Gene regulatory networks and conserved noncoding elements

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We miss something important when we just look at the genome as a string of nucleotides with scattered bits that will get translated into proteins — we miss the fact that the genome is a dynamically modified and expressed sequence, with patterns of activity in the living cell that are not readily discerned in a simple series of As, Ts, Gs, and Cs. What we can’t see very well are gene regulatory networks (GRNs), the interlinked sets of genes that are regulated in a coordinated fashion in cells and tissues.

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Oh, no, not the Aquatic Ape hypothesis!

I’m getting a lot of email asking me to talk about the aquatic ape theory, the idea that humans went through a semi-aquatic stage in their evolutionary history. It’s complete nonsense; its proponents spew out a lot of inconsistent and mutually contradictory noise to ‘support’ their claims, and there is no evidence anywhere for such a stage. I don’t need to say more, though, because Jim Moore’s Aquatic Ape page is the definitive web resource for dissecting this fringe theory.

The evolution of Hedgehog

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PLoS has recently published a highly speculative but very interesting paper on how a particular signaling pathway, the Hedgehog pathway, might have evolved. It’s at a fairly early stage in hypothesis testing, which is one of the things that makes it interesting — usually all you see published is the product of a great deal of data collection and experiment and testing, which means the scientific literature gives a somewhat skewed view of the process of science, letting the outsider mainly see work that has been hammered and polished, while hiding the rougher drafts that would better allow us to see how the story started and was built. It’s informative in particular for those who follow the creationist “literature”, which often crudely apes the products of actual working science, but lacks the sound methodological underpinnings. In particular, creationism completely misses the process of poking at the real world to develop ideas, since they begin with their conclusion.

So take this description as a work in progress — we’re seeing the dynamic of building up a good working model. As usual, it starts on a sound foundation of confirmed, known evidence, makes a reasonably hypothesis on the basis of the facts, and then proposes a series of research avenues with predicted results that would confirm the idea.

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What caused the Cambrian explosion? MicroRNA!

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No, not really — my title is a bit of a sensationalistic exploitation of the thesis of a paper by Peterson, Dietrich, and McPeek, but I can buy into their idea that microRNAs (miRNAs) may have contributed to the pattern of metazoan phylogenies we see now. It’s actually a thought-provoking concept, especially to someone who favors the evo-devo view of animal evolution. And actually, the question it answers is why we haven’t had thousands of Cambrian explosions.

In case you haven’t been keeping up, miRNAs are a hot topic in molecular genetics: they are short (21-23 nucleotides) pieces of single stranded RNA that are not translated into protein, but have their effect by binding to other strands of messenger RNA (mRNA) to which they complement, effectively down-regulating expression of that messenger. They play an important role in regulating the levels of expression of other genes.

One role for miRNAs seems to be to act as a kind of biological buffer, working to limit the range of effective message that can be operating in the cell at any one time. Some experiments that have knocked out specific miRNAs have had a very interesting effect: the range of expressed phenotypes for the targeted message gene increases. The presence or absence of miRNA doesn’t actually generate a novel phenotype, it simply fine-tunes what other genes do — and without miRNA, some genes become sloppy in their expression.

This talk of buffering expression immediately swivels a developmental biologist’s mind to another term: canalization. Canalization is a process that leads organisms to produce similar phenotypes despite variations in genotype or the environment (within limits, of course). Development is a fairly robust process that overcomes genetic variations and external events to yield a moderately consistent outcome — I can raise fish embryos at 20°C or at 30°C, and despite differences in the overall rate of growth, the resultant adult fish are indistinguishable. This is also true of populations in evolution: stasis is the norm, morphologies don’t swing too widely generation after generation, but still, we can get some rapid (geologically speaking) shifts, as if forms are switching between a couple of stable nodes of attraction.

Where the Cambrian comes into this is that it is the greatest example of a flowering of new forms, which then all began diverging down different evolutionary tracks. The curious thing isn’t their appearance — there is evidence of a diversity of forms before the Cambrian, bacteria had been flourishing for a few billion years, etc., and what happened 500 million years ago is that the forms became visible in the fossil record with the evolution of hard body parts — but that these phyla established body plans that they were then locked into, to varying degrees, right up to the modern day. What the authors are proposing is that miRNAs might be part of the explanation for why these lineages were subsequently channeled into discrete morphological pathways, each distinct from the other as chordates and arthropods and echinoderms and molluscs.

