davegodfrey: South Park Me. (Default)
When I was a lad I read every dinosaur book I could get my hands on. And this being 20+ years ago much of what I read then is now out of date. Pterosaurs are now always shown as furry, when then there were somewhat brief dismissive mentions of this "Hairy Devil" from the USSR. Sauropods have been rescued from near-certain death by suffocation from snorkeling about in lakes. (The pressure from water at this depth would have crushed their lungs and irreparably damaged their hearts had they tried this. The German physiologist Robert Stigler tried breathing through a six-foot tube and suffered heart damage as a result.)

But one thing was almost universal. Sauropods weren't doing very much in the Cretaceous other than dying out. From their heyday in the Late Jurassic, when Diplodocus Apatosaurus and Brachiosaurus stumped about the place, by the Late Cretaceous the world was full of horned dinosaurs, flamboyantly crested hadrosaurs, spiky club-tailed ankylosaurs and the like. Occasionally you'd find mention of Alamosaurus, a 21 metre 30 tonne sauropod from New Mexico. But it was usually in the "A-Z" type books and tended to get three lines if that.

Now it turns out that a fair bit of this is the result of historical bias. The USA and Canada were the scene of some very intensive collecting during the 19th and early 20th centuries, followed by Roy Chapman Andrews expedition to Mongolia. The rest of the world didn't get much of a look-in. Which is a shame, because in the rest of the world there doesn't seem to have been much of a change. Hadrosaurs and ceratopsians were largely an Asian and American specialisation, and in North America the sauropods seem to have died out completely for 30 million years before Alamosaurus turns up to see out the Cretaceous. But in South America, for example, the sauropods thrived, and grew to even bigger sizes than the Jurassic Morrison Formation ones that everyone knows (Brachiosaurus, and its African cousin Giraffatitan)- despite being relatively poorly known (and in some cases poorly measured) Futalognkosaurus, Argentinosaurus and Puertasaurus were among the largest dinosaurs known, dwarfed only by the semi-mythical Amphicoelias fragillimus.

The impression that I got all those years ago was that this dinosaur was small (relatively), and not exactly common. Which is utterly and completely wrong. Alamosaurus crops up all over the place, and is a very common dinosaur. And while the size estimates might not have got much of a mention (we are talking about the era when Brachiosaurus was supposedly weighing in at 80 tonnes- roughly double the modern estimate), Alamosaurus was still the biggest dinosaur in the USA at the time. And yet faced with all the crazy horned, crested, spiky chaps it still doesn't get much of a look in.

But with a bit of luck this might change, and poor ignored Alamosaurus might get back into the kids books. Denver Fowler and Robert Sullivan would like to introduce you to SMP VP-1625, SMP VP-1850, and SMP-2104. A portion of the femur, a neck vertebra and a tail vertebra respectively. They're big. Really big. Argentinosaurus-sized big.

So all those fantasies about T. rex versus the uber-sauropod just became scientifically viable. Woohoo!

Lehman, T.M. & Coulson, A.B. 2002. A juvenile specimen of the sauropod Alamosaurus sanjuanensis from the Upper Cretaceous of Big Bend National Park, Texas. Journal of Paleontology 76(1): 156-172.

D’Emic, M., Wilson, J., & Thompson, R. (2010). The end of the sauropod dinosaur hiatus in North America Palaeogeography, Palaeoclimatology, Palaeoecology, 297 (2), 486-490 DOI: 10.1016/j.palaeo.2010.08.032

Denver W. Fowler and Robert M. Sullivan (2011) The first giant titanosaurian sauropod from the Upper Cretaceous of North America. Acta Palaeontologica Polonica in press available, online 07 Feb 2011 DOI:10.4202/app.2010.0105
davegodfrey: Coelacanth (Science)
When discussing the fact that Torosaurus never existed, I mentioned that something similar had happened with Iguanodon.

Iguandon is one of the world's most famous dinosaurs, and its famous for being one of the first discovered. Initially described from teeth, by Gideon Mantell, it was reconstructed first as a colossal lizard, and then as a rhino-like quadruped with a horn on its nose. Later finds near the town of Bernissart in Belgium allowed Louis Dollo to show that the animal's "horn" was a thumb-spike, and the arms were considerably shorter than the hind limbs, giving the characteristic Fonz-style pose that many people are familiar with. Later work by David Norman, showed that Dollo had dislocated large chunks of the tail and that in fact the animal was largely quadrupedal.

Iguanodon being initially based on relatively poor material, as is so often the case has ended up as something of a "wastebasket taxon", with lots of indeterminate bits and bobs ascribed to it, and several species all lumped together. At the last count there was Iguanodon anglicus / I. mantelli, described by Mantell based on his teeth and other material, the gracile, I atherfieldensis, the Belgian I. bernissartensis, the American species I. lakotaensis, the Mongolian species I. orientalis,  and several other species from the UK, I. hollingtoniensis, I. fittoni, I. dawsoni (named after the perpetrator of Piltdown, Charles Dawson), and I. hoggi, often referred to the related genus, Camptosaurus. And that's just the species known from good material, or that have stayed in Iguanodon for more than a few years. There are several other species that are either based on very poor material, that are either undiagnostic, were fairly rapidly shifted into other genera (Iguanodon prestwichi has been happily residing in Camptosaurus for over 100 years now), not from ornithopods, or aren't even dinosaurs.

The beginning of a solution to this mess was in 2000, when the ICZN (International Commission of Zoological Nomenclature) designated Iguanodon bernissartensis as the type species of Iguanodon, primarily because this species is known from 37-odd individuals, many of which are complete, whereas I. anglicus was based on several teeth  One specimen of I. bernissartensis appeared to be rather more gracile than the others, and was later referred to I. atherfieldensis.

