This article is reposted from the old WordPress incarnation of Not Exactly Rocket Science. The blog is on holiday until the start of October, when I’ll return with fresh material.

Imagine that one day, you make a pact with your brother or sister, vowing to never have children of your own and instead spend your life raising theirs. You’ll agree to do the grocery shopping, cook for them, clean their rooms and bathe them, until you die.

That seems like a crazy plan, but it’s one that some of the most successful animals in the world – the social insects – have adopted. It’s called ‘eusociality‘ and it’s a puzzle for evolutionary biologists. Why should an animal forgo the chance to reproduce in order to help rear its siblings and their young?

The strategy makes sense if you share enough genes with your close relatives. In helping them, you indirectly ensure the transmission of your own genetic material. But even if this explains the existence of eusociality, it doesn’t explain how such an extreme form of co-operation evolved.

Now, Amy Toth and colleages at the University of Illinois have found a clue in the genes of the paper wasp, Polistes metricus, which suggests that their altruistic actions evolved from motherly behaviour.

Scientists have suggested this theory before as a possible origin for eusociality. It doesn’t take a great leap of imagination to picture how a group of wasp sisters living together and communally looking after their young could become a society in which only a few individuals reproduce and the others share the care. But until now, that theory had never been tested at a genetic level.

Truly eusocial insects like honeybees have physically distinct castes with strongly segregated jobs. The queen’s sole purpose is to lay eggs and she never takes on the menial foraging and brood care of the smaller workers.

Paper wasps are only halfway down the road to eusociality, which makes them an ideal choice for studying its evolution. They have different castes, but they all look much the same and their castes are far less strictly segregated. The roles that individuals perform depends on the age of the colony and fall into four different groups.

Foundresses, females that establish new colonies and care for young as well as laying eggs. After creating the first generation, these females become queens and focus solely on laying more eggs. Their daughters, the workers, take up the task of caring for their new siblings to the exclusion of their own reproduction. Later on in the colony’s life, the queen gives birth to gynes, that neither care for young or lay eggs – their job is to mate with males and become foundresses themselves in the following spring.

Toth decided to look at the patterns of gene activity in these four groups. She reasoned that if the workers’ altruistic actions had originated in maternal care, they would share similar genetic profile to the foundresses, the only other group that also cares for young.

Complex behaviours like caring for young and foraging were hardly going to be the province of a single gene. Toth needed a way to analyse a myriad of genes across the entire wasp genome – a genome that has not yet been fully sequenced.

To overcome this problem, the team took a streamlined approach. They specifically looked at genes that were strongly activated in the brains of 87 wasps from all four groups. Using a powerful sequencing technique from the 454 Life Sciences company, they identified almost 400,000 stretches of relevant DNA across their genomes.

Toth matched these hits to the genome of the closely related honeybee (Apis mellifera), which was fully sequenced last year. They focused on 32 genes, whose honeybee counterparts are involved in worker behaviour. Even though bees and paper wasps started down different evolutionary roads some 100 million years ago, the proteins encoded by these genes have remained very similar.

As predicted, Toth found that the activation pattern of these 32 genes was closest in workers and foundresses, and were distinct from those of queens and gynes, which don’t practice maternal care. Regardless of whether the wasps focused on their siblings or their young, their caring behaviour was governed by similar sets of genes, supporting the idea that eusociality evolved from maternal care.

Today, the vast majority of solitary wasps provide food for their helpless young, often in grisly or murderous ways. During the course of evolution, the twin behaviours of egg-laying and maternal care started to separate.

In the intermediary paper wasps, the behaviours are separated in time – the foundresses practice both at first and then focus on just one when they turn into queens. As this happens, their brain undergo dramatic changes and different sets of genes are switched on.

The final stage down this evolutionary path is the one seen in true eusocial wasps, where egg-laying and maternal care are separated in space, in the bodies of queens and workers.

The study also shows that many evolutionary problems can be addressed without the complete sequence of an animal’s genome. For every full genome we have, we can use next-generation sequencing technology to compare it to the partially sequenced genes of closely-related species, just as the bee and wasp proved here.

