Monday, July 23, 2012

Resolving why Confuciusornis has a modified wireframe nearly identical to juvenile Alligator

In my last post, I took Bhullar et al. (2012) to task for 1) their choice of Confuciusornis as being a close match in analyzed skull shape to juvenile Alligator; 2) Bhullar's own online statement it wouldn't matter which basal bird they used, since the Catalan enantiornithine embryo and others would come out very similarly; and 3) why their wireframes vary so much from the specimens themselves.  After communicating with Bhullar, we have answers to these issues.

Number three is easiest, and works to explain the rest.  As Bhullar explained (and Rodriguez noted on the DML), the wireframes in the paper are not actually the raw wireframes that result from placing landmarks on photos.  Instead, they are a combination of principal components.  Now morphometrics is not my thing, but as I understand it, Principal Component 1 is the horizontal variation in landmarks and Principal Component 2 is the vertical variation in landmarks, once the skulls have been resized and rotated to best agree with each other.  As their figure S6 below shows, each component has a hypothetical extreme on each end.  On each axis, a certain line will change from one extreme to another.  So on PC1, you can see the naris moving further back going left to right.  However, some features weren't common or consistent enough to show over those features that explain most of the variation.  So you'll notice nothing in any extreme has a large naris, since that didn't vary consistently with the main horizontal or vertical changes.  And that's why the Confuciusornis and juvenile Alligator both have modified wireframes with small, partially retracted nares- most of their horizontal measurements fall out to average a PCI of ~0.08-0.10, and at that (and every) point in the graph, skulls have small and partially retracted nares.  So you take the average wireframe of skulls on a certain point of the PC1 axis, and mix it with the average wireframe of skulls on a certain point of the PC2 axis, and ta-da!, you have your modified wireframe that doesn't really resemble the original much at all.

Bhullar said he should have noted this in their paper (especially in the oft copied figure 4 which purported to show the "nearly identical skull configuration" of Confuciusornis and juvenile Alligator, with almost complete overlap of every line) and I said I shouldn't have called his data seriously flawed before confirming his methods.  We've both apologized and are happy with how things turned out.  Bhullar sent me his Confuciusornis and juvenile Alligator raw wireframes, and while I would place a few points differently, they're accurate overall.  The above discussion also shows what Bhullar meant when saying the choice of Confuciusornis over e.g. the Catalan nestling wouldn't matter, since it's very close in PCA morphospace.  The reduced antorbital area of Confuciusornis doesn't factor in, since on average, taxa in that area of the graph don't have such reduction, so the PCA average wireframe the computer uses for Confuciusornis doesn't either.

So then, despite their wildly varying anatomy, Confuciusornis and juvenile Alligator are getting similar PCAs.  What actual anatomy is controlling most of the variation?  We both hypothesized that most of the variation is simply due to the general skull outline.  You'll remember from before that the snout length and slope match almost perfectly, and the braincase is just a little more expanded in Confuciusornis (though perhaps due to crushing). 
To test this, I suggested Bhullar eliminate all but the major landmarks outlining the skull- 1, 2, 3, 4, 16, 23, 24, 25, 29, 40 and 43.  He ran this reduced analysis based purely on the skull outline and found very similar results.
PCA plot by Bhullar using only 11 landmarks, all defining the lateral skull outline.  Figure shown upside down to more easily compare to their figure S6 above.  Juvenile Alligator highlighted in blue, Confuciusornis in brown.  Other taxon-number correlates given below.
Note Confuciusornis and juvenile Alligator as about as close as they are when all 45 points are analyzed, showing Bhullar et al.'s analysis mostly compared gross skull shape.

And that's that.  As I said at the beginning on my first post, I agree with their main thesis- that bird skulls are paedomorphic.  Before ending, I'd like to thank Bhullar for how gracious he has been toward me and my critique.  As he said in an email, such criticisms and responses are how science should work.

Supplementary data- 

Numbers representing each skull in Bhullar's reduced PCA plot.
ID=01 Alligator adult
ID=02 Alligator embryo
ID=03 Allosaurus adult
ID=04 Anchiornis adult
ID=05 Archaeopteryx adult
ID=06 juv Archaeopteryx
ID=07 Bambiraptor
ID=08 Byronosaurus adult
ID=09 Ceratosaurus adult
ID=10 Citipati adult
ID=11 Citipati embryo
ID=12 Coelophysis juvenile
ID=13 Coelophysis adult
ID=14 Compsognathus adult
ID=15 Confuciusornis adult
ID=16 Dilong adult
ID=17 Dilophosaurus adult
ID=18 Dromaius adult
ID=19 Eoraptor
ID=20 Erlikosaurus adult
ID=21 Eudromia adult
ID=22 Euparkeria adult
ID=23 Gallus adult
ID=24 Gallus juvenile
ID=25 Garudimimus adult
ID=26 Gorgosaurus adult
ID=27 Guanlong adult
ID=28 Herrerasaurus adult
ID=29 Incisivosaurus adult
ID=30 Majungasaurus adult
ID=31 Monolophosaurus adult
ID=32 Scipionyx juvenile
ID=33 Suchomimus adult
ID=34 Tarbosaurus adult
ID=35 Tarbosaurus juvenile
ID=36 therizinosaurid embryo
ID=37 Tyrannosaurus adult
ID=38 Tyrannosaurus subadult
ID=39 Tyrannosaurus large adult
ID=40 Velociraptor adult
ID=41 Zanabazar adult
ID=42 Haplocheirus adult
ID=43 enantiornithine juvenile
ID=44 Pengornis adult
ID=45 Shenqiornis adult
ID=46 Struthio adult
ID=47 Struthio juvenile
ID=48 Yixianornis adult
ID=49 Pterocles adult
ID=50 Chauna adult
ID=51 Opisthocomus adult
ID=52 "Byronosaurus" perinate

Does Confuciusornis really have a skull configuration like juvenile Alligator?

