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Fossilized Melanosomes and Extinct Dinosaur Colors

Posted by tigerhawkvok on February 14, 2010 16:24 in dinosaurs , evolution , research , paleontology

ResearchBlogging.org

I may have fallen off the face of the planet, but it doesn't mean science stopped going. So, beginning with a bit of admittedly old news — we've determined the color of a few coelurosaurian theropod dinosaurs' plumage. It's the subject of a few papers that came out in Science and Nature two weeks ago (DOIs 10.1126/science.1186290,10.1038/nature08740, summary: 10.1126/science.327.5965.508). The trick, it turns out, was to use a scanning electron microscope (SEM) to look at the microstucture of the preserved melanosomes in the feathers.

Figure 2, DOI 10.1038/nature08740

a, Optical photograph. b, Strongly aligned, closely spaced, eumelanosomes preserved as solid bodies. c, Mouldic (that is, preserved as moulds) eumelanosomes (at arrow) a short distance above a layer in which the eumelanosomes are preserved as aligned solid bodies. d, Area (at arrow) comprising more widely spaced mouldic phaeomelanosomes surrounded by less distinct, aligned eumelanosomes (top of image). e, Gradational boundary between areas dominated by eumelanosomes (longer arrows) and phaeomelanosomes (shorter arrows), both preserved as solid bodies. Scale bars: a, 50 mm; b—e, 2 µm.

If you can work your way through this paragraph, you can also see why this discovery is not just a novelty, but scientifically interesting (I don't think I can phrase it better):

Integumentary filaments occur both in non-avian theropods that possessed true pennaceous feathers (for example, Caudipteryx) and in those in which the latter are absent, such as Sinosauropteryx, Sinornithosaurus and Beipiaosaurus. The report of superficially similar unbranched filaments in the ornithischian dinosaurs Psittacosaurus and Tianyulong suggests that such structures might be common to all dinosaurs. Many investigators have accepted that these various filamentous to feather-like structures are epidermal in origin and represent feathers; others have disputed this view, arguing, for example, that in the theropod dinosaur Sinosauropteryx they represent degraded dermal collagen fibres, part of the original strengthening materials of the animal's skin. Resolving this fundamental difference in interpretation is important for our understanding of the biology of the taxa in which they occur, but also has wider implications; if epidermal in origin, these structures will inform models of the evolutionary origin of modern feather and the timing of steps in the acquisition of this evolutionary novelty.

Wikified for your convenience


Figure 4, DOI 10.1126/science.1186290

Anchiornis huxleyi, as rendered in Li et al..

Well, it turns out that the preserved microfeatures of the integument on Sinosauropteryx and Sinornithosaurus bear strong resemblance to modern microstructures in feathers known as melanosomes, which are responsible for giving color to feathers. Further, they are located inside the preserved feathers in physical locations analogous to those in living dinosaurs (ie, birds). The Nature paper thus conclusively demonstrates that they are epidermal features of the animals, ie, not degraded bits of skin, collagen, and scales that merely resemble feathers. As a fun fact, it showed that the animals they looked at had black, white, and russet feather colorations, and even color variations along single feathers and colored crests. The Science report suggests that Sinosauropteryx even had banding along its' tail.

Figure 5, DOI 10.1126/science.1186290

Cladogram of feather coloration, from Li et al..

In side-news related to the series of dino discoveries, the discovery of an early alvarezsauroid pretty much once and for all deflated the arguments of Alan Feeduccia. He had essentially resorted to temporal arguments (i.e., Archaeopteryx was older than the oldest found non-avian eumaniraptoran dinosaur) to state that Aves must have had a seperate, basal archosaurian/avesuchian ancestory, not nested within Dinosauria. Goodbye, so-called "temporal paradox". Now I just need to get people to stop saying the K-Pg event wiped out dinosaurs, and get them to insert non-avian in there. Remember, encourage evolutionary/cladistic thinking whenever you can!

Zhang, F., Kearns, S., Orr, P., Benton, M., Zhou, Z., Johnson, D., Xu, X., & Wang, X. (2010). Fossilized melanosomes and the colour of Cretaceous dinosaurs and birds Nature DOI: 10.1038/nature08740


Archosaur Lungs

Posted by tigerhawkvok on January 20, 2010 12:45 in dinosaurs , evolution , biology , herpetology

Just a quick update, before I head to Indiana to visit Purdue and my friend Jessica. I realize I missed yesterday's tetrapod, but I prefer to postpone a week and post a better update rather than a very breif post every week (look forward to sea snakes next week).