Reference: toth, Varala, Newman, Miguez, Hutchison, Willoughby, Simons, Egholm, Hunt, Hudson & Robinson. 2007. Wasp gene expression supports and evolutionary link between maternal behaviour and eusociality. Sceince

This article is reposted from the old WordPress incarnation of Not Exactly Rocket Science. The blog is on holiday until the start of October, when I’ll return with fresh material.

Science fiction loves to play off the potential threat of threat of alien viruses. But a new study suggests that space travellers are much more likely to be threatened by germs from our own planet that become more virulent in space.

Warding off infections is a real priority for astronauts, especially if longer space missions to the Moon and Mars are to go ahead. People have a tendency to get sick in space and over half of the astronauts on the Apollo missions became ill during their trips or soon after their return to Earth.

Earlier research has shown that prolonged weightlessness weakens our immune systems by preventing key sets of genes from switching on. But that’s only part of the problem. A team of researchers from NASA, Arizona State University and 12 other institutions has shown that bacteria also react to zero-gravity conditions, by becoming more virulent, or able to cause disease.

This time last year, they sent cultures of Salmonella typhimurium – one of the most common causes of food poisoning – into space aboard the Space Shuttle Atlantis. To protect the vulnerable crew, the bacteria were safely housed in three layers of containment. All the astronauts had to do to start the experiment was to push down a plunger.

That dropped the isolated bacteria into a nutritious broth that fuelled their growth. After 24 hours of growth, the astronauts pushed more plungers to either pumped in more growth solution, or immobilised the bacteria with a chemical fixative, preserving their genetic activity for the journey home.

Back on Earth, other scientists were doing the same thing with their own Salmonella samples grown in the same conditions (albeit with extra gravity). They spoke with the Shuttle crew through radios to synchronise their experiments.

When the Shuttle returned, the team recovered the space-bound bacteria and analysed the pattern of genetic activity across their entire genomes using microarrays. This modern and powerful technique allows scientists to measure the activity of thousands of genes at the same time. The researchers also measured the levels of every protein in the samples.

The team looked at the entire Salmonella genome and found that the expression of 167 genes and the levels of 73 proteins had changed in the space-travellers. Clearly, the environmental changes of space-flight had triggered changes in the bacteria at the molecular level.

When fed to mice, the altered bacteria were three times more virulent than their Earth-bound counterparts. The infected mice succumbed to much lower concentrations of space-faring bacteria and in much shorter times.

These results support earlier studies which showed that Salmonella grown in conditions that simulated space flight turned into super-bugs. They were more virulent and more resistant to high temperatures, acidic conditions and white blood cells.

When the team looked at the bacterial cells under the microscope, they found that they hadn’t changed in size or shape. The major difference was that the space-faring Salmonella were much more likely to form biofilms, massive communities of bacteria that clump together and live within a network of substances that they themselves excrete.

Our immune systems and antibiotics find it much more difficult to clear infectious bacteria once they form these biofilms and this could explain why Salmonella seems to be much more dangerous after a jaunt in space.

One protein in particular – Hfq – plays a crucial role in these changes. It lords over the activity of a large suite of genes, including some involved in the creation of biofilms. It sticks to small RNA molecules that control the expression of other genes, and ensures that the larger mRNA molecules are successfully translated into proteins in the face of environmental stress.

The researchers suspected that Hfq is a key player that orchestrates a slew of genetic chances responsible for Salmonella‘s hardier nature and increased virulence. They tested this idea by growing mutant Salmonella that lacked Hfq in a special chamber that mimicked incredibly low gravity. Sure enough, these mutants never developed the resistance to acid and white blood cells that normal Salmonella do.

Hfq is now an inviting target for drugs designed to guard the health of future astronauts, but these discoveries could also have implications for medicine on Earth.

So far, there is no vaccine for Salmonella and the bacterium is becoming increasingly resistant to antibiotics. Targeting Hfq and disrupting the bacteria’s ability to make biofilms could change that. Hfq is also very similar in a wide range of other bacteria so drugs that focus on it could find uses in treating a whole range of diseases.

Reference: Wilson et al. Space flight alters bacterial gene expression and virulence and reveals a role for global regulator Hfq. PNAS doi/10/1073/pnas.0707155104.

The two-toed sloth is a walking hotel. The animal is so inactive that its fur acts as an ecosystem in its own right, hosting a wide variety of algae and insects. But the sloth has another surprise passenger hitching a ride inside its body, one that has stayed with it for up to 55 million years – a virus.

