Friday, October 29, 2004

Friday Plant sorta-blogging

I'm a zoologist by training, dammit, not a botanist, so I really have to struggle when I read a paper on plant evolution. But I do feel obligated to at least every once in a while explore the world of our meristematic sisters in descent. So, despite understanding only one word in three in the paper, here is another lovely fossil, the proto-seed plant Runcaria heinzelinii from 385 million years ago:

Since I really can't say much about the details of this discovery other than what I can glean from my limited understanding of botany, I'll just reproduce the authors' conclusions. My less limited readers can discuss it among themselves.

This new evidence suggests that seed plants arose between 385 and 365 Ma, in the time interval separating Runcaria and the earliest known seeds. This is earlier than the ages ranging from 341 to 360.4 Ma that were recently estimated for this event on a molecular basis. Runcaria evolved in the Givetian, when progymnosperms were represented by aphyllous Aneurophytales and earliest representatives of the Archaeopteridales (3). This early occurrence of a seed plant precursor adds more credit to hypotheses that spermatophytes are nested in the Aneurophytales rather than the Archaeopteridales and supports views about nonfoliar origins of the cupule and integument of the earliest seeds. Finally, Runcaria demonstrates that, in addition to monomegaspory, endomegasporangy, and integumentation, possession of a cupule and differentiation of an unopened megasporangial apex preceded the acquisition of the pollen chamber and lagenostome characterizing the hydrasperman organization.

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Gerrienne P, Meyer-Berthaud B, Fairon-Demaret, Streel M, Steemans P (2004) Runcaria, a Middle Devonian seed plant precursor. Science 306:856-858.

Friday Leanchoilia blogging

Hmmmph. I'm a bit miffed. The New York Times is finding the news so slow (ha!) that they can write fluff about Friday cat blogging by the usual suspects, but week after week I tell you all about much more interesting beasties, and do I get any mention? Noooooo. Just because I'm more interested in things with suckers or spines instead of fur, or antennae instead of eyes, or tentacles instead of paws, or that are dead instead of playing with balls of yarn, I get no respect. Dang pandering felines—you know they're just sucking up to you with that purring crap and that soft, furry pelt.

Now here's an animal with integrity, one with a little self-respect that demands you to love it for what it is. It's called Leanchoilia superlata, a very pretty name. It was a blind arthropod bearing a pair of spectacular "great appendages" on its front end, each with a trio of whiplike lashes. This general layout seems to have been a successful morphological strategy in the Cambrian: Opabinia, Anomalocaris, Yohoia, and Fortiforceps all seem to have adopted the habit of carrying around great whacking claws or knives or clubs as their frontmost appendages. Leanchoilia probably used theirs as sensors, flicking them over the surface in search of prey, and as graspers, clutching their victims to their mouthparts for consumption.

The other distinctive feature is their gut—several papers have been written about the spectacular Leanchoilia gut. It fossilizes unusually well, preserving a fair amount of fine structure, revealing that it is thickly surrounded with glandular tissue. This also suggests a few things about taphonomy.

Phosphatization of soft tissues in the Burgess Shale is restricted to particular taxa, indeed to particular organs of particular taxa. In Leanchoilia, for example, it is limited specifically to the midgut and possible excretory organs on the third podomere of its great appendages. Such specificity suggests that the source of the phosphorus ions was internal, i.e., derived from the organs themselves. Likewise, the absence of any Santana-type preservation of muscle argues convincingly against a significant external source of phosphorus. In this light, it is interesting to note the abundance of unordered “mineral” spherites characteristic of many arthropod midgut glands, sometimes to the extent that they constitute a substantial fraction of the solid feces. Rich in both phosphorous and calcium, these offer a ready source of permineralizing ions, as well as abundant, localized nucleation sites.

Isn't a bizarre chitin-covered nektobenthic predator with guts and half-billion-year-old fossilized poop much more interesting than yet another boring cat?

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By the way, at least The Modulator's Friday Ark pays attention to a little zoological diversity. And at least one other person recognizes the intrinsic interest of invertebrates.

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Butterfield NJ (2002) Leanchoilia guts and the interpretation of three-dimensional structures in Burgess Shale-type fossils. Paleobiology 28(1):155–171.

Wednesday, October 27, 2004

Homo floresiensis, Flores Man

A long-lost cousin has been discovered, Homo floresiensis, or Flores Man. It's especially dramatic for a number of reasons. It's relatively recent, with the youngest specimen only 18,000 years old, but it is most closely related to Homo erectus. This species was also minute, only 3 feet tall, and tiny-brained. Here we have a group of small, specialized human relatives, living contemporaneously with Homo sapiens, on isolated islands in Indonesia. It's like discovering that Munchkins were real. You can read more here:

• Nature has special online section on Flores Man, with several articles on its discovery free to the public.
• Carl Zimmer has a summary of the significance of the discovery.

A real pleasure of working in a historical science like biology is that sometimes you can be completely surprised by some unexpected, odd, and entirely accidental discovery. Flores Man is such a wild surprise.

A new human-like species - a dwarfed relative who lived just 18,000 years ago in the company of pygmy elephants and giant lizards - has been discovered in Indonesia.

