gene duplication

The copied gene that gave dachshunds and corgis their short legs

edyong — Thu, 16 Jul 2009 11:00:36 +0000

The copied gene that gave dachshunds and corgis their short legs

Compare the elegant grace of a running wolf with the comical shuffle of a waddling dachshund, and you begin to understand what millennia of domestication and artificial selection can do to an animal. As dachshunds develop, the growing tips of their limb bones harden early, stunting their growth and leading to a type of dwarfism called chondrodysplasia. The same applies to at least 19 modern breeds including corgis, Pekingese and basset hounds, all of which have very short, curved legs.

These breeds highlight the domestic dog's status as the most physically diverse of mammals. Now, a team of scientists led by Heidi Parker from the National Human Genome Research Institute have found the genetic culprit behind the stumpy limbs of all these breeds, and its one with surprising relevance for dwarfism in humans.

All cases of stunted legs in domestic dogs are the result of a single genetic event that took place early on in their evolution. Some time ago, a gene called FGF4 (short for fibroblast growth factor 4), which plays an important role in bone growth, was copied and reinserted into a new site in the dog genome. It's this extra errant copy - a retrogene - that has retarded the growth of so many domestic breeds.

Parker's team sequenced genes from over 835 dogs across 76 different breeds, including 95 short-legged individuals, and found a genetic signature unique to these stunted animals. This included a handful of genetic variants - each consisting of a single altered base pair or "DNA letter" - that were overrepresented in the short-legged breeds and that clustered in the same site. One of these variants was 30 times more common in the short-legged breeds than their long-limbed peers.

The team found that this mystery region exactly matched a gene called fibroblast growth factor (FGF4). That was puzzling, for FGF4 normally sits at a very different location, some distance away on the dog genome. In fact, Parker found that the short-legged breeds have two copies and the one associated with their abnormal growth has been inserted in an unusual site. Not only did all the stunted animals have this errant FGF4 gene, but 96% of them had two identical copies of it.

Genes that code for proteins, like FGF4, first need to be transcribed into a molecule called messenger RNA (mRNA). A group of enzymes called ribosomes "read" this transcript and assemble a chain of amino acids - a protein - based on the information it encodes. That's the usual story, but sometimes, an mRNA molecule is converted back into DNA through a process called reverse transcription; some viruses have the ability to do this.

The DNA molecule can then be inserted back into the genome it was originally transcribed from, often in a new place. But to be active, these reinserted genes need to be surrounded by the right "promoter" sequences. Without these promoters, most inserted genes just sit around doing nothing, slowly building up debilitating mutations. However, a lucky few hop back into just the right place where they can "borrow" promoters from other parts of the genome. They can go on to produce functional proteins and these active copies are called retrogenes.

Parker found clear evidence that the extra FGF4 of dachshunds and corgis is indeed a retrogene. When genes are transcribed into mRNA, useless chunks of sequence called introns are edited out of the transcript. An mRNA molecule that is then reverse-transcribed would produce a shorter, more streamlined stretch of DNA than its original gene. That's exactly what the second FGF4 of short-legged dogs is - an intron-less version of the original.

Parker's team isn't yet clear what this extra copy of FGF4 does to stunt the growth of their bearers, but they have a very good idea. They suggest that with two copies of the gene, the dogs overproduce the FGF4 protein, which docks at, and turns on, another protein called FGFR3. In humans, overactive FGFR3 is responsible for virtually every case of achondroplasia, the most common type of dwarfism. It seems that FGFR3 and its partner proteins are responsible for shortness in both man and man's best friend.

The short-legged varieties were developed in many different countries and they don't sit on an exclusive branch of the dog family tree. Nonetheless, the sequence of the FGF4 retrogene strongly implies that it arose only once, very early on in the evolution of domestic dogs and before they split into the various modern breeds.

This means that for the longest time, domestic dogs had the potential for dwarfism, which was independently maintained and nurtured by breeders all over the world. Originally, they were shaped for specific jobs like flushing out burrowing animals. Later on, breeders would have kept imposing strong evolutionary pressure on their animals to meet the conditions set by dog-breeding associations. The big question is whether a single retrogene can be as potent as force in the evolution of wild species as it so clearly has been in a single domestic one.

