Larva of a crocodile icefish. Photo by Uwe Kils.

Few fish would survive a swim in Antartica’s ice-covered waters. Temperatures can drop to -1.9 ℃, whereas a typical fish starts to freeze at -0.8 ℃. If the water is colder, microscopic ice crystals will soon infiltrate the fish through gills and skin and start growing from within. Nerves are severed, tissues damaged, and the fish dies within minutes.

But crystals don’t bother Antarctic icefish. These cold-adapted creatures carry antifreeze proteins in their blood and body fluids. The antifreeze proteins bind ice crystals and smother them by dividing the long and growing crystal fronts into many small and curved fronts. This inhibits crystal growth just enough to prevent the icefish from freezing.

The Antarctic Icefish rule the seas that lie over Antarctica’s continental shelf. Here, more than 90% of all fish are icefish. There are over 132 different species of Antarctic icefish known to science. Some are native to the coastal waters of Australia and South-America, but the majority of them dwell near Antarctica.

Many biologists assume that the antifreeze proteins were the key to the icefish’s evolutionary success. Antarctica went through a major period of cooling around 24 million years ago. Ice sheets formed and glaciers scoured over the continent. In a study that was published last year, German biologists found that the onset of this cooling event coincided with the origin icefish and the evolution of antifreeze proteins. Their conclusion was simple: the antifreeze proteins were the evolutionary innovation that triggered the diversification of icefish. With their newly acquired cold resistance, the ancestral icefish and their descendants invaded the frigid waters of the Antarctic and multiplied.

These ancestors were bottom dwellers. When they first spread out over the Antarctic shelf, a world of plenty awaited above their heads, full of tasty krill and opportunities. But this world was out of reach: icefish don’t have a swim bladder. To rise up from the sea floor, ice fish evolved other tricks. Some replaced bone with cartilage, others store fatty molecules in sacs between their muscles and under their skin, as a kind of visceral floating devices.

But now a team of ecologists and biologists suggests there’s more to this simple two-stage model. Their DNA analyses confirm that the last common ancestor of all Antarctic Icefish lived 22.4 million years ago, but also reveal that the majority of icefish diversity evolved 10 million years after these first origins. The Trematomus family originated 9 million years ago, the crocodile icefish 6 million years ago, and the Artedidraconidae 3 million years ago. These additional pulses of speciation occurred long after the first antifreeze proteins evolved.

Many icefish lineages diverged long after antifreeze proteins evolved.

The evolutionary path towards buoyancy was not straightforward either. In general, closely related species share similar ways of life. For example, one icefish family could have dominated the sea floor, whereas another lineage inhabits the upper waters. But when the biologists compared the buoyancy measurements of different icefish, they found a different pattern. Within each icefish family there were many species that had adapted to life at different depths. For icefish, there exists no link between niche and lineage.

Antarctica’s harsh and erratic climate might explain this lack of direction in icefish evolution. While Antarctica has been a cool place for millions of years, the degree to which the continent and its surrounding waters have been covered by ice has varied. Sometimes the ice expanded as far as the edges of the continental shelf, wiping out the animal communities that lived there, only to suddenly retreat again, leaving a few isolated ice caps behind.

In 2008, polar researchers describe how Antarctic life might have ‘hung by a thread‘ during such glacial periods. Fish and other creatures might have persisted in so-called ‘polynyas‘, areas of open water surrounded by sea ice. Or in this case, oases in a desert of ice. Once the ice retreated again, the survivors had an empty sea floor all for themselves. The cycle of creation and destruction of ice would have brought in new waves of colonists every time, explaining why the different lineages of Icefish repeatedly colonized the different layers of the Antarctic Ocean.

The Emerald rockcod, or Trematomus bernachii. Photo by Zureks

This goes to show that nothing in evolution is as simple as it might first seem. ‘Antifreeze proteins triggered icefish diversification’ makes for a simple story, but it does not hold up once we take a closer, deeper look. Even with antifreeze, Antarctic life has treated icefish harshly.

For creatures so familiar with extreme cold, it remains to be seen how they will cope with a warming world. The authors conclude: “In a tragic twist of fate, the development of polar climatic conditions that shaped the radiation of Antarctic icefish is now reversing, and the increasing temperature of the Southern Ocean, with the associated potential for the arrival of invasive species and disruption of foodwebs, is the greatest threat to the survival of this unparalleled radiation of fish.”

Climate change could be more than the icefish can take. There might be no icy oases this time.

Geothermal pond near the Mutnovsky volcano, Kamtchatka. Copyright Anna S. Karyagina

“But if (and oh what a big if) we could conceive in some warm little pond with all sorts of ammonia and phosphoric salts, light, heat, electricity etcetera present, that a protein compound was chemically formed, ready to undergo still more complex changes [..] ”
~Charles Darwin, in a letter to Joseph Hooker (1871)

All life on earth is related. Trace back the separate lines of descent of all organisms that ever lived, and they will converge to a single point of origin – the beginning of life. Charles Darwin was reluctant to publish his views on life’s origin. His only speculations on the subject are known from a private letter to his friend and colleague Joseph Hooker, in which he speaks of a ‘warm little pond’ in which the first molecules of life could have formed.

A new and controversial study suggests Darwin’s stab in the dark hit close to truth. In the article that was published earlier this week, researchers claim that the first cells evolved in volcanic pools. This new hypothesis brings the origin of life debate back from the depths of the oceans to the surface of the earth – other scientists believe hydrothermal vents in the deep sea are the most conducive environments for nascent life.

The researchers, led by Armen Mulkidjanian, presume that the chemistry of modern cells mirror the original environment in which life first evolved. Since oceans and cells are chemically dissimilar, they think it is unlikely life evolved there. The chemical nature of volcanic pools, or ‘warm little ponds’, resembles the cell’s composition of its cytoplasm much more closely.

The researchers invented the term ‘chemistry conservation principle’ for their idea that organisms retain their chemical traits throughout time. They reason that the membranes of the first cells must have been simple and leaky. Metal ions could have flowed in and out unhindered, leading to a equilibrium between environment and protocell. As the cells adapted to the ion levels in their surroundings, they came to depend on them. Circumstance became necessity. Cells evolved ion pumps and iontight membranes to maintain the ion balance that was initially forced upon them – hence the assumption that cells themselves are reflections of their ancestral environment.

The occurrence of some key ions in oceans and cells.

This is not a new approach. The Canadian biochemist Archibald Macallum applied it as early as 1926, when he noted that ion levels were similar between blood and sea water and concluded that animals must have evolved in the sea. “Maccallum was also the first to measure the concentrations of ions within cells”, says Mulkidjanian. “He discovered that all modern cells contain more potassium than sodium.”

This century old observation is one of the cornerstones of Mulkidjanian’s argument: potassium outnumbers sodium in living cells, yet in oceans and lakes, sodium dominates. Other ions, like zinc, magnesium and phosphate are also present in much higher concentrations in modern cells than they are in oceans of past and present.

The same small set of ions is built into the core machinery of the cell, inherited from the last common ancestor of life. The backbone of DNA is made of phosphate, many ancient proteins require zinc, and the cell needs potassium ions to solder amino acids together in the manufacture proteins, one of the most important chemical reactions in life.

From these observations, Mulkidjanian and his colleagues conclude that it is unlikely life evolved in the sea. They think terrestrial springs, like those in Yellowstone Park, are much better candidate environments for the earliest evolution of life. They argue that geothermally active pools are the only places on earth where potassium, zinc, magnesium and phosphate are found in high enough quantities to explain the ionic content of cells.

Aside from containing the right mix of ions, the researchers list several other features that make volcanic pools suitable cradles for early life, borrowing heavily from the theories that were developed to explain how life could have formed in hydrothermal vents. “In water that flows through hot rock, organic molecules are spontaneously produced through a process called serpentinization“, says Mulkidjanian. “Michael Russell was the one who first brought this reaction under the attention of origin of life researchers. He also noted that hydrothermal vents are not solid, but porous. He suggested these pores could serve as hatcheries for the first cells.”

Mulkidjanian incorporated both these ideas in the volcanic pond model. “Serpentinization can also proceed in continental rocks. Indeed geochemists find organic molecules in the vapour that escapes from the surface. And our geochemical analyses show that in the past, porous minerals would have been deposited on the bottom of geothermic pools rather than mud, because of the lower acidity at the time. Cells could have used these honeycomb structures to survive. In a sense we took these ideas that were developed by Russell for the origin of life in the deep sea, and brought them to the surface.”

In their paper, the researchers write that ‘the terrestrial scenario outlined here incorporates all the features of the hydrothermal vents that favour the origin and early evolution of life, and adds more.’ But not everyone is convinced.

Heated vapour escapes the earht near the Mutnovsky volcano. Copyright Anna S. Karyagina

“The ‘principle of chemistry conservation’ is a postulate rather than a proven principle”, says Jim Cleaves from the Carnegie Institution of Washington. “It may be true on short time scales, but who can say what has happened since the origin of life?”