In this week's science, there is a paper describing unidirectional airflow in alligator lungs, strongly suggesting that this formerly "avian-style lung" is in fact an archosaurian synapomorphy. That is to say, this paper gets as close as a single paper can get to outright saying that this is a mechanism that helped nonavian dinosaurs get so large. Archosaurs just keep being awesome.

On somewhat related news, I think I'll try to put up a few evolutionary YouTube videos. Rather than a pure bash-on-creationist style, though, it'll be focused on describing particular evolutionary lineages and evidence. We'll see how that works out, though I need to become much more familiar with movie editing software.

Basal theropod, with interesting implications

Posted by tigerhawkvok on December 10, 2009 15:35 in dinosaurs , evolution , paleontology

Now, this is actually an interesting piece. according to LiveScience, a new basal theropod dinosaur, Tawa hallae has been found in lower Triassic New Mexico rocks, dated at ~213 MYA. The paper is due to be published in the December 11th issue of Science, after which I'll post more.

However, LiveScience implies that there is reason to believe that T. hallae was covered in filamentary integumentary structures, adding to the evidence suggesting filamentary integument was at least basal to dinosauria (interesting blog post on that topic, though this find, if LiveScience's implications are correct, would invalidate his point (5).)

To avoid needless speculation, though, I'll avoid talking more about it right now, and instead post a longer entry on it in the next few days when I can look at the actual paper. But I'm looking forward to it!

Crowdsourcing Science

Posted by tigerhawkvok on September 10, 2009 19:37 in dinosaurs , research , paleontology , internet

Mike Taylor, Matt Wedel, and a bunch of other folks have gotten together with an ambitious project: to crowdsource science. While this may seem bizzare at first glance, the idea is that there are many, many papers out there, with all sorts of information that can be useful — and in this case, they're looking for measurements on ornithischian limb bones. So, enter the Open Dinosaur Project. For science, for acknowledgements, or for possible co-authorship, just head on over, give it a quick read, and start contributing!

If you want to dive right in, just go straight to the page for contributors.

On a more personal note, this project has re-invigorated me to start looking at the last bits of data for my paper ... it's been sitting idle for too long, it's time for it to get out! It means I need to do some more proofing of it, in addition to filling in the empty bits — if anyone is interested in proofing, let me know.


Dinosaur Proteins

Posted by tigerhawkvok on May 04, 2009 18:45 in dinosaurs , biology , paleontology

ResearchBlogging.org

So, a quick read over the Science news this week led to an interesting news brief (DOI: 10.1126/science.324_578) about a paper that expanded on the 2007 claim that T. rex collagens were recovered (DOI: 10.1126/science.1165069 ; 2007 article DOI: 10.1126/science.1137614). [Edit: And my lagging on my Nature RSS also shows that Nature also had a very similar report (DOI: 10.1038/news.2009.422) ]

Brachylophosaurus composite image

Composite picture of Brachylophosaurus. Color pictures from Wikipedia, reconstruction copyright Scott Hartman.

So, a refresher for those who don't remember: Back in 2007, Science published a paper that stated proteins from collagen fibers were recovered from a T. rex sample. While fascinating, the paper received much skepticism over the method, and this paper attempts to address that issue with a new genus and much more strictly controlled procedures.

By demineralizing the bone matrix of the fossil, and comparing it to a Struthio sample, the authors identified protein fragments with FESEM analysis and then checked for reactivity with antibodies to avian collagen I, ostrich whole bone extracts, and a specific epitope. The first two showed reactivity, but the last did not, indicated that this was either a novel epitope or simply not preserved. There were further antibody test against elastin, laminin, and hemoglobin (all associated with blood vessels), with were all also positive.

One of the more interesting points brought up in the article that wasn't really addressed in the news brief (though it certainly need much more research and a larger sample size) was that the antibodies (to ostrich bone extracts) used in the preparation to test binding to the proteins bound more strongly to the hadrosaur proteins than to G. gallus (chicken) proteins. If this result is consistent across more testing, it actually provides another reference point to the (uncontroversial) status of Paleognathene birds being basal to Neognathae.

Another big issue with the 2007 paper was the mass spectrometry. Its results were considered to be possibly contaminated with bacteria, and too close to noise level. In this experiment, the machine used was more sensitive, and analysed at two labs. The authors still found collagen peptide sequences.

< !-- Clade Image --> Cladogram from the paper

Cladogram from the paper. Copyright the authors.