Reference: Science 10.1126/science.1173275

Image: Dachshund by Lily M; image by Science/AAAS

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edyong Thu, 07/16/2009 - 07:00

Interesting, but can you give the reference for this paper. The doi you cite is invalid.

No it's not - you just need to wait a while. There is a time-lag of a few hours before the embargo on a Science paper lifts and the paper becomes available online.

So wait a second, I'm confused. "Dwarfism" in dogs evolved only once, but arose several times among different breeds? Or was it the potential for dwarfism that evolved only once, and was taken advantage of around the world? So there'd always be a few stubby-legged pups in a litter?

I have a Pembroke corgi named Ozzie. Corgis are one of my favorite breeds (the other being the shiba inu) precisely because they look so ridiculous, but they have a great temperments and are very intelligent. Originally bred as herding dogs, you know. It seems they are too short to be kicked.

Or was it the potential for dwarfism that evolved only once, and was taken advantage of around the world? So there'd always be a few stubby-legged pups in a litter?

That was my understanding of it.

the comical shuffle of a waddling dachshund

As a former owner of a dachshund I'm offended. A dachshund waddles only if he's too fat.
Dachshund at work

It's all your fault. I just spent two hours watching videos on youtube of dachshunds running/doing tricks/chasing stuff/being bathed/going crazy after they have been bathed.
Liked (the not-dachshund-discriminating part of) your post, though. ;)

Very interesting - thanks.

Very interesting, thanks Ed. Any thoughts on whether the mutation would have survived without selective breeding imposed by humans? I vaguely remember reading that several dog breeds suffer from health problems caused by the very feature that sets their breed apart: daschund legs, cocker spaniel eyes etc.

Corgis are evil. Is that genetic too?

Ever see a long-legged corgi or dachshund?

Corgis are not evil. Bad dog owners produce bad dogs. I have a long legged corgi and he is very sweet.

Extra genomes helped plants to survive extinction event that killed dinosaurs

edyong — Mon, 23 Mar 2009 16:00:55 +0000

Extra genomes helped plants to survive extinction event that killed dinosaurs

Sixty-five million years ago, life on Earth was sorely tested. One or more catastrophic events including a massive asteroid strike and increased volcanic activity, created wildfires on a global scale and dust clouds that cut the planet's surface off from the sun's vital light. The majority of animal species went extinct including, most famously, the dinosaurs. The fate of the planet's plants is less familiar, but 60% of those also perished. What separated the survivors from the deceased? How did some species cross this so-called "K/T boundary"?

Jeffrey Fawcett form the Flanders Institute for Biotechnology thinks that the answer lies in their genomes and specifically how many copies they have. Geneticists have found that the majority of plants have duplicated their entire portfolio of genetic material at some point in their evolution. They are called "polyploids" - species with multiple copies of the same genome.

By dating these doublings, Fawcett had found that the most recent of them cluster at a specific point in geological time - 65 million years ago, at the K/T boundary. It suggests that having extra copies of their genomes on hand gave these plants the edge they needed to cope with the dramatic environmental changes that wiped out the dinosaurs and other less well-endowed species.

Time and again, scientists have found that flowering plants, from trees to grasses, have multiple copies of their genomes. The exact number and timings are being debated, but most agree that the oldest doubling took place very early on in the evolution of this group. It may even have contributed to the lineage's success. Within about 5 million years, the lineages that would eventually produce about 97% of all flowering plant species had exploded into existence and an extra genome copy may have acted as the catalyst for this rapid expansion.

But this ancient doubling was just the beginning. Recent studies have found evidence of another, more recent duplication in the genomes of many species. To date these events, Fawcett looked at several plant species whose entire genomes have been completely sequenced - the thale cress Arabidopsis, the California poplar, barrel clover the common grape vine and rice - and many others that we have plenty of genetic data for, including cotton, tomato, lettuce, Californian poppy and American sweet flag.

Fawcett used these sequences to build a family tree of these different species. He used known evolutionary splits to put dates on the tree's branches and he used this information in turn to date the recent genome duplications in the various species.