This already sounds confusing, but in practise what tended to happen was that specimens were either referred to I. atherfieldensis if they were relatively slender, and I. bernissartensis for the chunky guys, regardless of how old the specimen was. This is clearly unsatisfactory. Especially as these animals start looking rather different when you look closely and start including the other species in the mix.

In 2006 Gregory Paul separated Iguanodon atherfieldensis into the separate genus Mantellisaurus, in honour of Gideon Mantell. A year later he erected a new genus and species for the Belgian I. atherfieldensis specimen, calling it Dollodon bampingi. Iguanodon lakotaensis was also separated into a new genus (Dakotadon), and I. orientalis regarded as a "Nomen Dubium". He did not attempt to redescribe I. hoggi, I. dawsoni, or I. fittoni and I. hollingtonensis, regarding them as "Iguanodontidae" of uncertain affinity- and possibly not even not particularly close to Iguanodon at all. This was for two reasons, one, they were clearly morphologically distict from each other, and also of a significantly different age. Warm-blooded species tend not to last more than 2 million years, but Iguanodon would have had a range of over 40 million years, spanning most of the northern hemisphere. Which seems unlikely to say the least. Lumping everything together like this masks diversity and evolutionary trends and generally makes it much harder to work out what's really going on. He didn't entirely approve of the ICZN's decision to have I. bernissartensis as the type species, but there isn't a better option, and I agree that its prefereable to have the well known dinosaur from Dollo's iconic reconstruction that is familiar to public and professionals alike for such a historically important genus.

In 2010 David Norman looked at some of the other species that hadn't been officially removed from the genus, "tacitly accepting" Paul's erection of the genus Mantellisaurus, but disagreeing with the separation of Dollodon and Dakotadon, for reasons that he didn't elaborate on other that to say "wait for the paper". "Iguanodon" hollingtonensis and "Iguanodon" fittoni were synonimised into the new genus Hypselospinus fittoni, meaning "high spine" named for the shape of the vertebrae. "Iguanodon" dawsoni was renamed Barilium dawsoni "heavy flank" because, well its got a big arse.

So "Iguanodon" turns out to be far more diverse than you'd first think there's room for at least four, if not six or more genera in there, spanning the gap between the Jurassic camptosaurs to the familiar duck-billed hadrosaurs with their dental batteries, and flamboyant crests. And of course there's the promise of more research to follow, and an interesting (if somewhat esoteric) debate about haow different species have to be before you start putting them in different genera.
davegodfrey: Coelacanth (Science)
About a month ago John Scannella and Jack Horner published an article "Torosaurus Marsh, 1891, is Triceratops Marsh, 1889 (Ceratopsidae: Chasmosaurinae): synonymy through ontogeny" in the Journal of Paleontology*

*Note. Ceratopsidae are the "horned dinosaurs", including Styracosaurus, Triceratops/Torosaurus, Chasmosaurus, and Pachyrhinosaurus to name but a few. The Chasmosaurines are a subgroup which had long brow horns, short nasal horns, and big frills, (Chasmosaurus and Triceratops/Torosaurus are fairly typical.) The other group (the Centrosaurinae) had short, or absent brow horns, a long nasal horn, and a relatively short frill (Styracosaurus and Pachyrhinosaurus are good examples of this group).

What this paper attempts (and I think succeeds) to show is that the fossils attributed to Triceratops are all juveniles, and the fossils attributed to Torosaurus are all adults. They looked at all the skulls they could get their hands on, and looked at what was happening to the bones, and they are fairly confident that they've identified a growth sequence between Triceratops and Torosaurus.

As it grew Triceratops first developed the long brow horns, and a short solid frill. When it reached maturity then holes in the frill opened as bone was absorbed, and the frill itself then grew significantly longer. There are one or two Triceratops specimens that show that the bones in the frill were starting to thin as this happened.

So all in all, a reasonably convincing study. So why the hoo-ha?

Because journalists (and the sub-editors responsible for their headlines) can't read, and then the internet gets hold of their shoddy penmanship, and before you know it people are clutching their pearls and comparing this to "Pluto not being a planet anymore". (Breaking Daily News are particularly precious, I really can't see how this could delight creationists at all.)

Anyway. The ICZN (International Commission of Zoological Nomenclature) has some pretty strict rules about how you go about naming things. Generally the first name given has priority. Its why Brontosaurus was renamed Apatosaurus (Apatosaurus was published first). Its why Laelaps had to be renamed Dryptosaurus (a mite had already been given the name). Its generally a very sensible rule, and only causes problems when you discover that another name was previously published for the same species, but completely ignored, or if the type species, or the specimen on which the name was originally based turn out to be fairly poor for identifying, well anything.

When this happens you appeal to the ICZN and they think about it, ask for comments and make a decision. Often they'll agree with you. If no-one's used a name for ages there's no point in keeping it if everyone else uses something different. There's a application currently going through the ICZN< to replace Cetiosaurus medius with Cetiosaurus oxoniensis as the type species of the sauropod Cetiosaurus, primarily because the material of C. medius is crap, and everyone uses C. oxoniensis when talking about Cetiosaurus. Something similar happened to Iguanodon a little while ago, and there was a paper recently that made everything really confusing. Some day I'll write about it.

Anyway, in this case strict priority is going to rule. Torosaurus was described three years after Triceratops. The species included in Torosaurus will be reclassified as species of Triceratops. Scannella and Horner don't go so far as to synonymise the individual species however, so Triceratops gets several new species and a new look for the adults.
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davegodfrey: South Park Me. (Default)
Day 22 A Website

I've already mentioned Mike Everhart's Oceans Of Kansas website elsewhere, so I'll point you somewhere else instead.

Palaeos is one of the greatest websites I have ever found. It discusses pretty much the whole of palaeontology, covering thousands of taxa, providing primers on cladistics, morphology, biogeography, etc, etc. And its just been wikified, so if you think you can help then jump aboard.

