Magnificent momma

This is one beautiful plesiosaur, Polycotylus latippinus.

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(A) Photograph and (B) interpretive drawing of LACM 129639, as mounted. Adult elements are light brown, embryonic material is dark brown, and reconstructed bones are white. lc indicates left coracoid; lf, left femur; lh, left humerus; li, left ischium; lp, left pubis; rc, right coracoid; rf, right femur; rh, right humerus; ri, right ischium; and rp, right pubis.

The unique aspect of this specimen is that it’s the only pregnant plesiosaur found; the fore and hind limbs bracket a jumble of bones from a juvenile or embryonic Polycotylus. It’s thought to actually be a fetal plesiosaur, rather than an overstuffed cannibal plesiosaur, because 1) the smaller skeleton is still partially articulated, and it’s large enough that it is unlikely it could have been swallowed whole, 2) the two sets are of the same distinctive species, 3) the juvenile is incompletely ossified and doesn’t resemble a post-partum animal, 4) the bones aren’t chewed, etched by acids, or accompanied by gastroliths. I think we can now confidently say that plesiosaurs were viviparous, which is what everyone expected.

There are other surprising details. The fetus is huge relative to the parent, and there’s only one — so plesiosaurs had small brood sizes and invested heavily in their offspring.

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Reconstructions of female P. latippinus and newborn young. Gastralia were present in both animals but have been omitted for clarity.

The authors speculate beyond this a bit, but it’s all reasonable speculation. That degree of parental investment in fetal development makes it likely that there would have been extended maternal care after birth, and rather more tenuously, that they may also have lived in larger social groups. The authors suggest that their lifestyle may have resembled that of modern social marine mammals — picture a pod of dolphins, only long-necked and lizardy.

O’Keefe FR, Chiappe LM (2011) Viviparity and K-Selected Life History in a Mesozoic Marine Plesiosaur (Reptilia, Sauropterygia) Science 333 (6044): 870-873.

(Also on FtB)

Planet of the Apes

Isn’t it obvious that the story of Planet of the Apes is about apes from one planet dominated by apes finding themselves on a planet dominated by apes of a slightly different species?


Also, this comic bugs me a little bit: I’m flying off to give a talk in which I argue that the hallmark of human evolution isn’t brutality and conquest, but cooperation.

(Also on FtB)

Vox Day and the status of Xiaotingia

I told you all the batty creationists were crawling out of the woodwork to crow over Xiaotingia‘s redefinition of Archaeopteryx‘s status as a victory for their ideology, when it really isn’t. Now another has joined the fray: Vox Day, creationist and right-wing lunatic. He makes a lot of crazy, ignorant claims in this short passage that I’ll answer one by one.

Precisely when has any evolutionist reconsidered either a) the basic hypothesis that species evolve into different species through natural selection1 or b) the corollary and requisite hypothesis that life evolved from non-life2, as a result of the falsity of one, ten, or even a hundred predictions that relied upon one or both of them? If it weren’t for DNA, which was not discovered or developed with any assistance from evolutionary theory3, evolutionary biology would already be openly recognized by every intelligent, rational, science-literate individual as being about as useful as phrenology and astrology.4

Darwinian biologists are very much like Keynesian economists. It doesn’t matter how many times their predictions fail5. It doesn’t matter how often their models are proven to be wildly wrong6. It doesn’t matter how many times they have been wrong in the past even with the benefit of margins of error consisting of millions of years7. They continue to insist that their position is based on evidence even when the evidence demonstrates precisely the opposite of what they have been claiming8.

First, the details:

1Of course biologists have considered alternate mechanisms! Coyne argues for selection as a mechanism of speciation (by pleiotropic side effects of genes that are selected for other functions), and Futuyma argues for speciation by drift.

2Similarly, mechanisms of abiogenesis have been proposed that suggest selection, but also chance or as a necessary outcome of the physico-chemical properties.