In almost all cases, from rice to tomatoes to cotton, flowering plants showed a peak in or genetic duplication between 60 and 70 million years ago - a time that precisely matches the Earth's most recent mass extinction. Ten million years may seem like a long time to us but geologically it's a blip. The world's climate was changing long before the asteroid impact that truly sparked the extinction event, and the strike's aftermath lasted long after it happened.

Fawcett recognises that dating these events can be an unexact science, but he feels that the cluster of dates round this point is significant and unlikely to change. Only Arabidopsis and the poplar didn't fit this narrow band of time - they most recent genome duplications took place about 43 and 48 million years ago respectively.

In the case of Arabidopsis, Fawcett cites another study which suggests that this species, so favoured of geneticists, has copied its entire genome twice in the last 70 million years. It may be that this current study has only picked up the most recent event. In the case of the poplar, its family of trees have a tendency to evolve very slowly, which may mean that Fawcett's methods underestimated the date of its most recent whole-genome duplication.

During the KT boundary, the planet's environment changed dramatically. Dust clouds thrown up by asteroid collisions would have choked plants of sunlight and led to freezing ground temperatures that prevented seeds from germinating. There's plenty of evidence that these prehistoric plants were severely hit by these conditions. Studies of fossilised pollen, spores and leaves have suggested about 60% of plant species went extinct, including a "global forest dieback". The abundance of decaying vegetation provided nourishment for fungi, and their populations boomed at the KT boundary.

Fawcett thinks that double-genomes provided some lineages of plants with advantages that saw them through the environmental upheaval. Some studies have suggested that plants with multiple copies of their genomes are better able to cope with changing environmental conditions. Spare copies kicking around mean that the plant is more resistant to harmful mutations cropping up in any one gene.

But far from just being identical back-ups, spare copies can also be repurposed to new jobs or be used in new locations and at new times. This division of labour can be set up very quickly and provides the plant with the ability to swiftly adapt to new conditions - they get more bang for their genetic buck. You can see this happening in artificial selection experiments - cotton plants partition different copies of the same gene towards different ends if they are placed in difficult environments, like cold or too much water. By doing this, the plant ensures that neither copy is redundant; both quickly take on important roles and evolve independently.

Finally, plants with extra genome copies find it difficult to mate with other individuals with just the one, so they are biased towards fertilising themselves and reproducing asexually. That could actually be a perk in an environment where populations are crashing and mates are becoming scarce.

All these benefits combined to give polyploid plants a valuable advantage in a harsh world. Perhaps even further genome duplications will give some plants an edge in the rapidly changing climate of 21^st century Earth.

There are signs that this might happen. The Arctic Circle is a haven for polyploid plants and there's evidence to suggest that those with many genome copies are better than those with just the one at colonising areas where glaciers have vanished More recently, the industrial wastelands of York have been colonised by a new species of plant, the York groundsel, that evolved when two other species - the Oxford ragwort and common groundsel - crossbred to form a polyploidy hybrid.

Reference: PNAS doi:10.1073/pnas.0900906106 to be published this week

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edyong Mon, 03/23/2009 - 12:00

The death and resurrection of IRGM - the "Jesus gene"

edyong — Thu, 05 Mar 2009 19:00:16 +0000

The death and resurrection of IRGM - the "Jesus gene"

The world of genetics is filled with stories that are as gripping as the plot of any thriller. Take the IRGM gene - its saga, played out over millions of years, has all the makings of a classic drama. Act One: setting the scene. By duplicating and diverging, this gene thrived in the cells of most mammals as a trinity of related versions that played vital roles in the immune system.

Act Two: tragedy strikes. About 50 million years ago, in the ancestors of today's apes and monkeys, the entire IRGM cluster was practically deleted, leaving behind a sole survivor. Things took a turn for the worse - a parasitic chunk of DNA called Alu hopped into the middle of the remaining gene, rendering it useless. IRGM was, for all intents and purposes, dead and it remained that way for over 25 million years of evolution.

Act Three: the uplifting ending. The future looked bleak, but IRGM's fortunes were revived in the common ancestor of humans and great apes. Out of the blue, a virus inserted itself into this ancient genome in just the right place to resurrect the long-defunct gene. A fall from grace, a tragic demise and an last-minute resurrection - what more could you ask for from a story?