“Overall, I think it is questionable that organisms would have kept their original composition, given the variability observed in present cells. Is it not at least equally likely that they have modified their cytosolic composition once they had control over this process? Any modern environment which matches this composition would then be purely coincidental. In summary, I don’t get much from this paper that I would hang my hat on.”

Jack Szostak, professor at Harvard Medical School and 2009 winner of the Nobel Prize, has similar doubts about the chemical conservation principle, but he does not dismiss volcanic pools entirely. ” If there is a reason that a high potassium/sodium ratio is biochemically a good thing, then a prebiotic scenario that provided such a ratio might have been more favorable for the origin or early evolution of life”, says Szostak. “But we can’t rule out an origin in a low potassium environment followed by selection for high internal potassium.”

“Independent of these arguments, I do not think the oceans were a favorable environment for the origin of life. Fresh water ponds seem more favorable due to the lower salt and ion concentrations, which would allow for fatty acid based membranes to form. The accumulation of organic compounds in ponds is also easier to imagine than in the ocean, and geothermally active areas provide numerous advantages, as expressed by the authors.”

Michael Russell, one of the pioneers of the hydrothermal vent hypothesis, did not want to comment on the study.

Do I think life began in volcanic waters myself? I don’t know. What I do know, is that the origin of life has always been a topic that has divided scientists and poisoned debates. This is not surprising. The questions about who we are and where we come from incite controversy, precisely because they are dear to us all. Still I think it’s important to not dismiss new ideas outright, especially if they have been thought through. The wider our gaze, the higher our chance that we will one day find our warm, little pond.

Henry Lee (1826-1888) adored octopuses. As the resident naturalist at the Brighton aquarium he wrote regular columns about these creatures, which he bundled in the short but delightful book “The Octopus”. Lee shared his fascination for all things tentacles with the Victorian gentry. In the chapter ‘Octopods I have Known’ he describes how the aquarium’s public had grown bored with the exotic fish that had been on display for so long. In those days, in the words of Henry Lee, “an aquarium without an octopus was like a plum-pudding without plums”. So when the Brighton aquarium obtained its first octopus in October 1872, the public rejoiced.

“The new octopus became “the rage.” Visitors jostled each other, and waited their turn to obtain a peep at him – often a tantalizing exercise of patience, for the picturesque rock-work in the tanks provided so many hiding places, that the popular favourite only occasionally condescended to show himself.”

In the winter of 1873, disaster struck the Brighton Aquarium.

“[It] became necessary to clean out a tank in which were some “Nurse-hounds”, or “Larger spotted dog-fishes”, Scyllium stellare. No hostility between them and the octopus being anticipated by their attendant, they were temporarily placed with it, and, for a while, they seemed to dwell together as peaceably as a ‘happy family’ of animals.”

A predator and prey, in one happy family. Splendid!

“But one fatal day – the 7th of January, 1873 – the “devil-fish” was missing, and it was seen that one of the “companions of his solitude” was inordinately distended. A thrill of horror ran through the corridors. There was suspicion of crime and dire disaster. The corpulent nurse-hound was taken into custody, lynched and disembowelled, and his guilt made manifest. For there, within his capacious stomach, unmutilated and entire, lay the poor octopus who had delighted thousands during the Christmas holidays. It had been swallowed whole, and very recently, but life was extinct.”

A nursehound swallowed the Brighton octopus whole.

Needless to say, Lee was shocked by this untimely death. At least there was some consolation to be found in the ‘brilliantly written’ and ‘kindly sympathetic’ articles that appeared in the newspapers. One of the daily papers of London reported on the tragic death of the Brighton octopus as follows:

“Thus was an end put to a most distinguished and useful life. Octopuses doubtless die every day, but seldom has there been an octopus who will be so much missed as the octopus at Brighton.”

It took almost two months before the aquarium had found a suitable replacement for the popular star. But the novelty had faded, and the public lost its interest in the shy creatures. Not before the invention of embeddable video clips would octopuses rise to fame again.

This stuffed coelacanth, described by Smith in 1939, achieved worldwide fame. Source.

It was supposed to be extinct. Yet here it lay, with fins round and fleshy, scales as hard as bone and a tail unlike any living fish. “Lass, this discovery will be on the lips of every scientist in the world”, James Smith said to Marjorie Courtenay-Latimer, curator of the East London Museum. Smith had good reasons to make such a grand claim. This was a coelacanth.

Naturalists had known about coelacanths for a long time – but only as fossils. It was Louis Agassiz who first described the group in 1839. Paleontologists had found dozens of different coelacanth species since then, but always in rocks older than 70 million years. The lack of coelacanth fossils in younger strata led them to conclude that coelacanths had gone extinct a long time ago. But the fish that now lay before Smith was no fossil. This creature had been caught only weeks ago, as bycatch by a fishing trawler off the coast of South Africa.

It was 1939, and the discovery of the first living coelacanth was on the lips of scientists around the world. The press heralded the fish as a ‘missing link‘, ‘prehistoric fish’ and ‘living fossil’. In doing so, they branded the coelacanths as a backwards fish for years to come.

The same stereotypes have haunted the coelacanth to this very day. In most popular accounts, the coelacanth is portrayed as a a forgotten survivor that has been left at the evolutionary wayside. In this modern fable, coelacanths had been trapped in a private bubble of time for millions of years until they re-emerged in the 20th century.

Axelrodichthys araripensis, an extinct coelacanth from South America. Photo by Ghedoghedo.

But the truth is that evolution leaves no fish behind. Coelacanths are as much affected by evolution as finches, ferns and flying lemurs. They have their own evolutionary history – we only need to look for it. This is what Japanese and African coelacanth researchers did not long ago when they took stock of the genetic diversity amongst coelacanths in the Indian Ocean. Through their research, they uncovered a small part of the coelacanth’s history of change.

Coelacanths have popped up in many places along the East African coast. Figure from first reference.

Coelacanths have popped up in several places in the Indian Ocean over the years, but the majority of them has been found in the Comoros archipelago. In the late eighties, Hans Fricke filmed how coelacanths inhabit rocky crevices and caves around the Comoros. At night he saw them drifting along the up- and downwelling currents, using their fins as stabilizers, to sneak up on unsuspecting fish. A short stroke with its fan-like tail, a sudden and forceful bite and its prey is gone.

Other coelacanths have been captured off the coast of Madagascar, South Africa, Mozambique and Kenya, but these fish have been dismissed as strays. Biologists reasoned that coelacanths would not be able to survive on the flat and sandy sea floors near Mozambique and South Africa. They presumed that strong ocean currents had swept the creatures away from the Comoros. These dead-end drifters were destined for death.

But there’s evidence that these stragglers represent distinct coelacanth populations. Geologists have identified several marine canyons near South Africa and Mozambique in which coelacanths could live. A dozen coelacanths have been caught near Tanzania every year since 2003. It’s unlikely that these are all strays. Indeed – when marine biologists let a remotely operated submersible descend in Tanzanian waters, they were able to capture footage of nine living coelacanths. Could this be the second home of coelacanths in the Indian Ocean?

In the paper that was published a few months ago, researchers have compare the DNA of Tanzanian and Comoran coelacanths. They found that some Tanzanian fish carry unique genetic variants. These variants were not found in any Comoran fish or anywhere else. This was especially true for coelacanths captured off northern Tanzania. The team believe their results indicate that coelacanths from northern Tanzania form a separate breeding population from the coelacanths from the South and the Comoros. These last two populations are much closer to each other genetically.

The researchers think the last common ancestor of the Tanzanian and Comaran coelacanths lived at least 200,000 years ago. For your sense of time: this was around the same time when the first modern human walked the earth. The researchers arrived at this estimate with a simple technique, known as the molecular clock: the more genetic differences exist between two lineages, the longer ago they diverged. But calibrating the clock can be tricky. Using a different calibration point, the researchers dated the split between the two populations to a few millions years ago.

Whatever the exact figure is, fact is that the Indian Ocean harbours distinct populations of coelacanths. If the Comoros Archipelago is the ancestral home of coelacanths, some fish have packed their things and settled somewhere else. Given enough time these populations might evolve into distinct species. We know this has happened in the past, for there are two species of coelacanth alive today. Aside from the West Indian Coelacanth, there exists a second species of coelacanth that was discovered at a local fish market two decades ago, near Indonesia.

Scientists have just started to collect and sequence coelacanth DNA. The amount of DNA analyzed in genetic studies (including this one) has been tiny so far. As more sequences will become available, more evidence of the continued evolution of the coelacanth will come to light.

Let’s leave the silly concept of ‘living fossils’ behind. Watch the movie above, and see the coelacanth sail the currents with subtle movements of its fins. Marvel at the mysterious headstand these creatures perform. Peer into its eyes, and see how the light is reflected back at you. These creatures are no fossils. They are very much alive.

As Smith wrote in the paper that announced the discovery of a second specimen:

“Numbers of successful modern fishes appear less well equipped for survival than the coelacanth. [..] Coelacanths can scarcely be regarded as degenerate fish. They are apparently full of vigour.”

