Tag: Evolution

A life in the trees is a longer one

By Ed Yong | February 22, 2010 3:00 pm

An assortment of tree-living mammals

In The Descent of Man, Darwin talked about the benefits of life among the treetops, citing the “power of quickly climbing trees, so as to escape from enemies”. Around 140 years later, these benefits have been confirmed by Milena Shattuck and Scott Williams from the University of Illinois.

By looking at 776 species of mammals, they have found that on average, tree-dwellers live longer than their similarly sized land-lubbing counterparts. Animals that spend only part of their time in trees have lifespans that either lie somewhere between the two extremes or cluster at one end. The pattern holds even when you focus on one group of mammals – the squirrels. At a given body size, squirrels that scamper across branches, like the familiar greys, tend to live longer than those that burrow underground, like prairie dogs.

These results are a good fit for what we already know about the lives of fliers and gliders. If living in the trees delays the arrival of death, taking to the air should really allow lifespans to really take flight. And so it does. Flight gives bats and birds an effective way of escaping danger, and they have notably longer lives than other warm-blooded animals of the same size. Even gliding mammals too tend to live longer than their grounded peers.

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CATEGORIZED UNDER: Ageing, Evolution, life history

Evolving guppies shape their environments

By Ed Yong | February 1, 2010 3:00 pm

The streams of Trinidad and Tobago are home to the most unexpected of landscape gardeners. They’re guppies – tiny and beautifully coloured fish, just an inch or so long. Without tools or plans, they shape the environment around them, tweaking everything from the numbers of different species to the nutrients in the water.

The guppies are quick to adapt to different environments and particularly to which predators are around. The number and types of predators affect the guppies’ lifespan, how big they get and when they become sexually mature. This, in turn, affects what they eat, and that influence ripples across the entire stream.

We’re used to the idea that environments can shape the bodies and behaviour of living things, as species evolve adaptations that allow them to thrive in their surroundings. But the opposite also happens. Living things are both the product and the architects of their environment, with evolution and ecology affecting each other in a grand cycle. This whole process rests on the idea that evolution, though often assumed to move at glacial pace, can happen at rapid speed on a small scale. And the guppies are clear proof of that.

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CATEGORIZED UNDER: Animals, Ecology, Evolution, Fish

Echolocation in bats and whales based on same changes to same gene

By Ed Yong | January 25, 2010 12:00 pm

Millions of years before humans invented sonar, bats and toothed whales had mastered the biological version of the same trick – echolocation. By timing the echoes of their calls, one group effortlessly flies through the darkest of skies and the other swims through the murkiest of waters. It’s amazing enough that two such different groups of mammals should have evolved the same trick but that similarity isn’t just skin deep.

The echolocation abilities of bats and whales, though different in their details, rely on the same changes to the same gene – Prestin. These changes have produced such similar proteins that if you drew a family tree based on their amino acid sequences, bats and toothed whales would end up in the same tight-knit group, to the exclusion of other bats and whales that don’t use sonar.

This is one of the most dramatic examples yet of ‘convergent evolution’, where different groups of living things have independently evolved similar behaviours or body parts in response to similar evolutionary pressures.

It is one of a growing number of studies have shown that convergence on the surface – like having venom, being intelligent or lacking enamel – is borne of deeper genetic resemblance. But this discovery is special in a deliciously ironic way. It was made by two groups of scientists, who independently arrived at the same result. The first authors even have virtually identical names. These are people who take convergence seriously!

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Evolution without genes – prions can evolve and adapt too

By Ed Yong | December 31, 2009 2:00 pm

If you search for decent definitions of evolution, the chances are that you’ll see genes mentioned somewhere. The American Heritage Dictionary talks about natural selection acting on “genetic variation”, Wikipedia discusses “change in the genetic material of a population… through successive generations”, and TalkOrigins talks about changes that are inherited “via the genetic material”. But, as the Year of Darwin draws to a close, a new study suggests that all of these definitions are too narrow.