I think probably my favourite essay on there, and its hard to choose there are so many, is the essay "What Is A Tetrapod?"
davegodfrey: Coelacanth (Science)
A Non-Fictional Book

Just the one? But there are so many more books that are real than ones that aren't. Um. I'm going to take this to mean "Non-Fiction book", I'm going to recommend Mike Everhart's Oceans of Kansas, a book that owes much to his website of the same name. There are lots of lovely photos of specimens, the spectacularly weird pterosaur Nyctosaurus, which has no fingers- and just look at that crest, mosasaurs that were clearly eaten by sharks, Sabre toothed "herring",
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"birds with teeth", and one of the largest turtles ever.

Each chapter begins with a little fictional vignette of life in the Kansas Seaway, describing moments in the life (and death) of its inhabitants, and several are backed up with fossil evidence (the famous fish-within-a-fish fossil for instance) Its wonderfully illustrated by Dan Varner, and I recommend it to everyone with an interest in fossils. More importantly its not a technical book, so everyone can enjoy it.
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davegodfrey: Coelacanth (Science)
There's a new paper on the origin of primates. Now I've not looked into primate evolution much (other than criticising the hype around some recent discoveries). But this seemed interesting. In a "Yer what?" way.

Michael Heads has calibrated the origin of the various primate groups to several tectonic events involved in the breakup of Pangaea.

New and Old World Monkeys diverged 120 million years ago when the Atlantic opened. Lemurs diverged from their closest relatives when the Mozambique Channel opened 160 million years ago, and the deepest split in the primate tree, between the haplorhines (monkey, apes, and tarsiers) and strepsirrhines (lemurs and lorises) is 180 million years ago in the Early Jurassic.

This is a problem. The earliest known primate fossil is Purgatorius from the Upper Cretaceous of the USA. (Well maybe. A recent paper in Nature indicates that it isn't a primate but the sister group to placentals as a whole.) Other than that the earliest primates turn up in the Eocene, about 56 million years ago. Molecular divergence times however put the split between primates and their closest living relatives the Dermopterans (the Colugos or "flying lemurs") at about 80 million years.

He is right in pointing out that the previously accepted dates are indeed the minimum dates. Any new fossil discovery could shift them by several million years. Just a week or so ago some tetrapod footprints were found that indicated that tetrapod evolution occurred about 10-20 million years earlier than we thought, creating "ghost lineages", spans of time where no fossils are known, but are expected.

If Heads' model of primate evolution is correct then it creates ghost lineages of 100 million years. This, to me, seems rather excessive. Defending this he points out that several groups do not have a fossil record, yet must be very old, while other modern groups are only known from a few very early fossils (he mentions proscopiid grasshoppers from 110 million years ago). Fair enough, but the molecular dates indicate a ghost lineage of about 25-30 million years from the earliest fossils to the latest divergence times. Increasing this by four times really needs rather more support than he gives it. A new fossil would be enough to make people think.

He is correct in his statements that molecular dates (however they are calibrated) are generally minimum dates, but he repeatedly states that they are "transmogrified" into maximum dates. I can't find any detailed criticism from this paper as to how this is done (do the authors just swap words around? Or are there mathematical tricks that can get you this result?)

Moreover where Heads' paper also falls down is in his refusal to accept that rafting can play a part in evolution and dispersal. It is generally accepted that chameleons originated on Madagascar and then spread. Frogs have made it to Madagascar from Indonesia, and this week a paper was published in Nature showing how ocean currents in the Eocene would have allowed lemurs to raft across the Mozambique Channel, but would prevent them doing so today. He also fails to take into account that the separation of continents is not a simple matter. The North Atlantic began to appear in the Cretaceous, but there were extensive connections between Europe and North America throughout the Eocene, allowing animals to island hop across. I see no reason why South America and Africa would be different.

He doesn't address the issue of why we have a nice transitional sequence of various primate groups in the Eocene, but that isn't necessarily a problem- the footprint paper in Nature gave us the same problem to deal with. However the footprints are evidence for the existence of tetrapods at a particular time period. Heads has not presented any physical evidence to back up his claims, rather he's taken the current distribution of primate groups as evidence that they always lived in these areas, and matched them up with past events. Would he have got the same results if he had used a different group? And if not what does that say about his methods?

Finally, other than ascribing a date of 185 million years to the split at the base of the Archonta (the larger group uniting Primates, Tree Shrews, and Colugos) he says nothing about what this data means for the diversification of other placentals, marsupials or indeed the origin of mammals as a whole. Without running the mathematics I can't help get the feeling that were this paper correct it would push the origin of mammals somewhere into the Permian. Which seems, shall we say, extremely unlikely given the fossil record we have there.

As they say, extraordinary claims require extraordinary evidence.

Michael Heads: Evolution and biogeography of primates: a new model based on molecular phylogenetics, vicariance and plate tectonics, Zoologica Scripta, Published Online: Nov 10 2009 4:44AM DOI: 10.1111/j.1463-6409.2009.00411.

J. R. Wible, G. W. Rougier, M. J. Novacek & R. J. Asher: Cretaceous eutherians and Laurasian origin for placental mammals near the K/T boundary, Nature 447, 1003 - 1006 (21 June 2007)
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davegodfrey: Coelacanth (Science)
Does anyone have access to November' 2009's Zoologica Scripta? I'd like a copy of the following paper please.

Michael Heads. Evolution and biogeography of primates: a new model based on molecular phylogenetics, vicariance and plate tectonics. Zoologica Scripta, 2009.

