…and this is a 
Amphioxus and the evolution of the chordate genome
Category: Development • Evolution • Genetics • Molecular Biology • Organisms • Science
Posted on: June 26, 2008 3:29 PM, by PZ Myers
This is an amphioxus, a cephalochordate or lancelet. It's been stained to increase contrast; in life, they are pale, almost transparent.
It looks rather fish-like, or rather, much like a larval fish, with it's repeated blocks of muscle arranged along a stream-lined form, and a notochord, or elastic rod that forms a central axis for efficient lateral motion of the tail…and it has a true tail that extends beyond the anus. Look closely at the front end, though: this is no vertebrate.
It's not much of a head. The notochord extends all the way to the front of the animal (in us vertebrates, it only reaches up as far as the base of the hindbrain); there's no obvious brain, only the continuation of the spinal cord; there isn't even a face, just an open hole fringed with tentacles. This animal collects small microorganisms in coastal waters, gulping them down and passing them back to the gill slits, which aren't actually part of gills, but are components of a branchial net that allows water to filter through while trapping food particles. It's a good living — they lounge about in large numbers on tropical beaches, sucking down liquids and any passing food, much like American tourists.
These animals have fascinated biologists for well over a century. They seem so primitive, with a mixture of features that are clearly similar to those of modern vertebrates, yet at the same time lacking significant elements. Could they be relics of the ancestral chordate condition? A new paper is out that discusses in detail the structure of the amphioxus genome, which reveals unifying elements that tell us much about the last common ancestor of all chordates.
But first, a little question that needs to be resolved. This is an ascidian, a member of the subphylum urochordata.
Like us and like amphioxus, it also has a central notochord, and it also has segmental blocks of muscle and a dorsal nerve cord, and in this case you can also see that it has an expansion of the front of the nerve cord into something that looks rather brain-like. Ascidians are also more diverse and successful than the cephalochordates.
A major difference, though, is that amphioxus maintains its chordate morphology throughout its life — the picture at the top of this page is an adult. Ascidians, on the other hand, only look like tadpoles in their larval stages, which is only a dispersal form. They swim away from their parent and settle down on a solid surface and throw away their tail and brain and squat permanently as a sessile filter feeder called a sea squirt. This opens a debate about chordate ancestry. Did we 1) evolve from an ascidian-like animal, that maintained it's larval stage throughout life and refined its form to become something like an amphioxus, which then evolved into the vertebrates? Or was 2) an amphioxus-like animal at the base of the family tree, and the ascidians are the weird cousins who went off and evolved a specialized adult form?
I've discussed ascidian evo-devo before, and the consensus so far is that the second model is most likely, and ascidians are a highly derived descendant of the last common ancestor of all chordates, which have gone off in some radical and very interesting directions. The current paper on the amphioxus genome confirms that, and in particular reveals an interesting fact: while the ascidian genome has undergone some major remodeling that makes it very different from our own, the amphioxus genome seems to have conserved many ancestral features and may very well be a good proxy for examining the genetics of the last common chordate ancestor.
Before we move on to the genetics, though, look at the diagram above. At the bottom are two embryos at the 8-cell stage, with the prospective fates of some regions marked: cells that form in the area with the horizontal hatching will become notochord, and those with the vertical hatching will become the neural tube. The two are very similar; the one on the left is an ascidian embryo, and the one on the right is an amphioxus embryo. Both exhibit a pattern of mosaic development, in which the fates of regions of the egg are mapped out by a pre-pattern of molecular determinants. Vertebrates do not do this, or do so to a much lesser degree; we have regulative development, in which early cells are much more plastic, and gradually and progressively determine their role in the embryo. This suggests, though, that mosaicism may be an ancestral property of the chordate lineage, and we are the weirdos who have departed far from the traditional pattern in this regard.
Let's also have a brief video interlude. Below is a time-lapse movie of amphioxus development. You'll see the 8-cell stage illustrated above, and then it flies through a series of transformations into a hollow ball, folding in a portion of the structure to make a cup-shape organism, then elongating to make a kind of canoe-shaped beast, which then differentiates the various muscles and tissues to make an embryonic amphioxus. Isn't it lovely?
The recent paper in Nature by Putnam and others describes the completion of the draft genome sequence for the amphioxus species, Branchiostoma floridae. The genome is about 520 megabases long (a sixth the size of ours) and contains about 22,000 protein coding regions, or genes, and so is about the same size as ours. All this data means that a better phylogenetic tree can be assembled, which is shown below and which supports the conclusion that amphioxus diverged early in chordate history, followed by a later split between the urochordates and the vertebrates.