3The structure of DNA was analyzed by its chemistry, not it’s evolutionary history, obviously, but as this paragraph even concedes, the consequences of DNA biochemistry were profoundly important in their effects on evolution.

4Nope. Structure of DNA was determined in 1953; the neo-Darwinian synthesis occurred in the 1930s-1940s with the integration of genetics into evolutionary biology. It was genetics (especially population genetics) that established evolution as the only reasonable explanation for the history of life on earth.

5The precise taxonomic status of Archaeopteryx was not a specific prediction of evolutionary theory. Finding more data in the form of more fossils of feathered dinosaurs strengthens the idea of avian descent from dinosaurs.

6If you examine the family tree of Archaeopteryx and Xiaotingia, what you should see is that the taxonomic re-evaluation of Archeopteryx merely moves it from the Paraves branch to the nearby Deinonychosaurian branch…hardly a “wildly wrong” model.

7Vox Day has not described anything yet which shows evolution being wrong. Adjusting the precise timing of evolutionary events by millions of years is a reasonable response to new data which does not falsify the underlying hypotheses of relatedness.

8Again, this discovery does not demonstrate the opposite of what evolutionary biologists have been claiming, and actually makes for a better fit with other data about ancient bird ancestors; moving Archaeopteryx from a first cousin to a second cousin of the ancestor of modern birds isn’t a radical idea that invalidates evolutionary biology.

The big picture is even more damning for Vox Day. Of course we have huge volumes of information supporting the theory of evolution, that suite of mechanisms and principles that describe the broad course of evolutionary history, including common descent and descent with modification. And also there are a multitude of details that aren’t completely known — we have millions of species on this planet, and only a fraction have been studied in depth. The theory of evolution does not hang on the exact lineage of any two species out of those millions…it hangs on the fact that there is a lineage.

Vox Day is quite the poseur — he pretends to know better than real scientists, when he can’t even tell the difference between hypothesis and data.

Xiaotingia zhengi

A lovely new dinosaur fossil from China is described in Nature today: it’s named Xiaotingia zhengi, and it was a small chicken-sized, feathered, Archaeopteryx-like beast that lived about 155 million years ago. It shares some features with Archaeopteryx, and also with some other feathered dinosaurs.

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a, b, Photograph (a) and line drawing (b). Integumentary structures in b are coloured grey. cav, caudal vertebra; cv, cervical vertebra; dv, dorsal vertebra; fu, furcula; lc, left coracoid; lfe, left femur; lh, left humerus; li, left ilium; lis, left ischium; lm, left manus; lp, left pes; lpu, left pubis; lr, left radius; ls, left scapula; lu, left ulna; md, mandible; rfe, right femur; rfi, right fibula; rh, right humerus; ri, right ilium; rm, right manus; rr, right radius; rt, right tibiotarsus; ru, right ulna; sk, skull; ss, synsacrum.

Now here’s why this particular fossil has some paleontologists in a dither. Systematics uses a set of objective, computer-based tools to objectively build phylogenetic trees: you plug a set of character parameters for a set of organisms into it, and it analyzes them and determines the most likely or most parsimonious tree to describe their relationships. Plugging in data from modern birds, Archaeopteryx, and dromeosaurs, for instance, generates trees in which Archaeopteryx clusters with the birds, and not the dromeosaurs. Archaeopteryx was not a direct ancestor of modern birds, but was thought to be related to the basal avians — so it was a kind of close cousin.

When Xiaotingia‘s data is tossed into the calculation, though, the results change. Xiaotingia doesn’t cluster so tightly with birds; it’s a more distant relative. However, Archaeopteryx shares enough significant features with Xiaotingia that they now cluster together, pulling Archaeopteryx out of the basal Aves and into a new classification. It says that Archaeopteryx is now a kind of second cousin, a little less closely related to the birds than previously thought.

