Here’s a nice video about pachycephalosaurs describing a little exercise in taxonomic consolidation.
Pharyngula
Evolution, development, and random biological ejaculations from a godless liberal
Here’s a nice video about pachycephalosaurs describing a little exercise in taxonomic consolidation.
Shubin had a tough act to follow, coming after Kingsley’s great talk. I’m sure it will be good, though — last night I got a tour of his lab, saw the original Tiktaalik specimens and some new ones, and some of his work in progress (which I won’t tell you about until it’s published), so I’m confident I’m going to have a happy hour.
Darwin pulled together diverse lines of evidence to document his ideas. The different lines all reinforce each other making the argument even stronger, and what we’re seeing now is new syntheses, which is the theme of this talk: how do we use different lines of evidence to make a case that is more the sum of its parts.
The questions is the origin of limbs, fins to legs. Fins and legs look very different, with fins having rays and many bones, while legs have few bones in a fixed pattern. Intermediate taxa show us the changes, with transitions with bony core of the limb pattern and fish-like rays. He uses geology and extant fossils to make predictions about where to find intermediates, and paleontology also informs his understanding of developmental processes that build the limb.
Began his work in Pennsylvania, which was like the Amazon delta 360 million years ago. They followed the PA dept. of transportation around looking at road cuts that exposed the rocks of that age. They found many fossils, but one that changed his thinking was a fin of sauripterus, with fin rays and a core of tetrapod-like limbs. Definitely fishy, but contained precursors to the pattern.
They searched in Ellesmere Island for Devonian age rocks and fossils that would reveal the history of the limb. The logistics were very difficult, since the area is inaccessible. First started working in 1999, in rocks that were from marine sources and didn’t yield much. Moved east to freshwater sources. Found a layer of rock that was rich in bone, and found a snout of a flat-headed fish poking out. Eventually exposed about 20 specimens of this animal. Took months to fully expose the details of the specimen.
He showed off a cast of Tiktaalik — physical objects are really good at capturing people’s imagination.
It took a year and a half to prepare out the fins; the bones show articular surfaces, so you can actually see how the structure bent in life. What does this tell us about extant fins?
A tetrapod limb has 3 components: 1 bone, then 2 bones, then multiple bones in wrist and fingers. The limb forms in phases, with an early phase of hox expression that sets up the proximal bone, then phase II in which hox genes switch on in a patterned way to form digits. Are there elements of phase 2 in fish fins?
Looked in Polyodon, and embryos do have a distal phase of hox expression, not identical to tetrapod pattern, but definitely a phase 2.
What is a limb and how did it develop? The AER sets up the proximo-distal axis, ZPA sets up anteriorposterior axis. Cutting off the AER at different stages produces progressive deletions of portions of the limb. ZPA is a source of Sonic Hedgehog and sets up a gradient of positional information.
Does the common ancestor of all fish have these same two-axis signals? Chondrichthyans do, with patterns that can be manipulated in the same way as we do in chickens. The appendage patterning system is general to all vertebrate appendages.
How do fins differ from other outgrowths? Branchial arches have the same patterning, with an AER and ZPA. Seems to be a universal way for vertebrates to set up the patterning of outgrowths. Gill, fin, and limb have similar toolkits of patterning genes.
The patterning mechanisms may have originated in a general outgrowth and been coopted for limbs and gills. Shubin proposes to do targeted collecting of Ordovician vertebrates, expecting to find novel non-limb outgrowths that may be precursors to the patterning mechanism. Paleontology guided by developmental biology!
Oops, missed the first part of this talk due to the distractions of Lunch. Walked in as he was talking about tree vs. ladder thinking (people have a hard time conceptualizing trees) and history as a chronicle — barebones description of events — or a narrative — events linked by causal explanations.
It took a century for biologists to use systematics to make testable hypotheses about evolution. Darwin himself talked at length about all kinds of evidence for evolution, but strangely neglected fossils and dinosaurs altogether. Sereno blames this on rivalry with Richard Owen, who was the big dinosaur man of the day. One fossil Darwin was pleased with was Archaeopteryx, and Huxley in particular made the link between Archy and birds. Sereno brought in fossil of Confuciusornis — very cool.