This twisting tale lies hidden in the genomes of the world's mammals and it was discovered and narrated by Cemalettin Bekpen from the University of Seattle. To reconstruct the evolutionary story of the IRGM gene, Bekpen searched for it in a variety of different species.

(Oh come on - you try to find an image to illustrate this story!)

Most mammals, such as the dog and the mouse, have three copies located one after the other. This trio of genes are "paralogs" - slightly different duplicates of a single ancestor. Two species of lemur - the ring-tailed and mouse lemurs - also share the same three genes, but all monkeys have just the one. This suggests that the IRGM cluster shrank from a trinity into a single gene in the last common ancestor of all apes and monkeys, which lived about 40 million years ago.

If that decline wasn't bad enough, Bekpen found that the remaining IRGM gene of monkeys is actually a dead remnant. It's much shorter than those of other mammals, and it has been so heavily abridged that it has lost the ability to encode a protein. In technical terms, it's a "pseudogene" and to paraphrase the Python boys, it's an ex-gene.

The villain that struck the killing blow to the IRGM family will be familiar to geneticists - it's a mobile piece of DNA called Alu. It could well be described as a genetic parasite, for it has the ability to cut itself out of its resident genome and insert itself into new locations. And it's a common feature of primate genomes - as much as 11% of our own DNA is made up of Alu sequences.

In the ancestor of monkeys and apes, an Alu sequence jumped into the middle of the last remaining IRGM, disrupting its sequence. Every three "letters" of a gene's sequence corresponds to one amino acid. To make a working protein, the gene needs to be "read" from the right position in order to manufacture the right chain of amino acids. With the insertion of Alu, that process starts from the wrong place leading to a wholly different chain of amino acids, and one that ends prematurely. It's called a "frameshift mutation" and it renders the gene useless.

Across 15 species of monkey from around the world, from marmosets to macaques to baboons, Bekpen found the same frameshift mutation. This means that Alu must have infiltrated the primate genome before the various monkeys diverged from one another, about 40 million years ago.

For 25 million years, the IRGM gene was effectively dead. But then, in the common ancestor of humans and the great apes, something unexpected happened. The gene somehow regained its ability to produce a protein, albeit a shortened one. The gene had been resurrected, and ironically enough, its saviour was another genetic hitchhiker that inserted itself in just the right place.

The new intruder was an "endogenous retrovirus" - a group of viruses that can integrate their DNA into the genomes of their hosts. The virus jumped into a position at the very start of the gene and its own sequence then drove how the gene was read and activated. Its presence negated the harmful effects of Alu, effectively getting rid of the frameshift mutation.

We humans have this resurrected IRGM gene, and Bekpen found that it's active in a variety of different tissues including the heart, brain, kidneys and particularly the testicles. The results don't provide direct evidence that the gene actually produces a working protein, but there's good reason to believe that it does.

Mutations in the IRGM gene are associated with Crohn's disease - an inherited disease, where the immune system attacks the digestive tract, leading to chronic inflammation. That strongly suggests that the IRGM gene has regained some sort of role in the immune system, and it was one of the reasons why Bekpen started investigating the gene in the first place.

But as he says on his homepage, "Who cares about Crohn's disease? We just discovered the Jesus gene!"

Reference: Cemalettin Bekpen, Tomas Marques-Bonet, Can Alkan, Francesca Antonacci, Maria Bruna Leogrande, Mario Ventura, Jeffrey M. Kidd, Priscillia Siswara, Jonathan C. Howard, Evan E. Eichler (2009). Death and Resurrection of the Human IRGM Gene PLoS Genetics, 5 (3) DOI: 10.1371/journal.pgen.1000403

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edyong Thu, 03/05/2009 - 14:00

A burst of DNA duplication in the ancestor of humans, chimps and gorillas

edyong — Wed, 11 Feb 2009 12:00:09 +0000

A burst of DNA duplication in the ancestor of humans, chimps and gorillas

This is the sixth of eight posts on evolutionary research to celebrate Darwin's bicentennial.