Skeletal remains show that the hominins, nicknamed 'hobbits' by some of their discoverers, were only one metre tall, had a brain one-third the size of that of modern humans, and lived on an isolated island long after Homo sapiens had migrated through the South Pacific region.

"My jaw dropped to my knees," says Peter Brown, one of the lead authors and a palaeoanthropologist at the University of New England in Armidale, Australia.

The find has excited researchers with its implications—if unexpected branches of humanity are still being found today, and lived so recently, then who knows what else might be out there? The species' diminutive stature indicates that humans are subject to the same evolutionary forces that made other mammals shrink to dwarf size when in genetic isolation and under ecological pressure, such as on an island with limited resources.

Flores Man adds an interesting twist to our hominid phylogenies. As you can see in this diagram, we now have to add this slender thread from the great Homo erectus dispersal, a relic species that survived long after it's closest relatives.

Cryptozoologists are going to have a ball. Henry Gee already has an article up, mentioning "that other species of recently extinct humans might be discovered on other isolated islands", and even mentioning the possibility of extant hominids.

The accompanying paper on the archaeology also shows the tools found with these little hominids; these weren't simple apes. They were making some wicked weapons and carving tools.

Despite its ability to make tools, though, Flores Man was small-brained, small even for its diminutive size.

Look at that: 1m tall, with a 380 cm³ brain. And shaped stone tools. That is simply amazing.

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There's also an article on Flores on the National Geographic site, including the nice reconstruction to the left.

National Geographic provided funding for the research, and are going to be airing a documentary on the subject next year.

They also summarize the little guy's life style:

The Flores people used fire in hearths for cooking and hunted stegodon, a primitive dwarf elephant found on the island. Although small, the stegodon still weighed about 1,000 kilograms (2,200 pounds), and would pose a significant challenge to a hunter the size of a three-year-old modern human child. Hunting must have required joint communication and planning, the researchers say.

Almost all of the stegodon fossils associated with the human artifacts are of juveniles, suggesting the tiny humans selectively hunted the smallest stegodons. The Flores humans' diets also included fish, frogs, snakes, tortoises, birds, and rodents.

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Morwood MJ, Soejono RP, Roberts RG, Sutikna T, Turney CSM, Westaway KE, Rink WJ, Zhao J-x, vandenBergh GD, Rokus Awe Due, Hobbs DR, Moore MW, Bird MI, Fifield LK (2004) Archaeology and age of a new hominin from Flores in eastern Indonesia. Nature 431-435.

Brown P, Sutikna T, Morwood MJ, Soejono RP, Jatmiko, Saptomo EW, Rokus Awe Due (2004) A new small-bodied hominin from the Late Pleistocene of Flores, Indonesia. Nature 431:1055-1061.

How do octopus suckers work?

Whoa, it's been a while since I've said anything about my infatuation with cephalopods. Let's correct that with a nifty paper I found on octopus suckers.

Here's a typical view of a tangle of octopus arms, all covered with circular suckers. The octopus can cling to things, grasp prey and other objects with those nifty little discs, and just generally populate people's nightmares with the idea of all those grappling, clutching, leech-like appendages.

Octopus suckers are actually beautiful little tools, though, with a fair amount of sophistication in their organization. Don't compare them to the simple rubber suction cups on kids' toy dart guns; these have their own elaborate muscular regulatory mechanisms. This diagram illustrates the internal structure of a single octopus sucker.

There are two main regions, an infundibulum (IN) on the attachment face of the sucker, and a deeper chamber called the acetabulum (A) (if you don't recall any Latin, "infundibulum" just means "funnel", while "acetabulum" is "vinegar cup"—anatomy is littered with funnels and cup-shaped structures, so these are actually very generic names). Both regions are muscular, covered with a dense sheet of radial muscles (R) and rings of circular and meridional muscles (C and M).The whole thing is surrounded by supple sheets of connective tissue and epithelia.

The way it works is that the sucker is pressed against a surface, and the flexible outer margin of skin conforms to it, forming a seal. Then the radial muscles contract. Now muscle is a relatively incompressible tissue; when it contracts, it changes its length, but it cannot change its volume. When you make a muscle in your arm to show off to the girls, you are reducing the length of the bicep, so it has to bulge outwards to maintain a constant volume. This principle is also how your tongue works: when muscles contract to flatten it, the volume has to stay the same so it protrudes.

When the radial muscles in the sucker contract, the walls of the acetabulum and infundibulum get thinner. The muscle volume has to go somewhere, so the circumference of the cup-shaped acetabulum has to increase, increasing the volume of the acetabular chamber. Since the infundibulum is sealed against a surface, water can't get in; so we have the same quantity of water in a larger chamber, which means the pressure is reduced, generating suction. They can release their grip by relaxing the radial muscles, or contracting the circular muscles, which would reduce the volume of the acetabulum.

An octopus can generate a respectable amount of force with this mechanism. At sea level, they can create a pressure differential of 100-200 kPa (kilopascals; 100 kilopascals is approximately equal to one atmosphere), and at greater depths, where the water pressure is greater, they can generate correspondingly greater amounts of force.

A closeup view of the sucker reveals other details.