The bald uakari has a distinctive, but simple, face. Photo by Ipaat

Specks. Stripes. Red fur. Black fur. Eye masks. Bald spots. Beards. Moustaches. New World monkeys are nature’s motley crew. Their faces display an extraordinary range of colours and patterns. Some are simple and straightforward, others intricate and complex. Take the bald uakari. Its hypervascularized, red skin is striking, but uniform. The uakari’s nose is just as red as its forehead. Other species have more complex facial patterns, such as the marmosets. Large tufts of hair extend from around their ears. Specks of white and brown are islands in a sea of grey.

Evolutionary biologist Sharlene Santana was struck by this diversity. She wanted to know what evolutionary forces shape the colours and patterns on a primate’s face. Why is the marmoset’s face so much more complex than the uakari’s?

For us primates, faces are an important source of information. We are visual and social animals, reading faces is what we do. A face can tell to which group or species a primate belongs (species recognition), or reveal the identity of a fellow group member (individual recognition). Santana came up with two hypotheses to explain how these two modes of recognition affect the evolution of the colours and patterns on primate faces.

Wied's marmosets have intricate facial patterns. Photo by grendelkahn.

Santana’s first hypothesis is that a complex face aids in the recognition individuals. A face that consists of multiple distinct components also has more potential variations and combinations. If Mico has longer hair tufts and a darker eye mask than Sue, it’s easier to tell them apart. According to this scenario, primates living in large, social groups should have the most complex faces. Seeing who’s who at a glance is more important for them than it is for solitary animals.

In Santana’s second hypothesis, species recognition is the main driver of facial complexity. The roles are reversed in this explanation: solitary primates or primates living in small groups should now have the most complex faces. They only meet others of their kind sporadically, so they have to be able to rapidly identify that potential mate or territorial aggressor when they see one. This is easier when faces are distinctive and intricate.

To test these hypotheses, Santana collected photo’s of 129 different primate species, together with colleagues from the University of California. She scored all these faces on their facial complexity. She first divided the faces in 14 different regions and then tallied how many different colours occurred across these regions. A simple approach, but it is the first time that the facial colours and patterns of so many different species have been measured and compared. “Past work has been mostly focused on particular species or one feature of the face”, Santana says.

Emperor Tamarins have massive moustaches. Photo by Mila Zinkova.

Sure enough, Santana found a correlation between facial complexity and sociality: primates living in smaller groups have more complex facial patterning. This is in line with Santana’s second scenario, where species that rarely interact with others of their kind have to identify and classify other primates as quick as possible. When species live in the same habitat as a high number of closely related species, they also tended to have more complex faces. A distinctive and recognizable face is even more important when things get crowded.

The New World monkeys that live in large groups must have other means to recognize their fellow group members. Perhaps they can distinguish between subtle differences in shape and structure of noses, lips and eyes, or on differences in colour intensity, rather than the shape of facial patterns. Social primates also display a wider range of expressions on their faces. Perhaps there’s a trade-off between the evolution of complex facial musculature and of complex facial patterning. No one can see your grin if it is covered by a massive moustache, after all. These are interesting ideas, but they cannot be resolved until more primatologists have gathered more data on the expressions and facial musculature of New World monkeys.

When Santana compared the facial complexity of primates with their geographical distribution, she identified several other drivers of facial evolution, aside from sociality. Eye masks become darker towards the Equator and the east, to shield eyes from glare in open and sunny surroundings. In more temperate regions, beards, moustaches and hairs grow longer. In the forested west, monkeys have darker noses, to aid in camouflage. None of these ecological rules are absolute: a primate’s face is shaped by the combination of behavioural, ecological and social pressures.

It’s interesting that Santana never set foot in the Amazon rainforest or the Brazilian Caatinga for her research. She collected the primate pictures came from databases like All The World’s Primates and Arkive, she mined the information on average group size came from scientific publications and literature, and the data on their geographical ranges came from the database InfoNatura. All the data was there, but it Santana and her colleagues connected all the dots. “I think we are coming to an interesting point at which there is a ‘critical mass’ of data and resources for many species, all of which is allowing us to conduct these broad comparative and integrative studies. These would have been virtually impossible in the past”, Santana says.

Ever since Humboldt travelled Latin America, and Darwin described the emotions of man and animals, our collective scientific knowledge has increased. There are ever more dots to draw lines between and unforeseen patterns to uncover. Data-driven biology is the next chapter in study of life.

The newspaper scrap above is an excerpt of my very first article that ran in NRC, on the 2nd of December in 2010. In NRC newsroom jargon, this is a ‘shortie’. Shorties range from 80 to 150 words in length and contain a short description of a single research paper’s results and findings. This one is about how oxytocin, a chemical often branded as the ‘love hormone’, can also induce negative memories. I remember spending a good 5 to 6 hours reading the paper and writing this piece.

So did it feel good to have made the newspaper for the first time? While I was relieved that my writing was deemed good enough for print (after several rounds of editing and rewriting – the first blow is never half the battle), the blogger inside me felt betrayed. As a blogger I was used to wrote long stories on subjects I was deeply familiar with. Here I was writing about oxytocin, a hormone I knew nothing about, in the tersest way possible. This is how science blogger extraordinaire Ed Yong covered the same research, using over 820 words. My 130 words looked stale in comparison. They were missing depth, context and nuance.

But before judging the shortie for what it isn’t, I should have realized that NRC Handelsblad is not the internet. Unlike Ed, a newspaper doesn’t have the luxury of unlimited white space. NRC publishes five science pages a week (and a larger science supplement in the weekend), so every inch of paper should be an inch well spent. A column full of shorties contains a diverse mix of science news in a short amount of space. They’re like chocolate sprinkles on a daily science dessert. And in a sense, their brevity is their forte (‘it’s not a bug. it’s a feature!’). Its length reflects its importance, relative to the other articles of that day. This kind of hierarchy is hard to come by on a blog, where every post seems as important as the next.

That said, short articles still make me uncomfortable. My biggest worry is that they contain enough information to pique a reader’s interest, yet not enough to satisfy her curiosity. Often I get questions from readers that were covered in the original research, but which didn’t fit into my story. And there’s always the danger of oversimplification. It’s impossible to trim down a research paper of 6 pages full of details and caveats to a hundred words without cutting some corners. Therefore, in my ideal newspaper, the last line of each short piece would read ‘click here to read more’.

If short stories made the blogger inside of me cringe, he should feel comfortable with the large feature articles that I’ve written, right? Yeah, that’s not true either. I’ve found that even in 2,300 words, there are always opportunities missed, details left out and ground left uncovered. A paper I mention might be a single part a much larger body of research. A person I interviewed might feel misquoted because I highlight key quotes from an hour long interview. Online, I could have linked to papers, additional sources, graphs and transcripts. Offline, the article is the article.

Forward-looking mainstream media organizations should recognize the potential of online reporting. I try to sneak in links into the newspaper whenever I can, but I’d like to see the integration of offline articles and online resources carried much further. And while I’ve been dipping my toes in this cross pollination already, with some of my blog posts becoming newspaper articles, and vice versa, I hope there’s a bigger role for me and other young bloggers to play in this transition in the future.

The story of a frog-killing fungus also became a story in NRC Handelsblad. Photo by Brian Gratwicke

Online-offline discussions aside, I am glad I had the opportunity to work in MSM. I acquired journalistic skills that I didn’t even know existed when I was a rogue blogger. The first time I called a scientist to interview them about his research, I was nervous. The interviews went horrible. In hindsight, I was trying to impress my conversation partner more than I was asking relevant questions. ‘Hey, I have a MSc degree in biology, I know what you’re talking about’. It took some time before I realized that it’s all right to ask basic questions.

This is but one example of many, and there is still much left to learn. Blogging made me a writer, but it is thanks to editors and colleagues, who were honest enough to criticize and give advice when it was necessary and kind enough to guide me as I stumbled onwards, that I became a better one.

Next week I’ll return to regular evolution blogging. Here’s to another year of genes, Neandertals, dinosaurs, Yeti crabs, ecology and evolution!

Protobalistum imperiale from around 50 million years old of Bolca, Italy.

Like most evolutionary tales, this one could have started on the Galapagos Islands. Instead we find ourselves in an ancient sea, near the end of the Devonian, 360 million years ago. A mass extinction has struck life underwater. The armoured placoderms, once an abundant class of fishes, have gone extinct. Other groups of fishes have been decimated and are struggling to survive. But, as a Dutch saying goes, one man’s death is another man’s breath. For the ray-finned fishes (fishes whose fins are supported by a ray of spines) this time of trouble is a time of opportunity. With their direct competitors out of the way, they are free to evolve into a multitude of shapes and species, from stream-lined hunters to plump grazers. The fish are dead. Long live the fish!

