The new family tree of birds (spot the nightjar!)

April 6, 2015 • 9:39 am

Last December 12, the journal Science included a paper by Erich Jarvis et al. (reference and free download below) that undertook an ambitious revision of the family tree of birds. Although I read it when it came out, I didn’t post about it as I simply didn’t have the time (it takes about 4 hours to read and prepare one of these scientific posts). But I was reminded that I was remiss by a short piece by Sarah Lewin appearing online in March the Scientific American site, “The bird family tree gets a makeover“. The advantage of Lewin’s piece is that it compares both the old and new family trees (“phylogenies”) of birds to show how drastically our view of their evolution has changed from the Jarvis et al. paper. And there’s also a nightjar in both—can you spot it?

I’m only going to show the results, which are based on DNA sequencing of 48 birds spread across all avian orders. Three types of DNA were used: protein coding genes, introns (which are spacer segments separating protein-coding regions of DNA), and UCEs, as described below:

. . . we identified a high-quality orthologous gene set across avian species, consisting of exons from 8251 syntenic protein-coding genes (~40% of the proteome), introns from 2516 of these genes, and a nonoverlapping set of 3769 ultraconserved elements (UCEs) with ~1000 bp of flanking sequences. This total evidence nucleotide data set comprised ~41.8 million bp (table S3 and SM4), representing ~3.5% of an average avian genome.

The tree that resulted rested largely on noncoding intronic sequences, as one expects, since noncoding DNA is expected to be largely free of selection, and thus its evolution simply reflects the passage of time (evolution by “genetic drift”). This noncoding DNA is precisely the kind of DNA you want when you’re constructing a phylogeny. After all, a family tree simply describes which species’ ancestors branched off at different times, which and that time-branching is the relatedness of moden species. Anything affected by natural selection, whose action is usually not as clocklike, is likely to make the phylogeny noisier. At any rate, here is the new tree presented by Lewin, followed by her conclusions:

B9C45B72-C01A-4B24-BBC80D64B66859C2_landingbannerLewin’s take:

The new tree confirms many past observations, such as the common ancestor of the core landbirds. It also resolves some controversial links. Who might have guessed, for instance, that pigeons and flamingos are close cousins?

In addition to 48 bird genomes, the researchers sequenced three crocodilian genomes to pinpoint early descendent relationships.

The separation of penguins, pelicans and ibis from flamingos and grebes (and pigeons) implies that the waterbird trait evolved independently multiple times.

Because of how quickly both land birds and waterbirds evolved, the data suggests that the original ancestors might have been birds that lived along the coastline.

Chickens share the most DNA with the first bird ancestor, closely followed by hoatzin and emu.

You can see how drastically things were revised. What strikes me is first of all, that vocal learning, the ability to imitate and learn new sounds, evolved three times independently: in songbirds like starlings, in parrots (of course), but also in hummingbirds! I was completely unaware that hummingbirds had any imitative capacities.

Other things I find intriguing are that parrots are much more closely related to songbirds than previously thought; that pigeons and doves are now more closely related to flamingos than to other songbirds; that hummingbirds are a sister group to the swifts; that falcons are more closely related to parrots than to either eagles or vultures; and that owls are more closely related to trogons, woodpeckers and trogons than to falcons.

We have many bird experts as readers, so if I’ve made any errors in my elementary explanation, or if there are any other important or suprising findings I’ve failed to highlight, please add them to the comments.

h/t: Amy


E. D. Jarvis et al. 2014. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346: 1320-1331.

81 thoughts on “The new family tree of birds (spot the nightjar!)

      1. You mean all of them — ravens and crows and grackles and the rest — are in that single branch at the very top in yellow? Along with all the tweety birds?

        I think we need a bigger chart….


          1. Damn it, Jim. I’m sequencing as fast as I can. But yes, lots more. Wouldn’t put the priority on more passerines, though. For one thing, there’s no stork, and that’s actually a live question.

        1. Ben, to a first approximation, all bird species are in those top two branches (about 60% of all birds). And most of those are in the very top branch.

          1. Depends how you scale the ratio. The ratio of beetles (specifically Coleoptera) to insects (class Insecta) is actually lower than the ratio between passerines and all modern birds. Roughly speaking, one third of insects are beetles, but over 60% of birds are passerines.

            To put it briefly and roughly, songbirds beat beetles twice over.

          2. Beetles/skinks/colubroids/percomorpharians/rodents etc.; many phylogenies turn out to be dominated (in species number) by a single deeply-nested clade. Darwin wrote about this sort of pattern a lot, and probably understood it about as well as anybody does now (despite having no real method for inferring phylogenies).