It suggests that lemurs and lorises diverged from the new and old-world monkeys about 180 million years ago, (the early Jurassic). I'd like to post a criticism of it, but I'd rather wait until I've read the paper. After all, he might have included some important data that hasn't made it into the press reports that explains why placentals should be found in the Permian, or that he's produced a ghost lineage based on no fossil evidence whatsoever that's about 100 million years long. Like I say. I don't want to be prejudiced.
davegodfrey: Coelacanth (Science)
So  having had a look at the paper, and watched the video courtesy of Nature I thought I'd see how the various newspapers reported this new and interesting discovery.

As far as I can see The Daily Express doesn't cover it at all. But as their astrologer is writing a guide to getting fit in 2010 I think they might have given up on being a newspaper these days.

The Mail throws the "Missing Link" phrase around in the first paragraph. Which is a shame, because I've not seen it mentioned anywhere in the reporting or the press release. If anything this is something that would have been largely ignored if it was contemporaneous with the body fossils- "Oh neat, tetrapod trackways. Oh they're marine. That's interesting, virtually everything else is freshwater" would have been the response. However the rest of the article is not bad- the quote from Ahlberg reads like the abstract, and they've lifted some quotes from Phillipe Janvier's "News and Views" article accompanying the Nature paper. I think they fumbled it a bit, but made a decent recovery. Just don't look at the comments.

The Guardian is pretty good actually. Doesn't use the "missing link" phrase, which I think is a win. Quotes Janvier (who made the important point that the sequence of fossils probably hasn't changed, its just that the timing of the actual transition is way off). It also quotes Ahlberg and Jenny Clack (though it initially spelt her name wrong- but this is the Guardian, so that's to be expected). Where I think it does best is online, where there's the blog by Adam Rutherford providing more information I mentioned last time.

The Indy is generally very good, and provides more information about the circumstances leading up to the find- they were thought to be dinosaurs until they had another look at the fossils in the surrounding rocks to work out how old they really were. It probably explains why the article says "They occurred in a rock formation several metres beneath a younger rock formation." because otherwise that's a totally pointless statement- there's no information about why this younger formation is important. Did it contain the conodonts that they used to work out how old the rocks were? Was it just a pretty colour? What? Enquiring minds wish to know.

The Times however seems to be making stuff up. It describes the creature that made the tracks as looking like a stout crocodile, which is not an inaccurate description of the typical early tetrapod. However it says that; "However, unlike the modern-day crocodile, the ancient creature appears to have held its body up from the ground as there is no trace of it being dragged along. It may have been closer to a dog in terms of posture." No. Seriously. Just No. Crocs have legs that stick out from the side less than that of lizards or salamanders, giving them a semi-erect gait that raises their bodies off the ground. Dogs have a very different gait, their legs are directly under their bodies like dinosaurs, and mammals. All the early tetrapods have sprawling gaits- we don't see body or tail trails because the animal was supported by water in the intertidal zone, and because it had a sacrum which allowed it to support its tail with the hind limbs. Dogs don't enter into this anywhere.

Its also not true that the rocks "teemed with marine fossils". Tracks are common, but body fossils are extremely rare, and this is not uncommon. There seems to be something about environments that are good for preserving tracks, but lousy for preserving the organisms that made them. I think however they may have redeemed themselves by solving the question of why they were thought to be dinosaur tracks- the man who first discovered them didn't know how old the rocks were.

The red-tops seem to have completely ignored it, which is not surprising- Metro gave it a sentence or two, and I can't find it on the intertubes.

So not a bad showing for the papers this time round. Shame the creationists turn up with their "how can you know so much from a footprint?" crap. Well dear, lots. There's a whole science out there that you're completely ignorant of called ichnology.


Jan. 7th, 2010 12:34 am
davegodfrey: Coelacanth (Science)
Scientists in changing mind based on new data shocker!

Grzegorz Niedźwiedzki, Piotr Szrek, Katarzyna Narkiewicz, Marek Narkiewicz, and Per Ahlberg (late of the NHM, now firmly ensconced in Sweden) appear to have thrown a cat among the pigeons. Actually what they've done is thrown a tetrapod among the fishes.

Until last tonight we thought we'd got a handle on tetrapod evolution. First you get things like Eusthenopteron, often cited as the standard Devonian "Lobe-Finned Fish". While clearly a fish it has rather limb-like fins. A little while later (385 million years ago to be precise) a group called the Elpistostegids turn up, the most famous of these is probably Tiktaalik which did the rounds couple of years back. These are much more tetrapod-like. The heads have a long snout, the front fins are even more limb-like, with the beginnings of a shoulder and wrist, but the back legs are relatively small, and while Tiktaalik could probably do push-ups, it certainly couldn't walk anywhere.

Finally at about 370mya tetrapods which actually have proper legs with fingers and everything turn up. Animals like Acanthostega, Ichthyostega, and friends. None of these was ideally suited to life on land- Acanthostega was still dependant on gills, and would have died if you'd taken it out of the water. Ichthyostega would have fared better, but wasn't going to go anywhere terribly quickly. The most recent reconstructions indicate it was rather seal-like. Around about this time the elpistostegids disappear, so we have a nice rough evolutionary sequence, with all the usual (or indeed unusual) branching and diversification that entails- Livoniana's seven rows of teeth are my favourite example.

Or rather "did", now the nice Polish scientists have borked it all up. They've just found the earliest tetrapod footprints and trackways. And they're 397 million years old. Over 10 million years older than the elpistostegids and 18 million older than the "proper" tetrapods. Oh dear. Actually, no. Not "oh dear" "How awesome is that?" They went looking for fossils and trackways where no-one expected to find evidence of tetrapods, and they found it anyway. Adam Rutherford justly celebrates the fact that it was pure research with no applications- and Per notes that not even the guys who's job it is to give money for just those sort of projects would have forked out.