Fast forward to today. With over 23.000 species alive, ray-finned fishes are the largest and most diverse group of vertebrates of this day. Their rapid evolution after the Devonian mass extinction was the turning point that ensured them their evolutionary success. Biologists have come across similar explosive patterns of diversification across the tree of life, and call them ‘adaptive radiation’. Adaptive radiations are evolution’s way of hitting the jackpot. The payout is twofold: a single lineage spins of many new species (speciation) that adapt to diverse ways of life (adaptation).

A species may radiate when it finds itself in an environment where plenty of ecological opportunities await exploitation, such as when it has just colonized an island or lake, or after mass a extinctions. Darwin’s Galapagos finches are the iconic examples of such an adaptive radiation. A single ancestral species arrived to the Galapagos archipelago and split into a dozen species, each one adapted to the local circumstances of its island. The finches with the heaviest beaks eat the largest seeds, whereas those with slender, sharp beaks ones that catch insects.

The beaks of Darwin's finches are adapted to different food sources.

These little finches have been studied in great detail ever since Darwin first set foot on the Galapagos, but biologists still know little about how adaptive radiations unfold. Some think that species and their different shapes evolve in a single burst. This explosive diversity is then followed by periods of relative stability. Others disagree, and think that radiations occur in stages. They argue that new species first adapt to their environment or habitat, by changing their body shape and size, before they adapt to a specific diet or way of life, by changing their skulls and jaws. In this model, wings evolve before beaks, fins before mouths and legs before teeth.

Biologists have argued both ways, but neither side has delivered convincing evidence so far. This is where fossils of ray-finned fish come in. The biggest advantage dead fish have over living finches is that we know both their past and future. This makes it possible to track their radiation through time and see whether their different shapes evolved in steps or not. The fossil record of ray-finned fish is rich, and they underwent multiple adaptive radiations. For the first time after the Devonian mass extinction, and a second time at the end of the Cretaceous period (around 65 million years ago), when a massive asteroid struck earth and killed off many species of animals, including the dinosaurs.

Lauren Sallan and Matt Friedman investigated both these radiations by digitalizing the shapes of 69 Devonian fish and 304 fish from the Cretaceous. They first mapped several landmarks onto their skulls and skeletons, such as the positions of their jaw joints and fins. In the next step they determined which axes of these landmark maps explain the major differences between fish. They then analyzed how these differences changed through time.

Ray-finned fish evolved their heads before tails. Skull diversity starts to increase right after the Devonian (orange range), in the Tournaisian (darkest green). The diversity of body shapes lags behind.

Sallan and Friedman found that for fish from both era, heads evolved before tails. The heads of Devonian fish started to diversify right in the aftermath of the mass extinction. Some skulls became longer and flatter, while skeletons lagged behind. Only after a couple of million years did some evolve the shape of flat spades, in addition to the classical torpedo-shape. The Cretaceous fish also went through a head-first phase. Their skulls grew more elongated and streamlined before the main extinction event at the end of the Cretaceous, and long before their bodies followed suit.

This head-first trend in the evolution of ray-finned fish contradicts the biological big bang model of adaptive radiations, and it is a direct reversal of the idea that radiating species first adapt to their habitats. So why would fish evolve their skulls before anything else? The answer seems simple: to bite, crush, rip, nibble and suck. Certain niches might have been left vacant after the Devonian and Cretaceous mass extinctions, and ray-finned fishes evolved the jaws to exploit them. Large predatory fish died out after the Cretaceous extinction for example, making room for creatures such as the sword-fish like Blochius to evolve.

But skulls did not only evolve earlier, they also reached their peak diversity in a shorter span of time than body shapes did. This suggests that it’s also easier to evolve most variations on a skull than it is to evolve most body forms.

Blochius was a swordfish that lived 56 to 34 million years ago, in what is now Italy.

Friedman and Sallan are careful to generalize their findings to other adaptive radiations. “The real world is more complicated than any model”, is what they write in their final paragraph. A lot more studies need to be done before either theory can be discounted. That said, Sallan thinks the head-first model has the potential to explain a large portion of adaptive radiations. “There’s anecdotal evidence for many groups: lungfishes, sharks, birds, mammals, insects and even worm lizards“, she says. “And in a way it makes sense. When an animal is faced with limited food relative to the total population size, which is likely in a successful group, it has two choices. It can either find a new resource, or move to a new habitat and hope the same resource is there. Changing diets in probably easier and more likely to be successful.”

Do these findings mean that shifts in behaviour are the ultimate drivers of adaptive radiations? A bird first has to change its diet before it can change its beak, after all. Sallan thinks this might be the case. “Animals can be plastic in what they eat”, she says. “You hear about deer eating squirrels, squirrels eating birds, etcetera. Marginal dietary behaviors could turn out to be beneficial and some individuals might be better at exploiting a new food source than others, due to variation already present in the population. Directional selection then takes hold. So basically, you never know until you try!”

So white, so hairy.. I want to pet them!

Irene is a freelance illustrator who has specialized in nature and history. Every week, she draws an animal that has been in the news for the kids section of NRC Handelsblad‘s science supplement. You can find a selection of her illustrations here.

I love how realistic, yet playful and full of character these Yeti Crabs are. Judging from its carapace, the depicted species seems to be Kiwa hirsuta (which is the hot vent variety, not the species that lives near cold seeps).

I fell in love with Yeti Crabs from the moment I learnt about their peculiar existence below the sea. I’m delighted that the first piece of art I bought myself features these weird and wondrous creatures.

This bumblebee bat could be the smallest mammal in the world.

Isolation can be a blessing. I am most productive when I’m not connected to the web. If I’m writing in a train or plane, severed from the thoughts of others, it is easier to capture my own trails of thought and let them expand. Don’t get me wrong, my inner writer loves the internet. It’s where I go to learn about new research and get inspired by scientists and writers from all over the world. With every click I uncover a new idea or story, waiting for a mind to latch onto.

And this is why my inner writer loathes the internet. On the web it seems as if every idea has been thought of before and every story has been retold countless times. In an echo chamber filled with a thousand voices, it can be hard to find your own.

In nature life is not much different. Every animal, from the smallest bat to the largest cat, has to find a niche and voice of its own. Take Kitti’s Hog-nosed Bat, or the bumblebee bat. With a length of just 3 centimetres (1.2 in), this cute creature is a strong contender for the title of ‘smallest mammal of the world’. The bumblebee bat and occurs in two separate populations in Myanmar and Thailand. Its total natural range is restricted to a mere 2,000 square kilometres (770 square miles). For comparison: this is a region half the size of Rhode Island, and a little smaller than Luxembourg.

The natural range of the Myanmar (dark blue) and Thai (green) populations of bumblebee bat.

The Myanmar and Thai bumblebee bats are indistinguishable by eye, but not by ear. The echo calls of Myanmar bats have a somewhat higher pitch. The consequences of this difference extend beyond mere echolocation, because bats also use their echoes in personal communication. In some bat species, bats even prefer to mate with partners with similar echo calls. If the same is true for bumblebee bats, a small difference in echo frequency could have driven a wedge between the two populations in the distant past.

How so? Suppose that by chance, two groups arise within a population that each perceive the world in a slightly different way. If this small difference affects their choice of partners (such as with the bumblebee bats and their echoes, perhaps), these differences and preferences are passed on from generation to generation, become amplified and get locked in, up to the point where members of the two groups no longer recognize each other as potential mates. When they have stopped interbreeding, they have taken the first steps towards becoming different species.

Biologists have come up with several names for this process, such as ‘speciation through sensory drive’, but considering how these species-to-be ignore each other, I think ‘speciation through mutual ignorance’ is a better description. While it this makes for an attractive story, it is not the only explanation for the different echo frequencies of bumblebee bats. After all, these differences could also have evolved after the Thai and Myanmar bat populations became separated.

The Khwae Noi River (Kwai River) is part of the natural habitat of the bumblebee bat.

An international team of biologists, equipped with ultrasound detectors and mist nets, set out for the forests of Myanmar and Thailand to confirm whether bumblebee bats became isolated by ignorance or not. The team caught and released over 700 bats from Myanmar and Thailand, and took punctures of their skin or wings. A DNA analysis of these samples revealed that the smaller Myanmar population split from a larger Thai population around 400.000 years ago so. At such a coarse resolution, it is only possible to take a bat’s eye view of their evolutionary history. The researchers could only conclude that the Myanmar population likely originated from a small number of Thai bats, but not how or why they became isolated.

They therefore decided to ‘zoom in’ on the colonies that make up the Thai population, to see if they could catch isolation on the wing. Even though the Thai colonies form a continuous range, the team did find an abrupt change in echo frequency in the southern colonies. Southern calls had an increased frequency of 3 kHz, compared to the calls of bats from the north. This acoustic boundary was clear and sudden, but it wasn’t reflected in the DNA of the bumblebee bat. On average, colonies on both sides of the boundary did not differ more from each than other neighbouring colonies did.