The infundibulum is grooved. This allows the pressure differential to be distributed to the entire surface of the sucker as it is flattened against an object. Further, the surface of the infundibulum is covered with chitinous denticles that provide a fine network of channels that similarly transmit the force everywhere, and also provide a raspy surface that restricts lateral movement (remember how when you shot your rubber-tipped dart gun at a window it would stick, but you could easily slide the dart around? Octopus suckers wouldn't do that—they'd be locked firmly in one place.)

The authors mention that squid have an additional refinement that makes their suckers even more effective. They contain a piston-like structure inside an interior chamber, coupled so that when something tries to pull away from the sucker, it lifts the piston, further decreasing pressure inside and strengthening its grip—like a Chinese finger-trap, the more you struggle, the harder it is to get away.

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Kier WM, Smith AM (2002) The structure and adhesive mechanism of octopus suckers. Integr. Comp. Biol. 42:1146–1153.

Monday, October 25, 2004

Mouse models of Down Syndrome

We all know people with Down Syndrome. It's one of the most common serious congenital disorders, affecting one in 700 births, and the suite of stereotypical morphological changes make it readily recognizable. It's also usually traceable to what seems to be a discrete cause: a nondisjunction in meiosis that gives individuals an extra copy of chromosome 21, so that instead of the normal two copies, Down Syndrome individuals have three. Somehow, this trisomy, which changes gene dosage, disrupts development in subtle ways and leads to a wide range of characteristic modifications.

Other chromosomes than 21 can also occur in triplicate, but the difference is that they all (except for the sex chromosomes, which are a special case) are lethal. One reason Down Syndrome may be less destructive is that human chromosome 21 is our smallest chromosome in terms of nucleotide length. The total sequence length is 46,976,537 bases, but if you discount the telomeres, centromeres, and heterochromatic regions, it's 'merely' 33,924,742 bases long, with 200-300 genes (the number is in flux; just about every paper I read reports a different value). You can browse through chromosome 21 at NCBI, if you'd like. It is a bit overwhelming and obscure; you'll find things like "keratin associated protein 19-5" and "liver phosphofructokinase" reside there. Stare all you'd like, but it's hard to get any insight into which of those genes are responsible or why having an extra copy would be deleterious.

Thirty four megabases and 225 genes is too much. We need hints. It would be useful to be able to pare that long laundry list down to a more manageable collection of items.

One way to reduce the list is to look for rare individuals who have only partial duplications of chromosome 21. This does happen; a chromosome can break, and a fragment attach itself to another, and the individual carrying that translocation can subsequently pass on both an intact chromosome 21 and the fragment to their children, and together with the intact chromosome 21 from the other parent, the children will have 3 copies of each gene contained in the fragment. This kind of analysis of 'natural experiments', in which finding genetic accidents helps us associate smaller bits of the genome with a phenotype, is a useful research strategy. One result, for instance, is that it has allowed us to identify a smaller region, about 4-5 Mb long, that seems to be important in producing at least some of the Down Syndrome effect. That region of chromosome 21 is called the Down Syndrome Critical Region, or DSCR.

In many ways, this is not an entirely satisfying sort of analysis. It depends entirely on what genetic variations fate hands us, and you certainly don't get to tweak the methods, shave off a few thousand nucleotides here, add a few thousand there, or ask someone with an interesting deletion to breed a few dozen times with this other person with a promising duplication…people object to that sort of thing. We need an animal model.

You can't just make a trisomic mouse, though. Here's the catch: recall from my discussion of synteny that blocks of genes get scrambled around to different chromosomes during the course of evolution. The genes that we have on our chromosome 21 are scattered onto mouse chromosomes 10, 16, and 17; and each of these chromosomes contain orthologs of genes found on other human chromosomes. What you have to do is splice together a kind of artificial chromosome containing the pieces you want, and introduce that into a mouse. We have such a beast: it's called the Ts65Dn mouse, and what it contains is an extra piece of mouse chromosome 16 spliced to a small piece of chromosome 17, and contains 104 of the genes we find on human chromosome 21. It's not a perfect copy of Down Syndrome, but it produces mice that live into adulthood, with characteristic skeletal changes (a shorter, broader skull and jaw, for instance) and changes in brain physiology. There is also another mouse strain with a smaller duplication, called Ts1Cje, that has extra copies of 81 of the genes found on human chromosome 21—and it exhibits a similar phenotype.

These are powerful tools! Try searching PubMed for "Ts65Dn" or Ts1Cje". There is a bloom of papers dissecting these mouse models of Down Syndrome, digging into the precise mechanics of the various deficits and working out the details of the disorder.

The diagram below illustrates what these artificial segmental trisomies contain. On the left is the human chromosome 21 for comparison, with the DSCR marked. Next to it is the Ts65Dn mouse chromosome, showing that it isn't a complete copy of Human 21, but it does encompass the DSCR. On the far right is the still smaller Ts1Cje construct, which also includes the DSCR.

In a paper by Olson et al., this reduction has been carried a step further. They have made a mouse construct that is trisomic for only the genes in the Down Syndrome Critical Region, labeled Ts1Rhr above, and they've also made one with a complementary deletion, called Ms1Rhr/Ts65Dn, which allows them the ability to very thoroughly control the dosage of those genes.

Here's a small surprise, however: the Ts1Rhr mouse, which is trisomic for the DSCR, doesn't seem to be a very good model for Down Syndrome.