In the Cretaceous period, the genes of the sloth’s ancestor were infiltrated by a “foamy virus“, one of a family that still infects humans, chimps and other mammals today. They are examples of retroviruses, which reproduce by converting an RNA genome into a DNA version and inserting that into the genome of whatever animal they’re infecting. If these hitchhikers become permanent tenants, as so often happens, they become known as endogenous retroviruses or ERVs.

ERVs act as a sort of viral fossil record, telling us about the ancient viruses that infected ancestral animals. In the sloth’s case, its ERVs tell us that foamy viruses must have been doing the rounds among ancient mammals over 100 million years ago, back when the dinosaurs still ruled the planet.

Despite the passing of a geological age, their descendants still circulate today and are astonishingly unchanged. The modern viruses look very similar to the one that inserted its genetic material into the sloth’s ancestors. That’s especially amazing because retroviruses – take HIV as an example – have a reputation for mutating at incredibly high rates.

(more…)

Meet Raptorex, the “king of thieves”. It’s a new species of dinosaur that looks, for all intents and purposes¸ like the mighty Tyrannosaurus rex, complete with large, powerful skull and tiny, comical forearms. But there’s one very important difference – it’s 100 times smaller. Unlike the ever-shrinking world of music players and phones, it seems that evolution crafted tyrannosaur technology with much smaller specifications before enlarging the design into the giant predators of the late Cretaceous.

Raptorex is a new species of meat-eating dinosaur, discovered in northwest China by Paul Sereno from the University of Chicago. The specimen is a young adult, but it wouldn’t have grown to more than 3 metres in length. It stood about as tall as a human, and wouldn’t have weighed much more. And yet Raptorex looked very much like a scaled-down version of its giant future relatives. All the features that made tyrannosaurs so recognisable and such efficient killers (except their enormous size) were present in this animal.

It really is a beautiful transitional fossil. As Sereno says, “Raptorex really is a pivotal moment in the history of the group where most of the biologically meaningful features of tyrannosaurs came into being, and the surprising thing is that they came into being in such a small animal.” Raptorex clearly shows that natural selection initially honed the distinct body shape of these giant predators at a 1/100^th scale. This design was then scaled up with remarkably few modifications.

It had a skull that had clearly been developed into the animal’s primary weapon.  It was unusually big for its body size (40% of its torso length), it was structurally reinforced against the stresses of heavy bites, it had large places where powerful jaw-closing muscles attached and it was armed with sharp teeth.

Its limbs also had classic T.rex proportions – strong hind legs that that were fit for running, but miniscule forearms. In contrast, other early tyrannosaurids, such as Guanlong, Dilong, Eotyrannus and Stokesosaurus, looked very different with arms that were long and useful, and proportionally smaller heads (just 30% of its torso length). Only a few distinctive parts of their skeleton mark them out as early tyrannosaurids.

Raptorex brain was also large for its size. For comparison, the Jurassic predator Allosaurus had a brain that was just 60% bigger, despite having a body that was 10 times heavier! Raptorex‘s sense of smell was particularly well-developed, just as Tyrannosaurus‘s was. A scan of its skull showed a large area for its olfactory bulbs – the parts of its brain devoted to smell. These bulbs take up a full 20% of the brain’s total volume, a proportion that exceeds that of all meat-eating dinosaurs except the giant tyrannosaurs.

Despite what many newspapers will assuredly tell you, Raptorex isn’t the ancestor of Tyrannosaurus although it probably looked very much like what this hypothetical animal would have done. It’s more like an early cousin, but one that’s clearly more closely related to T.rex and its giant kin than any of the other smaller species so far discovered.

Based on his new fossil, Sereno tells a three-act story of tyrannosaur evolution. Act One was set in the Jurassic and early Cretaceous periods, with a cast that included Eotyrannus and Dilong.  Their snouts had become stronger and their jaws more powerful, but they were typical of other predators of the time. It was only during Act Two, around 125 million years ago, that this dynasty of predators started to become truly specialised, enhancing the skull, lengthening the legs, and shrinking the forearms.