One piece of DNA formed an exception. Bats from the north side of the echo border carried a different version than bats from the south. This stretch of DNA is located near a gene that is involved in producing hair cells in the bat’s hearing organ, so it might have played a role in the evolution of the different echoes of the Thai and Myanmar bats.

This is a CT scan of a complete skeleton of the bumblebee bat scan, provided by Digimorph.

The skewed distribution of this ‘echo location gene’ suggests that it provides an advantage of some kind. But what? Enter a second species of bat: Himalayan Whiskered Bat, or Myotis siligorensis. This bat is of a similar size and catches similar prey, but more importantly: it emits its echoes along the same bandwidth as the bumblebee bat. This could give problems if a bumblebee bat and whiskered bat would be out hunting and echoing in the same region. Their echo signals would interfere, and they would be unable to determine their distance to their prey.

The bats could avoid jamming each other’s frequencies if one of them would shift the pitch of its echo. Indeed this seems to be what happened to the bumblebee bats in the south of Thailand and in Myanmar. Recordings revealed that their caves were also frequented by whiskered bats, whereas in the north of Thailand not a whisker was seen.

The researchers conclude that it is unlikely that echolocation was the driving force behind the isolation of Myanmar and Thai bats. Given the large distance (for a bumblebee sized bat, at least) between the two populations and that Thai bats are genetically the most diverse, they suggest that a few bats were swept from Thailand to Myanmar by storm, cyclone or typhoon or perhaps one of the strong winter monsoons that occur about once every 100.000 years.

A handful of bumblebee bats, tumbling in the storm. As the winds die down, the creatures find themselves far away from home. From the woods sounds an all too familiar shriek, from an unfamiliar source. The bumblebee bats know what they must do. Time to find a voice of their own.

The hairy claws of these crabs are covered with bacteria. With every swing of their arms, they mix up the water column and provide their homegrown bacteria with additional nutrients. The submersible team that discovered this new species shot this amazing video of the gardening crabs in action:

These white and hairy crabs are a new species of ‘Yeti crab’. The species received the formal name of Kiwa puravida in PLoS ONE article last week, meaning ‘pure life’, which is a common saying in Costa Rica.

The first Yeti crab (Kiwa hirsuta) was discovered in 2006 off the coast of Easter Island. The team that discovered this crab already noticed that its bristled claws were covered with bacteria. They only collected a single specimen however, limiting the opportunities for a thorough investigation of the association between bacteria and crab. The nature of their relationship remained a mystery.

Until now, that is. Not long after these first Yeti crabs were found, more Yeti’s revealed themselves, over 6,500 kilometres away from Easter Island. This new species was discovered thanks to one submersible pilot. “Gavin Eppard is one of the pilots of the ALVIN submersible. He was in the sub when he spotted the new species of Yeti crab, standing on a carbonate block waving their claws back and forth”, says Andrew Thurber, one of the authors of the recent paper. “Gavin was on the original cruise that discovered the first Yeti. He immediately recognized that this was something new to science.”

The new species Yeti crab: Kiwa puravida (missing two walking legs, sadly).

The submersible team returned to collect more dancing crabs after this initial discovery. All the crabs were found waving their arms near cold seeps, where methane and hydrogen sulfide escapes from the ocean floor. You might think such environments are inhospitable places for life, but several species of bacteria thrive near such seeps. They liberate energy from methane and hydrogen sulfide by stripping the electrons from these molecules and passing them on to oxygen.

These species can form dense mats around cold seeps, but they also grow on the Yeti’s claws. Thurber and his colleagues found DNA belonging to two bacterial families that eat methane and hydrogen sulfide, respectively. Thurber thinks that the crabs perform their dance to make sure that the bacteria always have access to both oxygen from the ocean water and methane or sulfide from the seep. If the crabs would stand still, the symbiotic bacteria growing between its bristles could locally deplete either resource. But by waving their arms, Yeti crabs mix water and seepage, keeping bacterial productivity high.

The symbiotic bacteria of the Yeti crab were most similar to bacteria that live near hydrothermal vents and on the creatures that live there, such as the vent shrimp. Hydrothermal vents are similar to cold seeps, so Thurber suggests they disperse through the oceans using vents and seeps as stepping stones.

While these findings indicate that Yeti crabs grow their own food, Thurber and his colleagues also show that the Yeti’s harvest it. Thurber didn’t observe them snacking on bacteria in the wild, but he did film captured crabs that used their mouth parts to feed from their claws. “I initially put them in the aquarium to see if I could get them to dance. They wouldn’t, making me think that they sway their arms in response to the movement of water or a chemical queue. Instead they ended up feeding off their bacteria, which I was lucky enough to catch on film”, he says. Without seepage to farm in, this poor fellow probably went hungry:

The Yeti crabs themselves also contain traces of feeding symbiotic bacteria in the wild. Carbon comes in a heavy (C13) and a lighter (C12) variety. The enzyme that plants and bacteria use to derive energy from sunlight selects the lighter form of carbon slightly more often than the heavy form. However, the enzymes of microbes that consume methane or sulfide have a very strong preference for C12 over C13. As a result the ‘carbon signature’ of methane and sulfide munchers will be lighter than that of bacteria that obtain energy from sunlight. The carbon profile of the Yeti crab matched that of its symbionts, indicating that they are its main food source. The fatty acid distribution of Yeti crabs mirrored that of its bacteria in a similar manner.

All in all Thurber et al have made a compelling case that Yeti crabs grow and harvest their own bacteria. But don’t these crabs ever get tired from dancing? Thurber: “The crabs have to use energy to swing their arms back and forth – so by doing so they must gain more energy through their symbionts than they expend by waving their arms. I don’t think they get tired.”

The dancing yetis also seem to have more than enough energy to engage in some yeti wrestling from time to time. The ALVIN team captured a video of what seems to be two Yeti crabs fighting for a nice spot in the seep. The challenging crabs had recently molted, so perhaps it wanted a good position to regain its bacterial covering. But Thurber points out that this confrontation could also be a mating display, as crabs are known to mate after molting. Strife or love, you decide:

The Yeti crab’s rise to internet fame was swift. Proof: a compilation of crabs dancing to different pieces of music.

Who is to blame for this wave of extinction? While climate change, pollution and habitat destruction certainly play a supporting role in this amphibian drama, biologists now agree that a fungus is the major villain. The fungus in question is chytrid fungus, and bears the name Batrachochytrium dendrobatidis, or Bd for short, and causes a disease called chytridiomycosis.

This Limosa Harlequin Frog has died from chytridiomycosis. Notice the reddening of the skin and the lesions on its belly.

What Bd does to an amphibian’s skin is not pretty. The fungus grows right within the cells of the skin. When it has produced enough spores, they burst out of the cells and re-enter uninfected skin cells. This cycle of growth and infection causes lesions and a premature shedding of the top layer of the skin. Lee Berger, who first identified Bd in sick and dying frogs in 1998, wrote that “these specialized adaptations suggest that B. dendrobatidis has long evolved to live in skin.”

This seems strange. Bd only became a problem somewhere in the second half of the twentieth century. Analyses of museum skins show that Bd was absent from most affected localities prior to the 1970s. It has spread over the world at an alarming rate since then, killing frogs, salamanders and newts wherever it goes. But if Bd has really existed for a long time and kills its hosts with such vigour, shouldn’t it have burned itself out by now?

Biologists have come up with two general explanations for the sudden emergence and spread of Bd in the 20th century. Some have suggested that environmental changes make amphibians more susceptible to Bd. Others have proposed that Bd is a novel disease to which amphibians have no resistance. These two hypotheses are far from exclusive, and come with many flavours in between.

Feeling at home in skin

When the Bd genome was sequenced in 2006, biologists hoped it would reveal how Bd became a slayer of frogs. But without similar genomes to compare the Bd genome to, it was hard to draw conclusions about what makes Bd special. The chytrids, the branch of fungi that Bd belongs to, turned out to be particularly understudied.

Conventional chytrids are quite harmless. They are microscopic fungi that usually live in water or wet soil where they degrade leaves and other organic material. The closest known relative of Bd is Homolaphlyctis polyrhiza (or Hp). This fungus was isolated from leaf litter in Maine by Joyce Longcore. Erica Bree Rosenblum, evolutionary biologist at the University of Idaho, and her colleagues have now sequenced the DNA of this leaf muncher, to see what makes it different from Bd.

Rosenblum discovered several types of genes that are abundant in the Bd genome, but not in the Hp genome. The proteases were on of them. Proteases are like molecular scissors. These enzymes recognize, cut and cleave other proteins. Rosenblum found that three different protease families have expanded in the Bd lineage. They have between between four to ten times as much members as the same families in the Hp genome.

Each of these petri dishes is filled with skin flakes from cane toads. The left dish is untreated, the second dish has been treated with Hp, the third dish has been treated with Bd.

Fungi that infect human skin or nails are known to carry similarly large and diverse sets of protein slicers. They help the fungus to invade tissues and obtain nutrients by breaking down the proteins and cells of its host. It’s likely that the numerous proteases in the Bd genome also play a role in the colonization of amphibian skin.