(Click for larger image)

Archaeopteryx has historically been regarded as the most basal bird (avialan), but the discovery of the closely related Xiaotingia led Xu et al.1 to pull these archaeopterygids out of avialans (birds) and into deinonychosaurs along with dromaeosaurids and troodontids. This new grouping better accounts for the evolution of feeding strategies among bird-like dinosaurs. Previous research suggested that herbivory was common among this group, as reflected in the tall, boxy skulls of oviraptorosaurs and basal avialans such as Epidexipteryx. The triangular, sharp-toothed skull of Archaeopteryx was incongruous among basal avialans, but fits better among the carnivorous dromaeosaurids and troodontids.

I have to say that I think it’s extremely cool that we have a new fossil from down around the roots of the bird family tree, and it does sharpen our knowledge of what was going on down there in the middle and late Jurassic. There was a whole assortment of delicate-boned, feathered, bipedal dinosaurs that were flourishing and diversifying in that window of time, and we’ve now got enough data that we can distinguish details in the family tree, which is absolutely fabulous.

However, a lot of the fuss over the specimen as somehow radically changing the importance of Archaeopteryx is a bit overblown. The relative status of Archaeopteryx and Xiaotingia is a bit of taxonomic detail — important details in working out the specific history of life — but it’s the equivalent of deciding that a fossil belongs in one pigeonhole rather than the pigeonhole next to it. Its shift in status means that there’s a bigger gap in the early history of the true birds than we thought, and it also means that there was a greater diversity of bird-like forms than we expected in the Jurassic. One other suggestion is that removing the carnivorous Archaeopteryx from the base of the bird family tree opens up the possibility that modern birds might have descended from the vegetarian side of the family — if the last common ancestor of birds was an herbivore, that has interesting implications for the paths evolution took.

But don’t worry, Archaeopteryx still represents a beautiful example of a transitional form. This new fossil is just another transitional form discovered. Creationists cannot take any consolation from it: Archaeopteryx isn’t suddenly gone, it’s become a part of a richer picture of bird evolution.

Xu X,
You H,
Du K
Han F (2011) An Archaeopteryx-like theropod from China and the origin of Avialae. Nature 475, 465-470.

A Skeptical Look at Aliens

OK, I’m feeling guilty: I’m off at The Amaz!ng Meeting enjoying myself, and totally neglecting the blog readers who aren’t lucky enough to be here too. And since I’ve been getting lots of requests to put the full content of my talk online, I figured…yeah, sure, I can do that. So here you go, all of the slides and what I said about them, mostly, below the fold. Criticize and argue and do your usual.

[Read more…]

The teeny-tiny bit of my TAM talk I had to cut short

I just gave my talk at TAM on likely paths of alien evolution (my conclusion: humanoids are extraordinarily unlikely), and there was one awkward bit I have to fix.

Here’s the problem: these were short talks, only a half hour long, so I designed it so there were some optional bits I’d only get to if time allowed, and I also had a couple of places where I could naturally bring it to a close if I ran over time. I was not able to show the last two slides I’d prepared, which was OK, I was ready for that. However, when we were setting up, the technician accidentally flashed the very last slide to the audience, which is a weird image, and it had to be left unexplained…so now I’ll explain it here on the blog.

Here it is, PZ’s TAM talk: the Lost Slides. This was to go right after I’d summed up the main reasons why we ought to expect great surprises in any alien morphology.

There’s one more brief and somewhat tangential point I have to make, because it’s weird and keeps coming up. I call it the Kirk effect: to boldly go and explore strange new worlds, and to hump all the women on them. This is not going to happen.


This is the most recent outrageous example of this, from the space fantasy movie Avatar. James Cameron consciously chose (for understandable dramatic and profit-making reasons) to completely ignore what science said and shape his aliens to fit human expectations. And that meant making them sexy.

This is more than just sticking large lumps of adipose tissue on the female’s chest. It’s deep and subtle changes to the shape of the face, the eyes, the whole of the body — cues that we all unconsciously recognize. You don’t even need to see a person face-on to recognize sex. All you heterosexual men and lesbians, you know this: sight of the nape of the neck, the curve of waist to hip, all those are enough to make your heart go pitta-pat. And all you heterosexual women and gay men: broad shoulders, narrow hips, muscular buns…they can do it for you, right?

