the eyes and in the lower jaw (antorbital and mandibular fenestrae), and an extra ridge (trochanter) on the femur. However, birds no longer have most of these traits, and the one trait that they do have (antorbital fenestrae) is not found in modern crocodilians. As such, this conclusion was not always intuitively obvious.

Nonetheless, here we have an excellent example of where DNA and fossils tell the same story. Fossils appear to document a transition from large reptilian progenitors to modern birds and DNA suggests that birds are not only relatives of reptiles, but are descendants of reptilian ancestors shared with crocodilians, turtles and lizards..

Questions for Creationists

Why do birds have DNA more similar to crocodilians than crocodilians do to turtles and lizards? Is it just a coincidence that bird DNA and the fossil record seem to be telling the same story, that birds are descended from reptiles? What kinds of evidence might overturn this hypothesis?

References

1. Chiari, Y., Cahais, V., Galtier, N., & Delsuc, F. (2012). Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria). Bmc Biology10(1), 65.

Photo credit

Alligator, caiman lizard, terrapin, tuatara, nightjar, cranes, sandgrouse, sunbird

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7 thoughts on “DNA points to reptilian ancestry of birds

  1. g

    so it’s basically the argument for common similarity as evidence for common descent. but the same can be evidence for a common designer too. for instance: lets say that we will have a self replicating car (with dna). can such a car will evolve into something like airplane in milions of years? another question: is such a car with dna is evidence for design or a natural process?

    1. Thank you for your comment, g!

      It’s not an argument for common similarity as evidence for descent. In fact, it’s the opposite.

      To restate, crocodilians, turtles and lizards all have so many similarities that they have been classified as “reptiles” for many years. Historically, taxonomists grouped them together in Class Reptilia, whereas birds had their own distinct Class Aves.

      This distinct classification was because birds are quite different from “reptiles”, such that it probably wasn’t until the discovery of Archaeopteryx that the bird-reptile connection became really convincing to some scientists.

      Which raises the questions: if birds look so different from reptiles, why are they genetically nested within reptiles? If the Designer created the DNA of these organisms, and similar DNA leads to similar physical traits (phenotypes), why is it that when we compare DNA that reptiles don’t group together separately from birds?

      1. g

        hey christopher. you said:

        “if birds look so different from reptiles, why are they genetically nested within reptiles?”-

        good question. there are 2 options under the creation model:

        a) it’s because internal morphology and not just external.

        b) they were created in a similar geological time. so the difference is only about neutral mutations that doesnt effect the morphology.

        and in the other hand: how evolution explain this? if morphology means nothing then any fossil or morhpological classification is meaningless.

        by the way: i have read several other interesting articles in your site. i think that i can answer many other questions from an id perspective.

        1. Hi g:

          “a) it’s because internal morphology and not just external.”

          So you point out something that is relatively difficult to quantify, but is certainly doable. I’ll mention a few internal features that distinguish birds from reptiles.

          (1) The first is a four chambered heart. This is shared in common with mammals, but genetically birds are nowhere near mammals. Crocodilians appear to have the beginnings of a four chambered heart, whereas turtles and lizards have a pretty typical three-chambered heart.

          (2) The skeletons of birds are very very different from those of reptiles, including the fusion of some leg and arm bones, reduction/fusion of the tail, large keel in the sternum, hollowed out bones, three forward and one backward facing toe (fifth toe lost), loss of several fingers, etc.

          (3) Birds have reproductive organs that are shrunk/absent most of the time, but grow back during the reproductive season.

          (4) The bird digestive tract includes a crop and a gizzard, features not found in reptiles.

          (5) Bird lungs are not anything like that of reptiles, consisting of sacs that create a unidirectional flow of air.

          (6) Bird brains have major differences from typical reptiles, including a large cerebellum for coordination, and tiny olfactory (smell) lobes.

          These are just some features that come to my mind, but the point is that a lot of both the external and internal anatomy of reptiles is relatively similar, whereas birds tend to stand out as being rather distinct. Regardless of the specific organs that are similar or dissimilar, you’ll get the same results if you compare the DNA from vision genes, bone genes, heart genes, nervous system genes, etc. So the gross morphology/DNA connection doesn’t always match up.

          “b) they were created in a similar geological time. so the difference is only about neutral mutations that doesnt effect the morphology.”

          I assume what you’re referring to is that over time neutral mutations may accumulate randomly, and just due to chance birds, may appear genetically nested within reptiles. Is this what you’re referring to?

          If I’m understanding you correctly, what you can do (and researchers often do) is eliminate all of the DNA sites that are prone to neutral mutations (usually nucleotides at the 3rd codon position) and just perform the analyses with sites that are typically important functionally (e.g., 1st and 2nd codon positions). What you’ll find is that you’ll get the same result, probably with even stronger support since neutral mutations indeed due cause problems with these sorts of analyses.