        2. “I think we need a bigger chart….”

          As Ugh, the flint knapper, said returning from his first mammoth hunt, nursing a broken spear with a teensy-weensy little sparrow-hunting flint tip …
          (I can envisage the cartoon ; but I couldn’t draw it to save my life. I know, I’ve tried competitive cartooning while in all too brief periods of free fall. At least that’s how I explained the colourful pattern inside my wetsuit. Do I need to add that flint is a type of chert, and some other cherts are used for knapping as available? Or am I assuming too much of the audience. I’ll be here all night. Do you want fries with that?)

          1. So Ugh is the flint knapper!? Damn — should have known it!

            Next time you see him, tell him he better return my flint or he’ll rue the day he stole it!


  1. Exactly the sort of process religion does not do. The multiple vocal learning reminds me of the many separate evolutions of the eye.

    1. The multiple vocal learning reminds me of the many separate evolutions of the eye.

      For “the” eye, you need to add another thirty odd separate evolutions to the list to bring the two into competition. It’s still thirty-odd if you include the evolution of vocal mimicry in the close cousins of birds, their fellow fish, the anthropoid apes. (Just in case people need reminding of Shubin’s advice to “embrace your inner fish”.)

  2. Typo? “owls are more closely related to trogons, woodpeckers and trogons than to falcons.”

    Fascinating stuff. Hummers can talk? Who knew?

    1. I think it’s too early to comment on the position of the owls. If you look at the original paper the bootstrap support for the owl position is low, so that’s still pending further resolution.

    2. I’m now imagining hummingbirds imitating all sorts of things but because they are so small, we are all missing it. The next time I hear a really faint fire truck siren, I’m going to look around for a hummingbird!!

      1. A bad-tempered bureaucratic bird? That’d include the Secretary Bird?
        (No, I didn’t check that. I’m just (ka-boom…tish) winging it!)

      2. Don’t let a trogon read you any of its poetry, especially if you are fitted with a Babel fish.

  3. Very good. I had heard about the separation of falcons from the other birds of prey but it is good to see it very clearly laid out here.
    Also, I spotted the nightjar. First to post!

  4. I would just like to point out that the “old” bird tree has been dead for nearly 10 years now, ever since Ericsson et al. 2006 and Hackett et al. 2008. Most of the revolutionary conclusions you note were in those prior papers, and this new study confirms them.

    I’m also concerned by the claim down at the bottom of the tree that this new study has anything to do with re-ordering the relationships of tinamous and ostriches. In reality, Jarvis et al. didn’t sample any of the species needed to do that — it wasn’t one of their goals — and that was one of the conclusions of Hackett et al. 2008 and Harshman et al. 2008.

    This study was a great advance in avian phylogenetics. It doesn’t have to be oversold.

    Ericson, P. G. P., et al. 2006. Diversification of Neoaves: Integration of molecular sequence data and fossils. Biology Letters 2:543-547.

    Hackett, S. J., et al. 2008. A phylogenomic study of birds reveals their evolutionary history. Science 320:1763-1768.

    Harshman, J., et al. 2008. Phylogenomic evidence for multiple losses of flight in ratite birds. Proceedings of the National Academy of Sciences 105:13462-13467.

  5. One more thing: the dates assigned to the tree are very tentative and, in some cases, demonstrably wrong. Any molecular dating scheme should be accompanied with big error bars and many grains of salt. In particular, we know there were ducks in the late Cretaceous, but this tree has ducks and chickens diverging only in the Paleogene.

    1. Any molecular dating scheme should be accompanied with big error bars and many grains of salt.

      Do you want a dome with that?
      Just Messanian about.

  6. There do seem to be a number of interesting points in the new tree vis-a-vis the older one, but I think you might need to read it carefully to be sure for some of them. It sticks out to me immediately, for example, that the ostriches and tinamous are shown to be switching positions in the tree by the crossing of the green lines down at the bottom of the tree. But in fact ostriches and tinamous have the exact same relations in both trees– they just chose to rotate the twig about the common ancestor (which is a choice about drawing, not a statement of relationship). Since the figure gives its visual impression of change by the crossing of the lines pointing to lineages in the two trees, yet some of these crossed lines do NOT represent changes, you have to look at the trees carefully to see what has actually changed. Again, there are interesting changes in there, but you have to look carefully, and not get an overall impression from a macro-view of how the trees have been drawn.