(click for larger image)
Deuterostome phylogeny. Bayesian phylogenetic tree of deuterostome relationships with branch length proportional to the number of expected substitutions per amino acid position, using a concatenated alignment of 1,090 genes. The scale bar represents 0.05 expected substitutions per site in the aligned regions. Long branches for sea squirt and larvacean indicate high levels of amino acid substitution. This tree topology was observed in 100% of sampled trees. Numbers in red indicate bootstrap support under maximum likelihood. Unlabelled nodes were constrained.
Look at the magnitude of the substitutions in the urochordates! If you want to argue that any chordate group is "more evolved" than any other, you'd have to hand the title to those somewhat obscure organisms — they've been shedding genes and reorganizing and adapting in some amazing ways.
Now for the tricky part, the analysis of synteny. If you're not familiar with the concept, you might want to review yesterday's basic summary of synteny, but it is basically a search for conserved clusters of genes. In this work, they used the logic of synteny to work out the existence of 17 ancestral Chordate Linkage Groups (CLGs). A CLG may roughly compare to a single chromosome in the chordate last common ancestor — it's a set of genes that are associated with one another in multiple species, and are thought to represent the retention of an ancient organization.
Here's the wonderfully complicated summary diagram.
(click for larger image)
Quadruple conserved synteny. Partitioning of the human chromosomes into segments with defined patterns of conserved synteny to amphioxus (B. floridae) scaffolds. Numbers 1-17 at the top represent the 17 reconstructed ancestral chordate linkage groups, and letters a-d represent the four products resulting from two rounds of genome duplication. Coloured bars are segments of the human genome, shown grouped by ancestral linkage group (above), and in context of the human chromosomes (below).
First, along the top they have reconstructed the 17 ancestral CLGs, and they've color-coded them: for instance, the genetic contents of CLG #8 (or ancestral chromosome #8, if you'd rather think that way) has been deduced from a comparison of human and amphioxus genomic data, and all those genes have been colored yellow. Below the ancestral CLGs is a diagram of the human chromosome set, from chromosome 1 to 22, with the X chromosome, and homologs to each of the genes in CLG #8 have also been colored yellow. You can see that ancestral chromosome 8 has, over the 500+ million years since, broken up and scattered into human chromosomes 2, 4, 5, 11, 13, and X.
I have to qualify this image a bit, though: don't get the impression that big chunks of the ancestral chromosomes have survived perfectly intact for half a billion years! What's illustrated here is a pattern of macro-synteny — what it says is that within a swathe of a particular color, we can find many, but not all genes that can be mapped to a common linkage group. If we did a more fine-grained synteny diagram, where we only mapped continuous blocks of 3 or more genes that were the same, we'd have a much messier, more salt-and-pepper sort of picture.
Within a region of a single color, there has been much scrambling of the local gene order. There have also been additions of individual new genes in either the amphioxus or human genome, and losses of genes. Also, not all genes are included in this summary: approximately 60% of the human genes that have amphioxus orthologs are found in these linkage groups. What each bit of color means is that this is a region that is enriched for a common set of shared genes between amphioxus and human beings, but it has also been leavened with variation and scrambled about internally. What has been preserved is not a literal duplicate of an ancient chromosome, but a segment that retains enough signal above the noise of ages of slow rearrangement that we can detect its affinities.
Still, pretty cool, I think. Evolutionary change hasn't completely swamped out our origins, only made them fainter and trickier to discern.
There is one other significant detail to this illustration. If you look at the ancestral CLGs, you see that each has more than one colored bar descending from them — there's four for each. What's going on here? For each gene (more or less) identified in amphioxus, there tend to be multiple genes in the human. When aligning them, you'll get multiple roughly equivalent sets of genes lining up with each amphioxus group. What this reveals is that our history is marked by two rounds of whole genome duplications after we branched away from amphioxus. This is also very cool; it might explain some of the greater diversity we see in later chordates, that they have more potential for new combinations and variations of genes.
You might recall that I mentioned that humans and amphioxus have approximately the same number of genes, about 20,000, and be wondering how that jibes with the evidence that there were 2 rounds of duplications. Shouldn't we have four times as many genes? The answer is no. When a gene is duplicated, more often than not is that one of the copies will accumulate errors and drift away into nonexistence.