Prions.jpgJiali Li from the Scripps Institute in Florida has found that prions – the infectious proteins behind mad cow disease, CJD and kuru – are capable of Darwinian evolution, all without a single strand of DNA or its sister molecule RNA.

Prions are rogue version of a protein called PrP. Like all proteins, they are made up of chains of amino acids that fold into a complex three-dimensional structure. Prions are versions of PrP that have folded incorrectly and this misfolded form, called PrPSc, is social, evangelical and murderous. It converts normal prion proteins into a likeness of its abnormal self, and it rapidly gathers together in large clumps that damage and kill surrounding tissues.

Li has found that variation can creep into populations of initially identical prions. Their amino acid sequence stays the same but their already abnormal structures become increasingly twisted. These “mutant” forms have varying degrees of success in different environments. Some do well in brain tissue; others thrive in other types of cell. In each case, natural selection culls the least successful ones. The survivors pass on their structure to the “next generation”, by altering the folds of normal prion proteins.

This process follows the principles of Darwinian evolution, the same principles that shape the genetic material of viruses, bacteria and other living things. In DNA, mutations manifest as changes in the bases that line the famous double helix. In prions, mutations are essentially different styles of molecular origami. In both cases, they are selectively inherited and they can lead to adaptations such as drug resistance. In prions, it happens in the absence of any genetic material. 

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CATEGORIZED UNDER: Evolution, Medicine & health

Big-headed tiger snakes support long-neglected theory of genetic assimilation

By Ed Yong | October 30, 2009 9:34 am

Tiger snakes are a group of extremely venomous serpents found all over the southern half of Australia, and on many of its islands. Some were cut off from the mainland by rising sea levels more than 9,000 years ago, while others were inadvertently introduced by travelling humans and have been around for less than 30 years.

When the snakes first arrive on an island, they find prey that are generally larger than they’re used to on the mainland. That puts them under strong evolutionary pressure to have larger heads, in order to swallow larger meals. But by feeding snakes from different populations with prey of varying sizes, Fabien Aubret and Richard Shine have found that the more recent immigrants solve the need for larger heads in a very different way than the long-term residents. 

Young populations do it by being flexible. If growing tiger snakes from newly colonised islands are fed on large prey, their heads rapidly enlarge to cope with the sizeable morsels. This flexibility is an example of “phenotypic plasticity” and it doesn’t involve any genetic changes.

But Aubret and Shine found that older populations lack this flexibility – they have larger heads from birth and the size of the prey they eat doesn’t affect the way they grow. These adaptations are fixed in their genomes. In the heads of tiger snakes, Aubret and Shine have found evidence for a 67-year-old concept in evolution called “genetic assimilation“, which has very rarely been tested and is often neglected.


Its name might conjure up images of science-fiction and DNA-stealing aliens, but genetic assimilation simply describes a means of adaptation. It was proposed in 1942 by Conrad Waddington, who suggested that species initially cope with fresh environments by being flexible – through plasticity. All species have a certain amount of variation built in to their developmental program, which they can exploit according to the challenges they face. In this case, the tiger snakes can grow larger heads if they encounter bigger meals.

But as populations face constant evolutionary pressures, natural selection eventually favours genes that produce the same results, the ones that plasticity once achieved. This is the crux of Waddington’s theory – in time, natural selection eliminates plasticity by fixing genes for the same traits. Such genes as said to be “canalised”.

Back in the 1950s, Waddington demonstrated this using fruit flies. He exposed developing flies to ether vapour and found that some developed a second thorax (the middle segment between the head and abdomen). By anyone’s standards, that’s a radical change, but one that was triggered by an unusual environment. Over time, Waddington selectively bred the double-thorax individuals and exposed each new generation to ether. After 20 rounds of this, he found that some flies developed a second thorax naturally, without being exposed to ether. The double-thorax trait, which was initially induced by the environment, eventually became governed by the fly’s own genes.

