Thumbs down, what?

Bird fingers confuse me, but the explanations confuse me more, it seems.

I didn’t mean to post today, but I’ve just read a new review/hypothesis paper about the identities of the stunted little things that pass for fingers in the wings of modern birds. The review part is fine, but I’m not sure I get the difference between the hypothesis Čapek et al. (2013) are proposing and the hypothesis they are trying to replace/improve.

To recap: the basic problem with bird fingers is that fossil, genetic and developmental evidence seem to say different things about them.

1. Fossils: birds pretty clearly come from dinosaurs, and the early dinosaurs we have fossils of have five fingers on their hands with the last two being reduced. Somewhat closer to birds, you get four fingers with #4 vestigial. And the most bird-like theropods have only three fingers, which look most like digits 1, 2 and 3 of your ordinary archosaur. (Although Limusaurus messes with this scheme a bit.)

2. Embryology: in developing limb buds, digits start out as little condensations of tissue, which develop into bits of cartilage and then finger bones. Wing buds develop a short-lived condensation in front of the first digit that actually forms, and another one behind the last “surviving” digit. Taking this at face value, then, the fingers are equivalent to digits 2, 3 and 4.

3. Genetics: In five-fingered limbs, each digit has a characteristic identity in terms of the genes expressed during its formation. The first finger of birds is most like an ordinary thumb, both when you focus on individual genes like members of the HoxD cluster and when you take the entire transcriptome. However, the other two digits have ambiguous transcriptomic identities. That is, bird wings have digit 1 and two weirdos.

Add to this the fact that in other cases of digit loss, number one is normally the first to go and number four stubbornly sticks around to the end, and you can see the headache birds have caused.

So those are the basic facts. The “old” hypothesis that causes the first part of my confusion is called the frame shift hypothesis, which suggests that the ancestors of birds did indeed lose digit 1, as in the digit that came from condensation 1 – but the next three digits adopted the identities of 1-2-3 rather than 2-3-4. (This idea, IMO, can easily leave room for mixed identities – just make it a partial frame shift.)

Čapek et al.’s new one, which they call the thumbs down hypothesis, is supposedly different from this. This is how the paper states the difference:

The FSH postulates an evolutionary event in which a dissociation occurs between the developmental formation of repeated elements (digits) and their subsequent individualization.


According to the TDH no change of identity of a homeotic nature occurs, but only the phenotypic realization of the developmental process is altered due to redirected growth induced by altered tissue topology. Digit identity stays the same. Also the TDH assumes that the patterning of the limb bud, by which the digit primordia are laid down, and their developmental realization, are different developmental modules in the first place.

(Before this, they spent quite a lot of words explaining how the loss of the original thumb could trigger developmental changes that make digit 2 more thumb-like.)

I…. struggle to see the difference. If you’ve (1) moved a structure to a different position, (2) subjected it to the influence of different genes, (3) and turned its morphology into that of another structure, how exactly is that not a change in identity?

Maybe you could say that “an evolutionary event” dissociating digit formation and identity is different from formation and identity being kind of independent from the start, but I checked Wagner and Gauthier’s (1999) original frame shift paper, and I think what they propose is closer to the second idea than the first:

Building on Tabin’s (43) insight, we suggest causal independence between the morphogenetic processes that create successive condensations in the limb bud and the ensuing developmental individualization of those repeated elements as they become the functional fingers in the mature hand, thus permitting an opportunity for some degree of independent evolutionary change.

Am I missing something? I feel a little bit stupid now.



Čapek D et al. (2013) Thumbs down: a molecular-morphogenetic approach to avian digit homology. Journal of Experimental Zoology B, published online 29/10/2013, doi: 10.1002/jez.b.22545

Wagner GP and Gauthier JA (1999) 1,2,3 = 2,3,4: A solution to the problem of the homology of the digits in the avian hand. PNAS 96:5111-5116

Lotsa news

Hah, I open my Google Reader (damn you, Google, why do you have to kill it??? >_<), expecting to find maybe a handful of new articles since my last login, and instead getting both Nature and Science in one big heap of awesome. The latest from the Big Two are quite a treat!


By now, of course, the internet is abuzz with the news of all those four-winged birdies from China (Zheng et al., 2013). I’m a sucker for anything with feathers anywhere, plus these guys are telling us in no uncertain terms that four-wingedness is not just some weird dromaeosaur/troodontid quirk but an important stage in bird evolution. Super-cool.


Then there is that Cambrian acorn worm from the good old Burgess Shale (Caron et al., 2013). It’s described to be like modern acorn worms in most respects, except it apparently lived in a tube. Living in tubes is something that pterobranchs, a poorly known group related to acorn worms do today. The Burgess Shale fossils (along with previous molecular data) suggest that pterobranchs, which are tiny, tentacled creatures living in colonies, are descendants rather than cousins of the larger, tentacle-less and solitary acorn worms. This has all kinds of implications for all kinds of common ancestors…


Third, a group used a protein from silica-based sponge skeletons to create unusually bendy calcareous rods (Natalio et al., 2013). Calcite, the mineral that makes up limestone, is not normally known for its flexibility, but the sponge protein helps tiny crystals of it assemble into a structure that bends rather than breaks. Biominerals would just be ordinary rocks without the organic stuff in them, and this is a beautiful demonstration of what those organic molecules are capable of!