The diagram to the right illustrates the kind of morphological analysis that was done. Mice don't look like people, obviously, and while we may be good at recognizing the overall appearance of a Down Syndrome person, it's harder to do in a mouse. What you can do is identify specific landmarks in the skeleton, measure proportions, and make a mathematical comparison. For instance, the bottom diagram is a human jaw, and the lines represent angles and distances between points on that jaw that can be measured and compared in different individuals. The purple lines indicate measurements that are significantly different between Down Syndrome individuals and euploid (or unaffected) individuals. In Down Syndrome, all of those purple lines are shorter than they should be, so that the person has smaller jaws.

In the segmentally trisomic Ts65Dn mouse, in the top diagram, similar parameters can be measured (the purple lines again), as well as others (the red lines) that all indicate a net reduction in jaw size. This is comparable to human Down Syndrome.

The middle figure, though, is the Ts1Rhr mouse, the one that is segmentally trisomic for just the DSCR. Those blue lines are parameters that are longer than they are in the wild type mouse—instead of a shorter, smaller jaw, these mice have the opposite, a longer, slenderer skull and jaw.

Scientific American has a short summary of these results, and they draw a conclusion we really ought to take for granted.

In an accompanying commentary, David L. Nelson and Richard A. Gibbs of the Baylor College of Medicine note that the findings refute the notion that possessing three copies of the DSCR is the sole cause of the cranial and facial features of Down syndrome. For their part, Reeves and his colleagues posit that genes contained in the DSCR interacting with other genes could be to blame. “The simplistic idea that just one of the hundreds of genes on chromosome 21 affect development no longer holds up,” Reeves remarks. “Now researchers can take a deep breath, accept that the syndrome is complex, and move forward.”

The key concept there is that development and morphology are consequences of interactions between genes (and with the environment, I would add). We shouldn't expect that we can reduce a phenotype to the simply additive effects of a few genes, either. The paper I use to illustrate this in my classes is by Elkins et al., in a far simpler system, Drosophila. A gene that was expressed in a suggestive pattern in the nervous system, Fasciclin I, could be knocked out, but it had no apparent effect. Another gene that was thought to be important, a signal transduction molecule called Abelson tyrosine kinase, could also be mutated, but with again no visible effect. Knock out both genes in the same animal, though, and wham, gross errors in nervous system formation occurred.

It is entirely conceivable that you could give mice extra copies of each gene found on human chromosome 21 one by one, and see no effect at all. There is instead some threshold network of genes that need to be perturbed in order to see a change.

One other comment bothered me a bit, but I know what they mean.

The notion that a few genes might be of critical importance in this syndrome is particularly attractive because such a simple model would bode well for possible therapeutic intervention.

I think we should be clear on one thing: there will never be a cure for Down Syndrome. Down Syndrome is a genetic and developmental disorder; the phenotype is the result of complex genetic and epigenetic interactions during embryonic development, not the discrete expression of a defective gene product late in development. The only possible 'cure' for the wide spectrum of problems in Down Syndrome would require breaking an individual down to a few cells and replaying all of those embryonic events over again, and that's the kind of treatment nobody wants.

However, these studies do promise to help isolate pieces of the syndrome and identify treatments that could correct symptoms: Down Syndrome individuals have an increased frequency of childhood onset leukemia, testicular cancer, and early onset Alzheimer's pathologies, for instance, and identifying the parts of the genetic puzzle that contribute to those problems could help figure out strategies for reducing them in Down Syndrome individuals. And understanding how these factors induce such problems in people trisomic for chromosome 21 might also reveal the mechanisms that cause the same problems in us euploids.

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Akeson EC, Lambert JP, Narayanswami S, Gardiner K, Bechtel LJ, Davisson MT (2001) Ts65Dn—localization of the translocation breakpoint and trisomic gene content in a mouse model for Down syndrome. Cytogenet Cell Genet. 2001:270-6.

Elkins T, Zinn K, McAllister L, Hoffmann FM, Goodman CS (1990) Genetic analysis of a Drosophila neural cell adhesion molecule: interaction of fasciclin I and Abelson tyrosine kinase mutations. Cell 60(4):565-75.

Nelson DL, Gibbs RA (2004) The critical region in Trisomy 21. Science 306(5696):619-620.

Olson LE, Richtsmeier JT, Leszl J, Reeves RH (2004) Chromosome 21 critical region does not cause specific Down Syndrome phenotypes. Science 306(5696):687-690.

Friday, October 22, 2004

Pufferfish and ancestral genomes

The fugu is a famous fish, at least as a Japanese sushi dish containing a potentially lethal neurotoxin that was featured on an episode of The Simpsons. Fugu is a member of the pufferfish group, which have another claim to fame: an extremely small genome, roughly a tenth the size of that of other vertebrates. The genome of several species of pufferfish is being sequenced, and the latest issue of Nature announces the completion of a draft sequence for the green spotted pufferfish, Tetraodon nigroviridis, a small freshwater species.