When phylogenies were inferred from the collagen sequences, the results were consistent with inferences based on genetics and the fossil record. The sampled onithodirans ended up collapsing into a three-way polytomy, with Brachylophosaurus and Tyrannosaurus resolving as related to each other closely, but the relationship between the non-avian dinosauria and the sampled neornithines remained unresolved. This problem remained even with the removal of T. rex from the phylogeny, still leaving a three-way polytomy. The authors point out that there was, for obvious reasons, a fairly low resolution in Dinosauria, but B. canadensis still resolved as a derived archosaurian, more closely related to birds than to Alligator.

< !-- Ideal Clade --> Ideal cladogram

The predicted clade, based on extensive fossil evidence.

Now, its important to note that though this is incredibly cool, this is a far cry from Jurassic Park. The proteins recovered from the collagen fragments are incomplete, and it is highly unlikely that even an egg of an ostrich would provide a suitable oocyte for cloning. That said, however, this certainly has the promise of making paleontology gain a genetic basis for phylogenetics to complement the fossil record. Though, as this study showed, there's a way to go yet.

As an aside, does anyone think it'd be useful for me to put in a DOI search box on the right hand panel?

Schweitzer, M., Zheng, W., Organ, C., Avci, R., Suo, Z., Freimark, L., Lebleu, V., Duncan, M., Vander Heiden, M., Neveu, J., Lane, W., Cottrell, J., Horner, J., Cantley, L., Kalluri, R., & Asara, J. (2009). Biomolecular Characterization and Protein Sequences of the Campanian Hadrosaur B. canadensis Science, 324 (5927), 626-631 DOI: 10.1126/science.1165069

Commentary on Sauropod Neck Posture

Posted by tigerhawkvok on April 30, 2009 00:24 in biomechanics , dinosaurs , sauropods , biology , paleontology

If you look at a (yikes! month old) Science "Letters", there an interesting, if brief, back-and-forth about sauropod neck posture between RS Seymour and PM Sander.

Up front, I'd like to say like Sander, I don't necessarily disagree with Seymour's conclusion; my own work (still undergoing revision that is halting its review process) strongly suggests that the necks were mostly held laterally, due to energetics and biomechanical concerns. However, I do take issue with the blanket scaling argument used on several points.

DSCF4647

Ara ararauna (Blue and yellow macaw), Hawaii

First, it is important to note that the work done by Seymour is based on mammalian modeling. I have no comment as to whether it strengthens or weakens his argument this way; however, as a saurischian dinosaur, a bird would be a much more convincing model point. Second, their morphology is wildely divergent even from birds, the closest living species to them. The anology, even to birds, would be as problematic for me as the biomechanical study that based T. rex on Gallus gallus (chicken). Merely being a close relative does not ensure analogy; the musculature distribution, posture, and body shape in both cases are significantly different from the model animal. The results might very well be interesting, but they are not sure be relevant at all.

While I also have some issue with the "plug and chug" nature of the blood pressure calculations, those you can't really get around — though I'd at least like to know if it was based on mammals or birds.

Well, that's my 2 cents for now. More later.

More on Hesperonychus

Posted by tigerhawkvok on March 17, 2009 15:03 in dinosaurs , paleontology

ResearchBlogging.org

A little bit on Hesperonychus...

I managed to get a hold the paper on PNAS (DOI: 10.1073/pnas.0811664106), and I thought I'd flesh out what I thought was the most interesting report yesterday. First, a bit of clarification: I mentioned that it is the smallest, non-avian North American dinosaur yet found, but "small" is relative. Most people, thinking of carnivorous non-avian theropods, think of superpredators such as Allosaurus fragilis or tyrannosaurids.

Size Chart

Relative sizes of North American theropods

Now, for many reasons, smaller specimens are not likely to be fossilized, despite being much more numerous than their superpredator bretheren. Being light of frame, they are more prone to scavanging, or direct physical damage to their remains. Thus, the fossil evidence becomes much more scant at lower mass ranges, and Hesperonychus is the first animal found in North America under 10 kg, under-massing Sauronitholestes langstoni.