Imagine that we have a stretch of chromosome that has these genes on it:
A-B-C-D
A duplication occurs; now we have two regions:
A-B-C-D and A'-B'-C'-D'
Errors take out some of the copies, so we end up with this:
A-.-C-. and .-B'-.-D'
Now, you see, we've got a result where the organism hasn't gained or lost anything overall — it still has an A, B, C, and D gene — we haven't had a doubling of the total gene numbers, we still have four genes. If we look at the synteny, we'd see one stretch of chromosome, A-.-C-., that lines up with the ancestral A-B-C-D, and we'd also see a second region, .-B'-.-D', that also lines up with it — there'd be two matches. Even though we haven't seen a significant net increase in gene numbers, we still have a doubling of the number of syntenic regions.
That's what this paper is reporting: no major increases in the number of genes, but we are seeing the vestiges of that ancient doubling. Furthermore, the losses aren't entirely random. There has been a preferential retention of duplicate genes involved in signal transduction, transcriptional regulation, neuronal activity, and developmental processes, exactly what we'd expect to see if new avenues in developmental and behavioral complexity were being explored by our ancestors. So what probably happened is that there was a fairly abrupt duplication event in our history that was largely neutral in its initial effect, and was gradually pared back down, but that some of the duplications generated new capabilities that were promoted by natural selection.
Before our ancestors were even fish, they were Cambrian and pre-Cambrian filter-feeding torpedos, muscular tubes with springy tails that darted through clouds of bacteria and plankton in the seas, harvesting microorganisms in a branchial net, and that probably resembled modern amphioxus more than anything else. That was our primitive niche, motile grazers on suspended particles. Where we vertebrates came from was an accidental set of duplications that created new combinations of genes and new phenotypic variants, some of which had adaptive advantages.
Don't get too cocky and think that surges in complexity are always a good thing, and lucky for us that we are the outcome. Evolution is blind and sometimes the fortunate result can go the other way: look to the ascidians, which, rather than expanding their genetic library, have been successful by streamlining their genomes, chucking out unnecessary elaborations and juggling a smaller suite of genes around in more dramatic ways. There are many directions evolution can take, and there's no a priori reason to think our particular path is the most powerful.
Putnam NH, Butts T, Ferrier DE, Furlong RF, Hellsten U, Kawashima T, Robinson-Rechavi M, Shoguchi E, Terry A, Yu JK, Benito-Gutiérrez EL, Dubchak I, Garcia-Fernàndez J, Gibson-Brown JJ, Grigoriev IV, Horton AC, de Jong PJ, Jurka J, Kapitonov VV, Kohara Y, Kuroki Y, Lindquist E, Lucas S, Osoegawa K, Pennacchio LA, Salamov AA, Satou Y, Sauka-Spengler T, Schmutz J, Shin-I T, Toyoda A, Bronner-Fraser M, Fujiyama A, Holland LZ, Holland PW, Satoh N, Rokhsar DS (2008) The amphioxus genome and the evolution of the chordate karyotype. Nature 453(7198):1064-71.
Life Science
Comments
Thank you. I love this stuff!
Posted by: sjburnt | June 26, 2008 3:41 PM
Looks like an embryonic Mind Flayer.
Posted by: Jon H | June 26, 2008 3:44 PM
*bursts into song*
It's a long way from amphioxus, it's a long way, to us.
It's a long, long way from amphioxus, to the meanest human cuss
cause it's goodbye to fins and gillslits, and welcome lungs and hair
it's a long long way from amphioxus, but we all came from there
Posted by: Becca | June 26, 2008 3:51 PM
This reminds me of the Pikaia
Posted by: Peter Vaht | June 26, 2008 3:52 PM
That's the thing about evolution. Nearly all of the evidence for it is really based upon the limitations imposed by mutation, duplication, natural selection, etc. So that anyone who accepts the evidence that evolution occurred is implicitly admitting that it occurred by "natural" means.
All of the synteny is merely due to unfathomable whim, according to ID--that is, if anyone thinks their ideas through.
Anyhow, I appreciate this info as to its particulars (though I read much of it in Nature already), and the rather amazing conservation of genes and parts of the original organization over more than half a billion years. I simply thought it worth pointing out, yet again, that it has meaning only in theory, while with ID it's only a swarm of meaningless facts.