And finally, Japanese biologists think they know where the extra wings of ancient insects went (Ohde et al., 2013). Today, most winged insects have two pairs of wings, one pair on the second thoracic segment and another on the third. But closer to their origin, they had wing-like outgrowths all the way down the thorax and abdomen. Ohde et al. propose that these wing homologues didn’t just disappear – they were instead modified into other structures. Their screwing with Hox gene activity in mealworm beetles transformed some of the parts on normally wingless segments into somewhat messed up wings. What’s more, the normal development of the same bits resembles that of wings and relies on some of the same master genes. It’s a lot like bithorax mutant flies with four wings (normal flies only have two, the hindwings being replaced by balancing organs), except no modern insect has wings where these victims of genetic wizardry grew them. The team encourage people to start looking for remnants of lost wings in other insects…

Lots of insteresting stuff today! And we got more Hox genes, yayyyy!



Caron J-B et al. (2013) Tubicolous enteropneusts from the Cambrian period. Nature advance online publication 13/03/2013, doi: 10.1038/nature12017

Natalio F et al. (2013) Flexible minerals: self-assembled calcite spicules with extreme bending strength. Science 339:1298-1302

Ohde T et al. (2013) Insect morphological diversification through the modification of wing serial homologs. Science Express, published online 14/03/2013, doi: 10.1126/science.1234219

Zheng X et al. (2013) Hind wings in basal birds and the evolution of leg feathers. Science 339:1309-1312


My heart is a bit broken.

On my way to work this morning, I saw a crow tearing into the corpse of a small bird, possibly a greenfinch from the brief look I got. I don’t know if the crow had killed it or if it had dropped dead all by itself, but in the end it doesn’t really matter.

I love crows and I know they are opportunistic bastards that will eat anything, but I’ve never actually seen one feast on a small bird. And small birds are my little feathered antidepressants. It’s like seeing your beloved cat dismember your pet hamster.

I’ll console myself with Andreas Trepte’s gorgeous photos of a non-dismembered greenfinch. Isn’t he a beauty!

Birds invent the password!

This is quite outside my normal favourite topics, but it’s so cool I had to share anyway. (Though I guess it’s still not quite as far outside as, say, exoplanets :D)

A study of nesting superb fairy wrens (Colombelli-Négrel et al., 2012) suggests that these beautiful little birds use something akin to a password to defend against cuckoo infiltration. While the female sits on her eggs, she calls to them. The chicks inside listen, and when they hatch, their begging contains sounds that match a characteristic part of mum’s nesting calls. Learning is clearly going on – when you switch eggs between different nests, the chicks’ cries are most similar to their foster mother’s and not their genetic mother’s calls. (So while the technique might work against cuckoos, it’s no good against cuckoldry ;))

(Superb fairy wrens from Wikipedia. Female (left) by Fir0002/Flagstaffotos, male in breeding plumage (right) by JJ Harrison.)

The female uses the same password to tell her mate to feed her, so he also learns. The crucial thing is that cuckoo chicks don’t. Maybe it’s because they hatch earlier; since female fairy wrens stop making their calls when the first egg hatches, a hatchling cuckoo has had less time to memorise them than a hatchling wren. Either way, both parent wrens can tell the difference. By playing back the begging of wren chicks brooded in the target nest, wren chicks from elsewhere, and cuckoo chicks, the researchers determined that the parents react differently to “home” and “foreign” calls. When the begging cries contain the correct password, they feed the chicks more and spend less time on the lookout for intruders. Interestingly, it makes no difference whether the calls are from another wren nest or from a cuckoo. If you got the password wrong it doesn’t matter if it was by one measly typo 🙂



Colombelli-Négrel D et al., (2012) Embryonic learning of vocal passwords in superb fairy-wrens reveals intruder cuckoo nestlings. Current Biology in press, available online 08/11/2012, doi:10.1016/j.cub.2012.09.025

So… much… STUFF!

Gods, this is what I’m faced with all the time. Someone needs to tell me how proper science bloggers pick articles to discuss, because I just get my RSS alerts, start squeeing, and end up not writing about anything because damn, I WANT TO WRITE ABOUT EVERYTHING!

I give up. I’ll just dump all the cool stuff that’s accumulated on my desktop and bookmark bar here and return to lengthy meandering whenever I don’t feel like I’ve been caught in a bloody tornado 😉

So, here is some Cool Stuff…

(1) A group measured the rate of DNA decay in 158 moa bones of known age from three sites. Really cool stuff, to go out and directly measure how ancient DNA disappears from dead things under more or less identical conditions. The unsurprising result is that DNA decays exponentially, a bit like radioactive material. This suggests that the main cause of the decay is random breaking of the strands. The surprising bit is that this happens much more slowly than previously estimated, suggesting that in ideal (read: frozen) conditions, it might be worth looking for preserved DNA in samples as old as a million years.

