Your Inner Feather

Feathers are like eyes or or hands. They’re so complex, so impressive in their adaptations, so good at getting a job done, that it can be hard at first to believe they evolved. Feathers today are only found on birds, which use them to do things like fly, control their body temperature, and show off for potential mates. The closest living relatives of birds–alligators and crocodiles–are not exactly known for their plumage. At least among living things, the glory of feathers is an all-or-nothing affair.

But the more we get to know feathers, the more we can appreciate how they evolved. The general rule is that complex things–be they feathers, hands, or eyes–take a very long time to evolve. As I wrote in National Geographic in 2011, the fossil record has gone a very long way in helping us to understand how feathers took on the form we see today. Birds evolved from dinosaur ancestors, and those ancestors already had feathers. Feathers started out as simple filaments, turning to fuzz, and then diversifying into a lot of different forms–including the ones that eventually let birds take to the air.

A sampling of feathered dinosaurs and early birds. Xing Lida/National Geographic
A sampling of feathered dinosaurs and early birds. Xing Lida/National Geographic

Now a new study in the journal Molecular Biology and Evolution offers an even deeper look into the history of feathers. Instead of looking at fossils, the scientists look at the genetic recipe for feathers written in the DNA of birds. It turns out that a lot of that recipe already existed hundreds of millions of years before anything vaguely resembling a feather existed on Earth. In fact, you, my fine unfeathered friend, have most of the genetic information required for making feathers, too.

Scott Edwards, a Harvard ornithologist, and his colleagues couldn’t have carried out this study even a few years ago, because scientists have only recently figured out a lot of the details of how feathers develop. Bird embryos starts out featherless. But in their skin, they develop lots of tiny blobs of cells known as placodes in which cells are switching on genes in a distinctive pattern. The reason that certain genes switch on in the placodes and others don’t is that genes have little on-off switches near them. If a particular combination of proteins lands on a gene’s switch, the gene will start making a protein of its own.

Ng et al 2012.  PLoS Genet 8(7): e1002748
The development of a feather. The middle figure is a cross-section of the primordial feather shown on the left. Source: Ng et al 2012. PLoS Genet 8(7): e1002748

At first, the cells in the placodes multiply quickly. Then they start grow into shafts, which then split open to form feathers. Depending on the bird, and on the spot on the bird’s body where it grows, the feather may split into a downy plume, or into a paddle-shaped flight feather, or into an ornamental tail feather. Along the way, the cells differentiate, producing different combinations of proteins. The cells that make up the central shaft of the feather are stiffened with certain types of keratin, for example, while cells that are in the more delicate regions of the feather produce more flexible forms of the protein from different genes. Clusters of cells produce pigment molecules to give the feather colors and patterns. Every cell has an entire genome, which means it has all the genes for making any part of the feather. But its switches ensure that it only uses a certain combination of those genes.

Frizzled chicken. Photo by Alisha Vargas via Creative Commons https://flic.kr/p/7XmQqu
Frizzled chicken. Photo by Alisha Vargas via Creative Commons https://flic.kr/p/7XmQqu

Edwards and his colleagues combed the scientific literature for genes that are important for feather development. Scientists have studied frizzled chickens, for example, identified the mutation for the breed’s frizzles, and thereby identified a gene essential for developing feathers. All told, Edwards and his colleagues found 193 feather genes this way. Their list included 67 that encode variations of keratin, and 126 that help establish the pattern of feathers.

Next, the scientists searched for the switches that control those genes. This isn’t so easy. The switches are short stretches of DNA, often nestled deep inside much longer stretches of DNA that are just gibberish. What’s more, genes have distinctive segments that let you know you’re looking at a gene. The switches are much harder to distinguish from the gibberish.

The scientists used several strategies to zero in on the switches. They took advantage of the fact that most switches for a gene are close to the gene itself. So they only searched in the neighborhood of the 167 feather genes. They also took advantage of the fact that switches evolve relatively little, because most mutations will be harmful to them. So the scientists compared the DNA around feather genes in several different species and sought out the stretches that were noticeably similar from one species to the next. Using these two strategies, the scientists discovered a staggering 13,307 feather gene switches (technically known as conserved nonexonic elements, or CNEEs for short).

