Fly my pretties, fly!

This was originally posted at: http://blogs.egu.eu/palaeoblog/2013/03/20/fly-my-pretties-fly/

The origin of bird flight is one of the greatest stories evolution has ever told us in the history of life on this planet. To imagine how organisms that once ran around on the ground have descendants that soar through the skies is truly phenomenal, and represents a truly great leap in increasing the awesomeness of these animals. The secret of how it came about though is hidden away in the fossil record, with the mysterious tale ever-shifting as our understanding of early birds and feather precursors evolved.

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Gender confusion in Confuciusornis? Not any more!

Among the many issues with the fossil record is the case of gender identification. In modern organisms, it is usually pretty easy to tell which members of a particular species are the males and which are the females. This can either be through consistently perving on them to figure it out during copulation, or some aspect of their morphology, such as antlers, or you know, a penis or vagina. When it comes to fossil though, we often don’t find these typical gender-distinctive aspects of morphology preserved, as they are usually lost in one form or another to the ravages of time and the process of fossilisation.

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A new feathered dinosaur – worth getting ruffled for?

Two new feathered dinosaur articles appeared in the latest edition of Nature Communications; one on gender identification in a well-known theropod (the meat noshing ones), and the subject of a forthcoming blog post, and another on a new feathered fiend from, surprise surprise, China.

I normally really don’t like writing about theropods, especially of the feathered variety, as it just seems like I’m jumping on the bandwagon that they were awesome and every aspect of them needs extensive media coverage. Ok, yeah, they can be pretty cool. But only, for me, in the context of the larger evolutionary patterns that they can reveal to us, such as the evolution of feathers and flight. Each new fossil doesn’t exactly transform our knowledge of this, but they do help us to refine our theories to a certain extent; whether or not that’s worthy of excessive media coverage and Nature publications, is not my judgement to make (no, it’s not).

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How to destroy generations of childhood memories in an instant: Yutyrannus huali

Childhood memories of dinosaurs have received another shattering blow today. The latest culprit is Yutyrannus huali, a large basal tyrannosauroid from the lower Cretaceous of China, complete with elongate integumental filament structures, or ‘protofeathers’. The etymology is quite special, says lead author Xing Xu, translating into a blend of Mandarin and Latin as ‘beautiful feathered tyrant’. This species is the latest wonder to be exhumed from the fossil treasure trove known as the Yixian Formation, a series of volcanogenic and lacustrine deposits that are currently guiding and re-working our understanding of dinosaur evolution. Of course, being such prominent study, Nature saw fit to pop it behind a $32 paywall.

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Did Archaeopteryx Really Have Black Plumage?

Not surprisingly, the latest Archaeopteryx study has kicked up quite a stir within the media and scientific realms, considering the iconic status it has attained since discovery some 150 years past. This latest paper by Carney et al. and published in the journal Nature Communications claims to have resolved the plumage colour of a feather possibly from  Archaeopteryx, a pretty neat little addition to the reconstruction of this critical species. They use methods employed during previous studies, namely the morphological or structural analysis of melanin-bearing organelles within feathers called melanosomes to infer that Archaeopteryx possessed an entirely black plumage.

The notorious black feather (Image Copyright: WitmerLab at Ohio University)

There is no doubt that the structures are in fact melanosomes, and no doubt that melanosomes contribute to plumage colour. But the question is, how much do they contribute to the plumage colour..? Well, I don’t know. In fact, no-one knows, at least in extinct avian theropods. The authors don’t discuss this either. It has however been discussed elsewhere in similar studies, albeit only qualitatively and in passing.

One comment is from Zhang et al. 2010: “Melanosomes are lyosome-related organelles of pigment cells in which melanins are stored and are responsible in part for the colours exhibited by modern birds.”

And Li et al. 2010: “Other molecular pigments such as carotenoids and porphyrins also produce plumage colours but are not preserved morphologically, thus we cannot address their possible effects here.”

That seems like a pretty big caveat. It’s like saying if you mix green, yellow and red paint in unknown quantities, you get red every time. Or something similar, I suck at analogies. The point is, if in modern birds, there are other significant structures that dictate or contribute towards plumage colour, does it make sense to try and predict colour when these are absent?

UPDATE: Ryan has been kind enough to clarify this point in a comment below.

Furthermore, the 95% confidence intervals the authors use are practically useless. Look at the ordination provided in Figure 4 (not sure if I can copy it here, so won’t..).  These 95% confidence ellipses mean nothing in the slightest, or at least nothing meaningful. What they should have shown is an envelope includes 95% of all points within a sample, so that when you insert data ‘blind’, if it falls within a completely discriminated envelope, you can be 95% certain that it belongs to that group (i.e., 95 times out of 100, a blind data point will be correct). The envelopes shown in figure 4 clearly do not show this (if you don’t have access to the paper, ask me for a copy, or take my word for it). As a result, the points calculated for the particular Archaeopteryx feather analysed could really be grey or black, or maybe brown at a push (the number of colour choices is simply overwhelming..).

So was Archaeopteryx lithographica black?

Probably, probably not.

Carney et al. (2012) New evidence on the colour and nature of the isolated Archaeopteryx feather, Nature, DOI: 10.1038/ncomms1642

Li et al. (2010) Plumage patterns of an extinct dinosaur, Science, 327, 1369-1372

Negro et al. (2009) Porphyrins and pheomelanins contribute to the reddish juvenal plumage of black-shouldered kites, Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology, 153(3), 296-299

Zhang et al. (2010) Fossilized melanosomes and the colour of Cretaceous dinosaurs and birds, Nature, 463, 1075-1078