(On a side note, if you ever get a chance to see a talk by Eske Willerslev, one of the authors and a leading expert on ancient DNA, don’t miss it. The man is absolutely hilarious.)

– Allentoft ME et al. (2012) The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils. Proceedings of the Royal Society B FirstCite article, available online 10/10/2012, doi: 10.1098/rspb.2012.1745

(2) The beaks of the finches, or mixing and matching developmental recipes. This study examines the genetic basis of beak shape in three little birds closely related to Darwin’s famous finches. The three finches, just like Darwin’s, share the same basic beak shape, only bigger or smaller. However, there seem to be two distinct developmental programs at work, using different genes and parts of the skeleton to orchestrate beak development. One of the three newly investigated species (the one most closely related to Darwin’s finches) apparently uses the same developmental program as its more famous relatives, even though its beak is shaped more like the other two birds studied here. I told you – genetics, development and homology are complicated 😉

– Mallarino R et al. (2012) Closely related bird species demonstrate flexibility between beak morphology and underlying developmental programs. PNAS 109:16222–16227

(3) Armoured fossil links worm-like molluscs to chitons. There’s a little-known group (or groups) of molluscs called aplacophorans that have only a coat of tiny spicules instead of shells and look more like worms than “proper” molluscs. Exactly where they fit into our picture of mollusc evolution has been controversial to say the least – they could represent an old lineage separate from other molluscs, they could be related to cephalopods, they could be related to chitons, they could be one group or they could be two lineages in completely different places on the tree… Well, a new fossil named Kulindroplax seems to argue for the chiton connection: the animal has the characteristic armour plates of a chiton on an aplacophoran-like body. Similar creatures have been discovered before, but this guy with its detailed 3D preservation provides the clearest evidence of the link so far.

– Sutton MD et al. (2012) A Silurian armoured aplacophoran and implications for molluscan phylogeny. Nature 490:94-97

(4) More cool fossils – this time straight from my beloved Cambrian. Nereocaris, a newly described Burgess Shale arthropod, suggests to its discoverers that the earliest arthropods weren’t predators prowling the seafloor, but swimmers who might have been filter feeders and certainly weren’t predators. The animal has a bivalved shell around its front end, similar to many other Cambrian swimming arthropods, and a long abdomen with paddles at the end. It bears the arthropod hallmark of a hardened and jointed exoskeleton, but it lacks specialised limbs such as antennae or mouthparts. In a cladistic analysis of arthropods and their nearest relatives, the new species comes out on the first branch within true arthropods, and the next few branches as we move towards living arthropods all contain similar shelled, swimming creatures. Since the non-arthropods closest to the real thing (i.e. anomalocaridids) were also fin-tailed swimmers, this arrangement makes the transition between them and true arthropods smoother than previously thought. It also suggests that the hard exoskeleton so characteristic of arthropods originally functioned in swimming – perhaps as an anchor for swimming muscles.

– Legg DA et al. (2012) Cambrian bivalved arthropod reveals origin of arthrodization. Proceedings of the Royal Society B FirstCite article, available online 10/10/2012, doi: 10.1098/rspb.2012.1958


And … there was also

… but it’s almost bedtime, and if I wanted to summarise every one of those, I’d be here all weekend 😦

See, this is why being a science nerd today is both amazing and frustrating. There’s just so. Much. Stuff.

Birds are baby dinosaurs

Just a quick squee over something from the recent crop 😀

Paper: Bhullar BAS et al. (2012) Birds have paedomorphic dinosaur skulls. Nature advance online publication 27/05/2012, doi:10.1038/nature11146

New body forms often seem to evolve by tweaking the timing of developmental events. For example, axolotls are salamanders that become mature without ever losing larval traits such as gills, and many things about adult humans can be interpreted as retentions of baby ape characteristics. Now a new study in Nature argues that birds’ characteristic skull shape – big-brained, big-eyed, and usually small-snouted compared to their dinosaurian relatives – are similarly leftovers from dinosaur childhood. The team collected various skull measurements from young and adults of birds, non-avian dinosaurs, alligators and the early Triassic reptile Euparkeria, a distant cousin of both alligators and dinosaurs. When they analysed the variation in the data, they found that the skull of all of these animals changes in similar ways as they mature. However, adult dinosaurs more closely related to birds grouped with embryos and youngsters of more distant bird relatives, and modern birds were even further on the “baby” side of the diagram. Thus, it seems that the origin of birds was marked by the adoption of increasingly babylike faces. No wonder some of these feathery bastards are so disarmingly cute! (Blue tit above by Maximilian Dorsch, Wikimedia Commons)