Glen D
http://tinyurl.com;/2kxyc7
Posted by: Glen Davidson | June 26, 2008 3:53 PM
These occasional forays into our natural world you that you offer are beyond my scope of endeavor or expertise, but since they are here and to be known and studied, make evolution a true wonder and a realization that we areso much a part of it. I read this stuff each time you offer it, and though my command of the terminology is limited, it nevertheless fascinates me. Please continue in this regard, as since it is science, it will hold my attention.
Posted by: Holbach | June 26, 2008 3:55 PM
Is it known whether hagfish have the duplications?
Posted by: Andreas Johansson | June 26, 2008 3:57 PM
Argh! One of my favorite things to say was that vertabrates can't have larval forms because we ARE the larval forms. Now I see that may not be true.
Of course I know that sometimes just hatched fish are called larvae. I see this in my baby White Clouds and cherry barbs if I use a magnifying glass, but White Cloud suckers are still fish. The only maor anatomical revision once they become free swimming is that the mouth moves.
I've had such luck with the cherry barbs I'm thinking about moonshining some GloFish.
Posted by: Bacopa | June 26, 2008 3:58 PM
awwww
widdle itsy bitsy baby cthulhu fetus.
Posted by: ThePetey | June 26, 2008 4:03 PM
Thanks for the supporting article on synteny, that made the genetic switchup a bit easier to follow.
And excellent point on the a priori pathway evolution takes, it's hard not to think of evolution as a line to a higher progression of complexity, when species like this thrive on simplicity.
Cheers.
Posted by: Architeuthis | June 26, 2008 4:05 PM
Doh, quick clarification:
It's hard not to think of evolution as a line.... but when species like this thrive, it shows that complexity as a trait is not always the best survival mechanism.
Posted by: Architeuthis | June 26, 2008 4:07 PM
Fun with quote-mining!
"They... settle down on a solid surface and throw away their... brain and squat permanently as a sessile filter feeder called a" fundamentalist.
Once again, thanks for bringing the knowledge, PZ!
Posted by: Longtime Lurker | June 26, 2008 4:13 PM
as a relatively new follower/reader of the blog I can see that you are now on "summer break" and to satisfy your "compulsive" need to teach your personal subject you are posting these "lessons" to all to see. I for one am surprised and great full for the effort.
I personally had to end my formal science education long ago before I could really finish it for a bunch of reasons that were unavoidable at the time I have since at least acquired a tech degree. So I am pleased to read this to me new series of posts. It was biology I was studying long ago and the facts the plants and animals have been my fascination my whole live. The more I learn the deeper my appreciation becomes. I stand in awe to the way things are. thank you though I will have to study the text more before I will be able to really understand and remember it fully. your enthusiasm for and understanding of these details is great to see thanks again. uncle frogy
Posted by: uncle frogy | June 26, 2008 4:17 PM
This animal is no more "primitive" than humans are. Evolution is stupid.
Posted by: stanley | June 26, 2008 4:17 PM
Someone has to say it: I ain't no kin to no amphioxus.
Posted by: PatrickHenry | June 26, 2008 4:36 PM
NO no no no, its a living fossil ,santa , planted it............suckers
Posted by: RT NZ | June 26, 2008 4:36 PM
I never have to read so many big words when I read about Intelligent Design. My brain hurts.
Posted by: Badjuggler | June 26, 2008 4:37 PM
Hey stanley--speak fer yerself, eh?
--Sorry, I thought we were talking about Farfarman for a minute.
Posted by: Metro | June 26, 2008 4:39 PM
Hey stanley--speak fer yerself, eh?
--Sorry, I thought we were talking about Farfarman for a minute. He's busily soiling the thread over at Candid World.
As for me, what Holbach said goes double. My science education ended somewhere between planaria and my personal discover of human female biology, but you manage to give me handholds to clamber up and at least have a glimpse over the garden wall.
Posted by: Metro | June 26, 2008 4:42 PM
Though some of the advanced biology is lost on me, that is a pretty neat creature.
Posted by: Jason | June 26, 2008 4:44 PM
dear Stanely:
come on dear calm down stupid or not evolution describes what we see with in the world our eyes. I am not sure that I understand what you are trying to say.
do you mean by "primitive" inferior or crude than I would agree. they are highly adapted to the life they lead. evolution has nothing to do with developing "higher forms over lower forms" it is not directed to produce anything specific as can be observed all around us at any time it is not a ladder. I for myself look at it as more of a spreading creating opportunities (space)for other plants and animals and adopting to opportunities and space created by other plants and animals. and yes it is stupid if by that you mean mindless. or is it just you and you just want get off on argument.