We have begun to separate out the chronology from the narrative; chronology is a limiting factor in our hypotheses. We are interested in the trajectory of change over time, and Sereno confesses to baldly exploiting that to get a publication in nature of Raptorex, but he carefully omitted any causal discussion in the paper, trusting readers to infer a narrative from the story, because that’s what we do.
Deplores the thinness of work in the philosophy of phylogeny.
History: Darwin crystallized many of the pieces of an existing chronology into an evolutionary narrative. The next big breakthrough was Hennig (1950) who atomized morphological transformations and branching patterns, defining specific terms to describe phenomena important for understanding trees. Quantitative cladistics (1969) put it on a solid empirical foundation. Character states were coded as mathematical variables.
Problem: everyone has a different matrix for the analysis of characters for each phylogeny examined. The matrix is a black box. We are searching for a methodology that will link everything together. A modern comparative cladistics would open up the black box for universal analysis. Need to figure out what the characters are, and need to be able to do comparative analysis. There is no global understanding of what a character or character state are. There is currently a movement to develop a universal character ontology.
He makes a strong case that we have a serious problem with different investigators studying the same phylogenies, but using different characters and even scoring them differently. We need to standardize to enable full comparisons of multiple data sets.
It’s yet another transitional fossil! Are you tired of them yet?
Darwinopterus modularis is a very pretty fossil of a Jurassic pterosaur, which also reveals some interesting modes of evolution; modes that I daresay are indicative of significant processes in development, although this work is not a developmental study (I wish…having some pterosaur embryos would be exciting). Here it is, one gorgeous animal.
One important general fact you need to understand to grasp the significance of this specimen: Mesozoic flying reptiles are not all alike! There are two broad groups that can be distinguished by some consistent morphological characters.
The pterosaurs are the older of the two groups, appearing in the late Triassic. They tend to have relatively short skulls with several distinct openings, long cervical (neck) ribs, a short metacarpus (like the palm or sole of the foot), a long tail (with some exceptions), and an expanded flight membrane suspended between the hind limbs, called the cruropatagium. They tend to be small to medium-sized.
The pterodactyls are a more derived group that appear in the late Jurassic. Their skulls are long and low, and have a single large opening in front of the eyes, instead of two. Those neck ribs are gone or reduced, they have a long metacarpus and short tails, and they’ve greatly reduced the cruropatagium. Some of the pterodactyls grew to a huge size.
Here’s a snapshot of their distribution in time and phylogenetic relationships. The pterosaurs are in red, and the pterodactyls are in blue.
Darwinopterus is in there, too—it’s the small purple box numbered “7”. You can see from this diagram that it is a pterosaur in a very interesting position, just off the branch that gave rise to the pterodactyls. How it got there is interesting, too: it’s basically a pterosaur body with the head of a pterodactyl. Literally. The authors of this work carried out multiple phylogenetic analyses, and if they left the head out of the data, the computer would spit out the conclusion that this was a pterosaur; if they left the body out and just analyzed the skull, the computer would declare it a pterodactyl.
What does this tell us about evolution in general? That it can be modular. The transitional form between two species isn’t necessarily a simple intermediate between the two in all characters, but may be a mosaic: the anatomy may be a mix of pieces that resemble one species more than the other. In this case, what happened in the evolution of the pterodactyls was that first a pterodactyl-like skull evolved in a pterosaur lineage, and that was successful; later, the proto-pterodactyls added the post-cranial specializations. Not everything happened all at once, but stepwise.
This should be a familiar concept. In pterodactyls, skulls evolved a specialized morphology first, and the body was shaped by evolutionary processes later. We can see a similar principle in operation in the hominid lineage, too, but switched around. We evolved bipedalism first, in species like Ardipithecus and Australopithecus, and the specializations of our skull (to contain that big brain of which we are so proud) came along later.
As I mentioned at the beginning, this is an example of development and evolution in congruence. We do find modularity in developmental process — we have genetic circuits that are expressed in tissue- and region-specific ways in development. We can talk about patterns of gene expression that follow independent programs to build regions of the body, under the control of regional patterning genes like the Hox complex. In that sense, what we see in Darwinopterus is completely unsurprising.