Another abnormal group of genes in the Bd genome is the crinkler family. Crinklers have never been found in other fungi. They were originally discovered in oomocytes, which are single-celled organisms that infect plants and cause diseases such as late blight and sudden oak death. True to their name, crinklers cause the leaves of the plants they infect to crinkle. It is unknown what these proteins do to amphibian skin and whether they are important for infection, but their presence in the Bd genome is certainly intriguing.

Another group had described these Bd-crinklers earlier. They proposed that crinkler genes hopped from oomycetes to Bd and that this transfer of genes possibly led to the Bd-epidemic. Sophien Kamoun, who works with oomycetes and discovered crinklers in 2003, thinks that this conclusion is premature. “There are 62 crinklers in the Bd genome and they only resemble oomycete crinklers on a general level. If it is true that oomycetes are the source of the crinklers, they must have been transferred a long time ago.”

Rosenblum says the origins of Bd proteases are similarly ancient. “The Bd protease families expanded recently on an evolutionary time scale. This still means that most expansions are a millions years old. They certainly didn’t happen in the last 50 years.” So while the presence of crinklers and proteases might explain how Bd evolved to live in skin, but not why it became a global menace. These proteins loaded the gun, but they didn’t pull the trigger.

Conquering the world

I’ve painted a grim picture of Bd so far, but the truth is that not every strain of Bd is a global killer. In a recent PNAS paper, scientists describe two lineages of Bd from Switzerland and South Africa that are genetically distinct from the globally occurring lineage that is killing amphibians worldwide. They’re also not nearly as lethal. The researchers infected tadpoles with the South African strain and found that more than 7 out of 10 of them survived. Tadpoles that were exposed to global varieties of Bd were much worse off. In the most severe cases, less than 20% survived infection.

Isolated pockets of Bd such as those in South Africa and Switzerland have likely existed for a long time. Geneticists have uncovered some clues as to how a global killer fungus could emerge from such local varieties. To see what they found, we first have to take a short trip into basic Bd genetics. Bd is a diploid fungus, which means that it has two copies of each chromosome, just like humans have. Diploid organisms can thus carry two different versions of any given genetic variant, a situation which is known heterozygosity. When the same genetic variation is present on both chromosomes, this is called homozygosity.

Genomes of sexual organisms are a mixed bag of homozygous and heterozygous variants. But not that of Bd. Its genome is way more heterozygous than is normal. “The simplest explanation for this pattern is that the hypervirulent lineage of Bd is the product of two undiscovered parents”, says Matthew Fisher a geneticist from Imperial College London and co-author of the PNAS paper. In other words, the killer lineage of Bd is a hybrid fungus. It has received two different sets of chromosomes from its parents, which explains the high degree of heterozygosity in its genome. “Sex is rare for this species. But when it happens, a new strain with new properties might emerge”, says Fisher. “We think this is how hypervirulent Bd originated, somewhere in the 20th century.”

Not every frog is susceptible to Bd. Bullfrogs tolerant to the disease, but they can still spread it. Bd was introduced in Kent (UK) from North American bullfrogs.

Fisher thinks the international trade in amphibians is directly responsible for the emergence of Bd. “From the 1950s onwards the African clawed frog (Xenopus laevis) was shipped all over the world, first as a pregnancy test and later as a laboratory animal. This global trade in amphibian increased the possibility that two divergent lineages of Bd come into contact with each other. I’m pretty sure that hypervirulent Bd wouldn’t have evolved without the amphibian trade. We can clearly see the ongoing effects of this trade as it spreads the killer lineage ever more widely.”

Fisher’s team used the genetic relationships between the different lineages to date the emergence of Bd to 35 to 257 years ago, depending on which genome segment they analysed. Rosenblum points out that this analysis depends on a number of assumptions, each of which could affect the outcome. “My suspicion is that our next wave of analyses will suggest these genetic transitions are more ancient than that”, she says. Fisher admits that it is hard to argue what the exact emergence date is. “But since it underwent its spread in the 20th century, we think it is likely that the recombination event took place in recent history.”

A firmer answer to the questions where and when Bd evolved will have to await the sequencing of more genomes, from other lineages of Bd and from additional chytrids. Each genome will provide another piece of the puzzle. There are still corners of this world where Bd hasn’t penetrated yet, such as Madagascar. The sooner we understand this amphibian scourge, the better we can prevent its spread. The frogs will thank us for it.

We vertebrates work for our O₂. Whether we’re a fish or antelope, we all have gills and lungs to filter oxygen out of air or water. We also have beating hearts to transport oxygen-rich blood to the most distant corners of our bodies. But not the lancelet. This little fishlike creature breathes directly through its skin. The lancelet does have gills, but it only uses them to filter food particles from the water, not oxygen. It doesn’t even have a heart to direct the flow of its blood.

The way vertebrates and lancelets handle oxygen also differs on a molecular scale. We vertebrates have evolved a whole suite of proteins for carrying and storing oxygen that the lancelets lack. The most well-known member of these proteins is hemoglobin, which makes up 95% our red blood cells. Hemoglobin is a perfect oxygen transporter. It takes up oxygen where its concentration is high (lungs) and releases it where concentrations are low (muscles and other organs). We also have globins that specialize in storing oxygen, such as myoglobin our muscles and cytoglobin in our brains.

The lancelet has neither heart nor hemoglobin.

The origins of all these oxygen-manipulating tools can be traced back to a dramatic event in our evolution. Almost half a billion years ago, not long after the lancelet and vertebrate lineage had parted ways, the entire genome of the vertebrate ancestor was carbon copied by accident. Twice. Our distant ancestor thus had four times as many genes as before. This opened up evolutionary pathways that were closed before. How so? Imagine your Lego collection quadrupled in size. Not only can you now build a larger castle, the extra bricks also bring added flexibility. You can combine them in new ways, while leaving the core of the castle intact. It’s much the same for duplicated genes. Their redundancy allows them to specialize, divide labour and evolve new functions.

In a paper that was published last month, scientists show that our globin genes were born from these two rounds of genome duplication. The team, lead by Jay Storz from the University of Nebraska, first retrieved all the globin sequences of lancelets, sea squirts and fifteen different vertebrates (birds, lizards, fish and mammals) and determined the evolutionary relationships between them.

They found that all vertebrate globins occupied four branches in the globin family tree. They were myoglobin, cytoglobin, hemoglobin and GbY, a globin that has only been found in reptiles and the platypus. These four lineages corresponded to a single lineage of lancelet globins. While such as a 4:1 distribution fits the double genome duplication scenario, the history turned out to be a bit more complex.

The genetic neighbourhoods of the three globins are similar - not identical.

Storz and his colleagues reasoned that if the four globin lineages really arose through genome duplications, their genetic neighbourhoods should look alike. After all, all the genes of our ancestor were copied in one go. As genes tend to retain their relative positions over time, the genetic neighbours of the copied globins families should be similar. Of course they won’t be identical after 500 million years of evolution. Genes are lost, gained and reshuffled all the time time. Nevertheless, the ‘neighborhood signal’ (geneticists call it synteny) is a strong one, and should still be recognizable millions of years later.

The team found three of these globin-containing neighbourhoods, spread out over different chromosomes. They dubbed them Mb (myoglobin), Cygb (cytoglobin) and Hb (hemoglobin). GbY turned out to be a more recent addition to the hemoglobin family rather than the fourth globin type. The researchers discovered that this fourth globin was missing altogether. Its former neighbours are still there, on our nineteenth chromosome, but the globin itself went extinct a long time ago. For want of a globin, the researchers named this region Gb^-.

The researchers show how the initial duplication produced the Mb/Cygb and a Hb/Gb^- cluster. This is an interesting split, as the proto-hemoglobins (the blood globin) evolved to become oxygen transporters while myo- and cytoglobin (the muscle and brain globin) became oxygen storage proteins. The authors write that “the first round of WGD may have initially set the stage for the physiological division of labor between the evolutionary forerunners of [myoglobin] and [hemoglobin] by permitting divergence in the tissue specificity of gene expression.” In other words, it was the genome duplication that allowed these globins to evolve specific functions in separate tissues.

After 500 million years of evolution, lancelets are small, mud-dwelling filter feeders. We vertebrates have evolved into free-roaming grazers, predators and 180 tonne heavy filter feeders. It’s thanks to the combined evolution of a complex circulatory system (our hearts and gills/lungs) and an elaborate oxygen transport system (the globin family) allowed our ancestors to become larger and live a more active lifestyle than our distant cousins. Hemoglobin is the key to a healthy heartbeat indeed.

Welcome to the cell!

Inside the machine

Can you hear the hum? That’s the sound of biochemistry. Inside the cell, thousands of proteins are carrying out their tasks with clockwork precision. Cooperation is key here. Some proteins mesh together like gears: they depend on each other to function. Gemma Atkinson explains how such protein pairs co-evolve, hummingbird and flower as an analogy.

