Tag: genes

Elephants and humans evolved similar solutions to problems of gas-guzzling brains

By Ed Yong | November 16, 2009 5:04 pm

At first glance, the African elephant doesn’t look like it has much in common with us humans. We support around 70-80 kg of weight on two legs, while it carries around four to six tonnes on four. We grasp objects with opposable thumbs, while it uses its trunk. We need axes and chainsaws to knock down a tree, but it can just use its head. Yet among these differences, there is common ground. We’re both long-lived animals with rich social lives. And we have very, very large brains (well, mostly).

But all that intelligence doesn’t come cheaply. Large brains are gas-guzzling organs and they need a lot of energy. Faced with similarly pressing fuel demands, humans and elephants have developed similar adaptations in a set of genes used in our mitochondria – small power plants that supply energy to our cells. The genes in question are “aerobic energy metabolism (AEM)” genes – they govern how the mitochondria metabolise nutrients in food, in the presence of oxygen.

We already knew that the evolution of AEM genes has accelerated greatly since our ancestors split away from those of other monkeys and apes. While other mutations were reshaping our brain and nervous system, these altered AEM genes helped to provide our growing cortex with much-needed energy.

Now, Morris Goodman from Wayne State University has found evidence that the same thing happened in the evolution of modern elephants. It’s a good thing too – our brain accounts for a fifth of our total demand for oxygen but the elephant’s brain is even more demanding. It’s the largest of any land mammal, it’s four times the size of our own and it requires four times as much oxygen.

Goodman was only recently furnished with the tools that made his discovery possible – the full genome sequences of a number of oddball mammals, including the lesser hedgehog tenrec (Echinops telfairi). As its name suggests, the tenrec looks like a hedgehog, but it’s actually more closely related to elephants. Both species belong to a major group of mammals called the afrotherians, which also include aardvarks and manatees.

Goodman compared the genomes of 15 species including humans, elephants, tenrecs and eight other mammals and looked for genetic signatures of adaptive evolution. The genetic code is such as that a gene can accumulate many changes that don’t actually affect the structure of the protein it encodes. These are called “synonymous mutations” and they are effectively silent. Some genetic changes do, however, alter protein structure and these “non-synonymous mutations” are more significant and more dramatic, for even small tweaks to a protein’s shape can greatly alter its effectiveness. A high ratio of non-synonymous mutations compared to synonymous ones is a telltale sign that a gene has been the target of natural selection.

And sure enough, elephants have more than twice as many genes with high ratios of non-synonymous mutations to synonymous ones than tenrecs do, particularly among the AEM genes used in the mitochondria. In the same way, humans have more of such genes compared to mice (which are as closely related to us, as tenrecs are to elephants). 

These changes have taken place against a background of less mutation, not more. Our lineage, and that of elephants, has seen slower rates of evolution among protein-coding genes, probably due to the fact that the duration of our lives and generations have increased. Goodman speculates that with lower mutation rates, we’d be less prone to developing costly faults in our DNA every time it was copied anew.

Overall, his conclusion was clear – in the animals with larger brains, a suite of AEM genes had gone through an accelerated burst of evolution compared to our mini-brained cousins. Six of our AEM genes that appear to have been strongly shaped by natural selection even have elephant counterparts that have gone through the same process.

Of course, humans and elephants are much larger than mice and tenrecs. But our genetic legacy isn’t just a reflection of our bigger size, for Goodman confirmed that AEM genes hadn’t gone through a similar evolutionary spurt in animals like cows and dogs.

Goodman’s next challenge is to see what difference the substituted amino acids would have made to us and elephants and whether they make our brains more efficient at producing aerobic energy. He also wants to better understand the specific genes that have been shaped the convergent evolution of human and elephant brains over the course of evolution. That task should certainly become easier as more and more mammal genomes are published.

Reference: PNAS doi:10.1073/pnas.0911239106

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Autism linked to common gene variants that affect the connections between neurons

By Ed Yong | April 28, 2009 1:00 pm

Blogging on Peer-Reviewed ResearchThe autism spectrum disorders (ASDs), including autism and its milder cousin Asperger syndrome, affect about 1 in 150 American children. There’s a lot of evidence that these conditions have a strong genetic basis. For example, identical twins who share the same DNA are much more likely to both develop similar autistic disorders than non-identical twins, who only share half their DNA.

Autistic-child.jpgBut the hunt for mutations that predispose people to autism has been long and fraught. By looking at families with a history of ASDs, geneticists have catalogued hundreds of genetic variants that are linked to the conditions, each differing from the standard sequence by a single ‘letter’. But all of these are rare. Until now, no one has discovered a variant that affects the risk of autism and is common in the general population. And with autistic people being so different from one another, finding such mutations seemed increasingly unlikely. Some studies have come tantalisingly close, narrowing down the search to specific parts of certain chromosomes, but they’ve all stopped short of actually pinning down individual variants.

This week, American scientists from over a dozen institutes have overcome this final hurdle. By looking all over the genomes of over 10,000 people, the team narrowed their search further and further until they found not one but six common genetic variants tied to ASDs. This sextet probably affects the activity of genes that connect nerve cells together in the developing human brain.

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Genetic neoteny – how delayed genes separate human brains from chimps

By Ed Yong | March 24, 2009 8:30 am

Blogging on Peer-Reviewed ResearchBe it in sports or comedy, they say that timing is everything. In evolution, it’s no different. Many of the innovations that have separated us from other apes may have arisen not through creating new genetic material, but by subtly shifting how the existing lot is used.

