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Why the genome project missed a gene that shaped our brains

The Human Genome Project was officially completed in 2003, but our version of the genome is far from truly complete. Scientists are still finishing the last parts, correcting errors in the official sequence, and discovering new genes. These new genes did not go unnoticed because they are useless or insignificant. Some of them may be key players in our evolutionary story.

Two groups led by Evan Eichler and Franck Polleux have found that humans, alone among all animals, have three extra copies of a gene called SRGAP2, which is involved in brain development. The second of these copies, SRGAP2C, is particularly interesting because it affects the development of neurons, and produces features that are distinctively human. It also emerged between 2 and 3 million years ago, during the time when our brains became much bigger.


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Two fish families evolved electric powers by tweaking the same gene


The rivers of Africa and South America are full of shocking conversations. Both continents are home to fish that can talk to each other using electric fields: the elephantfishes of Africa, and the knifefishes of South America (including the famous electric eel). Both groups live in dark, murky water where it’s hard to see where you’re swimming. Both have adapted by using electricity to guide their way. Their bodies have become living batteries and their muscles can produce electric currents that help them communicate, hunt, navigate and court.

But both elephantfishes and knifefishes evolved their electric powers independently. Their common ancestors had no such abilities. They are a great example of how two groups of animals, faced with a similar problem, can arrive at the same solution. And this similarity is all the more striking because it is based on the same gene. For a fish, it seems there are only so many ways to be electric.


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The copied gene that gave dachshunds and corgis their short legs

Blogging on Peer-Reviewed ResearchCompare 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.

Dachshund.jpgThese 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.


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Extra genomes helped plants to survive extinction event that killed dinosaurs

Blogging on Peer-Reviewed ResearchSixty-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.



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The death and resurrection of IRGM – the “Jesus gene”

Blogging on Peer-Reviewed ResearchThe 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!)


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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.

Blogging on Peer-Reviewed ResearchPhysically, 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.