All of these features were present in Raptorex, setting the stage of the final act in tyrannosaur evolution – getting really big. The lineage grew in bulk by around 100 times. By the end of the Cretaceous, the meat-eating scene in the northern continents was dominated by tyrannosaurids – predators such as Albertasaurus, Gorgosaurus, Daspletosaurus and Tarvosaurus, each weighing in at 2.5 tons or more.

It would be fascinating to see if the same story could be told for other lineages of predators, if the abelisaurids, carcharodontosaurids and spinosaurids all had their own mini-prototypes.

Reference: Science 10.1126/science.1177428

Images: Reconstruction by Todd Marshall; other images from Science/AAAS

More on dinosaurs:

• Evidence that Velociraptor had feathers
• Dinosaurs provide clues about the shrunken genomes of birds
• Tianyulong – a fuzzy dinosaur that makes the origin of feathers fuzzier

For humans and most other mammals, sex is a question is chromosomes. Two X chromsomes makes us female while an X and a Y makes us male. Birds use a similar but reversed system, where males are ZZ and females are ZW. But for reptiles, including crocodiles, turtles and many lizards, sex is determined not by genes, but by temperature. 

In crocodiles, males hatch from eggs incubated at cooler temperatures while warmer conditions produce females. In turtles, it’s the other way around, and lizards use a variety of criteria including some very complicated combinations of genes, temperature and even size of egg.

But what did extinct reptiles do? It’s not exactly easy to tell for genes and temperature don’t fossilise. However, fossils can tell us about how such animals reproduced. For example, we know that three groups of marine reptiles – the serpentine mosasaurs, the dolphin-shaped ichthyosaurs, and the long-necked, paddle-flippered sauropterygians – gave birth to live young through a series of stunning fossils of pregnant females, and even one case of a birth in progress (see below). Around 20% of living reptiles (excluding birds) do the same and the ability probably evolved at least 100 times in lizards and snakes alone.

Chris Organ from Harvard University thinks that, in all three lineages of marine reptiles, the evolution of genetic sex determination preceded the evolution of live births. By studying the reproductive styles and sex-determining methods of 94 species of amniotes (mammals, birds and reptiles), he showed that the two traits often co-evolve. Live birth almost always depends on first having a gene-based method of assigning sex, while egg-layers can use either chromosomes or temperature.

Organ suggests that these important changes were instrumental for the success of these prehistoric swimmers, allowing them spread throughout the open oceans, where temperatures can’t be relied on to determine sex. And without the need to return to land to lay their eggs, they were free to live permanently at sea and evolve more extreme physical adaptations to an aquatic life, including paddle-like limbs, back fins, streamlined bodies and fluked tails.

(more…)

People with red-green colour blindness find it difficult to tell red hues from green ones because of a fault in a single gene. Their inheritance robs them of one of the three types of colour-sensitive cone cells that give us colour vision. With modern technology, scientists might be able to insert a working copy of the gene into the eye of a colour-blind person, restoring full colour vision.

 You might think that the brain and eye would need substantial rewiring to make use of the new hardware, but Katherine Mancuso from the University of Washington thinks otherwise. She has used gene therapy to give full colour vision to adult squirrel monkeys that had been red-green colour-blind since birth, opening up a world of formerly invisible reds and oranges, right in front of their eyes.

Her success proved that adding a third cone cell into a retina with just two isn’t as much of a technical challenge as it initially seems – the new cells slot in with all the ease of plug-and-play hardware.  The experiments suggest that early mammals could have evolved three-colour vision simply by developing a third type of cone cell, with little in the way of extra genetic control or neural wiring. If anything, the third cone probably exploited the circuitry that was already in place to process the signals from one of its siblings.

The human eye has three types of cone cells – the S cones that are sensitive to short violet-ish wavelengths, M-cones that are sensitive to medium greenish-blue wavelengths, and L-cones that are sensitive to longer reddish wavelengths. Each type of cone cell contains a different light-sensitive pigment – an opsin – and each of these is produced by a single gene. Red-green colour-blindness is what happens when the genes for the M-opsin or the L-opsin are flawed.

In squirrel monkeys, females see a more colourful world than males. While they have the same three opsins that humans do, males lack the gene for L-opsin and can’t see red.  Mancuso changed that by loading the human L-opsin gene into a virus and injecting it into the monkeys’ retinas. As a result, around 15-30% of each animal’s M-cones were also producing L-opsins. It’s a trick that other researchers have used to give mice the ability to see red and it clearly worked for monkeys too.