Next, the scientists asked when each part of this feather cookbook evolved. If they found a gene or a switch only in the DNA of birds, then they could be confident that it had evolved after the ancestors of birds split off from the ancestors of alligators and crocodiles. But if they found a gene or a switch in birds and alligators and crocodiles, then it must have evolved earlier, in their common ancestor.

(You may be asking, how did these new genes evolve? The short answer is that they can evolve through the duplication of old genes, or the transformation of genetic gibberish–a k a noncoding DNA. If you want to get more details, watch this TED-Ed video I wrote the script for.)

To see how far back the evolution of feather genes went, the scientists compared birds to a wide range of vertebrates, including humans, turtles, and pufferfish. They found that the instructions for making feathers got their start a long, long time before feathers themselves (see the tree at the bottom of the post or embiggen it here). The genes that establish the basic pattern of placodes already existed in the common ancestor of living fish and birds (and us)–in other words, about half a billion years ago. Even more feather genes evolved as our common ancestors climbed ashore and walked around on land 350 million years ago. Many switches for feather genes also emerged during this period, too.

About 300 million years ago, our ancestors began to lay hard-shelled eggs. Those early animals would give rise to mammals, reptiles, and birds (collectively known as amniotes, named for the amniotic egg). Edwards and his colleagues found that the first amniotes already had the entire complement of feather patterning genes. That means you, as an amniote, have them too.

Later, the early amniotes split away into their major lineages. The lineage that includes alligators, birds, and extinct dinosaurs–called archosaurs–originated about 250 million years ago. Edwards and his colleagues detected many new keratin genes evolving during the origin of archosaurs, along with 86 percent of their 13,000 or so feather gene switches.

It would not be another 100 million years or so before the oldest known birds flew. And yet just about everything you need to make a feather, genetically speaking, was already in place.

It may seem strange to consider the fact that you, as a mammal, have all the known genes required to pattern a feather, and yet you do not look like Big Bird. The reason for this discrepancy is that genes can do different jobs. Depending on where and when they make their proteins, they can build different kinds of anatomy. But it didn’t take much rewiring of genetic switches to turn the scaly skin of early reptiles into feathers. Indeed, the deep history of feathers could explain why paleontologists are finding so much evidence of simple feather-like filaments not just in dinosaurs, but in their close relatives like pterosaurs. Evolution was tinkering with the same toolkit.

Edwards and his colleagues noticed something else intriguing in the genomes of birds. They found a lot of switches that were not near feather genes, but were unique to birds. When the scientists looked for the nearest genes, they noticed that many of the genes help birds grow. They control the size of bird bodies, for example, or the size of their limbs.

This is an intriguing finding, because the fossil record reveals that as dinosaurs evolved into birds, their bodies shrank, while their arms got long for their size. The shift made it possible for birds to generate a lot of lift with big wings, which only had to keep a small body aloft.

Edwards and his colleagues may have found the molecular signature of that change. If they’re right, the cookbook for feathers is very old, but it took the evolution of a new kind of body for birds to use their feathers to fly.

From Lowe et al 2014
From Lowe et al 2014 (Click to embiggen)

With apologies to Neil Shubin for riffing on his title.

20 thoughts on “Your Inner Feather

  1. Interesting article. The phylogeny is off a bit though. At reptileevolution.com you’ll find, as I did, that when more taxa are added to the amniote family tree pterosaurs are derived from a third clade of lepidosaurs between rhynchocephalians and squamates. So they’re not related to dinosaurs, but developed their own unique ‘hair.’ Mammals, it turns out, are more closely related to archosaurs (including birds and mammals). The varanopid synapsids were basal to the Permian diapsids that ultimately evolved into archosaurs, dinosaurs and birds.

    [CZ: While I will allow this comment, I will also direct readers to this critique of these claims.]

  2. One minor correction: birds are included within reptiles (birds are archosaurs: archosaurs are reptiles) so to say that Amniota includes “mammals, reptiles, and birds,” while technically true, implies that reptiles and birds are separate groups. This is really more of a problem with the historical baggage attached to the term “reptile,” but it’s something I always feel the urge to correct.