    1. It is amazing that the graphic would make such a misleading representation of the findings. It would have been easy to fix it so that those lines did not cross.

    2. I believe the ostrich/tinamou thing was an attempt to recognize that the (estimated, of course) relationships of ostriches have indeed changed in the last few years. Just not as a result of Jarvis et al.

  7. Great graphic! I like to imagine the surviving dinosaurs taking wing and blossoming into new species. Reminds me of the story of mammals returning to the sea.

  8. (spot the nightjar!)

    Found it! Two down from hummingbirds in the new system. Heh.

    Where would the emus, cassorwarys, rheas, and other similar large flightless birds fit? I know I may be mixing widely differing lineages there, I suspect “with the ostriches” is probably wrong for at least some of the species I list.

    1. I think they would be lumped in with the ostriches in this illustration. 1 branch = a lot of species.

          1. Practicing it’s aim?
            Trying to mimic the apes so they can come down form the trees and develop bipediality?

  9. Am I correctly interpreting the trees to indicate that tropicbirds (formerly Pelecaniformes) and sunbitterns (formerly Gruiformes) are now considered to be more closely related?

    1. Yes, that’s what the tree says, and it’s probably true. What’s certain is that the tropicbirds aren’t pelecaniforms and the sunbitterns aren’t gruiforms.

      1. I’d read about the tropicbirds being placed in their own order, Phaethontiformes, but wasn’t aware of the taxonomic status of sunbitterns nor of their relationship to tropicbirds.

        Also interesting that ibises (and presumably spoonbills) are no longer allied with flamingos, and that loons and grebes (allied in field guides at least) are more distantly separated in the new tree.

        1. Flamingos and grebes have been together (and far separated from ibises and loons, respectively) since 2001, and most of the rest has been known since 2006 or 2008. One thing new here is the close connection of tropicbirds and sunbitterns (including kagus, though this study didn’t sample those).

          van Tuinen M, Butvill DB, Kirsch JAW, Hedges SB. 2001. Convergence and divergence in the evolution of aquatic birds. Proceedings of the Royal Society of London, Series B 268:1345-1350.

          1. Cool – thanks for the reference!

            I’m a cancer biologist now, and a long way from my undergraduate roots in zoology. Way behind in the field of avian evolutionary biology, obviously.

  10. So many interesting things. I have nothing intelligent to say but to laugh a bit that we are looking at a tree with birds in it.

          1. Of course! There’s a website dedicated to their protection, after all.

  11. Thank you for again spending the four hours this kind of post requires. Surprising to me that grebes and flamingoes are each other’s closest relative.

          1. I still can’t read my own writing….

            All hail the, errr, nameless Chinese engineer who invented movable type, and indirectly the typewriter.

  12. I am not surprised that pigeons and flamingos are so close, I’ve long thought that the beak of the dodo looked a bit like the flamingo’s beak. That parrots are close to songbirds also makes sense. I love that NZ wrens get their own box, and this is the first time I have ever found a nightjar.

  13. Because of how quickly both land birds and waterbirds evolved, the data suggests that the original ancestors might have been birds that lived along the coastline.

    But we’ve had a significant suspicion that this was the case, with Archaeopteryx being found in an area of islands and shallow seas ; with the lacustrine environment of the Liaoning fauna, again it’s well hinted at.
    There’s probably a evolutionary rule of thumb that borderline environments are good for spreading groups descendants. You’ve a linear environment to spread along, and environments to either side to which you’re somewhat pre-adapted. If you have an environmental change, then your interface environment is likely to move laterally and continuously, rather than discontinuously. All handy characteristics, compared to “island” environments (including mountain tops).

    1. I think that Lyell made a very similar point in the Principles (which I recently read for the first time, in the much-shortened Secord edition; light was thrown on the origin of Origin, which is really structured as a series of footnotes to Lyell, also explaining why Darwin was annoyed with Lyell’s habit of constantly putting out new editions – making it a moving target).

      1. [guilty face] Never actually sat down to read my Principles – which ever edition. Dipped into it, but not cover-to-cover read. It struck me, from what I did read, as being an unnecessary piece of masochism.

  14. Very cool – thanks for the summary. I will have to take a look at that paper myself when I get a chance.

    Does anyone know where the gull family, Laridae, fits in to the new tree? I don’t see Charadriiformes mentioned anywhere.

  15. I didn’t comment originally but I very much enjoyed this article! The Falcon/eagle distinction was particularly neat, as I just assumed they were very closely related

Leave a Comment

Your email address will not be published. Required fields are marked *