The individual prints are clearly from a tetrapod, and preserve digits. (6 in the case of the photos I've seen. This sounds odd but was expected- Acanthostega had eight fingers, and Ichthyostega seven). The trackways aren't so well preserved, but indicate that the animal would have had a side-to-side gait like that of a salamander. This is decidedly weird- Tiktaalik and Panderichthys shouldn't produce those sorts of trackways. And "walking" seems a bit too advanced for Acanthostega- it couldn't place its feet flat on the ground if it tried. The more I think about it the more important this find gets.

What's going on then? Obviously the biggest problem we have is the spottiness of the fossil record. There's a similar problem with all the lovely Chinese dinobirds. They're mostly from the Early Cretaceous, but the "first bird" is from the Jurassic, and significantly older. My guess is that the changeover is an artefact of the fossil record. Somewhere out there are earlier "fishapods"
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, and as for why Tiktaalik and co hung around for so long after they should have got out of the way for these shiny real tetrapods I shall defer to Grzegorz Niedźwiedzki, who suggests that the elpistostegids were the first to colonise the environments where we've been lucky enough to find their bones. Ichthyostega's great grandmother seems to have been happy to have frolicked around the stromatolite studded tidal flats leaving her footprints, but little else behind.

As always the sciencebloggers have excellent commentary. Ed Yong has talked to Shubin and Daeschler who described Tiktaalik, as well as Jenny Clack, Laelaps, discusses it with reference to work done by Owen in the 19th century, and is very excited by all the new questions that this work raises.

Or you could watch the video, which discusses the environment the fossils were found in, and new ideas for why tetrapods might have started out on land (warning, hot field-trip action depicted)

(There's also really nice shot of the fuzzy Dilophosaurus model Darren Naish blogged about a little while ago in the intro)

Hopefully I'll get a post up in the next couple of days about how the press have reported mangled the reports.

Grzegorz Niedźwiedzki, Piotr Szrek, Katarzyna Narkiewicz, Marek Narkiewicz & Per E. Ahlberg
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 Tetrapod trackways from the early Middle Devonian period of Poland: Nature 463, 43-48 (7 January 2010)
davegodfrey: Coelacanth (Science)
Remember Ida? (or Darwinius massillae to give her full name)? Remember how six months ago she was unveiled to the world in a whirlwind of hype? Remember how the blogging community despaired of this, while noting what a lovely fossil she was?

This week more research has been published, after the discovery of Afradapis, a related species from the Late Eocene of Egypt. Not nearly as nice as Ida its a jaw and teeth. This is not unusual- most of our ideas about mammalian evolution were based on teeth until genetics came along and morphology had to play catch-up. And when dealing with extinct groups such as adapids its the best thing we have going- teeth are the most robust parts of your body, and withstand the processes of decay and weathering the best. The fossils shows some features present in the catarrhine primates (the group that include apes and Old-World monkeys). Which is very interesting. However...

...all is not as it seems. The team did a phylogenetic analysis, of 117 living and extinct species, using 360 characters. This is only about 3 characters per taxa, and I'm sure more would be nice- but you can guarantee that not all characters will be preserved in each group (its rather hard to say what features are present in the ankle of a genus only known from its teeth for example), and its the first phylogenetic analysis I'm aware of that includes Darwinius which is a very Good Thing. Sadly for most people, its published in Nature, which means anyone who doesn't have a subscription only gets the abstract and whatever mangling the newspapers put this and the press release through.

This analysis shows that Ida, Afradapis and the other Adapoids are not stem anthropoids, and are not even haplorhines (the group that includes monkeys [and apes] and tarsiers). In fact they fall out as the sister group to the living strepsirrhines (lemurs, lorises, and bushbabies). To me thats far more interesting than if the adapids were on the line to humans, because it means the features they share with us either evolved twice (once in anthropoids and once in adapids- the position the paper's authors take) or are primitive to a wider group of primates. Without having read the paper I can't say why the author's favour one over the other.

ETA: Brian Switek over on Laelaps has a very nice post, (with a lovely drawing of Afradapis' jaw). The features that link adapids and anthropoids (but are not present in the earliest anthropoids) are details of the mandibular symphysis (the joint between the two halves of the lower jaw) and the loss of the second premolar. Neither of these features are likely to be lost and re-evolved, when evolution discards things they tend to stay discarded, and when they come back, they're usually subtley different.

Before we start questioning how effective the analysis was- and believe me scientists will, plugging more species in, pulling others out, re-examining specimens, poking holes everywhere they can to see how good this tree really is, taking the analysis at face value raises a whole series of interesting questions. If we're seeing convergence between anthropoids and adapids, then what were these two different groups doing that was similar, and if the features we are seeing are primitive, then why did lemurs and other groups lose them.

And this to me is the beauty of science. When scientists are wrong it is very often for interesting reasons- lack of data, working within a theory that could not account for new observations, etc. And when they are shown to be wrong, a whole vista of new questions open up, new ways to be interestingly wrong, but at the same time inch closer to a greater understanding of the universe. And people wonder why I love science so damn much.

Seiffert, E., Perry, J., Simons, E., & Boyer, D. (2009). Convergent evolution of anthropoid-like adaptations in Eocene adapiform primates Nature, 461 (7267), 1118-1121

I recommend reading this interview with Seiffert.

davegodfrey: Coelacanth (Science)
From XKCD- Break-ups are better with junior synonyms.

Well, sex is like a velociraptor: despite your movie-fueled lifelong neurotic obsession, unlikely to be found in your house.

Brontosaurus excelsus was named in 1879, two years after Apatosaurus ajax. in 1903 Elmer Riggs decided that the two species were close enough to belong to the same genus, and by the laws governing zoological nomenclature Brontosaurus had to be sunk. The "mistaken combination" comes not from work done re-evaluating bones mistakenly assigned to A. excelsus, but the mount at the Peabody Museum that used skull material from the more distantly related Camarasaurus to restore the missing pieces. Later it was realised that Apatosaurus would have had a lower, more delicate skull, similar to that of its relative Diplodocus. But even then the name carried on, although given textbooks (especially children's textbooks) habit of copying from one another, they were still copying Knight's restorations, long after they should have known better.