          “and in the other hand: how evolution explain this? if morphology means nothing then any fossil or morhpological classification is meaningless.”

          I’m going to give you a two-sided answer to this:

          Yes, you’re right to question morphological classifications. In fact, this has been a major point of contention among molecular biologists and paleontologists ever since DNA began to be used for these sorts of analyses. In many cases, DNA overturned the classifications created by paleontologists and morphologists, such that “reptiles” are no longer considered a real group because birds are placed within them, artiodactyls or even-toed hoofed mammals (deer, cows, pigs, etc.) are no longer considered real thanks to whales plopping down right in the middle of them, and snakes are simply considered lizards that have lost their legs.

          However, the vast majority of morphological classifications have held up. Carnivores are all considered a single group, both by morphology and DNA. Within carnvores, cats, bears and dogs are all still considered real groups. Bats, odd-toed hoofed mammals (horses, tapirs, rhinos), falcons, parrots, snakes, sharks, etc. are all united by both DNA and morphology.

          So morphological classifications aren’t meaningless. Rather, these results seem to be suggesting that some researchers have in many cases been fooled by evolution (e.g., convergent evolution of anatomy, where different lineages evolve different features) or have let their biases in choosing traits to compare influence their results. This is the beauty of DNA: you compare lots and lots of characters (we’re now doing analyses comparing millions of letters of DNA), removing most of the statistical error coming from choosing too few characters, and taking away almost all of the biases that come from comparing characters discerned by human judgment, since a particular position in a string of DNA is largely, objectively discernible.

          But I should also point out that morphological classifications were originally based on comparing features between species from the present era. For example a bird looks almost nothing morphologically like a reptile, whereas reptiles all have many similarities. Therefore, researchers reasoned, birds should be classified as one group (Aves) whereas reptiles as another (Reptilia). However, comparisons between organisms originally lacked the element of time implicit in evolution. So as we go back in the fossil record, birds look a little more like reptiles, a little less like birds. You go back further and we see birds that look even more like reptiles, and less like birds. You go all the way back to Archaeopteryx and you find that calling it a bird or a reptile becomes an intractable issue of semantics. Then we go back further and see reptiles that sort of look like birds, but don’t have wings, and we call those dinosaurs. And so on.

          So the general picture conveyed by evolutionary theory is one where several lineages of organisms generally retained a certain body plan (reptiles), whereas one lineage (birds) changed drastically relative to their ancestors. This was largely, it is assumed, due to the functional demands associated with flight. So while birds today look very little like most reptiles, past or present, their DNA seems to be pointing to a shared ancestry with their reptile kin.

          “by the way: i have read several other interesting articles in your site. i think that i can answer many other questions from an id perspective.”

          I would love to read your thoughts if you would like to discuss them! 🙂 Since you identity as a subscriber to ID, I assume some of my posts aren’t points of contention for you the way they might be for young earth creationists.

          1. g

            hi again. first; thanks for that imformation. secondly: i meant that maybe the genetics only reflect the geological time that this creature appeared on earth. so this could explain why a whale is more similar (in the genetic level) to a cow then then say to a whale shark (because they both appeared closer to each other in the fossil record). i also doesnt understand if you accept that the internal morphology could explain it too (whale is more similar to a cow then to a shark in it’s internal morphology). by the way: it’s also important to note this interesting finding:

            https://www.newscientist.com/article/dn9402-bats-and-horses-get-strangely-chummy/

            “I would love to read your thoughts if you would like to discuss them!”-

            of course:). please chose your best evidence for a common descent and i will try to explain it by a common design. on the other hand: do you think that if we will find a self replicaiting robot with DNA it will be evidence for design or evolution in this case?

            by the way; english isnt my native. so sorry if i doesnt understand some of your words.

            1. “secondly: i meant that maybe the genetics only reflect the geological time that this creature appeared on earth. so this could explain why a whale is more similar (in the genetic level) to a cow then then say to a whale shark (because they both appeared closer to each other in the fossil record).”

              Oh okay, I think I understand. But again, you’ll get the same results if you eliminate the DNA letters that are typically associated with neutrality and just kept the functional ones (i.e., first and/or second codon positions). Or you could simply do the analyses with amino acids (which are functional elements), and you’ll still get the same results with birds being found within reptiles.

              Regardless, what you’re proposing is something that I’m not sure would be easy to test. Perhaps help me think this through: what you’re saying is that many kinds of organisms were created at the same point in time. Given enough time, they might appear more similar to each other genetically due to chance via the accumulation of neutral mutations. Correct?