It was a neat idea, but finding other natural examples has been very tricky. Aubret and Shine thinks that genetic assimilation tends to happen over such short timescales (geologically speaking) that you can only really detect it under unusual circumstances. And the spread of tiger snakes across Australia certainly fits that bill.

Aubret and Shine’s experiments show that snakes from newly colonised areas had the greatest degree of plasticity when it comes to head size while those from the longest-colonised islands had the least. These differences become abundantly clear when you compare snakes from three populations.

Tiger snakes have only been on Trefoil Island for 30-40 years and the jaws of their hatchlings are still small. However, they’re also plastic – if they eat big meals, they’ll grow bigger. On Carnac Island, tiger snakes have been around for 90 years and there, the hatchlings have moderately sized jaws and a relatively high degree of plasticity. On Williams Island, the tiger snakes have been cut off from the mainland for 9,100 years and their jaws are not only large from birth but their growth has very little plasticity. 

The differences between the Trefoil and Carnac serpents are particularly interesting, because they suggest that the process of genetic assimilation can take place over a very short span of time, as others have predicted. It starts manifesting within just a few decades, even in animals like tiger snakes that only breed after their second or third birthday. This rapid pace could explain why it’s very difficult to observe this process in the wild.


Reference: Current Biology 10.1016/j.cub.2009.09.061

Images: Tiger snake by Ian Fieggan

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CATEGORIZED UNDER: Animals, Evolution, Reptiles, Snakes

Venomous shrews and lizards evolved toxic proteins in the same way

By Ed Yong | October 29, 2009 12:00 pm

The Northern short-tailed shrew is a small, energetic mammal that lives in central and eastern North America. The Mexican beaded lizard is a much larger reptile found in Mexico and Guatemala. These species are separated by a lot of a land and several million years of evolution, yet they share astonishing similarities. Not only are they both venomous, but the toxic proteins in their saliva have evolved in very similar ways from a common ancestor, converging on parallel lethal structures independently of one other. 

This discovery, from Yael Aminetzach at Harvard University, shows that adaptations are sometimes very predictable. Despite the many changes that could have shaped the course of venom proteins in lizards and shrews, they seem to have gone down a consistent and similar route.

Northern short-tailed shrew by Giles Gonthier; Mexican beaded lizard by PiccoloNamek

The northern short-tailed shrew is one of the few venomous mammals, but its poisonous bite is painful to humans and can kill smaller animals. The key to its venom is a protein called BLTX, whose job is to cut another protein in two. This chemical reaction frees a molecule called bradykinin, which widens blood vessels and lowers blood pressure. It’s a necessary job, but BLTX is so active that if floods the body with bradykinin – an overdose that leads to paralysis and death.

BLTX is a dark, hyperactive descendant of an ancestral protein called kallikrein-1, which does the same thing but in a much more restrained way. Aminetzach found that BLTX is a longer version of kallikrein and the extra amino acids it has gained have changed the structure of the protein’s ‘active site’.

The active site is the protein’s business end – it allows BLTX to latch onto the right targets and catalyse the relevant chemical reactions. It’s also the part of the protein that has changed the most from the harmless kallikrein model; amino acids around BLTX’s active site have changed about twice as much as the rest of the protein. As a result, the site is larger, more flexible and better at drawing in its target, and the protein as a whole has become hyperactive.

And amazingly, the Mexican beaded lizard has gone through similar changes. Its venom relies on a protein called GTX, which is also descended from kallikrein. Like BLTX, it too is a longer version of its ancestor, and while its extra amino acids have been shoved into different places, the results are the same. The changes have altered the protein’s active site so that it’s larger, more flexible and better at drawing in its target.

These changes are very specific to these toxic proteins. By studying 24 relatives of kallikrein, Aminetzach found that none of the non-toxic members of the family have any of the changes that BLTX and GTX share.