Pelvic girdle

Hesperonychus pelvic girdle

Hesperonychus is further an interesting find in that it is a microraptorine dromaeosaurid (first one in North America), unlike other Dinosaur Park Formation dromaeosaurids found to date. The holotype pelvic girdle was discovered in 1982, but remained unidentified for a number of years (UALVP 48778, figure at right), but like many specimens, remained unstudied for a long time (25 years in this instance!). In addition to the holotype pelvis, Longrich et al. discovered a number of toes, including the typical sickle claw of basal dromaeosaurids. While superficially similar to the more infamous ones of Deinonychus, Utahraptor, and Velciraptor, the claw is less blade-like and resembles on close inspection (including on cross-section) that of microraptorines such as Rahonavis. The claw was quite small, only about a 1.5 cm long (projection, not along curve), but well-preserved. The precise cladistic placement of Hesperonychus is not particularly well defined, residing in a polytomy of various members of Microraptorinae. The number of phalaxes found (particularly phalanx II-3) suggest that there at least ten speciments in the TMP collections — when recognizing species by that element, for comparison, only 2 Dromaeosaurus specimens have been found, suggesting that Hesperonychus might have in fact been quite common in its day. This is especially true in light of how difficult preservation would have been!

Phalanx

Hesperonychus "sickle claws"

It is finally worth noting that even though this is a tiny dinosaur at 1900 g, it outmasses the largest metatherian (early marsupial mammal) Eodelphis by 150% (600 g). Yep, mammals — still puny!

Longrich, N., & Currie, P. (2009). A microraptorine (Dinosauria-Dromaeosauridae) from the Late Cretaceous of North America Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0811664106

Please respect image copyright of the authors, and contact them for permission if you plan to use their images. Thanks!

Fossil finds, oh my!

Posted by tigerhawkvok on March 17, 2009 03:24 in dinosaurs , sauropods , news , paleontology

Seems that the news has been an bit heavy on the fossil finds! How about a rundown.

Hesperonychus claw, hotlinked via National Geographic. The claw is on a Canadian penny.

First up is Hesperonychus ("western claw") — as yet, the smallest theropod found in North America. At the time of this writing, the PNAS paper isn't up yet, but in particular PhysOrg has a pretty good synopsis. As the name suggests (via a linguistic kinship to Deinonychus), Hesperonychus elizabethae is a diminuitive dromaeosaurid, approximately 2 kg and 50 cm tall "beating" Albertonykus borealis for title of "smallest North American non-avian dinosaur". It retains the trademark "sickle claw" of the dromaeosaurids, and the hip configuration was one of the primary diagnostic traits used to pin it to dromaeosauridae. The pelvis is also fused, suggesting that this was a mature adult. It's dated to about 75 million years ago (which the PhysOrg article accidentally writes as 45 million years ago, obviously in error at 20 MY after the K-T event).

Picture of the Svalbard excavation, from the New York Times.

The next big find announced today was of an unnamed, massive pliosaur found in the Svalbard region. I'm outright going to say I wish Kit had something to say about this, as I vaguely recall him mentioning this almost a year ago, and he knew some basics about it already. Never mind how he knows, considering it hasn't been published yet — the NYT article is already a pre-publishing press release.

At any rate, this guy was massive. This pliosaur had a skull measuring over 3m long, and the entire animal was probably longer than 15m at over 40 tonnes. Its "nickname" for now is "Predator X". Particularly novel about this find is that it might represent a new family of pliosaurs, which would be rather significant, paleontologically. Initial biomechanical work suggests its bit force would be 2-4 times that of T. rex and more than 10 times that of any extant animal. It was estimated to live about 150 MYA.

Figure 1 from Mud-trapped herd captures evidence of distinctive dinosaur sociality by Varricchio et al. 2008. (property of the authors)

Sinornithomimus dongi (Chinese bird mimic)is the next guy to hit to press. It has the slightly dubious distinction of being discovered when a large immature herd got stuck in a mud trap. It is siginificant in that the herd was apparently all juveniles, and in the number of animals found. With 25 individuals found (aged 1-7), this promises to make Sinornithomimus particularly well described. This was a bit of a late reporting on a December 2008 paper by Varricchio et al., which I've not had a chance to go over yet. I might update this with more detailed information once I get the chance.

Finally, SV-POW has an interesting piece up on Brachiosaurus. I'd strongly suggest you read it. And, for kicks, I adapted Matt's image into something nice and widescreen-background sized:

I swear, I will post Higgs and the mouse post ...

Nature: Chixulub impact did not create global wildfires

Posted by tigerhawkvok on February 23, 2009 17:06 in dinosaurs , news , paleontology

An interested news update from Nature today: apparently, the K-T impact's (Chixulub event) [wiki, UCMP] global soot layer was not caused by vegetation, and was probably due to hydrocarbons. That is to say, the impact probably burned sequestered gas and oil.

