Archive for December, 2008



Pteranodon sternbergi

pteranodonI rediscovered this image in my files this week and thought it would make for a great short post. It was done for me by palaeoartist / palaeontologist Andrea Cobbett (who is working on her PhD at Bath University) as part of a series of articles on pterosaurs I did for the kids geology magazine Rockwatch.

This is the head of Pteranodon sternbergi, by far the lesser known of the two species of Pteranodon. The infinitely more familiar P. longiceps has the elongate crest that extends to the rear and which largely mirrors the general shape of the head, whereas P. sternbergi has a far wider, shorter and more erect crest. Apart from that there is little to separate the two species, but it’s a pretty dramatic difference.

Monophyletic, Paraphyletic and Polyphyletic

Having covered the basics of taxonomy and how to read phylogenetic trees it is long past the time I should have dealt with the concept of monophyly and it’s ‘ugly sisters’, paraphyly and polyphyly. While the terms might be unfamiliar, the concepts behind them are simple and practical and I suspect at least a few readers will actually know them even if they couldn’t actually say what they were (so to speak). The three terms all describe different ways of grouping taxa together and are most easily demonstrated on a phylogentic tree (though they don’t need one as such).

Monophyly, paraphyly, polyphyly

Monophyletic groups and lineages are the fundamental basis of taxonomy and evolution as a whole really. Everything within a monophyletic group is the descendent of a single common ancestor and thus are the clades we typically talk about in biology and palaeontology. Here the clade comprising taxa A, B, C and D is monophyletic. Everything that descends from the ancestral lineage or organism that existed at the point marked by the red arrow belongs in that clade and thus it is a monphyletic group. Should we later discover any new relatives that fit anywhere in the tree above that point then they would also by definition be part on that monophyletic clade. Obviously the clade A-D is not the only monphyletic one in this tree, one could name a clade of just A & B, or A-F and this would still be monophyletic.

Paraphyletic groups do not include all of the descendents of a single common ancestor. This means that while the group has a common ancestor, we are artificially ignoring a subset of its descendents. Here the green arrows indicate first the monophyletyic group which we are considering (A-F) and then the second monophyletic group (A & B) that we are not considering, thus leaving us with the paraphyletic clade of C-F. As before, there are other ways of creating a paraphyletic group on this tree and I am merely illustrating one.

This might sound odd, but paraphyletic groups are still used as they have a practical value for describing some groups. The most obvious ones to readers here are the dinosaurs. Birds are dinosaurs, that is, they are the direct descendents of an ancestor that spawned the dinosaurs, yet palaeontologists typically refer to dinosaurs while explicitly not referring to birds. Thus one should formally call them non-avian dinosaurs (basically all dinosaurs except birds) and this does happen quite regularly, thought not always, and certainly not in the press. Two others are worth of mention, one as it relates to this blog regularly and another as a striking example of a paraphyletic group. First off the rhamphorhynchoid pterosaurs (or more properly ‘rhamphorhynchoids’ as the quotes denote it as paraphyletic) which often come up here in my frequent posts on pterosaurs. As with non-avian dinosaurs, the term persists as one of convenience as basically it’s easier to write than “non-pterodactyloid pterosaurs” (or a more extreme example, one can call Plaetosaurus a ‘prosauropod’, or a “non-sauropodan sauropodomorph”). Finally there is the most obvious group of all – fish, or rather ‘fish’. Yes fish are obviously paraphyletic since all vertebrates have a single common ancestor, but tetrapods descended from them but no-one calls mammals or birds fish do they?

Polyphyletic groups are those which have multiple origins and thus do not share a common ancestor or indeed much in common at all aside from whatever trait holds them together. Here the various blue highlighted taxa have been pulled together into a polyphyletic group, and again one could do this in a great many ways on even this small tree. Polyphyletic groups are rarely mentioned (for obvious reasons), but they do come up occasionally when a revision has led to a previously monopyletic or even paraphyletic group being declared polyphyletic as a result of some systematic rearrangement (e.g. ‘we have found that taxa X and Y are not members of clade Q and actually belong to two different clades, thus the clade Q under its current definition is polophyletic and a new definition is required that excludes X and Y’). One obvious example from history is the pachyderms (elephants, rhinos and hippopotamuses) which of course all belong in different mammalian families and were put together based on a few minor characters of their skin.