This study demonstrates that evolution doesn’t work with infinite possibilities. Often, there are only a few roads leading to the same destination. Through different amino acid changes, both BLTX and GTX have evolved similar structures and have turned into weapons. This predictability of venom evolution may be useful to us – for example, Aminetzach suggests that it could allow scientists to more easily identify toxins from others species, even distantly related ones.

Reference: Current Biology 10.1016/j.cub.2009.09.022

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CATEGORIZED UNDER: Animals, Evolution, Lizards, Mammals, Reptiles

Breaking the Link – Darwinius revealed as ancestor of nothing

By Ed Yong | October 21, 2009 1:00 pm

Cast your mind back to June, when a stunning fossil animal called Darwinius (alternatively Ida or “The Link”) was unveiled to the world to tremendous pomp and circumstance. Hyperbolic ads declared the day of Ida’s discovery as the most important for 47 million years. A press release promised that she would “change everything”, headlines proclaimed her a “missing link in evolution” and the scientists behind the discovery billed her as “the closest thing we can get to a direct ancestor“.

Darwinius.jpgAnd according to a new study, none of that is true. Mere months later, Erik Seiffert from Stony Brook University has done a comprehensive analysis of the bones of 117 primates, both living and extinct, which throws Ida’s supposed direct line of ancestry to humans into serious doubt.

Central to this new work is a new fossil called Afradapis, a member of the same group of extinct primates – the adapids – that Darwinius belonged to. The two were closely related but separated by around 10 million years. Like its more famous cousin, Afradapsis‘s jaw and teeth contain features that are similar to those of  anthropoids – monkeys, apes and humans. But far from being a sign of direct ancestry, Seiffert thinks that these features represent convergent evolution – the two groups evolved them independently.

His team compared and contrasted 360 features in the bones of over 117 living and extinct primates. Among them were 24 adapids, including Darwinius, Afradapis and eight other that had not been previously analysed. This comprehensive set of data revealed the group’s family tree, charting their relationships using their overall anatomy as a guide.And it clearly shows that adapids (and Ida among them) were more closely related to modern lemurs than to anthropoids (monkeys, apes and humans). The two groups sit on a different branches of the evolutionary tree.

The analysis also reveals that even though the adapids were a successful and widespread group, they left no living descendants. For all the hype, Ida turns out to be the ancestor of bugger all.

New evidence

To those who followed the criticisms of the Darwinius hype, this volte face shouldn’t come as a surprise. The the paper describing the fossil was criticised for juggling the structure of the primate family tree to shift Ida’s branch closer to ours. To recap, there are three groups vying for position as the ancestors of the anthropoids: the bizarre, large-eyed tarsiers, the related and extinct omomyids, and the equally extinct adapids. The general consensus places the first two groups closest to us; Ida’s discoverers think the adapids should be there instead.

To support that view, they looked at 30 traits that might help to settle the question and noted whether Ida had them or not, and concluded that placed the adapids next to the anthropoids on the basis of this single species. That approach seems positively minimalist compared to the one that Seiffert took, which included 12 times as many anatomical features and 117 times as many animals!

Seiffert’s tree places the tarsiers and omomyids as the closest relatives of the anthropoids – this is the so-called haplorrhine group. The adapids, however, are part of the strepsirrhine dynasty, the group that includes lemurs, lorises and bushbabies. This is the sort of analysis that was sorely lacking in the Darwinius paper.


There is no doubt that Ida is a beautiful fossil, but Seiffert questions its worth in understanding the evolution of primates. Not only was she a growing youngster, but most of her bones have been crushed or distorted in ways that obscure important body parts. Much was made of the fact that Ida lacked a toothcomb (a set of flattened, forward-facing incisors) and a grooming claw (a special ankle bone). These are two features that modern lemurs possess and modern anthropoids don’t – their absence in Darwinius was presented as evidence of a close tie to anthropoids but not lemurs. But Seiffert thinks that these body parts – the ankle and teeth – have been damaged enough that analysing them is difficult.