Impact, artist rendition

The writing was on the wall for the vegetation idea for a few years, since 2003 studies showed a comparative lack of charcoal, which one would expect for global wildfires. This was supplemented by research done by Belcher et al in a PNAS paper showing that polycyclic aromatic hydrocarbons (PAHs) ratios match that of burnt hydrocarbons better than that of vegetation. So, no global wildfires. However, it *is* important to note that the massive amount of soot produced itself had a global environmental impact. No matter how you dice it, the K-T event was not a fun time to be around.

Velociraptor wrists

Posted by tigerhawkvok on February 19, 2009 02:49 in biomechanics , dinosaurs , biology , paleontology

The promised science post!

Rewatching Jurassic Park, I wanted to correct a rather small, but important and understated error.

There's a hint in the URL, of course. The answer? The claws — they're held horribly, horribly wrong.

Jurassic Park Velociraptors are named after Velociraptor mongoliensis, and modeled after a hybrid between the genera Deinonychus and Utahraptor. At the time the novel was written, there was some talk of moving Deinonychus into the genus Velociraptor, which was the convention followed by Micheal Crichton, though this didn't play out. However, all of these were dromaeosaurids, which are eumaniraptorans. In fact, Dromaeosauridae is the group closest to but outside of Aves. So, all members of eumaniraptora have a synapomorphy list that includes a "semilunate carpal".

Sinoris manus

Sinornis santensis manus

Tanycolagreus manus

Tanycolagreus topwilsoni manus. Scale in cm.

Cathayornis manus

Cathayornis sanctis manus.

All three of the pictures above show this semilunate carpal in other maniraptorans. Unlike most mammalian wrists, it cannot flex perpendicular to the radius-ulna plane (ie, what we would most commonly accept as perpendicular to the groud). Instead, its motions were restricted to that plane, giving a jacknifing motion, much like a flight stroke. This was an optimal grasping motion for prey, and good for grappling large prey, and was easy to adapt into a flight stroke (particularly given the presence of primary feathers on some dromaeosaurids).

Sadly, this does mean that the raptors couldn't open doors. They would have broken their wrists trying to make the motion!

Image citations:

  • Carpenter K., Miles C., Cloward K. New Small Theropod from the Upper Jurassic Morrison Formation of Wyoming. In "The Carnivorous Dinosaurs" (ed. Kenneth Carpenter), 2005.
  • Sereno PC., Chenggang R., Jianjun L. Sinornis santensis (Aves: Enantiornithes) from the Early Cretaceous of Northeastern China. In "Mesozoic Birds: Above the Heads of Dinosaurs" (ed. Luis M. Chiappe and Lawrence M. Witmer), 2002.
  • Zhonghe Z. and Lianhai H. Mesozoic Birds in China. In "Mesozoic Birds: Above the Heads of Dinosaurs" (ed. Luis M. Chiappe and Lawrence M. Witmer), 2002.

Paper Creep

Posted by tigerhawkvok on May 29, 2008 17:13 in General , biomechanics , dinosaurs , sauropods , computers

As I've been working on the sauropod paper (aside from feeling a bit neglectful of Kepler), I've definitely felt the wish to "feature creep". For those unfamiliar with the term, its one I borrowed from computer program development; its the wish to include ever more "new" stuff into a program that you're writing, often to the detriment of timeliness. Aside from finding ever more species to want to add to my analysis, I find that I am having a difficult time finding the line where I say "enough -- I've explained this to my satisfaction." There are some legitimate holes that are left over from its "essay" form, such as comparisons on different ways of getting the taper constant, ways of extrapolating neck length and accuracy, and even I can't remember what I did to find the trunk length.

I also was a bit lax about my citing in the initial essay (oh, the usefullness of BibTeX -- I wish I knew it sooner. Kudos to Kit for helping me out there), I also really want it to look nice.

So, with its current state of revisions, it is being looked at by Sara W, Sarah W, Sarah K, and Andrew. Hopefully, it will be ready for submission by the end of June, July at the latest. Sarah (K) brought up a good point though -- where to submit it? Its hardly Nature or Science quality, but that still leaves:

1) Journal of Paleontology
2) Paleontology
3) Historical Biology

As the prime candidates at the moment. Hm. I'm leaning towards Historical Biology, but we'll see.

Hopefully this will be out of my system by the time Hawaii is over -- then I can do some solid astronomy. Helps that that's the one I get paid for, too.