Tetraodon has about the same number of genes as we do, 20,000-25,000, but they are contained in a total genome length of 340Mb vs. our huge 3.1Gb. One major difference is that in Tetraodon, transposable elements are rare: they have 73 types, present in less than 4000 copies, but humans have about 20 different types present in millions of copies. Transposable elements may be reverse transcriptases that blindly copy RNA sequences back into the DNA (called LINES) or shorter sequences that are processed by LINES, called SINES. These really are parasitic bits of selfish DNA, and somehow, pufferfish seem to be largely free of them.

One of the interesting things one can do with a pair of genome sequences is to start mapping synteny. Synteny represents the preservation of small regions of order within a chromosome; while the overall organization may have been scrambled by millions of years of chromosome breaks and fusions and duplications and deletions, we can still identify smaller blocks that maintain the same series of genes within them. For example, if we look on a chromosome of one organism and we see the series of genes A-B-C-D-E-F, and we look in another organism and find a chromosome with the genes W-X-C-D-E-Y-Z, we can see that the C-D-E chunk can be mapped directly to one region of that second organism's chromosome.

A way to diagram this is to color code all the syntenic regions from each chromosome in one organism, and see how those regions are distributed in a second organism. For instance, in the first diagram below, imagine that human chromosome 15 has been colored yellow (the key along the bottom of the diagram tells you how they've been color coded.) Then, we take each synteny with chromosome 15 in the Tetraodon genome and color it yellow; you can think of it as if we've taken human chromosome 15, and all the other chromosomes, and broken them apart and reassembled them into the Tetraodon genome, and the colors allow us to see where each fragment came from. For instance, you can see that large pieces of human chromosome 15 are found in Tetraodon chromosomes 5 and 13.

You can also do this in the other direction, and take each Tetraodon chromosome, color code them, break them apart, and reassemble them into the order they would be in in the human genome, as in the second diagram.

What you are seeing in the scattered colors in these diagrams is a rendering of the history of chromosome reorganization that occurred during evolution. Hundreds of millions of years of juggling, and the order is still not completely randomized—there are still recognizably preserved blocks of local structure.

Of course, don't be misled by the synteny diagrams into thinking that what happened in evolution was the reorganization of the human genomic organization into the Tetraodon pattern (or vice versa). There was a common ancestor with some arrangement of genes on its chromosomes, and those chromosomes got broken apart and juggled around in our history, and those chromosomes were independently scrambled in the Tetraodon lineage.

Here's something else we can learn from synteny. Looking more closely at the map, below, reveals a curious pattern: some of the Tetraodon chromosomes can be mapped in an alternating or interleaved arrangement on the human chromosomes.

For instance, look at human chromosome 16 (Hsa16). Blocks of genes from Tetraodon chromosome 5 (Tni5) and Tetraodon chromosome 13 (Tni13) are both found in a larger syntenic region here…and this defies probability. If chromosome reorganizations were random, we shouldn't be seeing only Tni5 and Tni13 alternating exclusively here, and we shouldn't be seeing these other associations all over the place. You can also see Tni5 and Tni13 alternating on Hsa15, and Tni1 and Tni7 alternating on HsaX.

Why are Tni5 and Tni13 found together, and Tni1 and Tni7, and Tni2 and Tni3, and so forth? The simplest answer is that there was a whole genome duplication in the Tetraodon lineage. In the last common ancestor of humans and Tetraodon, there was a single chromosome that mapped onto that region of Hsa16. After Tetraodon diverged, that chromosome was duplicated, forming Tni5 and Tni13, and over time, many of the duplicated genes were secondarily lost, but which copy was lost, whether the one on Tni5 or the one on Tni13, was random. The regions of doubly-conserved synteny (DCS), where we've got pairs of Tetraodon chromosomes clustering together in lockstep with regions of the human chromosome, represent ghosts of a single ancestral chromosome. In this diagram, those hypothetical ancestral chromosomes have been outlined and colored in the pastel colors surrounding the interleaved regions, and given the names AncA, AncB, AncC, etc. There are 110 of these DCS blocks scattered through the genome, and they can be grouped into 12 ancestral chromosomes.

And here you are, those ancestral syntenic fragments can then be reordered into a their simplest arrangement, and we have an ancestral genome.

I don't know about you, but I find this use of genomic evidence and logic to identify the long-lost chromosomes of a 350 million-year-old organism to be extremely cool. Hella cool. Kick-ass, far-out, mega-cool.

Jebus, but I am so happy to be a member of the reality-based community.

Anyway, comparative genomics now lets us put together a comprehensible story of the evolution of vertebrates. In the diagram below, we start with an ancestral bony fish with 12 chromosomes, and then split into two lineages that lead to us tetrapods on the left, and modern fish on the right.

Our lineage was marked by a period of intense amplification of transposable elements, LINES and SINES and repeated junk that copied itself over and over, leading to our current grossly bloated genome, containing 20-25 thousand genes swimming in 3 Gb of mostly useless dead DNA. Meanwhile, the fish went through a whole genome duplication (WGD), followed by a thorough pruning back of many of the excess copies, leaving them with a similar 20-25 thousand genes. In the Tetraodon lineage, at least, there was no amplification of junk, so their protein-coding genes reside in a lean, trim 340 Mb.

Comparative genomics is a powerful tool that is going to be telling us much, much more about our evolutionary history.