Afradapsis, ironically, poses no such problems. While most of its skeleton has yet to be recovered, its teeth and jaws are in excellent condition. Like those of Darwinius and some other adapids, these teeth bear a suite of features typically found in living and extinct anthropoids. The joint between the two jawbones is fused and the part of the jaw containing the teeth is deep, as is the crater in the jawbone where the chewing muscles attach. The main cusp of its upper molars – the hypocone – is very large. It’s missing the second premolar, but the third has become bigger with an edge that sharpens its matching canine.

But this doesn’t mean that Afradapis is an ancestor, or even a close relative, of the anthropoids. For a start, the most primitive fossil anthropoids, such as Biretia and Proteopithecus, lack these traits. If adapids were their ancestors, the early anthropoids must have jettisoned these adaptations, only to re-evolve them at a later stage. The more plausible explanation, and certainly the one Seiffert subscribes to, is that both groups evolved independently, and happened to converge on the same adaptations.

The price of hype

The arrival of a paper like this was almost inevitable given the interest that Ida stirred up. Obviously, Seiffert’s analysis isn’t the final word on the subject (although his study looks more convincing to me) and I’m sure that there will be a healthy debate for days to come. But what of the public impact?

Jorn Hurum, one of the key ringleaders in the Ida circus, famously said, “Any pop band is doing the same. We have to start thinking the same way in science.” The key differences, of course, are that pop music is impossible to analyse objectively and its quality depends on personal taste. The same cannot be said of scientific truth, and that changes the extent to which you can use marketing tactics to promote a discovery.

 Hurum and his colleagues have played a dangerous game – they may claim to have been marketing science but they were, in fact, marketing their opinions and ones that may not stand the test of time. It’s debate by media, and it’s fantastically dangerous.

Consider the fact that for all the interest that the new paper will undoubtedly instigate, there will still be a book, website and documentary out there firmly enshrining the increasingly dubious view that Ida is our direct ancestor. Consider also that contradicting that view now makes the scientific establishment look like buffoons, given all the publicity and to-do a few months back. When John Hurum makes grandiose statements, he gains in the eyes of the public. When those statements are later shown to be dodgy, it’s science as a whole that takes a beating.  

It’s also worth noting how the different publishers handled the two papers. This time, Nature made the paper available to reporters several days ahead of its publication, giving us time to analyse the paper, prepare our stories and, if necessary, contact experts for their views. The situation with the original Darwinius paper couldn’t have been more different.

As Mark Henderson notes, select journalists were allowed to see the paper at a specific location and under non-disclosure contracts that prevented them from seeking further opinions. PLoS ONE admitted to rushing the publication of the paper in time for John Hurum’s press conference, and indeed, it became publicly available mere minutes before said conference kick-started a blitzkrieg of media attention. In rushing the publication of the paper, the journal allowed itself to be held hostage to hype and actively hindered science writers who were trying to do their job responsibly.

Update: Already up on the Times blog is an excellent interview with Seiffert. Brian Switek has his typically thorough take on the new paper too.

Reference: Nature doi:10.1038/nature08429

More on Ida: Darwinius changes everything

Robots evolve to deceive one another

By Ed Yong | August 17, 2009 3:00 pm

Blogging on Peer-Reviewed ResearchIn a Swiss laboratory, a group of ten robots is competing for food. Prowling around a small arena, the machines are part of an innovative study looking at the evolution of communication, from engineers Sara Mitri and Dario Floreano and evolutionary biologist Laurent Keller.

They programmed robots with the task of finding a “food source” indicated by a light-coloured ring at one end of the arena, which they could “see” at close range with downward-facing sensors. The other end of the arena, labelled with a darker ring was “poisoned”. The bots get points based on how much time they spend near food or poison, which indicates how successful they are at their artificial lives.

They can also talk to one another. Each can produce a blue light that others can detect with cameras and that can give away the position of the food because of the flashing robots congregating nearby. In short, the blue light carries information, and after a few generations, the robots quickly evolved the ability to conceal that information and deceive one another.