Physically, we are incredibly different from our ape cousins but genetically, it's a different story. We famously share more than 98% of our DNA with chimpanzees, our closest living relatives. Our proteins are virtually identical and our chromosomes have more or less the same structure. At the level of the nucleotide (the "letters" that build strands of DNA), little has happened during ape evolution. These letters have been changing at a considerably slower rate than in our relatives than in other groups of mammals.

But at the level of the gene, things are very different. Entire parts of the genome can be duplicated or deleted and the rate at which this happens has actually accelerated in the primate lineage. Some families of genes (including many that play important roles in the brain) have expanded and contracted with remarkable speed.

Duplication provides raw fuel for rapid evolution by creating back-up copies of parts of the genome. If mutations with harmful effects crop up in one of these copies, there's always a spare kicking around to take up the slack. So duplicated segments of the genome become relatively free to pick up new mutations and unsurprisingly, they are often very dynamic places that change with incredible speed.

Today, they make up about 5% of the human genome and have probably been a major driving force in the ape evolution. Now, Tomas Marques-Bonet from the University of Washington has reconstructed the evolutionary history of these duplications by comparing them across the genomes of four primates - humans, chimpanzees, orang-utans and macaques.

Using computer programmes, he produced a "comparative map" that revealed duplications unique to each of these four genomes, along with those that are shared between them. The map showed that about a third of the duplications in the human genome are unique to us, and most of the remaining duplications are ones we share with chimps.

The rate at which these duplications cropped up had greatly accelerated in the part of the primate family tree that includes humans and the African great apes. These rates doubled and hit their peak in the last common ancestor of ourselves and chimpanzees. As a result, both chimps and humans have far more of these doubles than either orang-utans or macaques. This burst of activity coincided with a time when other types of mutation, such as changes to single nucleotides, were slowing down. Marques-Bonet thinks that these accelerated rates of gene duplication played a pivotal role in the success and evolution of the great apes.

More duplications, genes and a puzzling mystery

No one know why this burst of duplication happened, especially since in most cases, duplicating large chunks of the genome must have some pretty negative effects. But Evan Eichler, the head of Marques-Bonet's group, has some ideas. For example, he suggests that the ancestral ape may have hit a population bottleneck. It's easier for harmful genetic changes to persist In smaller populations where they are less frequently exposed to the purifying force of natural selection.

Alternatively, it's possible that this ancient ape developed a mutation that destabilised its genome and made subsequent mutations more likely - a so-called "mutator phenotype". That's certainly a reasonable idea, and it's backed up by the fact that the very presence of gene duplications seems to make further duplications even more likely. Marques-Bonet's map shows that they didn't crop up in random locations. For example, almost half of the duplications that we share with chimps are very close to duplications that we share three ways with chimps and orang-utans.

Many of the duplicated pieces of DNA contain actual genes; the human-specific duplications, for example, included at least fifty-six. Many have been linked to human adaptations in the past, and while chimps share the same genes, Marques-Bonet's analysis showed that we have more copies than they do.

Duplications that are shared between all four primates include several genes involved in breaking down amino acids. Those that are unique to the different species are very different; they include genes with roles in nerve cell activity, muscle contraction and chemical communication between cells. So not only has the rate of duplication sped up in the ape dynasty, but the types of genes that have been copied have shifted too.

The importance of these sequences becomes obvious when their numbers change. Today, further doublings or deletions at certain "duplication hotspots" have been associated with mental and developmental disorders, including autism, schizophrenia and retardation. Evan Eichler, who leads the group Marques-Bonet works in, said, "The genes responsible for these [conditions] have not yet been mapped, but one possibility may be the rapidly evolving genes that are embedded within the duplications."

The map has thrown up a few big puzzles too. For a start, some regions were duplicated extensively in other apes but never copied in humans. One region, on the ape equivalent of our tenth chromosome (green circle in the image below), has been duplicated up to 100 times in the chimp, gorilla and bonobo genomes (red arrows). In ours, there's just the one copy. This pervasive sequence turns up in very different locations in the various apes - a clear sign that it has been copied independently in each species. Its location even appears to be changing in modern gorillas. When Marques-Bonet looked for it in four living gorillas, he found that half of the locations in any individual were unique.