…the remarkable preservation of the Tetraodon genome after WGD makes it possible to infer the history of vertebrate chromosome evolution. The model suggests that the ancestral vertebrate genome was comprised of 12 chromosomes, was compact, and contained not significantly fewer genes than modern vertebrates(in as much as the WGD and subsequent massive gene loss resulted in only a tiny fraction of duplicate genes being retained).

The explosion of transposable elements in the mammalian lineage,subsequent to divergence from the teleost lineage, may have provided the conditions for increased interchromosomal rearrangements in mammals; in contrast, the Tetraodon genome underwent much less interchromosomal rearrangement. With the availability of additional vertebrate genomes (dog, marsupial, chicken, medaka, zebrafish and frog are underway), it will be possible to explore intermediate nodes such as the last common ancestor of amniotes, of sarcopterygians and of actinopterygians, and to gain an increasingly clearer pictureof the early vertebrate ancestor. Because the early vertebrate genome is 'closer' to current invertebrates, this should in turn facilitate comparison between vertebrate and invertebrate evolution.

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Jaillon O, Aury JM, Brunet F, Petit JL, Stange-Thomann N, Mauceli E, Bouneau L, Fischer C, Ozouf-Costaz C, Bernot A, Nicaud S, Jaffe D, Fisher S, Lutfalla G, Dossat C, Segurens B, Dasilva C, Salanoubat M, Levy M, Boudet N, Castellano S, Anthouard V, Jubin C, Castelli V, Katinka M, Vacherie B, Biemont C, Skalli Z, Cattolico L, Poulain J, De Berardinis V, Cruaud C, Duprat S, Brottier P, Coutanceau JP, Gouzy J, Parra G, Lardier G, Chapple C, McKernan KJ, McEwan P, Bosak S, Kellis M, Volff JN, Guigo R, Zody MC, Mesirov J, Lindblad-Toh K, Birren B, Nusbaum C, Kahn D, Robinson-Rechavi M, Laudet V, Schachter V, Quetier F, Saurin W, Scarpelli C, Wincker P, Lander ES, Weissenbach J, Roest Crollius H (2004) Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431:946-957.

Yet another Chinese enantiornithine bird!

I'm beginning to think China is a country paved with interesting fossils; every week I'm seeing something new published. This is another enantiornithine bird like the one I mentioned yesterday, only this fellow was caught as an embryo—it's all coiled around within a tight oval, a confusing jumble of bones with the skull on the left, looking down (if you can't sort it out in this picture, click on the image for a larger image with a diagrammatic key.)

The authors note a few interesting features: the bird is precocial, with feather traces present. It would have hatched as something a bit more advanced and active than your typical naked peeper. It's also lacking an egg tooth, but it's got regular teeth in its beak—as well as a long bony tail that make it look rather different from modern birds.

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Zhou Z, Zhang F (2004) A precocial avian embryo from the lower Cretaceous of China. Science 306(5696):653.

Thursday, October 21, 2004

"Four-winged" bird?

Here's a fossil enantiornithine bird. Note that, unlike modern birds, the hindlimbs are covered with long feathers:

The authors of this report speculate that there was a "four-winged" stage in the evolution of flight in birds, where the hindlimbs made a significant contribution to lift and maneuvering.

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Zhang F, Zhou Z (2004) Leg feathers in an Early Cretaceous bird. Nature 431:925.

Wednesday, October 20, 2004

A new announcement from the Human Genome Project

The human genome project has reached another landmark, the effective completion of the euchromatic sequence. It's still not 100% done, but the remaining small bits are going to require some new tricks to ferret out. You may recall announcements all over the place back in 2001 that the genome had been sequenced, but that was the draft sequence; 90% of the euchromatic genome was done, but there were still about 150,000 gaps scattered through it. You have to think of this project as something like assembling a colossal jigsaw puzzle—when the draft was done, we had a pretty good idea of the structure of the picture, and maybe had the borders done, but there were still these broad patches of solid colors that hadn't been pieced together yet. At this point, though, most of those have been filled in and the gaps are smaller and sparser.

Some numbers: the completed sequence so far consists of 2,851,330,913 nucleotides. There are only 341 gaps left in the sequence. and 33 of those are in the heterochromatin (the mildly boring, repetitive chunks of the genome, which correspond to those regions of solid color in a jigsaw puzzle), representing 198 megabytes of stuff that still has to be sequenced. In the euchromatin (the more interesting and complex stuff) there are more gaps, 308, but they are much smaller, so only 28 Mb of mystery remains. The total length of the genome is 3.08 Gb, with 2.88 Gb of it in the form of euchromatin.

The new, better defined sequence allows for a more accurate count of total gene number, and that number has dropped once again. We're down to 20-25,000 protein-coding genes. Some may think that knocks us off our pedestal a bit more, but that sounds like plenty to me.

One thing that leaps out at anyone reading the announcement is the importance of evolution in analyzing and understanding the genome. They used alignment with the chimpanzee draft sequence, for instance, to search for deletions. They are identifying recent duplications by their degree of divergence from neighboring genes, and have found 1,183 new genes that have arisen since the human and rodent lineages split. They're tracking the death of genes by identifying sequences with small numbers of disabling mutations (we seem to be losing olfactory genes at a rapid clip, relative to rodents).

The bottom line is that the HGP has provided us with a better tool for all kinds of research.