Let me show you. I know this is a family audience, so if you’re shy about female nudity or assertive sexual displays, I’m going to show you a bit of porn to make my point. So if you’re a little prudish, put your hands over your kids eyes or your own, because this may be an arousing image…

[Read more…]

The greatest science paper ever published in the history of humankind

That’s not hyperbole. I really mean it. How else could I react when I open up the latest issue of Bioessays, and see this: Cephalopod origin and evolution: A congruent picture emerging from fossils, development and molecules. Just from the title alone, I’m immediately launched into my happy place: sitting on a rocky beach on the Pacific Northwest coast, enjoying the sea breeze while the my wife serves me a big platter of bacon, and the cannula in my hypothalamus slowly drips a potent cocktail of cocain and ecstasy direct into my pleasure centers…and there’s pie for dessert. It’s like the authors know me and sat down to concoct a title where every word would push my buttons.

The content is pretty good, too. It’s not perfect; the development part is a little thin, consisting mainly of basic comparative embryology of body plans, with nothing at all really about deployment of and interactions between significant developmental genes. But that’s OK. It’s in the nature of the Greatest Science Papers Ever Written that stuff will have to be revised and some will be shown wrong next month, and next year there will be more Greatest Science Papers Ever Written — it’s part of the dynamic. But I’ll let it be known, now that apparently the scientific community is aware of my obsessions and is pandering to them, that the next instantiation needs more developmental epistasis and some in situs.

This paper, though, is a nice summary of the emerging picture of cephalopod evolution, as determined by the disciplines of paleontology, comparative embryology, and molecular phylogenetics, and that summary is internally consistent and is generating a good rough outline of the story. And here is that story, as determined by a combination of fossils, molecular evidence, and comparative anatomy and embryology.

Cephalopods evolved from monoplacophoran-like ancestors in the Cambrian, about 530 million years ago. Monoplacophorans are simple, limpet-like molluscs; they crawl about on the bottom of the ocean under a cap-like shell, foraging snail-like on a muscular foot. The early cephalopods modified this body plan to rise up off the bottom and become more active: the flattened shell elongated to become a cone-like structure, housing chambers for bouyancy. Movement was no longer by creeping, but used muscular contractions through a siphon to propel the animal horizontally. Freed from its locomotor function, the foot expanded into manipulating tentacles.


These early cephalopods, which have shells common in the fossil record, would have spent their lives bobbing vertically in the water column, bouyed by their shells, and with their tentacles dangling downward to capture prey. They wouldn’t have been particularly mobile — that form of a cone hanging vertically in the water isn’t particularly well-streamlined for horizontal motion — so the next big innovation was a rotation of the body axis, swiveling the body axis 90° to turn a cone into a torpedo. There is evidence that many species did this independently.

The tilting of the body axes of extant cephalopods. This was a result of a polyphyletic and repeated trend towards enhanced manoeuverability. The morphological body axes (anterior-posterior, dorso-ventral) are tilted perpendicularly against functional axes in the transition towards extant cephalopods.

We can still see vestiges of this rotation in cephalopod embryology. If you look at early embryos of cephalopods (at the bottom of the diagram below), you see the same pattern: they are roughly disc-shaped, with a shell gland on top and a ring of tentacle buds on the bottom. They subsequently extend and elongage along the embryonic dorsal-ventral axis, which becomes the anterior-posterior axis in the adult.

In extant cephalopods the body axes of the adult stages are tilted perpendicularly versus embryonic stages. As a con- sequence, the morphological anterior-posterior body axis between mouth and anus and the dorso-ventral axis, which is marked by a dorsal shell field, is tilted 908 in the vertical direction in the adult cephalopod. Median section of A: Nautilus, B: Sepia showing the relative position of major organs (Drawings by Brian Roach). C: shared embryonic features in embryos of Nautilus (Nautiloidea) and Idiosepius (Coleoidea) (simplified from Shigeno et al. 2008 [23] Fig. 8). Orientation of the morphological body axes is marked with a compass icon (a, anterior; d, dorsal; p, posterior; v, ventral; dgl, digestive gland; gon, gonad; ngl, nidamental gland).