              But it wouldn’t necessarily be that appearing at the same time is what matters. It’s simply having been around long enough to have accumulated enough random/neutral mutations to group with another organism by chance. So perhaps organisms that appeared at 20 million years ago or 400 million years ago have each had enough time to ‘shuffle’ their DNA, so to speak, to allow them to appear genetically similar. Or even the organism that appeared just 5 million years ago may be genetically similar to the one that appeared 400 million years ago, because over those 400 million years there have been a ton of genetic changes that could randomly group it with the 5 million year old organism.

              But perhaps I’m not entirely understanding the context of what you’re saying. I’m guessing you accept a sort of model of Intelligent Design where the Creator created different groups of organisms in intervals over millions of years, but didn’t cause certain groups to go extinct? That way some organisms appeared 50 million years ago, others appeared 10 million years ago, and they coexist today? Or they have descendants that coexist today?

              “i also doesnt understand if you accept that the internal morphology could explain it too (whale is more similar to a cow then to a shark in it’s internal morphology).”

              No, you’re right, in theory I would agree with the idea of external morphology being dissimilar and internal morphology being similar, and somehow that being reflected in the genetic code. But then this raises the question: if reptiles look more similar to each other both internally and externally than they do to birds, why is it that analyses of DNA put birds right there in the middle of reptiles? And again, if you looked at genes encoding internal functions or external functions, you would get the same results: birds will come out within reptiles.

              Plus, I’d like to point out that the external/internal morphology idea definitely does not work for certain organisms. Just one that comes to mind is African golden moles and ‘true’ moles: https://evolutionforskeptics.wordpress.com/2016/04/15/molecular-phylogenetics-not-all-moles-are-moles/

              Golden moles and true moles look extremely similar externally, and are probably pretty similar internally too (at least for their skeletons they are). Yet golden moles are much more genetically similar to elephants and manatees, and true moles are much more genetically similar to horses and whales. I assure you that the internal anatomy of a golden mole looks hardly like that of an elephant, and the internal anatomy of a true mole looks almost nothing like the insides of a whale.

              “by the way: it’s also important to note this interesting finding: https://www.newscientist.com/article/dn9402-bats-and-horses-get-strangely-chummy/

              I wouldn’t put too much stock in that particular result, as those of us who have analyzed the genetic similarities between bats, horses and other mammals have found that a few of those relationships change depending on the data and the analyses used.

              So we call the group of animals that bats (Chiroptera) and horses, tapirs and rhinos (Perissodactyla) belong to “Laurasiatheria”. It also includes cows, pigs, camels, whales and relatives (Cetartiodactyla), dogs, cats, bears and relatives (Carnivora), pangolins (Pholidota) and ‘true’ moles’, shrews, hedgehogs and relatives (Eulipotyphla). Whenever we analyze enough DNA of mammals, these six groups always come out together pretty much regardless of the specific genes or analyses used. Eulipotyphla always branches of first, with the remaining five clustering together. Among these five, Carnivora and Pholidota always come out together. But the relationships of Perissodactyla, Cetartiodactyla, Chiroptera and Carnivora+Pholidota shuffle around depending on what you do. While the study you mentioned got Perissodactyla + Chiroptera, an analysis my colleagues and I did got something else (you can see it here: https://www.researchgate.net/publication/284185545_Spectral_shifts_of_mammalian_ultravioletsensitive_pigments_Short_wavelengthsensitive_opsin_1_are_associated_with_eye_length_and_photic_niche_evolution). So whenever someone confidently says they figured it out, people like me just sort of roll our eyes and move on. I personally think it’s unlikely to ever be solved.

              So why are they genetically similar? Well, they aren’t that genetically similar, truth be told, just more genetically similar to each other than they are to, say, humans or armadillos. Just like a lungfish isn’t that genetically similar to a human, but it’s more similar to a human than it is to an earthworm.

              Just for a moment, assume that evolution is true. After those lineages split some 75 million years ago (that’s around the estimate we got in our analysis), they started living in isolation and adapting to different things. They changed, they evolved, and eventually they looked very little alike. Running on the plains and eating grasses would lead to very different adaptations than flying around and eating insects. But, thanks to DNA, we think we have a sort of record of their ultimate relatedness. Analogously, Icelandic people and New Guinea pygmies are pretty different, as far as humans go, but they’re more genetically similar to each other than they are to gorillas. Think of the horse + bat example as just a more extreme case of that.

              “of course:). please chose your best evidence for a common descent and i will try to explain it by a common design.”