Take our brains, for example. In the brains of humans, chimps and many other mammals, the genes that are switched on in the brain change dramatically in the first few years of life. But Mehmet Somel from the Max Planck Institute for Evolutionary Anthropology has found that a small but select squad of genes, involved in the development of nerve cells, are activated much later in our brains than in those of other primates.

This genetic delay mirrors other physical shifts in timing that separate humans from other apes. Chimpanzees, for example, become sexually mature by the age of 8 or 9; we take five more years to reach the same point of development.

These delays are signs of an evolutionary process called “neoteny“, where a species’ growth slows down to the point where adults retain many of the features previously seen juveniles. You can see neoteny at work in some domestic dog breeds, which are remarkably similar to baby wolves, or the axolotl salamander, which keeps the gills of a larva even as it becomes a sexually mature adult. And some scientists, like the late Stephen Jay Gould, have suggested that neoteny has played a major role in human evolution too.

As adults, we share many of the physical features of immature chimps. Our bone structures, including flat faces and small jaws, are similar to those of juvenile chimps, as is our patchy distribution of hair. A slower rate of development may even have shaped our vaunted intelligence, by stretching out the time when we are most receptive to new skills and knowledge. Somel’s research supports this idea by showing that since our evolutionary split from chimpanzees, the activation of some important brain genes has been delayed to the very start of adolescence.

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Child abuse permanently modifies stress genes in brains of suicide victims

By Ed Yong | February 22, 2009 1:00 pm

Blogging on Peer-Reviewed ResearchThe trauma of child abuse can last a lifetime, leading to a higher risk of anxiety, depression and suicide further down the line. This link seems obvious, but a group of Canadian scientists have found that it has a genetic basis.

By studying the brains of suicide victims, Patrick McGowan from the Douglas Mental Health University Institute, found that child abuse modifies a gene called NR3C1 that affects a person’s ability to deal with stress. The changes it wrought were “epigenetic”, meaning that the gene’s DNA sequence wasn’t altered but it’s structure was modified to make it less active. These types of changes are very long-lasting, which strongly suggests that the trauma of child abuse could be permanently inscribed onto a person’s genes.

Child abuse, from neglect to physical abuse, affects the workings of an important group of organs called the “hypothalamic-pituitary-adrenal axis” or HPA. This trinity consists of the hypothalamus, a funnel-shaped part of the brain; the pituitary gland, which sits beneath it; and the adrenal glands, which sit above the kidneys.  All three organs secrete hormones. Through these chemicals, the HPA axis controls our reactions to stressful situations, triggering a number of physiological changes that prime our bodies for action.

The NR3C1 gene is part of this system. It produces a protein called the glucocorticoid receptor, which sticks to cortisol, the so-called “stress hormone”. Cortisol is produced by the adrenal glands in response to stress, and when it latches on to its receptor,  it triggers a chain reaction that deactivates the HPA axis. In this way, our body automatically limits its own response to stressful situations.

Without enough glucocorticoid receptors, this self-control goes awry, which means that the HPA is active in normal situations, as well as stressful ones. No surprise then, that some scientists have found a link between low levels of this receptor and schizophrenia, mood disorders and suicide. So, childhood trauma alters the way the body reacts to stress, which affects a person’s risk of suicide or mental disorders later in life. Now, McGowan’s group have revealed part of the genetic (well, epigenetic) basis behind this link.

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

By Ed Yong | February 11, 2009 1:00 pm

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.

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Solar-powered green sea slug steals ability to photosynthesise from algae

By Ed Yong | December 28, 2008 12:00 pm

Blogging on Peer-Reviewed ResearchSolar power is a relatively new development for humans but, of course, many living things have been exploiting the power of the sun for millions of years, through the process of photosynthesis. This ability is usually limited to plants, algae and bacteria, but one unique animal can do it too – the emerald green sea slug Elysia chlorotica. This remarkable creature steals the genes and photosynthetic factories of a type of algae that it eats (Vaucheria littorea), so that it can independently draw energy from the sun. Through genetic thievery, it has become a solar-powered animal and a beautifully green one at that.

Elysia_chlorotica.jpgThe cells of algae, like those of plants, contain small compartments called chloroplasts that are its engines of photosynthesis. As the Elysia munches on algae, it takes their chloroplasts into the cells of its own digestive system, where they provide it with energy and sugars. It’s a nifty trick that provides the sea slug with an extra energy source, but the problem is that it shouldn’t work.

Chloroplasts are not independent modules that can be easily separated from their host cell and implanted into another. They are the remnants of once-independent bacteria that formed such a strong alliance with the cells of ancient plants and algae, that they eventually lost their autonomy and became an integral part of their partner. In doing so, they transferred the majority of their own genes to their host so that today, chloroplasts only have a tiny and depleted genome of their own, containing just 10% of the genes it needs for a free-living existence.

So, shoving a chloroplast from an algal cell into an animal one should be about as effective as installing a piece of specialised Mac software on a PC. The two simply shouldn’t be compatible, and yet Elysia and its chloroplasts clearly are. Mary Rumpho from the University of Maine discovered the key to the partnership – the sea slug has also stolen vital genes from the algae that allows it to use the borrowed chloroplast. It has found a way to patch its own genome to make it photosynthesis-compatible.

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