The next division of the cephalopods occurred in the Silurian/Devonian, about 416 million years ago, and it involved those shells. Shells are great armor, and in the cephalopods were also an organ of bouyancy, but they also greatly limit mobility. At that early Devonian boundary, we see the split into the two groups of extant cephalopods. Some retained the armored shells; those are the nautiloids. Others reduced the shell, internalizing it or even getting rid of it altogether; those are the coleoids, the most successful modern group, which includes the squids, cuttlefish, and octopuses. Presumably, one of the driving forces behind the evolution of the coleoids was competition from that other group of big metazoans, the fish.

The nautiloids…well, the nautiloids weren’t so successful, evolutionarily speaking. Only one genus, Nautilus has survived to the modern day, and all the others followed the stem-group cephalopods into extinction.

The coleoids, on the other hand, have done relatively well. The number of species have fluctuated over time, but currently there are about 800 known species, which is respectable. The fish have clearly done better, with about 30,000 extant species, but that could change — there are signs that cephalopods have been thriving a little better recently in an era of global warming and acute overfishing, so we humans may have been giving mobile molluscs a bit of a tentacle up in the long evolutionary competition.

There was another major event in coleoid history. During the Permian, about 276 million years ago, there was a major radiation event, with many new species flourishing. In particular, there was another split: between the Decabrachia, the ten-armed familiar squid, and the Vampyropoda, a group that includes the eight-armed octopus, the cirroctopodes, and Vampyroteuthis infernalis. The Vampyropoda have had another locomotor shift, away from rapid jet-propelled movement to emphasizing their fins for movement, or in the case of the benthic octopus, increasing their flexibility to allow movement through complex environments like the rocky bottom.

Time for the big picture. Here’s the tree of cephalopod evolution, using dates derived from a combination of the available fossil evidence and primarily molecular clocks. The drawings illustrate the shell shape, or in the case of the coleoids, the shape of the internal shell, or gladius, if they have one.

A molecularly calibrated time-tree of cephalopod evolution. Nodes marked in blue are molecular divergence estimates (see methods in Supplemental Material). The divergence of Spirula from other decabrachiates are from Warnke et al. [43], the remaining divergences are from analyses presented in this paper. Bold lineages indicate the fossil record of extant lineages, stippled lines are tentative relationships between modern coleoids, partly based on previous studies [41, 76, 82] and fossil relationships are based on current consensus and hypoth- eses presented herein. Shells of stem group cephalopods and Spirula in lateral view with functional anterior left. Shells of coleoids in ventral view with anterior down. The Mesozoic divergence of coleoids is relatively poorly resolved compared to the rapid evolution of Cambro- Ordovician stem group cephalopods. Many stem group cephalopod orders not discussed in the text are excluded from the diagram.

The story and the multiple lines of evidence hang together beautifully to make a robust picture of cephalopod evolution. The authors do mention one exception: Nectocaris. Nectocaris is a Cambrian organism that looks a bit like a two-tentacled, finned squid, which doesn’t fit at all into this view of coleoids evolving relatively late. The authors looked at it carefully, and invest a substantial part of the review discussing this problematic species, and decided on the basis of the morphology of its gut and of the putative siphon that there is simply no way the little beast could be ancestral to any cephalopods: it’s a distantly related lophotrochozoan with some morphological convergence. It’s internal bits simply aren’t oriented in the same way as would fit the cephalopod body plan.

So that’s the state of cephalopod evolution today. I shall be looking forward to the Next Great Paper, and in particular, I want to see more about the molecular biology of tentacles — that’s where the insights about the transition from monoplacophoran to cephalopod will come from, I suspect.