Nonetheless, the euchromatic human genome can now be regarded as effectively known. The accuracy and completeness of the current near-complete human genome sequence has important consequences for biomedical research. It allows systematic searches for the causes of disease—for example, to find all key heritable factors predisposing to diabetes or somatic mutations underlying breast cancer—with confidence that little can escape detection. It facilitates experimental tools to recognize cellular components—for example, detectors for mRNAs based on specific oligonucleotide probes or mass-spectrometric identification of proteins based on specific peptide sequences—with confidence that these features provide a unique signature. It allows sophisticated computational analyses—for example, to study genome structure and evolution—with confidence that subtle results will not be swamped or swayed by noisy data. At a practical level, it eliminates tedious confirmatory work by researchers, who can now rely on highly accurate information. At a conceptual level, the near-complete picture makes it reasonable for the first time to contemplate systems approaches to cellular circuitry, without fear that major components are missing.

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International Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature 431:931-945.

Tangled Bank #14 exists!

We have another Tangled Bank—#14 is online at Prashant Mullick's Weblog. He had me worried for a while that darn few submissions were coming in, but as usual, there was a last-minute flurry and we have an entertaining and diverse assemblage of biology posts.

There will be more to come at The Sixth International in two weeks, so send us those links. Also, I'm still looking for more hosts, so if you're willing to collect and organize a few web links, volunteer!

Tuesday, October 19, 2004

Development of cavefish eyes

Here's a story that Darwin got completely wrong. He had observed that certain species had profoundly reduced or rudimentary organs, and he explained them not as a consequence of natural selection, but as evidence of the inheritance of acquired characters.

But we learn from the study of our domestic productions that the disuse of parts leads to their reduced size; and that the result is inherited.
It appears probable that disuse has been the main agent in rendering organs rudimentary. It would at first lead by slow steps to the more and more complete reduction of a part, until at last it became rudimentary,- as in the case of the eyes of animals inhabiting dark caverns, and of the wings of birds inhabiting oceanic islands, which have seldom been forced by beasts of prey to take flight, and have ultimately lost the power of flying.

It's easy to feel mildly embarrassed for Darwin on reading this now; it was an honest error, though, and since he had no good model for inheritance, he fell back on an old idea, that the use or disuse of an organ in the parent would have an effect on its progeny. Blind fish lost their eyes because Mom and Dad fish lived in the dark and never used their eyes, so Junior inherited weaker eyes.

As it is difficult to imagine that eyes, though useless, could be in any way injurious to animals living in darkness, their loss may be attributed to disuse.

Well, actually, Charles…it's not difficult to imagine at all. Eyes are fragile, pulpy things that represent a significant investment in energy. I could imagine that there would be a slight selective advantage to jettisoning something an animal isn't using, that costs it effort to develop or is a weak or sensitive point of attack. Since we've long discarded the hypothesis of the inheritance of acquired characters, that's one of the primary explanations for the loss of eyes in cave animals—their absence was an advantage.

Another explanation is that eyes are effectively a neutral character in dark environments, and that there is therefore no selective advantage in maintaining them. Cave organisms acquired mutations that knocked out the eyes, and in the absence of selection to maintain sight, these mutations accumulated until the entire population was lacking eyes.

There is a third possibility, now supported by observations in blind cave fish of the genus Astyanax. Despite being wrong on the mechanisms of inheritance, Darwin was no dummy, and he almost figured this one out. If he'd had just a little more intuition about development, he might have suggested this idea. Here's the tantalizingly close passage:

By the time that an animal had reached, after numberless generations, the deepest recesses, disuse will on this view have more or less perfectly obliterated its eyes, and natural selection will often have effected other changes, such as an increase in the length of the antennae or palpi, as a compensation for blindness.

The third possibility requires that one recognize that development is not infinitely plastic, that characters are linked in development, and that maybe the only way to develop these compensatory structures is at the expense of the eyes—that is, that there is a selective advantage to developing long antennae or palpi or other organs, but that the simplest developmental process to do so involves cannibalizing eye tissue. This explanation is an example of the way knowledge of developmental biology can inform our understanding of evolutionary biology.

Here, for example, are two species of a Mexican fish, Astyanax. The one on the left is found in surface streams, and the one on the right is found in caves, and has lost most of its pigment as well as its eyes. These two are sufficiently closely related that they can be interbred, and are thought to have diverged within the last ten thousand years. One has to wonder what is the cause of the differences between them. One answer is found in their development.

Here's how those two look as embryos; the surface fish is again on the left and the cave fish is on the right. The cave fish starts to form an optic cup (oc), but it never develops as far, and actually begins to regress, starting at the ventral edge, which is where the optic stalk is located (the optic stalk is the tissue connecting the embryonic eye to the brain.)

Looking earlier, when the optic cup has not yet formed the the primordium of the eye is called the optic vesicle (ov), we can see an obvious difference: the optic vesicle of the cave fish is much smaller than that of the surface fish. In addition, we can stain for various molecules present at this time, in particular pax2, which is expressed only in the optic stalk, and pax6 found in the optic vesicle itself. Below, the fish have been stained for pax2, and the cave fish is expressing it much more strongly.