Hopefully that makes everything clear and explains the fixation with the term monophyletic that often springs up on dinosaur forums (and indeed evolutionary ones in general). Monophyletic groups are the only taxonomically and systematically viable ones – that is they represent evolutionary history. As stated paraphyletic ones are useful for rhetorical simplicity, provided everyone is clear that they are paraphyletic and in what sense they are being applied. Polyphyletic ones are never used, except when referring to changes in taxonomic status, or of course in the most general terms (‘bipeds’ are polyphyletic).

 

………………………………..

Just a small and very late addition – I’ve noticed this one page gets a hell of a lot of traffic which is never brought in from search engines or linked from other sites and seems to boom and bust on certain days. I’m sure that’s because this is being used as a teaching resource and lecturers are pointing out the url to students. If so, great!, but I’d love to know if that’s the case. If you’ve been sent here by your professor, please put a comment in below and let me know which college / uni you are at. Thanks.

Limulus tracks

Despite the title of this blog, I am a genuine enthusiast of pretty much all animals, though like most I am certainly far more partial to hypercharismatic megafauna* (an apparent piece of horrible corporate-speak but actually a genuinely useful term, c/o Desmond Morris) than others. Despite my bias, this is one of my favourite fossils of all time, and sadly the photo really does not do it justice.

As many palaeontologists will tell you, and as I mentioned recently with the new Chinese theropod tracks, working out which animals left which tracks can be a very tricky thing indeed. What you *really* need therefore is something like this to help you out:

100_0619

This poor little Limulus (that’s a horseshoe crab) was tottering along on the bottom of a nice lagoon leaving a beautiful trial of tracks for future palaeontologists, right up to the point where he snuffed it and he himself was covered. Yep, this is one of only a handful of fossils worldwide where we have both the tack and trackmaker in direct association such that the identity is pretty much unambiguous. This is of course incredibly useful if you want to know what kind of tracks these animals leave, and also just an amazing fossil.

It comes, perhaps not surprisingly, from the German Solnhofen beds that yield Archaeopteryx (the urvogel), numerous pterosaurs (hooray) and plenty of other fossil life including numerous insects, plants, marine reptiles and rarities like squid and jellyfish (yep, they *do* have a fossil record). Even so it’s an exceptional piece about three metres long (it carries on to the right for soem way, the crab is only about 15cm across) and of course it is a wonder that not only was it found, but recognised for what it was (not may people bother to collect invertebrate trackways, well, not huge slabs of them) but that it was recovered unbroken and in superb condition. You can see it at the Jura Museum, base of the great Helmut Tischlinger and a number of other famous fossils including an Archaeopteryx, the dimunitive theropod Juraventaor, and plenty of important pterosaur specimens.

* If you had not worked it out, it basically means ‘big exciting animals’. It was originally intended to be somewhat tongue in cheek I think, but it has gained a certain popularity.

How to read a phylogenetic tree

Nowadays even the media seem quite happy to occasionally put up a phylogenetic tree as part of their scientific coverage, and they are proliferating on the internet on websites, research papers and blogs, in addition to books and magazines. However, while it is hardly difficult to get the gist of a tree, there is a certain skill and amount of knowledge that needs to go into pulling out all of the information correctly from a tree. It is easy to make mistakes about what a tree actually tells you so hopefully I can clear up a few misconceptions about tree creation and how trees should be read.

Continue reading ‘How to read a phylogenetic tree’

Batman

p1000215In my post on the Museo del Desierto. I noted that they have some nice innovations in their displays and this is one that I was especially impressed with (apparently in some bizarre way a left-over from a touring exhibit sponsored by Pepsi – how or why, I have no idea). As you can see they have mocked up a bat skeleton to the size of a person to really demonstrate the homology of all the various parts of the mammalian skeleton. It’s easy to see how all the main limb and trunk bones match, not just in terms of basic number and position, but also in terms of the articulations and subtleties of shape and so on. It’s simple enough, but nice and dramatic, and of course the details are easy to see when they are this size, and humans are always going to be a brilliant frame of reference for the average museum visitor or child.

No ado about much – new dinosaur footprints from China

There are great papers that get all the attention that they deserve, great papers that don’t get the attention they deserve, bad papers that get attention they don’t deserve and one that get just the right amount. This is one of the latter. Not, I would hasten to add, that it is not a good paper but simply that I would be surprised if many people outside of the dinosaur ichnology crowd would be particularly interested and perhaps not even them.

Continue reading ‘No ado about much – new dinosaur footprints from China’

Urvogels again

archaeo002Time for another Archaeopteryx, this time the Thermopolis specimen, the only one oused outside of Europe. I was fortunate enough to catch this while on display in Karlsruhe and though again the specimen was behind glass, a few photos came out weel enough that I thought people might want to see. This specimen, as some of you may know, caused a fiat botof controversy over it’s ownership, and to be perfectly honest I am really ot sure what its current status is.