EDIT: The issues have been resolved.  The short version is that the wireframes are not actually of the specimens, but rather what the average specimen with that same gross skull shape and the minor variables that correlate with it would look like.  The long version is here.

Bhullar et al. (2012) have a recent paper that is getting a lot of press.  Its thesis is that bird skulls resemble those of juvenile theropods, and I agree.  I do have a problem with one of their figures though, showing how juvenile Alligator and Confuciusornis supposedly have an almost identical skull configuration.  First I wondered why use Confuciusornis, as it has a skull which is "very unusual for basal birds, with its robust construction, highly reduced antorbital area, etc.".  I commented on this at Jaime's blog, and Bhullar replied there that "Confuciusornis was just one example; we could as easily have used one of the enantiornithines, for instance, and the skulls would have been almost as similar. The early avialans in general cluster with the juvenile/embryonic archosaurs. Moreover, apart from the premaxilla, which is a very separate developmental module derived from a different embryonic primordium and patterned by different genes, Confuciusornis does _not_ have an especially reduced antorbital region compared to other early avialans. Rather, it’s square in the middle, shorter than Archaeopteryx and similar to a juvenile enantiornithine."  Being skeptical, I made my own wireframes...

Bhullar et al.'s figure 4, with Confuciusornis and nearly identical juvenile Alligator outlines on the right.

Bhullar et al. used Confuciusornis specimen GMV-2132, which is a good choice as it is largely uncrushed and articulated, except for a posteriorly displaced lacrimal.  It can be seen in figure 10 of Chiappe et al. (1999).  Here's my attempt at making a wireframe based on the landmarks Bhullar et al. used.

Er... doesn't really look the same, does it?  Below are the wireframe superimposed on the skull (which has only been altered by moving the lacrimal forward, and erasing fragments that were in the orbit and naris), plus figure S1 from their paper to show the landmarks used, so you can judge my accuracy for yourself.  Some points had to be estimated, while others such as those involving the prefrontal don't exist in Confuciusornis.

Here's the closest fit I could get between Bhullar et al.'s wireframe and the skull.  So now my big concern is how Bhullar et al. even got their data.
The beak isn't even close, being too blunt with a tiny anteriorly positioned naris and anteriorly placed antorbital fenestra, while the braincase is too posterodorsally expanded.

Further, Bhullar claimed the juvenile enantiornithine would be almost as similar, and that its antorbital region is similar to Confuciusornis besides the premaxilla.  The enantiornithine in question is LP-4450-IEI, described by Sanz et al. (1997), whose reconstruction Bhullar et al. used for their wireframe.  Below is my attempt (Confuciusornis on the left, LP-4450-IEI on thr right), again with an overlay of figure 3C from Sanz et al. so you can judge the accuracy for yourself.  Notice that even ignoring the premaxilla, Confuciusornis has very short nasals and antorbital fenestra, a small, vertical and posteriorly placed ascending maxillary process (which is possibly all the medial wall of the antorbital fossa, making it even more dissimilar to the enantiornithine which preserves no medial wall), and no anterior lacrimal process, all of which show up in my wireframes.  I've also included Bhullar et al.'s version from their figure 3E, and I honestly don't see how they got it.

Here's the closest overlay of their wireframe with the skull I could manage-

The premaxilla is way too long, the snout decurved, the dorsal jugal process sitting in the orbit, they attached a point to the tip of the pterygoid/orbital process of the quadrate (which is not one of their points, as seen on Herrerasaurus), the naris is tiny, the squamosal is given a large ventral process...  What happened?!

I think the above comparisons show that Bhullar et al.'s data is seriously flawed.  Originally I was just questioning the use of Confuciusornis, but now I see that the wireframes don't even fit the skull.  Just comparing Confuciusornis with their juvenile Alligator (figure 1b) shows the wireframes couldn't possibly be that similar-

At the very least, there are three external naris landmarks, and Alligator's is small and anteriorly placed, while Confuciusornis' is huge and mostly at the level of Alligator's lacrimal.  Or how about the seven laterotemporal fenestra landmarks, considering Alligator's anteriorly placed weird crurotarsan fenestra with the anteriorly projected quadratojugal?  How did Bhullar et al. ever get this amount of overlap?!

I've emailed Bhullar with a link to this page, so hopefully there will be a response.

References- Sanz, Chiappe, Perez-Moreno, Moratalla, Hernandez-Carrasquilla, Buscalioni, Ortega, Poyato-Ariza, Rasskin-Gutman and Martinez-Delclos, 1997. A nestling bird from the Lower Cretaceous of Spain: Implications for avian skull and neck evolution. Science. 276, 1543-1546.

Chiappe, Ji, Ji and Norell, 1999. Anatomy and systematics of the Confuciusornithidae (Theropoda: Aves) from the Late Mesozoic of Northeastern China. Bulletin of American Museum of Natural History. 242, 1-89.

Bhullar, Marugán-Lobón, Racimo, Bever, Rowe and Norell, 2012. Birds have paedomorphic skulls. Nature. 487, 223-226.

Monday, July 2, 2012

Silently combining taxa

Just a brief rant today.  Senter et al.'s (2012) Yurgovuchia paper includes Linheraptor codings in its Tsaagan OTU, and the fairly complete IGM 100/99 and 100/120 codings in its Parvicursor OTU.  Would have been nice to at least mention this in the Methods section so that I now don't have to go back and delete those Tsaagan codings I thought were due to Senter examining it firsthand but were actually from a genus which has never even had its synonymy defended. grr...