    This study is fascinating, and I can’t wait to read it. As soon as you said they included turtles, my mind leapt to whether turtles share more feather genes with archosaurs than with lepidosaurs (if that’s shown). That finding could help determine where turtles sit on the Sauropsida family tree!

  3. I had to smile at the connection between the genetic diversity of birds used to tease out these effects and Darwin’s pigeons. I suspect that without the unnatural selection of genetic traits by artificial means (as demonstrated by the frizzled chicken), we might not have had enough variation to easily look at the effects of natural selection. That would have made finding those 193 genes and 13,307 (!) CNEE a lot more difficult.

    What fascinated the Master over 150 years ago still provides us with insights today.

  4. You say:
    “it took the evolution of a new kind of body for birds to use their feathers to fly”.
    What would be an example of an early taxon with that “new kind of body”?

    [CZ: There were a lot of very small feathered dinosaurs that were closely related to the first birds, such as Eosinopteryx brevipenna.]

  5. Is David Peters’ blog title an intentional echo of David Beatty’s comment at Jutland, “There seems to be something wrong with our bloody ships today”?

  6. Carl Zimmer, the 3rd link in your beautiful artical is’nt working. (Obama?drones? NSA?)
    Please help ! We want to know !

    kind regards,

    [CZ: All the links work for me.]

  7. Very interesting. I also appreciate that in the tree from Lowe that the turtles are embedded within the other ‘reptiles’, rather than being stuck outside the group as the olde Anapsids. I had heard that this is now the more likely place for turtles, but most texts still do not do it.

  8. ///Then they start grow into shafts, which then split open to form feathers. ///

    A “to” is missing here 🙂

    By the way, fascinating study and excellent reporting.

  9. Very interesting. Just a couple of comments.

    “About 300 million years ago, our ancestors began to lay hard-shelled eggs.”

    Did the hard shell really evolve that early?

    Also, even if fathers were around 150 million years ago, how modern were they? I read somewhere that it’s possible they were solid and not hollow as today’s feathers, and their anatomy in general were not as well suited to flying either. It would have been fascinating to know when the first modern feather evolved.

  10. You say:
    “it took the evolution of a new kind of body for birds to use their feathers to fly”.
    What would be an example of an early taxon with that “new kind of body”?

    [CZ: There were a lot of very small feathered dinosaurs that were closely related to the first birds, such as Eosinopteryx brevipenna.]

    But Eosinopteryx was flightless. They were not using their feathers to fly.
    http://en.wikipedia.org/wiki/Eosinopteryx

    [CZ: Exactly. Feathered dinosaurs underwent a long miniaturization before powered flight evolved. So Eosinopteryx is an example of small feathered dinosaurs that evolved before the origin of flight.]

  11. You say:
    “it took the evolution of a new kind of body for birds to use their feathers to fly”.
    What would be an example of an early taxon with that “new kind of body”?

    [CZ: There were a lot of very small feathered dinosaurs that were closely related to the first birds, such as Eosinopteryx brevipenna.]

    But Eosinopteryx was flightless. They were not using their feathers to fly.
    http://en.wikipedia.org/wiki/Eosinopteryx

    [CZ: Exactly. Feathered dinosaurs underwent a long miniaturization before powered flight evolved. So Eosinopteryx is an example of small feathered dinosaurs that evolved before the origin of flight.]

    If Eosinopteryx were a non-paraves maniraptor I would agree with you.
    However it is a member of Paraves. That leads to the conclusion that Eosinopteryx was secondarily flightless.

  12. Doug, keep in mind that Paraves includes birds but also deinonychosaurs, and the animals at the base of both groups will be virtually indistinguishable. It’s also not set in stone that paravians were ancestrally flight-capable. It’s entirely possible that basal deinonychosaurs (Dromaeosauridae + Troodontidae) developed their own “version” of flight apart from basal avialians.

    Either way, however, it’s clear that both groups were ancestrally miniaturized but were not necessarily flight-capable. Even basal birds, such as Confusiusornis, seemed to lack the skeletal requirements for a power stroke. And as you’re doubtlessly aware, dromaeosaurs and troodontids actually abandoned arboreality in favor of terrestriality and reverse-engineered larger body sizes.

    Meanwhile, birds were busy improving their flight apparatus.