Kröger B, Vinther J, Fuchs D (2011) Cephalopod origin and evolution: A congruent picture emerging from fossils, development and molecules: Extant cephalopods are younger than previously realised and were under major selection to become agile, shell-less predators. Bioessays doi: 10.1002/bies.201100001.

A little cis story

I found a recent paper in Nature fascinating, but why is hard to describe — you need to understand a fair amount of general molecular biology and development to see what’s interesting about it. So those of you who already do may be a little bored with this explanation, because I’ve got to build it up slowly and hope I don’t lose everyone else along the way. Patience! If you’re a real smartie-pants, just jump ahead and read the original paper in Nature.

A little general background.


Let’s begin with an abstract map of a small piece of a strand of DNA. This is a region of fly DNA that encodes a gene called svb/ovo (I’ll explain what that is in a moment). In this map, the transcribed portions of the DNA are shown as gray shaded blocks; what that means is that an enzyme called polymerase will bind to the DNA at the start of those blocks and make a copy in the form of RNA, which will then enter the cytoplasm of the cell and be translated into a protein, which does some work in the activities of that cell. So svb/ovo is a small piece of DNA which, in the normal course of events, will make a protein.

Most of the DNA here is not transcribed. Much of it is junk — changing the sequence of those areas has no effect on the protein, and has no effect on the appearance or function of the organism. Some of it, though, is regulatory DNA, and its sequence does matter. The white boxes labeled DG2, DG3, Z, A, E, and 7 are regions called enhancers — they are not translated into protein, but their sequence affects the expression of svb/ovo. One way to think of them is that they are small parking spots for other proteins that will bind to the DNA sequences in each enhancer. These protein/DNA complexes will then fold around to make a little landing zone for the polymerase, to encourage transcription of the svb/ovo gene. This is why this is called regulatory DNA: it doesn’t actually make the svb/ovo protein itself, but it’s important in controlling when and where and how much of the svb/ovo protein will be made.

Now for some jargon; sorry, but you have to know what it is to follow along in the literature. Those little white boxes of regulatory DNA are often called cis factors, because they have to be located on the same strand of DNA as the protein-coding gene in order to work. In general, when we’re talking about cis factors, we’re talking about non-coding regulatory DNA. The complement of that is the actual coding sequence, the little gray boxes in the diagram, and those have the general name of trans factors.

There is a bit of a debate going on about the relative importance of cis and trans mutations in evolution. Proponents of the cis perspective like to point out that cis mutations can be wonderfully subtle and specific; you can make a change in an enhancer and only modify the expression of the gene in one tissue, or even a small part of one tissue, while changing a trans factor causes changes in every tissue that uses that gene product. Also, most of the cis proponents are evo-devo people, scientists who study the small variations in timing and magnitude of gene expression that lead to differences in form, so of course the kinds of changes that affect the stuff we study must be the most important.

Proponents of the trans view can point out that small changes in the coding regions of genes can also produce subtle shifts in what the genes do, and that mutations can also produce very large effects. Those cis changes appear to be little tweaks, while trans changes can run the gamut from non-existent/weak to strong, and so have great power. They also like to point out that most of the data in the literature documents trans changes between species, and that a lot of the evo-devo stuff is speculative.

It’s a somewhat silly debate, because we all know that both cis and trans effects are going to be found important in evolution, in different ways in different organisms, and that arguing about which is more important is kind of pointless — it will depend on which feature and which species you’re looking at. But the debate is also useful as a goad to urge people to look more at the subtleties and ask more questions about those enhancers, as in the paper I’m about to describe.

What is this svb/ovo gene?


This is a drawing of just the back end of a fly larva, and what you should be able to see is that they’re very hairy. Dorsally, there’s a collection of small hairs called trichomes, and ventrally there are some thicker, stouter hairs called denticles. If you destroy the svb/ovo coding region, these hairs don’t form — svb is an important gene for organizing and making hairs on the cuticle of the fly. It’s name should make sense: svb is short for shavenbaby. The gene is responsible for making hairs, but when you break it with a mutation you get embryos and larvae lacking those hairs, a shaven baby.