Gears don’t turn themselves. We need a source of energy for our machine. We’re in luck: Christopher Dieni describes an enzyme that delivers sudden bursts of energy to keep the engines running. What’s more, this same enzyme can keep frozen frogs alive and assists in releasing insulin. Multipurpose design indeed!

While the main product of our cellular machine is life, there’s no reason we couldn’t tweak it to produce more. Lab Rat explains how we can let algae produce bioplastics, using a bacterial trick.

Woah.. Did you feel that rumble? Our cell is on the move! It unrolls its sticky proteins along the way to pull itself forward. The Leading Edge would like to study these sticky proteins in his or her test tube, but as it turns out, they prefer to remain attached to the surface instead.

Gremlins!

All machines are plagued by system failures, and sometimes even downright sabotage, and the cell is no exception. Viruses are the most notorious hijackers of cellular machinery. They usually come and go, but sometimes they become part of the machine themselves. EE Georgi describes how this happens.

Some gremlins cause more damage than others. HIV is one virus that certainly has earned its reputation of malevolence. EE Georgi joins in with another post, on whether gene therapy could eradicate this virus.

Bones can tell us about gremlins past. Lesions and pits in ancient bones sometimes represent the traces of ancient infections. Kristina Killgrove writes about palaeopathological evidence that the ancient Romans already suffered from Syphilis.

Connor Bamford continues along this line, and wonders if dinosaurs ever got the measles. Yes, he says! Or measle-like viruses, in any case. How do we know? Some dinosaur vertebra showed classical signs of Paget’s disease: remodeled bone and an increase in the amount of red blood vessels.

That’s it for this month’s edition of The MolBio Carnival. I hope you enjoyed this peek inside the machine, and you are welcomed to submit your best molbio blog articles to the next edition, which will be hosted by Connor (yes, that’s ‘dinosaur measles’ Connor!) from Rule of 6ix.

Images:
Crowded cell by TimVickers.

The lancelet resembles a lancet, a double-bladed surgical knife.

Few people will find delight in the dredge that is hauled from the ocean floor. But for the British biologist Ray Lankester, such hauls represented an unseen world of wonder. In his Diversions of a Naturalist he describes how an encounter with a creature from the bottom of the sea that filled him with so much joy that he completely forgot about his sea-sickness:

“I remember lying very ill on the deck of a slowly lurching ‘lugger’ in a heaving sea off Guernsey, when the dredge came up,and as its contents were turned out near me, a semi-transparent, oblong, flattened thing like a small paper-knife began to hop about on the boards. It was the first specimen I ever saw alive of the lancelet, that strange, fish-like little creature.”
~ Ray Lankester (1915)

Lankester had good reasons to be excited. For him and other naturalists, the lancelet was not merely another bottom dweller; it was a creature with the potential to resolve the ancient origins of the vertebrates, group of animals with a spine. But that’s running ahead of the story. What kind of creature is the lancelet, to begin with? The German zoologist Pallas was the first to describe the lancelet in the scientific literature. He worked with a preserved specimen, and mistakenly classified it as a slug in 1774. Perhaps he would have recognized how un-slug like the lancelet really is if he had seen one alive, wiggling and hopping about.

The 19th century naturalists Costa and Yarrell did have this opportunity. They were also the first to note that the lancelet resembles a vertebrate. Not only does the lancelet have a rudimentary spine that runs from their head to their tail, they also have segmented muscle bundles and a tail that extends past their anus, just like other vertebrates have.

The drawing of the lancelet as it appeared in Yarrell's History of British Fishes.

Lancelets and vertebrates share a similar anatomy, but a lancelet is not a vertebrate quite yet. There is still a huge gap between the complex tissues of vertebrates and the simple organization of their lancelet equivalents. The lancelet’s nerve cord is slightly swollen near its head, but this bulge is not yet a brain. Lancelets have contracting blood vessels that pump around blood, but no central heart. And then there are the organs that they lack entirely, such as a skull or a pair of eyes. Ernst Haeckel was right when he wrote that “the lancelet differs more from the fishes than the fishes do from man”.

As a creature on the border between vertebrate and invertebrate, biologists first regarded the lancelet as a ‘primitive vertebrate’ and later as ‘closest living cousin of vertebrates’ (and other almost-vertebrates, such as hagfish). It was clear to all that these little paper-knives were important creatures for studying the origins of the vertebrate lineage. No one believed that the lancelets were the unchanged descendants of some proto-vertebrate, but biologists reasoned that since all traits shared between lancelets and vertebrates have been inherited from a common ancestor, the lancelet still offered a glimpse of what these distant ancestors might have looked like.

Fossil unearthed in Canada and China show that there is some truth to this logic. The ancient Pikaia already had a flexible proto-spine and segmented muscles, resembles the lancelet in these regards. Pikaia is not a direct ancestor of either vertebrates or lancelets, but palaeontologists agree that they represent some of our earliest relatives.

In short, for more than a century, all the evidence seemed to indicate that the family ties between lancelets and vertebrates were close. Until 2006, when a team of molecular biologists drove a chain-saw into the stem of the vertebrate family tree. Their DNA-analyses revealed that not lancelets, but sea squirts and their ilk (the tunicates) are the closest living relatives of vertebrates. Common zoological sense turned out to be wrong. Somehow these shapeless sacks, hardly recognizable as animals, are closer related to us than the mobile and gracile lancelets.

The sea squirt Ciona intestinalis is a closer relative of yours than the lancelet is.

To be fair, biologists long knew that sea squirts occupy a branch close to the vertebrates in the tree of life. Adult sea squirts might be stationary filter feeding tubes, but their larvae look more like tadpoles than anything else. It was the Russian embryologist Alexander Kowalevsky who first noted that young sea squirts come complete with a head, tail and a proto-spine in 1866.

The lancelet genome, sequenced in 2008, confirmed that tunicates are the sister lineage of vertebrates and that lancelets branched off first. This redrawn family tree opens a whole new can of questions. If sea squirts really are our closest non-vertebrate cousins, how come we look so different from each other as adults?

Our genes hold some clues. The genomes of both tunicates and vertebrates show signs of widespread, but different kinds of, genetic upheaval. The first evidence that the genomes of the first vertebrates differed drastically from those of their forebears came from the observation that some of their gene families are overrepresented, often following a 4:1 ratio.

Sea squirt larvae (bottom) resemble tadpoles (top) in their earliest stages of development.

Take the famous Hox genes. These genes determine the shape of animals by regulating which segments develop into what kind of structure, such as a rib. Hox genes are arranged in clusters and are ‘read’ in a strict order during the development. Humans, mice, and chickens have four of these clusters, whereas invertebrates such as lancelets only have one. Confronted with this pattern again and again, biologists concluded that the entire genome of the ancestral vertebrate must have been duplicated twice, giving rise to a fourfold increase in genes. These two rounds of duplication were followed by massive gene losses where redundant and harmful copies were purged from the genome. Many biologists think that the genes that remained opened up the road to an increase in complexity, as genes acquired new roles and functions. More on this in a later blog post.

The genomes of sea squirts tell a different story. Instead of gaining genes, they have lost many of them over time. Of all the Hox genes that are present in the lancelet genome, 25 are missing from tunicate genomes. The remaining Hox genes have been shuffled around, generating scrambled versions of the traditional Hox clusters. As a cause or consequence, the development sea squirt larvae also proceeds in a way that is different from what we know of lancelet and vertebrate embryos. Their genes and genomes also seem to evolve at a higher rate and accumulating changes faster than the genes of lancelets and vertebrates do.

Vertebrates and tunicates thus seem to have evolved in completely opposite directions. Where the tunicates lost genes, the vertebrates gained them. As tunicates grew more simple and derived, the vertebrates became more complex. It’s thrilling to realize that their starting point was the same: a strange, little fish-like creature, not unlike the humble lancelet. If only it were possible to travel back 500 billion years in time on a lurching lugger, dredging the Cambrian oceans seeing what wonders come up.

These plague victims were excavated from the East Smithfield burial grounds between 1986 and 1988.

The plague bacteria that swept through medieval Europe had been declared extinct just over a month ago. A quick google search reveals articles with headlines such as ‘Medieval plague bacteria strain probably extinct’ and ‘Black death strain extinct’. Few writers mentioned that the original research on which they reported was a technical paper first and foremost, and not a comprehensive investigation into the evolution of the Medieval plague.

It’s ironic that a study that was published last week shows that the Black Death is far from extinct. On the contrary. The plague bacteria that still infect thousands of people every year trace back their ancestry to the plagues of the fourteenth century. Interestingly, this new research was carried out by the same scientists that published the other plague study in August, so what has happened here?

In their first paper, researchers lead by Johannes Krause and Hendrik Poinar announced that they had successfully extracted and sequenced some DNA of a medieval strain of Yersinia pestis, the bacterium that causes plague, from the teeth of a dozen Black Death victims. These remains had been excavated from the East Smithfield burial grounds in London by the Museum of London Archaeology before. During the height of the London plague epidemic, between 1348 and 1349, thousands of bodies were buried at East Smithfield.