  13. Fascinating post, Carl. I’m a bit unclear on this part, however:

    “Edwards and his colleagues found that the first amniotes already had the entire complement of feather patterning genes. That means you, as an amniote, have them too.”

    In an earlier post “The Continuing Evolution of Genes”, you mention that along with gene duplication, de novo genes can often arise from mutations in noncoding regions of DNA. Makes sense. But then you say that mutations can also deactivate genes by deleting entire segments of DNA. This would conceivably work as a sort of counterweight to genome size I would think. So how is it that we and other modern species have the “entire” genetic toolkit of flight and feather patterning? I would think that at least *some* of the genes would have been deactivated by the simple random process of mutations over the course of 100 million years.

    The only explanation I can come up with as to why this *wouldn’t* be the case is if all of those duplicated/de novo genes were co-opted by evolution to serve different functions, hence the reason they’re still sitting in our genome. Could you clear this conflict up for me?

  14. This ignoramasaur knows of at least five genus that developed the ability to fly or glide “independently” one fom the other: Birds, mammals (bats), reptiles, dinosaurs and insects, with arachnids and fish also able to travel through the air, one way or another. The pre-flight ancestors of these hugely variated genus would have been so stressed to the point that their gene sequences were influenced, either by food scarcity/availabilty, or the need to avoid being eaten! Is this environmental stress conveyed to genes by the “concious” experience of individuals or groups, or is it directly conveyed to genes by some other mechanism?

  15. Patrick, birds are dinosaurs, and dinosaurs are reptiles! All three didn’t develop flight independently because each groups nests within the other. Also, don’t forget pterosaurs like Pteranodon! They’re also reptiles, but not dinosaurs, so they DID develop their powers of flight independently of birds.

    1. Zack, by reptiles I was thinking about lizards. They are cold blooded, but the jury are still out on dinosaurs having been cold blooded. The “nesting” of one “group” within another I believe is proving to be a mistake, as is the drawing of scientificaly fixed evolutionary “trees”. Evolutionary “networks” would be a more accurate description of life’s “progress”.

  16. This article was very good ,you have searched well on it,it has very interesting things & very knowledgeable
    But i have one question :
    Can we put the genes of birds which helps to grow feathers in ours?
    If yes please mail it to me.

  17. It seems to me that Mother Nature provides very well and wisely for her children, equipping them with the potential for beneficial evolutionary modification where and when this is needed. Feathers apparently appeared independently, more than once, throughout dinosaur/paravian development, and for two different purposes: first, for the regulation of body temperature and possibly to enhance the courtship ritual; subsequently, in order to enable the birdlike theropods to have greater mobility and more chance of survival through the power of flight. If even man possesses the same POTENTIAL to grow feathers, but has never done so up until now, this would indicate that Homo Sapiens has alternative, demonstrably better ways of keeping his body warm, attracting mates and escaping from predators. And when the first airplane was constructed, Nature would have realized quite well that man did not require feathers or wings of his own for flight! So we remain featherless.

  18. @ Mary:

    “If even man possesses the same POTENTIAL to grow feathers, but has never done so up until now, this would indicate that Homo Sapiens has alternative, demonstrably better ways of keeping his body warm, attracting mates and escaping from predators. And when the first airplane was constructed, Nature would have realized quite well that man did not require feathers or wings of his own for flight! So we remain featherless.”

    I think we’re anthropomorphizing a bit too heavily here. Nature didn’t “realize” anything; it is not a conscious entity. Our invention of airplanes certainly had zilch to do with whether we did or did not evolve mutations for feathers.

    1. Daniel,

      You have failed to understand or appreciate my humorous remark about airplanes. As for Nature, I am not anthropomorphizing it; Nature, though certainly neither divine nor human, has a consciousness of its own; it is a logical force, and a compelling one, which strives to better species in a constant process of modification and selection. Nature tends to improve living organisms when these display certain deficiencies or needs; it operates toward their survival, and seems to “know” precisely when species are in need of modification. Don’t ask me how this works…I’m not a biologist…but time and again in the course of prehistory, Nature has brought about the evolution of the species. If Homo Sapiens had ever really been in need of feathers, the “feather potentiality” stored in his genes would have become a reality.

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