What is interesting, though, is that these modules, which we’re used to seeing within the finer-grained process of development, also retain enough coherence and autonomy to be visible at the level of macroevolutionary change. It caters to my biases that we shouldn’t just pretend that all the details of development are plastic enough to be averaged out, or that the underlying ontogenetic processes will be overwhelmed by the exigencies of environmental factors, like selection. Development matters — it shapes the direction evolution can take.
Lü J, Unwin DM, Jin X, Liu Y, Ji Q (2009) Evidence for modular evolution in a long-tailed pterosaur with a pterodactyloid skull. Proc. R. Soc. B published online 14 October 2009 doi: 10.1098/rspb.2009.1603
I should have mentioned that Darren Naish has a very thorough write-up on Darwinopterus!
What a day to be stuck in airplanes for hours on end; I had to slurp in a bunch of files on my iPhone and then look at them on that itty-bitty screen, just to catch up on the story of Ardipithecus. Fortunately, you can just read Carl Zimmer’s excellent summary to find out what’s cool about it.
For a summary of a summary: it’s another transitional fossil in our lineage. Ardipithecus ramidus is old, 4.4 million years or so — so it’s well before Lucy and the australopithecines. The latest result is a thorough analysis of a large number of collected specimens that shows it is an interesting mosaic of traits: it was bipedal, but not quite so well adapted to terrestrial locomotion as we are, and it had feet with an opposable big toe. And of course it had a small brain, only a little larger than a chimpanzee’s.
Ardipithecus is clearly different from (but related!) to us, and it’s also very different from a chimpanzee. One thing I’m finding baffling in all the commentary is the argument that this somehow shows that the last common ancestor of humans and chimpanzees would have been very unchimpanzee-like, and perhaps closer in morphology to us than to modern chimps. I’m not buying it. Has anybody actually ever suggested that chimpanzees have been in a state of relative stasis for 6 million years? Chimps have evolved in parallel with us for all of that time, so that argument is addressing a non-controversy, or at least, an argument that should have been recognized as silly all along.
We’re also going to have to push the fossil record back another couple of million years to get to that last common ancestor, and there’s no reason to presume that Ardi’s ancestors weren’t also rather different from Ardi. We also need to know more about the breadth of the primate family tree at that time; was Ardi a weirdly specialized sub-branch, or actually representative of a wider trend in the ape species that would lead to us? I think this image is a nice way to illustrate Ardipithecus‘s place in the family tree.
Don’t get me wrong: Ardipithecus is a magnificent addition to our family album, and the author’s of the multiple papers that have come out have done a very impressive job of analysis and documentation. We can all jump up and down with joy at these new data, and we can rightly point to this species and say, “Transitional form! Boo-ya, creationists!”
Unfortunately, I’m also seeing the press mangling the story already. National Geographic says, Oldest “Human” Skeleton Found—Disproves “Missing Link”, which is annoying. The article itself isn’t bad, but can we just kill the “missing link” nonsense altogether? It’s as if the only way some science journalists can grasp a new discovery is by relating it to a misbegotten misconception.
The prize for the very worst coverage has to go to Metro News and the Torstar News Service (is that from the Toronto Star?). They put up an article titled New theory may answer missing link question, which opens with the bizarre assertion, Man didn’t descend from apes. There is no new theory here. There is new evidence and further data documenting the details of one lineage’s descent. And if you put the phrase “missing link” in your headline any more, we’re going to have to put a silly hat on your editors and make them sit in a corner.
But the very worst part is this misinterpretation of the suggestion that the LCA of humans and chimps would have had characters we consider human-like. I guarantee you that this will be the core of the creationist response to Ardi in the near future.
The four-foot, 110-pound female’s skeleton and physiological characteristics bear a closer resemblance to modern-day humans than to contemporary apes, meaning they evolved from humanlike creatures — not the other way around.
Brace yourself, gang. The creationists are going to be claiming that this shows humans were created first, and all of these other hairy beasts the paleontologists are digging up are just degenerate spawn of the Fall.