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Werner Arber: Molecular Darwinism

This talk has me a little concerned: it’s proposing something rather radical, for which Arber is going to have to show me some unambiguous evidence to convince me, and I’m coming into it with a very skeptical mindset. Here’s the relevant portion of his abstract:

The theory of molecular evolution that we also call “Molecular Darwinism” is based on the acquired knowledge on genetic variation. In genetic variation, products of evolution genes are involved as variation generators and/or as modulators of the rates of genetic variation. These evolution gene products act together with several non-genetic elements that can be assigned to intrinsic properties of matter, to environmental mutagens and to random encounter. We conclude that natural reality takes actively care of biological evolution. The evolution genes must have been fine-tuned for their functions by second-order selection, so that spontaneous genetic variation with different evolutionary qualities occurs at quite low rates. This ensures a relatively high genetic stability to individuals, as well as an evolutionary progress at the level of populations.

The presence of evolution genes points to a duality of the genome: while many genes act to the benefit of the individuals for the fulfillment of their lives, the evolution genes act to the benefit of an evolutionary development, for a slow, but steady expansion of life and biodiversity.

You see the problem, I hope. These hypothetical genes that do not necessarily directly affect the fitness of the individual are assumed to be promoted in lineages by a higher level of selection. This is not easily supported by evolutionary theory: there isn’t a mechanism given for individuals to maintain a gene that will only help its many-times-great-grandchildren. It is inferring a kind of foresight to evolution that is doesn’t have a mechanism…unless, perhaps, Arber is going to give use one. We’ll see. This talk will start in about 15 minutes, and I’ll update this post as he fills us in.

A simple history lesson: modern evolutionary biology is the convergence of work that began with Miescher (1874: nucleic acids) which led to molecular biology, Mendel (1876) which led to genetics, and Darwin (1859) that approached the problem at the level of organisms and species. The neo-Darwinian synthesis fused the genetic and Darwinian line, molecular genetics brought together genetics and biochemistry/molecular biology, and molecular evolution brings all three together—he seems to claim some kind of intellectual ownership of the last concept, which is what he calls molecular darwinism.

How do bacteria generate new variants? By transformation, conjugation, or transduction. All are mechanisms that transfer genes from an external source to the bacterium. Work in the 1940s demonstrated that DNA was the carrier of genetic information.

Arber gave a little summary of E. coli gene structure, which I suppose would be helpful to all the chemists here. He defines mutation as an alteration of the nucleotide sequence; in classical genetics, it’s defined differently, as an altered phenotype that is transmitted to progeny.

Mutations are rarely favorable; often unfavorable, and very often silent or neutral. There is no good evidence for directedness of spontaneous mutations. Mutations do not appear in response to a need.

He argues that there are three elements to evolution: evolution is driven by genetic variation (mutation), directed by natural selection, and modulated by isolation as a mechanism for speciation. There are multiple mechanisms generating genetic variation: spontaneous DNA sequence alteration, DNA rearrangement or recombination, and DNA acquisition (horizontal gene transfer).

So far, this is all very unchallenging and basic, at least for someone with any background in genetics and cell biology. After sitting through one talk that completely lost me with a failure to explain the basic terms of the work, I can’t complain, but I confess, I’m having trouble staying alert through all this.

Some genes can affect the rate of occurence of mutations — these are modulators of the frequency of genetic variation. He calls these evolution genes. He says neatral reality actively takes care of biological evolution, and that this is an expansion of the biological theory of evolution. This leads to an expansion of biological diversity, and, he argues, higher complexity.

I’m not very impressed. This is a combination of the commonplace and some odd interpretations. Of course there is variation in fidelity of replication that is influenced by genetic variation. Some of it is simply thermodynamically necessary: perfect fidelity is impossible to achieve, and greater fidelity has a metabolic cost, so some of that variation is utterly unsurprising. Some is; when we have organisms that have specializations to directly generate greater genetic variation — and sex is the first to come to my mind — we have a problem to explain. I don’t see that Arber has proposed anything to explain the real problems.

At the same time, what Arber said here does not make him a friend to intelligent design creationism, or creationism of any kind, despite the claims of some unreliable creationist sources, a claim that Arber has directly rejected.

I’d have to say it was a nice enough overview, but didn’t really propose anything novel, and definitely didn’t demonstrate anything that can’t be explained in the context of modern evolutionary theory.

Visiting village dogs

I am horribly envious. I am speaking of the Village Dog Project, some current research going on that looks very cool.

Understanding the evolution and domestication in dogs requires genetic analysis of a global and diverse panel of non-breed-affiliated village dogs. With a network of worldwide and Cornell-affiliated collaborators, we plan to gather dog samples from remote villages, establish a genetic archive containing DNA and phenotypic information from these dogs, carry out genetic analyses on these samples, and develop computational methods for analyzing this dataset. In particular, we are interested in understanding the location, timing, and demographic conditions underlying domestication; the genetic changes involved in the transition of wolf to dog; the relationship between these village dogs and the breed dogs; and the effect that historical forces have shaped village dog diversity.