Posted by: uncle frogy | June 26, 2008 4:44 PM
Stanley more or less accidentally got to the truth. Evolution is stupid, hence it explains the unintelligent adaptations we see throughout life.
Intelligence is not stupid, so it does not explain biology.
Not that Stanley is likely to be intelligent enough to understand how he accidentally told the truth.
Glen D
http://tinyurl.com/2kxyc7
Posted by: Glen Davidson | June 26, 2008 4:50 PM
Are you sure that all those genes for humans weren't there in the first place and our creator didn't just "potentiate" them.
Sorry... I couldn't resist.
Great stuff as usual PZ. I particularly liked the synteny discussion yesterday.
Posted by: SiMPel MYnd | June 26, 2008 4:54 PM
You made that up. It's all a fabrication.
(I love this stuff PZ. You Rock)
Posted by: Alex | June 26, 2008 4:57 PM
Wow. I was actually able to follow that and understand it from beginning to end, without getting lost. And I have no training in evo-devo.
Excellent explanation, PZ, and really fascinating stuff. Thanks for making these kinds of things accessible for us non-scientists. :)
Posted by: Wes | June 26, 2008 5:01 PM
Was it accidental? As you rightly say, evolution is not intelligent or guided by intelligence. It is, quite literally, stupid. While rankings of organisms as more or less 'primitive' is one of those dangerous notions that leads many laymen astray. I recall SJ Gould warning us against ranking organisms, since evolution might lead in directions other than towards some purported pinnacle.
Posted by: Lee Brimmicombe-Wood | June 26, 2008 5:04 PM
I seem to remember Dawkins using the same metaphor in Ancestor's Tale. Probably around the page where our march back through the generations meets up with the urochordates. Except he used 'tenured professor' instead of 'fundamentalist'...
Posted by: stogoe | June 26, 2008 5:07 PM
Cool! Looks like something from Farscape.
Posted by: Patricia | June 26, 2008 5:07 PM
Hey Gordy,
Learning anything?
Posted by: CJO | June 26, 2008 5:10 PM
THIS is why I love this site.
Posted by: Spinoza | June 26, 2008 5:23 PM
Errr ... I'm pretty sure Stanley meant exactly what you mean - and think that he meant not.
Why else would he herald the Amphioxus as non-primitive? Wasn't there a three-post rule in effect at some point?
Thank you, PZed. So wonderfully clear. And I liked the pretty movie.
Posted by: Sili | June 26, 2008 5:26 PM
I'm sure Schlafly is going to ask for your data, PZ.
I got a fireball comin' online.
Posted by: Tulse | June 26, 2008 5:29 PM
Thanks for this!
Dear Dr. Putnam:
I haven't read your paper, and hardly feel it necessary to do so, but I find your results highly questionable. I demand that you send me all of your data forthwith, and in addition pay my airfare and expenses that I may travel to a tropical island to perform my own research on amphioxus. Otherwise, I shall find it necessary to proclaim the fraudulence of your work in the most public terms. Sincerely,
SC, Prep School Diploma, B.A., M.A., Ph.D.
Posted by: SC | June 26, 2008 5:36 PM
Great minds, Tulse. :)
Posted by: SC | June 26, 2008 5:38 PM
Stanley #14: This animal is no more "primitive" than humans are. Evolution is stupid.
This is one of the cases (which is most) where a word means something different in the technical jargon of a field vs. its common meaning. Primitive here means "more like the original state -- less changed". They have continued to evolve, "as much as" us, but the end result is a less changed ecological niche, and a less changed genome; aka, amphioxus's history has been more stable than ours.
It's got the same meaning in anthropology -- when an anthro says the folks in Niugini are primitive relative to us, all they mean is that their lifestyle is more similar to the ancestral state than ours is - not that they're simpler or "less culturally evolved", just that their cultural evolution has tended to involve fewer radical shifts.
This is a constant source of mis-communication. Bias in statistics doesn't mean the same thing as bias in common language; theory in science doesn't mean the same thing as theory in common-language; a "consideration of value" is different in law than in standard English.
Posted by: frog | June 26, 2008 5:38 PM
That is so cool. I've read that they're eaten by people and animals in other parts of the world, but they're only two and a half inches long.