This is a very cool fossil, a tiny T. rex cousin called Raptorex. Well, tiny is relative — it was still as big as a human being — but it has the same proportions, the oversized fanged head, the tiny forelimbs, etc., as it’s later relative, T. rex. It’s simply adorable, in a viciously evil predatory sort of way. Apparently the tyrannosaur body plan was successful at different scales.
It’s the 100th anniversary (we can’t say “birthday” for a deposit laid down half a billion years ago, I don’t think) of Walcott’s discovery of the Burgess Shale formation in British Columbia. I’m not quite sure what one does to celebrate on such a momentous occasion…maybe someone has a suggestion.
This is the skull of an arthrodire, an armored placoderm from the Devonian.
Somehow, 20 foot long predatory fish with a mouth lined with razor-edged bony shears has never made me think of sexy time…until I ran across this comparison image.
Oh, schwiiing. It really doesn’t take much to get a mammal to associate just about anything with sex. And then, what do you know, the latest Nature has a short article on an interesting fossil: it’s the pelvic region of an arthrodire, Incisoscutum ritchiei, and look what it’s got: an ossified clasper, comparable to the erectile organ of modern sharks. This is a bony rod that would have been the core of an intromittent organ in the living animal, so what we have here is a small relic of the sex life of a big fish from a few hundred million years ago.
Think about this, you over-sexed apes: what will be left of your manhood 300 million years from now?
Ahlberg P, Trinajstic K, Johanson Z, Long J (2009) Pelvic claspers confirm chondrichthyan-like internal fertilization in arthrodires. Nature 460:888-889.
Here’s an interesting use of tweening: take 5 fossil skulls, use the computer to interpolate between them, and animate the results. 3.5 million years just fly by in 5 minutes.
(The sound track is a bit superfluous though—turn the sound down if you’re at work)
How can anyone resist an article titled “Sexual Intercourse Involving Giant Sperm in Cretaceous Ostracode”? You can’t, I tell you. It’s like a giant brain magnet, you open the journal to the index, and there’s that title, and you must read it before you can even consider continuing on to anything else.
Some organisms have evolved immensely long sperm tails — Drosophila bifurca, for instance, has sperm cells that are about 60mm long, or 20 times longer than the length of the entire adult body. The excessively long sperm tail is obviously not a structure that has evolved for better swimming; instead, it is thought to act as a tangled barrier in the female reproductive tract to prevent other males from fertilizing the female, and there is also some very interesting evidence that sperm coevolves with the female reproductive tract, so some sexual selection at the level of the gametes is going on.
At the same time, sperm morphology is extremely diverse, and seems to evolve very rapidly. Perhaps these mega-sperm are a transient fad? Not all species of Drosophila exhibit the phenomenon, and those that do vary considerably from species to species. What we’d like to know is if there are any lineages that maintain these patterns of giant sperm over long periods of evolutionary time…so what do we need to do? We need to go spelunking for sperm in fossils!
That’s what this short letter in Science is about: the authors looked at ostracodes, a class of tiny crustacea that invests heavily in reproduction. About a third of their volume is their reproductive system, with males building giant (relative to their size) sperm pumps, and females having large seminal receptacles for sperm storage. The individual sperm are also large, often longer than the body length of the adult, and are also aflagellate — no flagellar tail at all, just a long, threadlike cell body. You can tell if a female ostracod is a virgin just by looking at those seminal receptacles, since they inflate hugely with all the giant sperm tucked inside.
So, if you look at the large orange blobs, the seminal receptacles, in this 3-D scan of a fossil female ostracod (bottom right of this image), you can tell that she was inseminated before she died, and that her mate had very large sperm. Her condition was also very similar to that of modern ostracodes (bottom left).
So, the conclusion is that boinking with giant sperm is an enduring property of at least some lineages: they’ve been going at it for a hundred million years. The authors also suggest that this kind of technique could be useful for measuring sexual selection by assessing pre-mating parental investment in fossil invertebrates.
Matzke-Karasz R, Smith RJ, Symonova R, Miller CG, Tafforeau P (2009) Sexual Intercourse Involving Giant Sperm in Cretaceous Ostracode. Science 324(5934):1535.
Miller GT, Pitnick S (2002) Sperm-Female Coevolution in Drosophila. Science 298(5596):1230-1233.