Another molecular player here is hedgehog, which is expressed in the midline. The authors have stained embryos for hedgehog and for other molecules downstream of it, looking for differences. Below are embryos stainded for ptc2, a hedgehog receptor, and nkx2.1a, a transcription factor that is regulated by hedgehog. What we see in the cavefish on the right is an expansion of hedgehog expression in the midline, and an expansion of the regions of expression of genes regulated by hedgehog.

What this is saying is that at the molecular and developmental level, eyelessness in the cave fish may not be a loss at all. Midline genes like hedgehog are in a balancing act with eye genes like pax6, and the eyelessness may be a side effect of tipping the balance towards wider expression of hedgehog, which secondarily represses eye formation.

This hypothesis can be tested by taking a surface fish embryo and artificially increasing the level of expression of hedgehog by injecting it with hedgehog RNA. The top two diagrams below are examples of surface fish embryos that were injected with hedgehog RNA on just the left side, and then stained with pax6. The eye on the injected side is visibly smaller.

The lower two images are older surface fish that had received the same kind of hedgehog RNA injection—the one on the left is reduced, while the one on the right has completely lost its eye, and is an excellent phenocopy of the cavefish.

What all this is telling us is that the failure of the eye to form in the blind cavefish isn't the result of a passive loss of eye genes, but the expansion of expression of genes that actively oppose eye formation. Other work from the Jeffery lab suggests that the expanding genes are responsible for an increase in jaw size and the number of gustatory receptors. The enlargement of sensory and manipulatory structures isn't to compensate for the loss of eyes, as Darwin suggested, but may actually be the developmental cause of the organism's blindness.

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Yamamoto Y, Stock DW, Jeffery WR (2004) Hedgehog signalling controls eye degeneration in blind cavefish. Nature 431:844-847.

Sunday, October 17, 2004

Tangled Bank is on its way

Remember! The next edition of the Tangled Bank> will be at Prashant Mullick on Wednesday. Send your submissions directly to Prashant, to host@tangledbank.net, or to me.

Friday, October 15, 2004

Friday Yunnanozoan blogging!

I'm traveling west, so I don't have a lot of time, but I've got to put up a new critter on a Friday…so here you go, a yunnanozoan, Haikouella jianshanensis:

Yunnanozoans are extinct deuterostomes from the Lower Cambrian of China, interesting because their relationship to chordates is thought to be close, but still a bit ambiguous in their exact position. I wrote about some of these relationships before, and here's the diagram I used; yunnanozoans either branch off the chordate line, or the hemichordates.

Once upon a time, though, these little guys had to be numerous. The authors reconstructed their anatomy from 1420 specimens.

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Shu D, Conway Morris S, Zhang ZF, Liu JN, Han J, Chen L, Zhang XL, Yasui K, Li Y (2003) A New Species of Yunnanozoan with Implications for Deuterostome Evolution. Science 299(5611):1380-1384.

Thursday, October 14, 2004

Abiogenesis looks a little bit easier now

I'm going to just briefly mention this nice article by Leman et al. in the current issue of Science, because I know someone at the Panda's Thumb is going to do a more thorough description when he gets time. For now, I'll point you to the abstract:

Almost all discussions of prebiotic chemistry assume that amino acids, nucleotides, and possibly other monomers were first formed on the Earth or brought to it in comets and meteorites, and then condensed nonenzymatically to form oligomeric products. However, attempts to demonstrate plausibly prebiotic polymerization reactions have met with limited success. We show that carbonyl sulfide (COS), a simple volcanic gas, brings about the formation of peptides from amino acids under mild conditions in aqueous solution. Depending on the reaction conditions and additives used, exposure of α-amino acids to COS generates peptides in yields of up to 80% in minutes to hours at room temperature.

That's interesting: bubbling a common volcanic gas through a solution of amino acids catalyzes the formation of peptide chains. The paper describes everything from dipeptides to traces of hexapeptides being formed in small volumes over the course of minutes to hours.

Don't ask me for all the details, though—it's a lot of organic chemistry. Keep your eye on the Thumb.

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Leman L, Orgel L, Ghadiri MR (2004) Carbonyl Sulfide-Mediated Prebiotic Formation of Peptides. Science 306(5694):283-286.

Wednesday, October 13, 2004

Mei long, the sleeping dragon

Those new fossils just keep pouring out of China. Here's a new troodontid dinosaur with the lovely name of Mei long, which was discovered intact as if caught abruptly in the instant of its death. Troodontids are long-necked bipedal dinosaurs that look rather ostrich-like. This one is a juvenile that died suddenly in its sleep, and is presumably in its normal resting posture.

Look at the bottom left view, which is also diagrammed to the right. The tail is arcing across the bottom of the image; it was coiled around the animal as it rested. The forelimbs are to the left, and are cocked back, elbows high, with the forepaws tucked under the chest. The hindlimbs are also folded foreward and held under the body, like a sleeping bird. And the long neck is coiled backwards towards the left side of the body, with its head (the triangular object with the huge open orbits labeled "sk")is tucked behind its left arm and looking backwards. Except for the long bony tail, you'd almost think this was a sleeping goose.

Mei long, by the way, is Chinese for "sleeping dragon."

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Xu X, Norell MA (2004) A new troodontid dinosaur from China with avian-like sleeping posture. Nature 431:838-841.

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