              Well, I’m not positive that it’s the best, but my favorite to talk about would be the case of the whales. I’ll point you to a series of posts I did on them. I’ll leave it up to you to decide what you care to read and address:

              There’s the fossil record pointing to whales transitioning from land to water and from toothed whales to toothless whales: https://evolutionforskeptics.wordpress.com/2014/05/18/transitional-fossils-3-through-11-from-land-mammals-to-the-ancestor-of-whales/

              DNA showing whales genetically nested within hoofed mammals pointing to a land to water transition:
              https://evolutionforskeptics.wordpress.com/2014/07/20/molecular-phylogenetics-whales-are-hoofed-mammals/

              The distribution of the whale-like fossils seemingly pointing to a transition from land to water:
              https://evolutionforskeptics.wordpress.com/2014/07/20/biogeography-whales-began-in-pakistan-2/

              Developmental evidence of teeth forming in toothless whales before disappearing:
              https://evolutionforskeptics.wordpress.com/2014/10/10/ontogeny-recapitulates-phylogeny-baby-baleen-whales-have-teeth-before-they-lose-them/

              Developmental evidence of hindlimbs forming in whales before they disappear:
              https://evolutionforskeptics.wordpress.com/2017/01/22/ontogeny-recapitulates-phylogeny-fetal-whales-have-hindlimb-buds/

              Genetic remnants of color vision genes in whales, which live in a relatively colorless environment: https://evolutionforskeptics.wordpress.com/2014/08/25/pseudogenes-whales-have-lost-the-ability-to-discern-colors/

              Genetic remnants of vomeronasal organ genes in whales, which lack a vomeronasal organ:
              https://evolutionforskeptics.wordpress.com/2014/09/10/pseudogenes-whales-have-lost-their-vomeronasal-organ-and-associated-genes/

              Genetic remnants of taste receptor genes in whales, which lack taste buds:
              https://evolutionforskeptics.wordpress.com/2014/09/17/pseudogenes-whales-can-only-taste-salt/

              Genetic remnants of tooth genes in toothless whales:
              https://evolutionforskeptics.wordpress.com/2014/10/05/pseudogenes-whales-have-remnants-of-tooth-genes/

              I have more posts to write on whales, but this is just what I’ve gotten to so far. Also, keep in mind, it’s important not just to explain each point individually, but to take all of the data into consideration and think about what story they’re telling together.

              “on the other hand: do you think that if we will find a self replicaiting robot with DNA it will be evidence for design or evolution in this case?”

              This is a tricky analogy, because we know that humans have created robots and we can see it happen perhaps every day of the year. By contrast, we don’t know that a Creator has ever created life.

              “by the way; english isnt my native. so sorry if i doesnt understand some of your words.”

              No apologies needed! Please let me know if I need me to clarify anything I’m saying. As someone currently living in a foreign country, I understand how difficult the language barrier can be. Thank goodness for things like google translate!

  2. g

    hi

    you said:

    “Oh okay, I think I understand. But again, you’ll get the same results if you eliminate the DNA letters that are typically associated with neutrality and just kept the functional ones (i.e., first and/or second codon positions).”

    yep. the result can be same since those mutations can be semi- neutral. so it’s not such a big different.

    “Perhaps help me think this through: what you’re saying is that many kinds of organisms were created at the same point in time. Given enough time, they might appear more similar to each other genetically due to chance via the accumulation of neutral mutations. Correct?”-

    true. but as far as we go back in time they actually need to be more different from each other (since they get more mutations). so if we will check 2 animals that appeared in the fossil record about 10 my ago, they should be more similar to each other then say 2 animals that appeared about 100 my ago (since they get far more mutations in 100 my).

    “Or even the organism that appeared just 5 million years ago may be genetically similar to the one that appeared 400 million years ago, because over those 400 million years there have been a ton of genetic changes that could randomly group it with the 5 million year old organism.”-

    it’s an interesting possibility.

    “, but didn’t cause certain groups to go extinct? That way some organisms appeared 50 million years ago, others appeared 10 million years ago, and they coexist today? Or they have descendants that coexist today?”-

    it’s possible that some of them indeed extincted. but it’s also possible that some of them still alive today. such as the lungfish or the horseshoe crabs.

    now let’s discuss the evidence for whale evolution.

    lets start with the first one about transitional fossils. i think that any series of fossils cant prove a common descent since we can arrange also objects that were designed in such hierarchy. see this figure for instance:

    https://imgur.com/a/OoZln

    and yet it doesnt prove any evolution. even if those vehicles were able to reproduce.

    another problem is this finding:

    http://news.nationalgeographic.com/news/2011/11/111116-antarctica-whales-oldest-evolution-animals-science/

    and if it’s true then it doesnt fit well with the fossil hierarchy.

    the second post may be explain by our discussion above about neutral mutations:)

    you also point out that whale has a vestigial flipper. but it may only prove that the dolphin ancestor may had an extra flippers. so this can be explain by the creation scenario too.

    “This is a tricky analogy, because we know that humans have created robots and we can see it happen perhaps every day of the year. By contrast, we don’t know that a Creator has ever created life.”-

    ok. but even if we will find such a robot in a far planet, we can conclude that this robot were designed, since we know that a robot cant evolve naturally.

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