Their evolution was made possible because each one was powered by an artificial neural network controlled by a binary “genome”. The network consisted of 11 neurons that were connected to the robot’s sensors and 3 that controlled its two tracks and its blue light. The neurons were linked via 33 connections – synpases – and the strength of these connections was each controlled by a single 8-bit gene. In total, each robot’s 264-bit genome determines how it reacts to information gleaned from its senses.

In the experiment, each round consisted of 100 groups of 10 robots, each competing for food in a separate arena. The 200 robots with the highest scores – the fittest of the population – “survived” to the next round. Their 33 genes were randomly mutated (with a 1 in 100 chance that any bit with change) and the robots were “mated” with each other to shuffle their genomes. The result was a new generation of robots, whose behaviour was inherited from the most successful representatives of the previous cohort.

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How the turtle got its shell through skeletal shifts and muscular origami

By Ed Yong | July 9, 2009 4:00 pm

Blogging on Peer-Reviewed ResearchThe turtle’s shell provides it with a formidable defence and one that is unique in the animal world. No other animal has a structure quite like it, and the bizarre nature of the turtle’s anatomy also applies to the skeleton and muscles lying inside its bony armour.

The shell itself is made from broadened and flattened ribs, fused to parts of the turtle’s backbone (so that unlike in cartoons, you couldn’t pull a turtle out of its shell). The shoulder blades sit underneath this bony case, effectively lying within the turtle’s ribcage. In all other back-boned animals, whose shoulder blades sit outside their ribs (think of your own back for a start). The turtle’s torso muscles are even more bizarrely arranged.

This body plan – and particularly the odd location of the shoulder blades – is so radically different to that of all other back-boned animals that biologists have struggled to explain how it could have arisen gradually from the standard model, or what the intermediate ancestors might have looked like. Enter Hiroshi Nagashima from the RIKEN Center; he has found some answers by studying how the embryos of the Chinese soft-shelled turtle (Pelodiscus sinensis) shift from the standard body plan of other vertebrates to the bizarre configuration of adult turtles.

By comparing the embryos to those of mice and chickens, Nagashima showed that all three species start off with a shared pattern that their last common ancestor probably shared. It is only later that the turtle does something different, starting of a sequence of muscular origami that distorts its body design into the adult version.

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Scientists tickle apes to reveal evolutionary origins of human laughter

By Ed Yong | June 4, 2009 12:00 pm

If you tickle a young chimp, gorilla or orang-utan, it will hoot, holler and pant in a way that would strongly remind you of human laughter. The sounds are very different. Chimp laughter, for example, is breathier than ours, faster and bereft of vowel sounds (“ha” or “hee”). Listen to a recording and you wouldn’t identify it as laughter – it’s more like a handsaw cutting wood. But in context, the resemblance to human laughter is uncanny.

Apes make these noises during play or when tickled, and they’re accompanied by distinctive open-mouthed “play faces”. Darwin himself noted the laugh-like noises of tickled chimps way back in 1872. Now, over a century later, Marina Davila Ross of the University of Portsmouth has used these noises to explore the evolutionary origins of our own laughter.

Davila Ross tickled youngsters of all of the great apes and recorded the calls they make (listen to MP3s of a tickled chimp, gorilla, bonobo and orang-utan). She used these recordings to build an acoustic family tree, showing the relationships between the calls. Scientists regularly construct such trees to illustrate the relationships between species based on the features of their bodies or the sequences of their genes. But this is the first time that anyone has applied the same technique to an emotional expression.

The tree linked the great apes in exactly the way you would expect based on genes and bodies. To Ross, this clearly shows that even though human laughter sounds uniquely different, it shares a common origin with the vocals of great apes. It didn’t arise out of nowhere, but gradually developed over 10-16 million years of evolution by exaggerating the acoustics of our ancestors. At the very least, we should now be happy to describe the noises made by tickled apes as laughter without accusations of anthropomorphism, and to consider “laughter” as a trait that applies to primates and other animals

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