(more…)

You may have seen rowing before, but I guarantee you that you know little about the sport unless you went to university at Cambridge or Oxford. There you will find a subspecies of human known as the “boatie” who seem perfectly happy to gather en masse at godforsaken times of the morning to paddle about on a river. In the rain. In winter. With a hangover. Later, in the pub, they will spend innumerable hours discussing their training schedules, talking about “catching crabs” without a hint of irony and comparing blisters.

For those of us who wondered what could possess grown men and women to forgo the comfort of a bed for several painful hours in the company of eight grunting companions, Emma Cohen from Oxford has some answers.

Group activities, such as rowing in an ‘eight’, increases the pain thresholds of the individual athletes, compared to rowing alone. These raised thresholds are probably the result of endorphins, natural pain-killing chemicals that our brains release when we exercise. Endorphins also produce a light euphoria and a sense of wellbeing that is important for bonding with our friends and peers, and gluing a group of rowers together, despite the smell and pain. 

Cohen worked with a dozen men from the University’s rowing squad and asked them to complete 45 minutes of continuous rowing on an ergometer – a gym machine that simulates the rowing experience and that crews use to train out of the river. They rowed for two sessions, either alone or in a “virtual boat” consisting of eight athletes using ergometers side by side.

(more…)

This article is reposted from the old WordPress incarnation of Not Exactly Rocket Science.

It’s not just us who like to go travelling in the summer – flu viruses do it too. After a busy winter of infection, they turn into the gap-year students of the virus world. They travel round the world, meet new viruses, swap genetic material, and returning back, changed and unrecognisable (at least to our immune systems).

The success of flu viruses hinges on their ability to rapidly fool our immune systems by changing the proteins that line their surface. Every year, they put on a new disguise that shield them from any immunity built up the year before, allowing them to constantly re-infect the same populations of people.

But when scientists looked for these fast evolutionary changes during the epidemic season (November to March in the northern hemisphere), they found surprisingly little. That suggests that the viruses evolve their new facades during their off-season and it could do so in two ways.

They could stay within the same host population in a dormant state, until changing climate stirs them into action. Alternatively, they could travel to other parts of the world, only to return the following year.

One of the problems with deciding between these theories is a lack of data. The World Health Organisation has an excellent network of influenza reference centres but for obvious reasons, they don’t keep an eye on the viruses outside of the epidemic season.

But Martha Nelson and colleagues form Pennsylvania State University and the National Institutes for Health realised that they didn’t actually need this data. They compared the genomes of virus samples collected during several epidemic seasons in America, Australia and New Zealand.

If they stayed in the same place, then viruses collected in different years at the same place would be genetically closer than viruses collected elsewhere. However, if the viruses travelled between busy seasons, their evolutionary relationships would be much more mixed, with some northern viruses being more closely related to southern viruses than their neighbours.

That’s exactly what Nelson found after sequencing the genomes of over 900 samples of the H3N2 influenza A virus. When she built an evolutionary tree of her samples, she saw clear signs of significant viral traffic across the equator in both directions.

In fact, she found no examples at all where viruses from the same place were genetically closely linked across different seasons. Even viruses from relatively isolated countries like Australia and New Zealand travelled and evolved elsewhere.

So during the off-season, flu viruses travel to foreign lands where they change their genetic make-up. Nelson’s study doesn’t tell us where this happens, but she thinks that the tropics are the best bet.

In the tropics, influenza is a year-round problem. Nelson believes that the tropical belt acts like a virus training camp. Every year, it receives recruits from temperate areas that have been recognised by the immune system, fits them with new mutations, and chucks them back out to start new epidemics. An increase in air travel could certainly be aiding the viruses in their journeys.

South-east Asia in particular could be a genetic melting pot for flu viruses because of the large populations there who live in close contact with their domestic animals. Of course, all of this is just an educated guess until the team can get their hands on some tropical flu samples.

Nelson also wants to find out why flu viruses in temperate zones take the summer off, when they happily infect all year round in the tropics. What climate-related cues quell the epidemics?

Again, she stresses that we’ll only get these answers by collecting more samples, throughout the year and in various parts of the world. That would be a vital step toward understanding the hidden life cycle of flu viruses, and how these can be disrupted.