By this time everyone not involved in actual science was using the name "Brontosaurus". Wikipedia blames the Peabody mount, I can see why, even now it still takes a while to update labels to reflect changes in taxonomy to pick a recent example close to home, Bob Bakker named the plesiosaur genus Attenborosaurus in 1993, but it took several years for the display at the NHM to be updated. I can see the same thing happenning at Yale, and by the time they did change the name on the label, everyone who people listen to (so not the scientists) is calling it "Brontosaurus".
davegodfrey: Coelacanth (Science)
The entire world seems to have gone utterly insane over this fossil, known colloquially as "Ida", but officially as Darwinius masillae. And it is a lovely fossil. It is also important because it will, I'm sure, tell us lots about what was going on in primate evolution 47 million years ago. I'm not going to go through the reports because there are too bloody many of them, but I will point out that while many have fallen for the "Missing Link" Found! angle plenty of others- especially the bloggers writing opinion pieces are being rather more restrained.

However utterly revolutionary it is not. At best it means a group of animals a bit like lemurs (Adapids) are more closely related to apes and monkeys than a group of animals a bit like Tarsiers (Omomyids). Be honest had you heard of either?

I quite like it because its another species published in PLoSOne (The Public Library of Science). This is an open access journal, so anyone can download and read a copy of the paper for free. There's a lovely long description of the fossil- it is young (under a year old), female (it lacks a baculum [penis bone] which you'd expect to see in male primates like this), and very nicely preserved (the body outline, hair and stomach contents are all preserved).

Its from the Messel deposits, which have yielded beautiful fossils of fishes, early horses, ants, weird mammals like Leptictidium, and all sorts of other things. Messel was covered in one episode of David Attenborough's 1980s series on fossils Lost Worlds, Vanished Lives, and also in the first episode of Walking With Beasts- though proto-whales aren't known from the area. I can't believe someone thought it was a good idea to turn the site into a rubbish dump. Fortunately they haven't, and it is now a World Heritage Site.

I am not qualified to say how much this fossil supports the conclusions that the authors are trying to draw- that the group to which Ida belongs are more closely related to monkeys and apes than tarsiers and their relatives are.  However the paper lacks a phylogenetic analysis and as Laelaps and The Open Source Paleontologist points out this is something one expects to see when claims for moving large groups around are made. Hopefully one will be done soon, and the question of whether Adapids (the group to which Darwinius belongs) is closer to lemurs or monkeys and apes will be better resolved.

I don't really have much to add to the criticism of the hype either. Both Ed Yong and Carl Zimmer have covered it far better than I could hope to. Especially Ed's post.

Personally the part that really annoys me- I wouldn't be at all surprised if the view of the Adapids in the paper turned out to be wrong. You just know that the creationists will have a field day because while I'm sure most of you know that the great strength of science is that whenever new information appears which contradicts its conclusions we change our minds- something the creationists seem incapable of appreciating as being A Good Thing. I just hope I am pleasantly surprised.
davegodfrey: Coelacanth (Science)
Today is the 200th birthday of Charles Darwin. Best known for formulating the theory of evolution by means of Natural Selection (which explains how the peacock got its wings), less well known for coming up with the theory of Sexual Selection (which explains how the peacock got its tail), and totally ignored for explaining how coral reefs formed.

What is remarkable about Darwin's theory is that the:

"...whole theory was thought out on the west coast of S. America before I had seen a true coral reef."

"But it should be observed that I had during the two previous years been incessantly attending to the effects on the shores of S. America of the intermittent elevation of the land, together with the denudation and the deposition of sediment. This necessarily led me to reflect much on the effects of subsidence, and it was easy to replace in imagination the continued deposition of sediment by the upward growth of coral."
Darwin observed volcanic islands in the Atlantic, and the second of his books on the geology observed on the voyage of the Beagle (Volcanic Islands, published in 1844) discusses the evidence for crustal uplift as caused by volcanic activity, and corresponding subsidence after the volcano became extinct. On the coast of South America he saw (and when caught in an earthquake, felt) the evidence for large-scale, and long-term movements of the Erth's crust. Having worked out how coral reef ought to form he was in a position to study real reefs to confirm or refute this hypothesis.

Gathering data from soundings taken by the Beagle's Captain Fitzroy, and from a wide range of other sources Darwin confirmed that the "polypifers" that created coral reefs were shallow water organisms. Darwin was unaware of the diversity of deep-water organisms, nor of the range of organisms that contribute to reef formation- had he been, he would have needed to qualify these observations. Rosen (1982) notes that this lack of knowledge probably helped Darwin to formulate the theory.

Darwin also considered the ecology of reefs, noting that the most exposed parts of the reef are mostly home to massive corals and red algae, and this was the area of most active reef growth. Once a reef has reached sea-level it then grows outwards. In the 130-odd years these basic observations have not been seriously challenged.

It was his work on coral reefs that earnt him scientific credibility, and made him a member of the scientific establishment. So by all means raise a toast to one of Natural Selection's founding fathers, but don't forget he was more than just a biologist. He was also a geologist, oceanographer, biogeographer and ecologist, long before many of these disciplines were recongised.
davegodfrey: Coelacanth (Science)
Further from my last post I mentioned a fossil whale most of you may never have heard of until this morning. Maiacetus inuus "Inuus' Mother Whale", named for the Roman god of fecundity, and important features of the holotype, which I will come to.

The whale comes from Pakistan, known for some time now as an important place for whale evolution, the earliest whales (placed in a family called the Protcetidae) are known from here- previous finds include Ambulocetus natans the "Swimming walking whale", Pakicetus, originally known only from a skull, and now known to be a rather wolf-like animal, (rather than the seal-like creature it was previously reconstructed as), in total 15 genera and 16 species are known ranging from South Asia and Africa into North America.