That looks informative and useful, and I’ll be looking forward to the publication of the research. That’s not what’s got me envious, though: for that, you have to look at their field work. The researchers are spending the summer traveling to exotic, remote locations (admittedly, to the kinds of places rife with scavenging village dogs, but still…) to collect blood samples. They have a travel blog that will be recounting their adventures, and also explains the science a little more.

After initial domestication, dogs probably lived “breed-less” lives as human commensals (hanging around humans, not really helping or harming them but living off their trash) for many thousands of years. During this time, dog populations quickly expanded and spread across the globe. In the last few hundreds of years, several hundred dog breeds were formed from local dogs in many parts of the world; these breed dogs have entirely replaced the non-breed “indigenous” dogs in some parts of the world, notably in Western Europe and the USA. However, most dogs throughout the world still live their lives as non-breed, indigenous, commensal dogs. We refer to these dogs as “pariah” or “village” dogs. They tend to be smallish (25-40 pounds), often tan, short-haired dogs, though the type varies a bit according to the region you’re in. The important point is that these dogs have not undergone the intense genetic bottleneck associated with breed formation. Thus, while breed dogs have only a small subset of the total genetic diversity of all dogs, it is likely that village dogs have a much greater range of the total diversity. Thus, they are very useful for looking at the original domestication event. They are informative of the original genetic bottleneck that led to the formation of domestic dogs many thousands of years ago.

Hmmm. We don’t seem to have many dogs running loose around exotic, remote Morris, Minnesota, but there are a few feral cats living off the dumpsters near the grocery store.

I probably wouldn’t try to read about visiting small midwestern towns to collect cats, though.

Big love among the ostracods

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How can anyone resist an article titled “Sexual Intercourse Involving Giant Sperm in Cretaceous Ostracode”? You can’t, I tell you. It’s like a giant brain magnet, you open the journal to the index, and there’s that title, and you must read it before you can even consider continuing on to anything else.

Some organisms have evolved immensely long sperm tails — Drosophila bifurca, for instance, has sperm cells that are about 60mm long, or 20 times longer than the length of the entire adult body. The excessively long sperm tail is obviously not a structure that has evolved for better swimming; instead, it is thought to act as a tangled barrier in the female reproductive tract to prevent other males from fertilizing the female, and there is also some very interesting evidence that sperm coevolves with the female reproductive tract, so some sexual selection at the level of the gametes is going on.

At the same time, sperm morphology is extremely diverse, and seems to evolve very rapidly. Perhaps these mega-sperm are a transient fad? Not all species of Drosophila exhibit the phenomenon, and those that do vary considerably from species to species. What we’d like to know is if there are any lineages that maintain these patterns of giant sperm over long periods of evolutionary time…so what do we need to do? We need to go spelunking for sperm in fossils!

That’s what this short letter in Science is about: the authors looked at ostracodes, a class of tiny crustacea that invests heavily in reproduction. About a third of their volume is their reproductive system, with males building giant (relative to their size) sperm pumps, and females having large seminal receptacles for sperm storage. The individual sperm are also large, often longer than the body length of the adult, and are also aflagellate — no flagellar tail at all, just a long, threadlike cell body. You can tell if a female ostracod is a virgin just by looking at those seminal receptacles, since they inflate hugely with all the giant sperm tucked inside.

So, if you look at the large orange blobs, the seminal receptacles, in this 3-D scan of a fossil female ostracod (bottom right of this image), you can tell that she was inseminated before she died, and that her mate had very large sperm. Her condition was also very similar to that of modern ostracodes (bottom left).

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Partial reconstruction of E. virens (extant) and H. micropapillosa (fossil). Anterior is to the left. Orange structures indicate central tubes of Zenker organs in males or seminal receptacles in females; brown, esophagus; turquoise, mandible; purple, upper lip; pink, lower lip; green, valves; and gray scales, whole-body reconstruction. All scale bars indicate 100 µm. (A) Lateral view of male E. virens with several organs included for comparison. (B) Male H. micropapillosa in lateral view with several organs in context of whole-body reconstruction. (C and D) Ventral views of several organs including tubes of Zenker organs of male H. micropapillosa. (E) Lateral view of female E. virens with several organs included for comparison. (F) Female H. micropapillosa in lateral view with several organs in context of whole-body reconstruction, including seminal receptacles.