Such an awesome looking animal.
Posted by: Steve | June 26, 2008 5:42 PM
Re #26 Posted by: Lee Brimmicombe-Wood:
I suppose we could refer to "early" and "late" organisms. I'm just groping. PZ probably has the terminology well in hand.
Posted by: PatrickHenry | June 26, 2008 5:43 PM
I don't, but I am wearing a greased helm of brilliance.
Posted by: PeteC | June 26, 2008 5:44 PM
Bah! Your greased helm of brilliance is no match for my half-githyanki half-gold dragon dire wereskunk archmage/forsaker!
Thanks for the education, PZ, from this Econ major/incurable D&D nerd.
Posted by: chancelikely | June 26, 2008 5:58 PM
Interesting write-up. I had to chuckle over this:
"This animal collects small microorganisms in coastal waters, gulping them down and passing them back to the gill slits, which aren't actually part of gills, but are components of a branchial net that allows water to filter through while trapping food particles. It's a good living -- they lounge about in large numbers on tropical beaches, sucking down liquids and any passing food, much like American tourists."
Posted by: Louise Van Court | June 26, 2008 6:03 PM
Well primitive works when used in conjunction with derived. The important thing is not to use the word "advanced" in this context. As Darwin said in his notebooks "Never say higher or lower".
Humans are significantly more derived than Amphioxus, which is therefore primitive. I don't think that Early and Late will work, because organisms (especially parasites) can be secondarily simplified and throw away all sorts of things. Tapeworms and flukes for instance are somewhere (I forget exactly) in the protostomes (complex invertebrates apart from echinoderms, hemichordates, and a few others), rather than down at the base of the animal tree with the acoelmate flatworms where they were traditionally classified.
Posted by: Dave Godfrey | June 26, 2008 6:06 PM
PZ, you must be brilliant in the classroom....If I'd had a bio teacher/professor like you, I'd probably be in the life sciences instead of math. And thank you for writing these things; this middle-aged technical person is finding his world vastly enhanced by your explanations.
There was another interesting bit of news in the paper today about an early quadruped fossil - in the same way as the amphioxus, the article said it was unclear where the new fossil sits with respect to the existing record, but it added some new info about how quadrupeds evolved.
Posted by: Matt H | June 26, 2008 6:15 PM
Wooooh, evolution of the hox gene clusters by tetraeuploidie, didn't know that.
hey PZ, it occurs to me that the 8-cell-stage fatemap of amphioxus looks more like the fatemaps of Xenopus and zebrafish than the ascidian fatemap, are there any thoughts on that in the paper? (can't get that now... registration wall)
first post!
Posted by: Danio | June 26, 2008 6:15 PM
stupid me..
"are there any thoughts on that in the paper?"
It wouldn't be in the same paper, so where is the picture from?
Posted by: Danio | June 26, 2008 6:19 PM
"They... settle down on a solid surface and throw away their... brain and squat permanently as a sessile filter feeder called a"
I'll see your 'fundamentalist' and raise Dawkins' tenured professor and point out that that is unpleasantly close to a functional description of 90+% of humans, especially western humans.
tim. trying not to qualify for the above.
Posted by: tim Rowledge | June 26, 2008 6:51 PM
especially western humans.
"Sessile feeders," perhaps, but, on the evidence, too many eschew the use of a filter.
Posted by: CJO | June 26, 2008 6:57 PM
Sometimes it's great to take a break from hammering at idiotic religious/spiritual people, and actually understand new and novel concepts. The fact that we're expanding upon our roots, striving for greater and greater understanding, far exceeds the petty imaginary hallucinations that religion has to offer.
My one question on the earlier post regarding Syntegy was what happens when genes are introduced into our genome since the split with the LCA? How would they be respresented? I guess those segments are the ones in black on that syntegy map. Is that a fair assumption?
Posted by: helioprogenus | June 26, 2008 7:00 PM
"It's a good living -- they lounge about in large numbers on tropical beaches, sucking down liquids and any passing food, much like American tourists."
..presumably without the loud shirts though.
Posted by: Bride of Shrek | June 26, 2008 7:29 PM
I love this stuff. I don't always understand the terminology, but it grabs my interest and holds it until the last word. It's so fascinating to see where we come from and the millions of other paths life has taken since we diverged from our cousins. Plus all these weird sea creatures are great fodder for monster ideas when I write stories.