Unlike later archaeocetes like Basilosaurus and Dorudon, Maiacetus and its relatives had strong back legs fused to the vertebral column. While strongly adapted to water they would have been able to move around on land, probably quite comfortably. Looking at the skeletal reconstructions I'm most strongly reminded of a cross between an otter and a crocodile. The limbs are strong, the snout long and narrow. The tail and limbs are strong, indicating that the animal probably swam rather like a modern otter. A 2.6m otter with a face full of teeth. Not as cute as the ones at the zoo then.

The animal shows some degree of sexual dimorphism. The second specimen is 12% bigger than the other, and has notably larger canine teeth. This specimen is also one of the most complete protocetes known, and clearly shows the "double-pulley" ankle that shows whales are actually artiodactyls (the "Even-Hoofed Ungulates", like cows, pigs and sheep). Molecular data shows their closest living relatives are the hippos.

But I've been skirting round the main reason why this species is so fascinating, and why the bloggers have been picking up on it- The holotype is a pregnant female. This is important for several reasons- its the first time a fossil whale has been found with a preserved fetus, and more importantly the fetus is lying head first in the birth canal.

We know that this is indeed a fetus and not the remains of her last meal because as the Phil Gingerich points out:

"Protocetids had shearing molars used to slice and chew their prey. The skull of the fetal skeleton could not have survived such mastication and be as well preserved as it is.

Because of their strong hind legs protocetes have been suggested as having given birth on land, but this fossil conclusively proves it. If Maiacetus had tried to give birth underwater junior would have drowned immediately. Later whales like Dorudon and Basilosaurus had to give birth to their young tail-first. Their legs are tiny and could never support their weight on land.

Another "missing link" found.

And if this wasn't awesome enough Gingerich PD, et al. (2009) New Protocetid Whale from the Middle Eocene of Pakistan: Birth on Land, Precocial Development, and Sexual Dimorphism. PLoS ONE 4(2): e4366 is freely available online at PLoS One

ETA: New Scientist has a nice gallery showing the various stages of whale evolution, including Pakicetus, Ambulocetus and co.
davegodfrey: Coelacanth (Science)
The following is adapted from a dissertation I wrote several years ago.

Fossils have been recognised as the remains of living organisms since the time of Leonardo da Vinci and before. At the close of the 18th century the French anatomist George Cuvier developed the idea of extinction, demonstrating that many fossils are not those of modern species. Erasmus Darwin and Jean Baptiste Lamarck formulated some of the first ideas suggesting that species were not immutable. At the same time James Hutton was formulating his theory of the earth, and demonstrated that the earth was much older than the ages biblical chronologies allowed (Bowler 1989). These three ideas were to become important questions and discussed much through the following century.

A (very) brief history of collecting )

Agassiz (1835) described osteostracean remains in his works on fossil fishes, creating the genus Cephalaspis for four species, C. lyelli, C. lewisii, C. lloydii, and C. rostrata. These species were not initially recognised as jawless. Of these four, Thomas Henry Huxley restricted Cephalaspis to C. lyelli, and created the genus Pteraspis for Agassiz’s other species in the genus (Huxley 1858). E. Ray Lankester separated heterostraceans and osteostraceans into separate groups in his 1868 monograph.

Ostracoderms. Some of the best fish ever... )

Revolutions in science are not instantaneous. New theories and ways of thinking take time to spread and gain respectability. The paradigms influencing the work of the second period, the work of Cope, William Patten, and others are the result of the publication of Charles Darwin’s Origin of Species in 1859, thirty years before, and the successful spread of evolutionary thinking in the latter half of the 19th century. Similarly, while Løvtrup produced one of the first cladograms of modern vertebrates in 1977, the cladistic method began with the entomologist Willi Hennig’s influential 1969 book Insect Phylogenetics where the principles of cladistics were first established.

References. )
davegodfrey: Coelacanth (Science)
This blog seems to have turned into a TV/Media reporting site recently. Never mind.
The Beeb have a new series out called "Fossil Detectives". Presented by Hermione Cockburn it is an 8-part series made by the OU. (So that should be a good indicator of quality.) Sadly, unlike the OU shows I remember as a child there's a distinct lack of beards, and less detail in some things than I would like. But being the OU what is there is top-notch stuff. This weeks episode concentrated on Central England, so we got a look at the Dudley Bug (the trilobite Calymene), the serial grinding work of Peter Sheldon that revealed a fossil sea-spider, David Attenborough reminiscing about his childhood collecting fossils, and the Ediacaran fauna of Charnwood Forest in Leicestershire.

What most excited me was the section on the BGS's work in rediscovering one of the more obscure Lagerstätten deposits, an Oxford Clay site in Wiltshire where volcanic eruptions poisoned the water, creating a predator trap, and preserving soft tissue in phosphate. The site had previously revealed beautiful cephalopod fossils, belemnites with their hooks in life positions, and squid with their arms, fins and ink sacs preserved. Sadly the site was lost as the local collector provided misleading information as to its location, but the BGS have rediscovered it.
 What was especially exciting for me is that I'd looked at the NHM's collection as part of my undergrad degree, so the thought of this site being rediscovered warms the cockles of my dead-squid-loving heart.

Next weeks episode is on London, so of course we get "hippos in Trafalgar Square", and the other episodes detail different regions , with input from the appropriate scientists, Jeff Liston discussing Leedsichthys in Peterborough for instance. I'm rather  looking forward to them.