So, the conclusion is that boinking with giant sperm is an enduring property of at least some lineages: they’ve been going at it for a hundred million years. The authors also suggest that this kind of technique could be useful for measuring sexual selection by assessing pre-mating parental investment in fossil invertebrates.

Matzke-Karasz R, Smith RJ, Symonova R, Miller CG, Tafforeau P (2009) Sexual Intercourse Involving Giant Sperm in Cretaceous Ostracode. Science 324(5934):1535.

Miller GT, Pitnick S (2002) Sperm-Female Coevolution in Drosophila. Science 298(5596):1230-1233.

Limusaurus inextricabilis

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My previous repost was made to give the background on a recent discovery of Jurassic ceratosaur, Limusaurus inextricabilis, and what it tells us about digit evolution. Here’s Limusaurus—beautiful little beastie, isn’t it?

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Photograph (a) and line drawing (b) of IVPP V 15923. Arrows in a point to a nearly complete and fully articulated basal crocodyliform skeleton preserved next to IVPP V 15923 (scale bar, 5 cm). c, Histological section from the fibular shaft of Limusaurus inextricabilis (IVPP V 15924) under polarized light. Arrows denote growth lines used to age the specimen; HC refers to round haversian canals and EB to layers of endosteal bone. The specimen is inferred to represent a five-year-old individual and to be at a young adult ontogenetic stage, based on a combination of histological features including narrower outermost zones, dense haversian bone, extensive and multiple endosteal bone depositional events and absence of an external fundamental system. d, Close up of the gastroliths (scale bar, 2 cm). Abbreviations: cav, caudal vertebrae; cv, cervical vertebrae; dr, dorsal ribs; ga, gastroliths; lf, left femur; lfl, left forelimb; li, left ilium; lis, left ischium; lp, left pes; lpu, left pubis; lsc, left scapulocoracoid; lt, left tibiotarsus; md, mandible; rfl, right forelimb; ri, right ilium; rp, right pes; sk, skull.

What’s especially interesting about it is that it catches an evolutionary hypothesis in the act, and is another genuine transitional fossil. The hypothesis is about how fingers were modified over time to produce the patterns we see in dinosaurs and birds.

Birds have greatly reduced digits, but when we examine them embryologically, we can see precisely what has happened: they’ve lost the outermost digits, the thumb (I) and pinky (V), and retain the forefinger, middle finger, and ring finger (II-IV), which have been reduced and fused together. This is called Bilateral Digit Reduction, BDR, because they’ve lost digits from the medial and lateral sides, leaving the middle set intact.

Dinosaurs, when examined anatomically, seem to have a different pattern: they have a thumb (I), forefinger (II) and middle finger (III), and have lost the lateral two digits, the ring and pinky finger (IV-V). This arrangement has been advanced as evidence that birds did not evolve from dinosaurs, since they have different bones in their hands, and getting from one pattern to the other is complicated and difficult and very unlikely.

The alternative hypothesis is that there is no conflict, and that dinosaurs actually underwent BDR and their digits are II-III-IV…but that what has also happened is a frame shift in digit identities. So dinosaurs actually have three digits, which are the index, middle, and ring finger, but they’ve undergone a subtle shift in morphology so that their forefinger develops as a thumb, and so forth.

Now we could resolve all this easily if only the physicists would get to work and build that time machine so we could go back to the Mesozoic and study dinosaur embryology, but they’re too busy playing with strings and quanta and dark matter to do the important experiments, so we’ve got to settle for another plan: find intermediate forms in the fossil record. That’s where Limusaurus steps in.

Limusaurus has a thumb, a tiny vestigial nubbin, and has lost its pinky completely. This is a (I)-II-III-IV pattern, and is evidence of bilateral digit reduction in a basal ceratosaur. In addition, the forefinger has become very robust, and while still distinctly a digit II, has been caught in the early stages of a transformation into a saurian first digit. It’s evidence in support of the dinosaurian II-III-IV hypothesis and the frameshift in digit identity! It’s almost as good as having a time machine.

Want to learn more? Carl Zimmer has a summary of the digit changes, while one of the authors of the paper, David Hone, also discusses the digits (the story is a little more complicated than I’ve laid out), and also has more on the rest of the animal—it’s a herbivorous ceratosaur, which is interesting in itself.

Xu X, Clark JM, Mo J, Choiniere J, Forster CA, Erickson GM, Hone DWE, Sullivan C, Eberth DA, Nesbitt S, Zhao Q, Hernandez R, Jia C-k, Han F-l, Guo Y (2009) A Jurassic ceratosaur from China helps clarify avian digit homologies. Nature 459(18):940-944.