Reference: Nelson, Simonson, Vibound, Miller & Holmes. 2007. Phylogenetic analysis reveals the global migration of seasonal influenza A viruses. PLoS Pathogens 3: e131.

The British Wildlife Centre is one of my favourite places in the country. It’s like a small zoo focusing solely on British wildlife and everything in it lives in lovely open enclosures with naturalistic environments (the otters have about three lakes to play around in). It’s a fantastic place to visit, especially for people who’ve most likely only ever seen a badger or a fox as a roadside carcass. Here are some photos from yesterday’s trip:

Badger

Buzzard

Eagle owl

Frog (pool frog?)

Harvest mouse (note size of blackberry for comparison)

Otter

Wotta lotta otter

Pine marten (Britain rocks for mustelids)

Red fox

Red squirrel

This article is reposted from the old WordPress incarnation of Not Exactly Rocket Science.

In Jurassic Park, the role of Velociraptor was played by computer-generated reptilian actors, that bore little resemblance to the real deal. The actual dinosaur was smaller, slower and used its infamous claw to stab (or possibly climb) rather than disembowel. And in 2007, scientists found good evidence that it was covered in feathers.

Since Jurassic Park aired, dinosaurs like Velociraptor have received something of a makeover. It began in the late 1990s when Chinese palaeontologists found a stunning series of dinosaur fossils with distinct traces of feathers around their bodies. Some were just covered in a downy fluff, while others like Microraptor had fully-formed wings and were probably capable of true flight.

These species were primitive members of the dromaeosaurids, a group of small, agile predators that Velociraptor also belongs to. With feathered ancestors and evolutionary cousins, it was always extremely likely that Velociraptor also had a feathered coat but until now, that was always an educated guess.

The breakthrough came from Alan Turner and Mark Norell from the American Museum of Natural History and Peter Makovicky of the Field Museum of Chicago. They were studying the forearm of a Velociraptor unearthed in 1998, when they noticed six evenly spaced knobs of bone on the back edge.

The team recognised these as quill knobs, small lumps of bone that act as attachment points for feathers. These knobs are direct evidence that Velociraptor carried a row of feathers on its forearm, probably about 14 by Turner’s count. You can see them in the top two images above. The bottom two show the equivalent structures in a modern vulture, and how feathers are attached to them.

The quill knobs also suggest that Velociraptor‘s feathers had a distinctly modern style. They probably looked much like those of today’s birds, rather than the hair-like proto-feathers of its ancestors.

Several well preserved Velociraptor skeletons have already been found but palaeontologists have never found the outlines of feathers that typifies the fossils of species like Archaeopteryx and Microraptor. Turner and co aren’t surprised – these outlines have only ever been found in the smallest of dinosaurs.

The most beautiful feathered fossils hail from special sites called lagerstätten, a kind of universal graveyard where an amazing diversity of prehistoric species is preserved. At these places, the specific mixture of sediment and low oxygen levels delays the process of decay long enough for soft body parts, like feathers, to become preserved. But this only works for small dinosaurs, smaller still than Velociraptor.

Feathers allow birds to fly and to keep themselves warm. But Velociraptor‘s forearm plumage probably fulfilled neither function. For its weight, its forearms were too small to provide powered flight, and feathers there wouldn’t have helped the animal to retain much heat.

Instead, Turner suggest that Velociraptor could have used its feathers to display to mates or rivals, to shield their nests from the cold, or to manoeuvre while running .

Its smaller ancestors probably did use their feathers for flight (or at the very least, efficient gliding), and Velociraptor kept them but co-opted them for other purposes. To their ancestors, Velociraptor and its kin would have been like prehistoric ostriches, having abandoned flying for a running life.

Feathers can join the list of bird features shared by dromaeosaurids, including wishbones, nest brooding and hollow bones. Discoveries like these further blur the distinction between this dinosaur lineage and their modern descendants.

Birds are now all classified as living dinosaurs, but some palaeontologists argue that there is a case for classifying dromaeosaurs as birds. As Norell himself says, “If animals like Velociraptor were alive today our first impression would be that they were just very unusual looking birds.”

Reference: Turner, Makovicky & Norell. 2007. Feather quill knobs in the dinosaur Velociraptor. Science doi:10.1126/science.1145076.