One of this week's "Charlie and Lola" was entitled "It is very special, and extremely ancient." Charlie is given an ammonite, and his sister Lola is very interested in it. Its even older than 25. Lola decides to look for fossils with her friend Lotta. Of course they start looking in all the wrong places (digging holes in sandpits, etc) before being taken to the beach where after an unsuccessful day they finally find something right at the end. Its a wavy line in the cartoon. Lola thinks its a centipede, Charlie isn't sure its a fossil at all, and it turns out to be a Nematode worm, and is Very Special and put on display in the museum.

There's definitely a degree of accuracy. Very often the most exciting finds occur on the last day of the dig (this happened to John Ostrom when he discovered Deinonychus, and seems to crop up in every other episode of Time Team). But the nematode fossil? That really would be something special. Nematodes are soft-bodied, so their chances of being fossilised are extremely rare. Some are known from Scotland, found inside the remains of a decaying sea-scorpion (Gigantoscorpio), others from Mazon Creek in Illinois (and I assume that Charlie & Lola don't live near Chicago), and still more from amber, including records of parasitism. However trace fossils resembling the wavy lines of nematode trails are known from Triassic and Eocene deposits, and Cochlichnus, a similar fossil is often attributed to nematodes, so perhaps that's what Lola found.

If a kids cartoon can get this sort of thing right, and it didn't take long to find the information via Google, then why can't newspapers?

Stormer, L. 1963. Gigantoscorpio willisi, a new scorpion from the Lower Carboniferous of Scotland and its
associated preying microorganisms. Skrifter Utgitt a v Det Norske Videnskaps-Akademi i Oslo, 8:1-171.

Valentine, J. W. 2004. On the Origin of Phyla. University of Chicago Press.
davegodfrey: Coelacanth (Science)
Some of you may have seen this paper at PLoS ONE. Its a rather nifty piece of work by Darren Naish and Mark Witton (who's very nice drawings accompany the article itself, and the various newspaper reports.)

Basically a group of pterosaurs called Azdarchids have always been a bit of a problem for palaeontologists working out their lifestyle. They're huge, with 10m wingspans, 2-3m jaws, and "it could look a giraffe in the eye". Originally suggested to be variously scavengers, "dip feeders" (like albatrosses), and mud probers, but they don't have the right sort of beak for any of those. Along with every other bloody pterosaur they've been suggested as a "skim feeder"- but no pterosaur is nearly as specialised as Rhychops the skimmer.

Naish and Witton therefore reconstruct them as stork-like predators. The fossils are mostly found in terrestrial deposits, and their footprints indicate their feet aren't adapted for wading (another popular hypothesis)

Yet again coverage is varied. The best place is of course the paper itself, freely avaliable online. Or you can read Darren's blog about it. I wouldn't bother too much about the rest of the media though. 

ETA: The Economist, another short article, and nothing wrong here either. States the research showed that they "were more like giant storks. Rather than skimming the sea, they plucked their prey from the ground." Better than the Sun article, but frankly not that much. Again, shorter seems to be better.
davegodfrey: Coelacanth (Science)

Yet another aberrant theropod from China. Called Gansus yumenensis, after the area it was found its 100 million years young. It looks a lot like the modern diver (or Hesperornis a large flightless toothed bird.) Feathers and the webbing between the toes is preserved. Sadly its missing a skull. But its still pretty. And ist shows the kind of diversity of bird species and ecotypes during the Early Cretaceous. The sad thing is that you won't see some of the variety of birds that probably existed because they lived on land, and never got fossilised. Our history of bird evolution is largely known from seabirds.

Its from another deposit in China with soft-tissue preservation, but not one I'd heard of before.  Still in a country that big I'm not suprised there are so many.

Metro thinks this is important. So important that it shows that birds evolved from fish! ARRRGH!!! I'm going to have to give up reading it. Its bad for my blood pressure.

davegodfrey: Coelacanth (Science)

Three updates in a day!

I used to admire and respect Robert Bakker, the enfant terrible of vertebrate palaeontology- many of his ideas in "The Dinosaur Heresies" were wrong, but at least they were interestingly wrong, in a way that made people say "that can't be right, lets go out and show the beardie hippie that he's wrong". Now I'm beginning to think he's going a bit daft. Ok so naming a plesiosaurus Attenboroughsaurus is perfectly sensible. But hogwarts?

And then Metro, ever the bastion of accurate scientific reporting states that this animal is important because:

A: Its named after bloody HP's bloody school, what next? Opusdeius danbrowni? The name you give an animal doesn't matter unless another animal already has it. I know it shouldn't annoy me, and to be honest it doesn't - not compared to reason B. However naming things after popular culture items is always a little dodgy. So many things don't last. I could name a species after Crom, Conan's god. But I don't think anyone else (other than [profile] steely_glint, and some of the other people I know would know what the bloody hell I was on about.)

B: Its the only dinosaur with a flat head known from the Cretaceous. Nooo! Its the only Pachycephalosaur with a flat head known from the Upper Cretaceous of North America- there's a couple of "flat-headed pachycephalosaurs" from Europe - Yaverlandia from the Isle of Wight fr'instance. Not to mention all the dinosaurs that aren't Pachycephalosaurs that have flat heads.

Damn you Metro and your utterly hopeless science reporting.

davegodfrey: South Park Me. (Default)

They've just found fossil phytoliths (the little silica granules in grass leaves) in some dinosaur poo! It seems that grasses are much older than we thought. The article notes that pollen had been recorded from India, South America and Africa and was a similar age (65-70 my).

Its certainly interesting and may mean a reinterpretation of several enigmatic fossils (maybe even some dinosaurs), and some early mammals. The article notes that previously a group called the gondwanatherians were thought to be beaver analogues, gnawing on wood, but the new finds indicates the hypsodont (hih-crowned) dentition is an adaptation to grazing (as in modern horses, etc).

Several email newsgroups are getting quite excited about this! I'm not surprised.


davegodfrey: South Park Me. (Default)
The Evil Atheist Your Mother Warned You About

November 2013

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