Posted by: Uncephalized | June 26, 2008 7:36 PM
What would you call a tadpole?
The phylogenetic position of Ventastega (which is in today's Nature rather than in last week's) is very clear, see below; what isn't clear is whether V. had fingers & toes and/or fin rays on its extremities, because the extremities haven't been found yet. There's just the skull & lower jaw, the shoulder girdle, the ilium (part of the hip girdle), possibly a rib, and possibly a fin ray of the tail fin.
--+--Eusthenopteron (f) `--+--Panderichthys (f) `--+--Elpistostege |--Tiktaalik (f; d?) |--Elginerpeton `--+--Ventastega `--+--Acanthostega (d) `--+--Metaxygnathus `--+--MGUH VP 6088 |--Ichthyostega (d) |--Densignathus `--+--Whatcheeria `--+--Pederpes (d) `--+--Greererpeton (d) `--+--Crassigyrinus (d) `--+--Baphetes `--+--Balanerpeton (d) |--Dendrerpeton (d) `--+--Silvanerpeton (d) `--+--Proterogyrinus (d) `--Eoherpeton (d)This is a strict consensus of 64 equally most parsimonious trees; this is where the divergences into more than two branches come from -- they represent uncertainties. (f) means fin rays are known, (d) means digits are known; Tiktaalik has fin rays and has what may or may not be homologous digits. MGUH VP 6088 is the specimen number of a new animal from Greenland that isn't yet described. Balanerpeton and Dendrerpeton are temnospondyls, so they would most likely have been found as sister-groups if more characters had been included, which wasn't done because they aren't the focus of this analysis; together they are most likely our closest relatives in this tree. Proterogyrinus and Eoherpeton are anthracosaurs.
Posted by: David Marjanović, OM | June 26, 2008 7:40 PM
PZ, when the heck is your book coming out? If your taking credit cards I'll pre order now. Oh, and what's with acsidians accumulating vanadium starting in embryogenesis?
Posted by: Fernando Magyar | June 26, 2008 7:45 PM
"there isn't even a face, just an open hole fringed with tentacles."
I misread that on the first skim through, and now I have a new favorite insult!
Excellent writeup as always PZ.
Posted by: pcarini | June 26, 2008 7:46 PM
You're not "your" Argh #$@^%%!
Posted by: Fernando Magyar | June 26, 2008 7:48 PM
Shit! never mind, I've had a very long day. Sheepish grin.
Posted by: Fernando Magyar | June 26, 2008 7:49 PM
David Marjanovic @ 50 I am truly awed with incomprehension, but still awed nevertheless! Science may at times be beyond the reach of the non-specialist, but it is still there to marvel for it's application to all that we know, and immaterial to the minds that don't wish to know.
Posted by: Holbach | June 26, 2008 7:57 PM
Have you got any more information about the putative digit in Tiktaalik? I don't recall anything being mentioned at the time.
Posted by: Dave Godfrey | June 26, 2008 8:01 PM
That's the tunicates department. :D
Posted by: Pandragon | June 26, 2008 8:04 PM
Bride of Shrek @ 48 "Presumably without the loud shits though(or was it shirts?)" If you want a peaceful spot on the beach, it is a lot easier to close your eyes than to stuff your ears, depending of course, on the offending shits or shirts.
Posted by: Holbach | June 26, 2008 8:40 PM
I can't believe no one else has commented on this!
That was freaking brilliant, and you are my new favorite human being, Becca.
I actually sang it to myself!
Posted by: Christopher Petroni | June 26, 2008 8:51 PM
anyone show me a mutation that creates a gill from a non-gill? Heck, or show me any mutation that adds a new structure (or part of a structure.)
Posted by: stan-the-man | June 26, 2008 9:21 PM
Evolution is indeed stupid. All you people are suckers for storytellers like PZ.
Posted by: stanley | June 26, 2008 9:22 PM
@54: It's been around for decades.
Posted by: Pandragon | June 26, 2008 9:28 PM
Previous post should have been directed to #59.
Posted by: Pandragon | June 26, 2008 9:30 PM
Well, I'm an IT nerd - but even I managed to follow most of that, and it is fascinating!
This is such a great blog!
"Pharyngula - come to kick the Fundies in the balls, stay for the Science!"
Posted by: Charlie Foxtrot | June 26, 2008 9:40 PM
@ 'stanley' - If you're really interested, there's a whole world of textbooks out there. Reject the ignorance and get reading.