Why this sequence took off so spectacularly in other apes but failed to do so in humans is a mystery. Eichler suggests that these regions are "simply unstable and dynamic". Once the original sequence copied itself, it greatly increased the odds of further duplications. It was by chance that this "initial cascading event" never happened in humans.

Addressing potential flaws

Marques-Bonet admits that his map has a few potential flaws. It obviously relied heavily on the software used to construct it, but he managed to show that this was reliable enough by using glowing molecules designed to stick to specific DNA sequences. These confirmed that the map predicted duplicated sequences with an accuracy of about 87-99%.

The map was also based on the genome of one individual per animal and it isn't clear how representative these single specimens are of their respective species. For example, the exact number of copies of each duplicated region could vary considerably from one individual to another. Further analysis showed that this was true, but it didn't change the fact that some regions were consistently duplicated across individuals and others were not.

As an example, Marques-Bonet compared duplications in James Watson's genome to the reference human sequence (a mix of samples from several people). The two genomes shared 89% of their duplicated regions. So whether a specific area of DNA is duplicated or not is fairly constant across members of a single species - it's just the number of copies that changes.

There is another caveat - two species may have duplicated the same parts of their genomes independently. That would make it look like the duplication happened in their shared ancestor, even though the two lineages converged on the same mutations of their own accord.

To account for that, Marques-Bonet focused on 103 different duplications that we share with chimps. In the two genomes, he found that 85% of these duplications have multiple copies that are found in the same spots. It's very unlikely that they are independent innovations - our last common ancestor with chimps almost certainly had these copies already.

Potential problems aside, the comparative map has already revealed tantalising bits and pieces about gene duplications, what they do, and the part they played in human and ape evolution.Even better, it provides raw material for scientists to test more ideas about these sequences in the future.

Reference: Nature 10.1038/nature07744

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edyong Wed, 02/11/2009 - 07:00

Ed, after looking at the pic, you may have to reconsider your first sentence.

Burn! Ow that hurts!

So redundancy rocks...sometimes.

I agree with Gerardo, though don't take it personally.

Whenever I look at the picture of a chimp I see me. Sure his ears are bigger, his nose is flatter and I'm hairier but otherwise we're the same.

Why the creationists can't see it is beyond my understanding.

NoAstronomer - Oh absolutely. But I submit to you that it's fairly easy to tell the difference with a quick glance ;-)

Lilian - yes indeed. But obviously the key point here is that one of the redundant copies soon becomes anything but.

Sorry for random advertising, but as someone whose interested in science communication I thought you might find this link interesting: http://www.thenakedscientists.com/

They are a small group of writers and radio-people based in cambridge, but the stuff they produce is really good. They really don't get enough coverage though.

Hence the random advertising :)

In order to post something vaguelly on topic, the MonkeyWorld zoo near us recently ran an advertising campaign called 'meet the relatives!' which had pictures of human and ape expressions and action next to each other looking spookily similar.

Cheeky ;-) I *have* heard of you, you know. See blogroll on right? Also I work with Kat, who I co-blog with at Cancer Research UK.

ah yes. heh. Didn't see that.

I'm not actually part of anything to do with Naked Scientists, I just found out about them recently and thought they were awesome.

I have heard a lot of people say that our DNA is 98% similar, but I have never seen this backed up. Do you know what study this is from? I don't see how it's possible, since humans have 24 pairs and chimps 23, which would alone account for more than 2% difference.

I have heard a lot of people say that our DNA is 98% similar, but I have never seen this backed up. Do you know what study this is from? I don't see how it's possible, since humans have 24 pairs and chimps 23, which would alone account for more than 2% difference.

It's the other way around - humans have 23 pairs of chromosomes*. And a lot of the genetic material in human chromosome 2 corresponds to genetic material in two pairs of ape chromosomes, as a result of chromosome fusion in humans. It's like if you fuse The Lord of the Rings in one volume instead of three, it doesn't mean that the result is only 33% similar to a set of three volumes.

*The figure above is a little misleading, since it shows the same (human?) set of chromosomes for all species. Where's the figure from?

OK, thanks. I just could never make the math come out on that one before.