Anyway, it is in superb condition and unlike the Solnhofen specimen I mentioned recently, was prepared superbly. Also important in Archeopteryx-ian terms is the preservation not only of excellent feet, but of the leg feathers as well (as notably lost in the Berlin specimen).

AABQOTW 4

This time out we move onto extant archosaurs and the question of why would some birds lose the power of flight?

As ever the answers are available here. This is a good illustaration of a few points on evolution however – birds went to quite a lot of trouble to evolve flight (so to speak) so why was it lost (really quite often – ostriches, kiwi, great auk, penguins, dodo, kakapo, Sephen’s Island wren among plenty of others)? Flight is of course just one component of bird life and bahaviour, and its evolution and maintenence is a huge energetic cost which between them can provoke a variety of situations under which flight may be lost.

The research hydra

I really should stop writing blog posts in exchange for doing some work, but no matter how self-inflicted my workload is, this is cathartic (and part of my lunch-break). It really does seem that for every project I finish (or finish contributing to) two more spring up (or even three or four) and I am buried right now in half-finished and unsubmitted papers.

While many are on temporary or long-term hold (waiting for contributions from colleagues, access to certain specimens, money or all three) more than enough are ‘active’ enough to keep me going for a couple of years. Which would be fine were it not for the fact that I certainly do not have two free years to get the work done in, and there is plenty on the back-burner that also needs attention. What I need to do is get some of them finished, but that is far easier said than done, and it takes a huge amount of time. You might get something out the door (i.e. submitted) but it will still be there for another year or two until it is actually in print, demanding your time on occasion.

Jerry Harris made the great point that “the hardest thing to learn was when to say no to cool projects”, I just wish he’d told me that a couple of years back.

Slackademic

slackademic

Ok, so I stole the pun from here , but it is brilliant. I sense a T-shirt series in the offing.

Taxonomy

Time for another ‘science basics‘ post and this time out I’m tackling the often complex and misunderstood field of taxonomy, quite simply the naming of things. It is quite possibly the most fundamental and important part of biology as a field and yet seems to be glossed over in the few undergraduate courses that even bother to mention it, which is both a shame and a worry. Why is it so fundamental? Well for the quite simple reason that if you do not know what species any given organism belongs to, then it becomes very hard to say anything meaningful about it. How do you protect a given species if you don’t even know what is and what is not a member of that species? Want to treat a snake bite? What species was it? Got a new drug from a rare frog, great! What frog was it? Are you working on a single species of a bunch of them in your lab that have just not been revised properly? You can see the issues – there is a basic one of clarity (all scientists want to be able to communicate clearly about what they are dealing with) but the consequences of making sure that is the case go far beyond that and touch every branch of biology.

Continue reading ‘Taxonomy’

More on bone degradation and disintegration

I recently wrote about scavenging and the odd effects it can have on corpses , and of course how that can affect what you might find as a palaeontologist. While I could always see how odd bones and body parts (like a whole hand) could go missing, one thing that had puzzled me was how you could find parts of skulls with others missing. Of course erosion can lead to pieces being worn away before the specimen is found, and perhaps not all of the cranium was buried originally and thus not fossilised. Some skulls of course also get smashed or broken, so that is another possible explanation, but these were not always in evidence, so what else could it be? Given how (in adult animals at least) the skull is often a tough piece and the sutures of the individual bones are all nicely sealed, it still struck me as odd that sometimes you could find several disparate parts of the skull apparently well preserved, and even in association with other parts of the skeleton but with the rest missing. What had happened to the rest? How had it broken along suture lines without damaging the individual parts? If it had taken a beating then why where the pieces in such good shape and where were the others since the rest of the skeleton was there?

p9196270

Well one explanation at least came up with this skull (another from the Mexican equid graveyard). As you can see it has simply been out in the sun a long time and while the bones are still in great condition, the sutures have all split and the skull is literally coming apart at the seams. I rather suspect this is as a result of alternating rain and sun, since the skulls I saw in the Chinese desert did not split like this, no matter how old and decrepit they were. It is only a partial explanation for the phenomenon of course, I am sure there are plenty of others out there, but it certainly appears to be one and interesting enough in it’s on right as a result.

Edit: not sure why some of the text went walk-about, I hope this has fixed it.


@Dave_Hone on Twitter

Enter your email address to follow this blog and receive notifications of new posts by email.

Join 548 other followers