It also has the synonym of ovo, because it has another important function in the maturation of oocytes, something I’ll skip over entirely. All you need to know is that svb/ovo is actually a large complex gene with multiple functions, and all we care about right now is its function of inducing hair development.

Now let’s look at embryos of two different species of fruit flies, Drosophila melanogaster at the top, and Drosophila sechellia at the bottom. D. melanogaster is clearly hairier than D. sechellia, and you might be wondering if svb is the gene making a difference here, and if you’re following the debate, you might be wondering whether this is a change in the trans coding region or the cis regulatory region.


One way to figure this out is to sequence and compare maps of the svb region in multiple fly species and ask where the actual molecular differences are. This isn’t trivial: D. melanogaster and D. sechellia have been diverging for half a million years, and there have been lots of little changes all over the place, many of them expected to be neutral. What was done to narrow the search was to compare the sequences of five different Drosophila species with hairy embryos to the relatively naked D. sechellia, and ask which changes were unique to the less hairy form.

A hotspot lit up in the comparison: there is one region, about 500 base pairs long, in the enhancer labeled “E” in the diagram at the top of the page, which contained 13 substitutions and one deletion unique to D. sechellia, in 7 clusters. This is very suggestive, but not definitive; these are consistent differences, but we don’t know yet whether these molecular differences cause the differences in hairiness. For that, we need an experiment.

The experiment.

This is the cool part. The investigators built constructs containing the E enhancer coupled to the svb gene and a reporter tag, and inserted those into fly embryos and asked how they affected expression; so they could effectively put the D. sechellia enhancer into D. melanogaster, and the D. melanogaster enhancer into D. sechellia, and ask if they were sufficient to drive the species-specific pattern of svb expression. The answer is yes, mostly: they weren’t perfect copies of each other, suggesting that there are other elements that contribute to the pattern, but the D. sechellia enhancer produced reduced expression in whatever fly carried it, while the D. melanogaster enhancer produced greater expression.

But wait, there’s more! The species differences were caused by differences in 7 clusters within the E enhancer. The authors built constructs in which the mutations in each of the 7 clusters was uniquely and independently inserted, so they could test each mutational change one by one. The answer here was that each of the seven mutations that led to the D. sechellia pattern had a similar effect, reducing very slightly the level of svb expression. Furthermore, they had a synergistic effect: the reduction in hairs when all 7 mutations were present was not simply the sum of the individual effects of each mutation alone.

What does it all mean?

One conclusion of this work is that here is one more clear example of a significant morphological difference between species that was generated by molecular modification of cis regulatory elements. Hooray, one more data point in the cis/trans debate!

Another interesting observation is that this is a phenotype that was built up gradually, by a set of small changes to an enhancer element. D. sechellia gradually lost its trichome hairs by the accumulation of single-nucleotide changes in regulatory DNA, each of which contributed to the phenotype — a very Darwinian pattern of change.

By modifying the regulatory elements, evolution can generate distinct, focused variations. Knocking out the entirety of the svb gene is disastrous, not only removing hairs but also seriously affecting fertility. The little tweaks provided by changes to the enhancer region mean that morphology can be fine-tuned by chance and selection, without compromising essential functions like reproduction. In the case of these two species of flies, D. sechellia can have a functional reproductive system, the full machinery to make functional hairs, but at the same time can turn off dorsal trichomes while retaining ventral denticles.

It all fits with the idea that fundamental aspects of basic morphology are going to be defined, not by the raw materials used to build them, but by the regulation of timing and quantity of those gene products — that the rules of development are defined by the regulatory activity of genes, not entirely by the coding sequences themselves.

Frankel N, Erezyilmaz DF, McGregor AP, Wang S, Payre F, Stern DL (2011) Morphological evolution caused by many subtle-effect substitutions in regulatory DNA. Nature 474(7353):598-603.