In my short time here I have seen that genuine questions are welcome here, indignant demands are not.
Go find some questions.
Posted by: Charlie Foxtrot | June 26, 2008 9:46 PM
Stanley @ 61 and possibly @ 60? No, what you meant to say is that all religionists are insane moronic cretins who believed that their shit imaginary god breathed life into them from massive rectums in the cesspit of dementia, and who are not worth the shit they were born from. Now you can call your ghost god down from wherever it isn't and lay waste to this site that treats your kind as the deranged product of religious insanity. Come on, let's see this imaginary shit god of yours, you slime mold cretin!
Posted by: Holbach | June 26, 2008 10:14 PM
Fascinating. Are they any good to eat?
Posted by: Geoff | June 26, 2008 10:21 PM
"...who believed that their shit imaginary god breathed life into them from massive rectums..."
Perhaps that's a little garbled and the god breathed life into their rectums, those being the first available chance. ("In the beginning, there was an asshole...")
Posted by: pcarini | June 26, 2008 10:38 PM
Damn - all this science stuff.
I came here because this blog has a reputation for verbal violence against faith and the faithful, and instead there's all this biology and explanations and guided tours through the labs.
Not even any dancing dodos, dammit.
I'm gonna go tell everybody that PZ's reputation is a fraud, and nobody should ever come here any more again!
Posted by: Pierce R. Butler | June 26, 2008 10:50 PM
A whole genome duplication would most certainly be a fatal mutation for the majority (all?) of modern vertebrates. Clearly at more than one point in the history of our lineage, genome duplications were neutral mutations. Does anyone know if a whole genome duplication is a neutral or non-neutral mutation for a modern amphioxus?
Posted by: amphiox | June 26, 2008 10:51 PM
I love how the people who believe that God breathed life into dust are the same ones who call the theory of evolution "a fairy tale". It's all bullshit; anyone with half a brain knows it was Prometheus messin' with his Play-Do.
Posted by: Kseniya | June 26, 2008 10:53 PM
It's all bullshit; anyone with half a brain knows it was Prometheus messin' with his Play-Do.
Oh damn, they must've totally screwed up that story when I heard it in school...
Posted by: pcarini | June 26, 2008 10:59 PM
any answer to #60 you evo losers?
Posted by: stanopoly | June 26, 2008 11:40 PM
Fuck off, ignorant fool.
Oh. I'm sorry. I meant to say, "Those answers are available to those who truly wish to learn."
Unfortunately, you're obviously an anvil troll, therefore you will not seek, because you do not wish to learn.
Enjoy your Dark Age.
Posted by: Kseniya | June 26, 2008 11:46 PM
Yeah, because goddidit is a much better explanation for the diversity of life than evolution, you ass-hat.
If you (Stan%whatev) weren't suffering from such a severe case of cephalo-caudal inversion you might have a chance to understand. But your head is so far up your own ass your burps smell like farts. Or something.
So I'll add my "fuck off, ignorant fool." to Kseniya's.
Posted by: bybelknap, FCD | June 27, 2008 12:11 AM
Kseniya, you poor miserable fool...why don't you stop running your mouth and answer my challenge.
Posted by: stanstrum | June 27, 2008 12:31 AM
Kseniya, you poor miserable fool...
this has GOT to be parody.
Posted by: Ichthyic | June 27, 2008 12:35 AM
Kseniya wrote:
Oh, I love that. From now on I will describe all creotard fundies as Skydaddy's Special Magical Play-Do Men™.
As for you stan(insert suffix here) - here's a hint: the posters won't bother to answer inane questions unless you do some reading first. I suggest you spend a couple of hours on Talk Origins.
Posted by: Wowbagger | June 27, 2008 12:40 AM
So don't you evos feel pretty stupid that of all the trillions of bodily structures in the universe that you cannot account for the arrival of even one of them via your theory (RMNS)? I mean you must feel like complete fools who've fallen hook, line and sinker for the fairytales told by the likes of storytellers such as PZ Nose-Miner! If you doubt this, prove me wrong; show me the scientific verfication of the addition of a new bodily structure via random mutation.
Posted by: stansmith | June 27, 2008 12:46 AM
you bunch of wackjobs.
Posted by: stan | June 27, 2008 12:48 AM
Stan, are you suffering from multiple personality disorder? Seriously, seek some help. With your faith being as strong as i