Since DNA degrades over time, the researchers used modern Yersinia DNA as bait to fish out the fragmented medieval sequences ( a technique called ‘targeted enrichment‘). The team found enough ancient DNA in this way to reconstruct a plasmid, a small ring of DNA, that belonged to medieval Yersinia. The paper is full of calibrations, controls and corrections that the researchers applied to make sure that their DNA wasn’t contaminated or damaged.

John Norden's map of Londen (1593), with the East Smithfield cemetery coloured red

So where did the conclusion that the medieval strains of Yersinia pestis are extinct come from? There is only one result in the entire paper that hints at this possibility: “[the medieval sequences] revealed the presence of two mutations that, to our knowledge, are not found in any Y. pestis sequences, either ancient or modern.” While these two mutations make an interesting observation, they do not provide enough evidence to justify some of the grand, sweeping claims about the Black Death’s demise that were made in the media. The researchers specifically mentioned that an investigation of the plague’s evolutionary history fell outside of the scope of this research.

I wrote a story about this disconnect between the media coverage and the research itself in NRC Handelsblad, the Dutch daily newspaper that I write for. The lead researcher of that paper, Hendrik Poinar, then told me that he was ‘flabbergasted’ with all the media attention that this study had received. The team hadn’t even prepared a press release about their work. They never expected that it would have interested anyone outside the field. Poinar later wrote me in an e-mail that “the PNAS paper was not the ‘landmark study’ people were making it out to be.”

At the time, Poinar was also careful to point that their findings didn’t prove the Black Death was extinct. “Only when we have the complete [medieval] genome, can we begin to reconstruct the evolutionary history of the plague”, is what he told me back then.

Little did I know that this medieval genome was almost ready to be published. Now, one and a half months later, the genome is there. Krause and Poinar reconstructed the entire DNA sequence of medieval Yersina pestis, with the same technique of targeted enrichment that they had used earlier. They found over two million pieces of medieval DNA and stitched these back together into a single genome. This is quite an achievement. It is the first time that scientists have managed to reconstruct the complete genome of an ancient, disease-causing bacterium. Even more exciting is that this genome reveals a story that directly contradicts the articles that were making the rounds on websites and newspapers earlier. The medieval Black Death isn’t extinct. Its descendants still cause disease today and have barely changed for over 660 years.

The Black Death appears to have been much more deadly in medieval times, but when the researchers compared the genomes of the medieval and modern Yersinia side by side, they hardly found any differences between them ^*. If the medieval Yersinia really was more dangerous than its modern counterparts, there’s no trace of its increased lethality in the bug’s DNA. Even the genes that are known to be important for causing death and disease have remained the same for over 650 years.

“For a long time we thought the bug was the culprit”, says Poinar, “but now we suspect that the interplay between the disease and humans was what made the medieval plagues so devastating. Fourteenth century London was a crowded, cold and damp. Large parts of the population were malnourished and many were carrying other diseases, such as the flu. Then suddenly the plague arrives with the merchant ships from Southern Europe. It was a perfect storm.”

Poinar and Krause believe that the plague grew less severe over time because the people of Europe adapted. This was a biological adaptation in part, since only the people able to muster some resistance to the deadly disease survived. But there was also cultural adaptation. Starting in the sixteenth century, many cities in the Netherlands constructed ‘plague houses’’for example, where bearers of the plague were quarantined and treated by specialized plague doctors. Nasty outbreaks still struck Europe every now and then, such as the Great Plague of London in 1665, but never again were they so deadly as in 1348.

Plague doctors wore beak-like masks to protect them from 'bad air'.

Another unexpected find was that all modern plagues seem to trace back their ancestry to plagues from medieval times. This raises some questions about another major pandemic in human history, the Justinian plagues that swept through the Byzantine empire in the sixth century. These plagues were always believed to be the same disease as the one that devastated medieval Europe. If this is so, these Justinian Yersinia strains have left no descendants that have survived into modern times. Another possibility is that the Plague of Justinian was a different disease altogether. “What caused the Justinian Plague has really become the next million dollar question”, Poinar says.

What about the two unique mutations that the team had found in August? They turned out to be an artifact. The ‘mutations’ turned out to be a form of DNA damage that is typical for ancient samples. When the researchers resequenced the same positions using next generation sequencing technologies that cover the same position multiple times, they found no trace of the ‘mutations’. The Black Death had been proclaimed dead to soon.

Pentastomes are true escape artists. Once they realize they’ve entered a reptile stomach, they use their sharp hooks to claw themselves a way to the victim’s lungs. In an experiment where pentastomes were implanted in a gecko’s stomach, the parasites invaded the lungs in as little as four hours.

Pentastomes use their hooks to burrow from the stomach to the lungs.

Despite their interesting and somewhat disturbing life cycle, pentastomes have always been a bit obscure. This is not at all surprising, said parasitologist John Riley, if you consider the nature of some their hosts: crocodiles, monitor lizards and various venomous and constricting snakes. With a sense of self-humour, he quipped: “To employ these hosts as vehicles for pentastomes in long-term studies is a particularly esoteric branch of parasitological research, with relatively few (one?) adherents!”

Aside from their hosts, the pentastome themselves are also problematic to handle. When a living pentastome is even slightly punctured, it deflates and contracts. For these and other reasons, parasitologists identify pentastomes using differences in the size and shape of the hooks. What pleads for using the hooks is that they are rigid and tough, and can easily be removed and measured.

But hooks don’t tell simple stories. Hook length and shape can vary within a single species, just like the length and shape of humans varies. Small differences in other body parts are also used for identification, such as male genitalia, but these measurements are more prone to errors if two specimens haven’t been treated in the same way.

There are more than enough examples where pentastomes were misidentified. A parasite from Taiwan first described as a new pentastome for example, only to be reassigned to an pre-existing species one year later. Twenty years later it turned out this second assignment was wrong too: the parasite was a member of a different species altogether.

In a recent paper in PLoS ONE, parasitologists have uncovered another case of mistaken identities. In a parasite survey of cane toads, they came across pentastomes with two kinds of hooks. Some were sharp, others blunt. The pentastomes with sharp hooks were known to infect amphibians, but the blunt-hooked pentastomes had only been seen in lizard lungs before. Indeed, the team also found these parasites inside the Asian house gecko.

If the researchers had followed taxonomic guidelines, they should have classified the pentastomes as belonging to two different species, Raillietiella indica for the sharp-hooked parasites and Raillietiella frenatus for the blunt ones. But the team suspected that something else was going on. A DNA analysis confirmed their hunch. All the parasites, with sharp and blunt hooks, from toads and geckos, were genetically identical to each other. This suggested that these parasites are not two species, but one.

A pentastome that has retained its younger, sharper hook by accident.

One strange pentastome provided additional evidence for this idea. By chance, this parasite had retained the hooks of previous molts. The oldest of its hooks were small and sharp, while the youngest were broad and blunt. So as the pentastome matures, the size and shape of their hooks change. Raillietiella indica is just an early stage of Raillietiella frenatus.

The team also discovered that body size and hook shape were correlated. In other words, larger pentastomes also tend to have blunter hooks. Combined with the observation that pentastomes grow to larger sizes in geckos than they do in toads, and it becomes easy to see why these parasites appear to be of different forms.

John Riley already warned for potential confusion that hooks can sow in his 1986 overview of pentastome biology: “In practice hook data can only be meaningfully compared between fully adult specimens, and a major obstacle arises in deciding what constitutes the adult stage.” He hit the hook on its head.

Chromosomes line up during the metaphase.

Most new genes are born through such accidental duplications. Duplicated genes have been described as the raw material that keeps the engine of evolution running. The basic idea behind this metaphor is that one gene acts as a safety net, while its sibling is free to mutate. Such a mutation could break the gene (without serious consequences – its intact twin is still there), or change its function. If the newly evolved function is useful enough, both copies are retained in the genome.

But duplicated genes are not without their downsides. Two identical genes also produce twice as much protein, and this can cause all sorts of troubles for the cell. Freefloating proteins could stick together and form toxic clumps, or bind other proteins which they shouldn’t bind for example.

To prevent such a protein overdose, the cell restores balance again by reducing the activity (expression) of both copies. Andrew Ying-Fei Chang and Ben-Yang Liao from Taiwan published a paper this week in which they describe how this works.

They found that the duplicated genes of mice and humans carry methyl groups (a simple chemical modification) than unduplicated ones. These methyl groups don’t affect the information that is encoded in the DNA: they are like little signposts that are added on top. Methylated DNA has a reputation for being less active than normal DNA. The methyl groups get in the way of the proteins that normally read the DNA. They also let the DNA coil in a more compact and rigid way, making it less accessible.

Chang and Liao were surprised to find that the cell rebalances duplicated genes with transient methyl groups: “[Such] changes [..] are not as permanent as modifications at the genetic level”, they write. Methyl group can be removed fairly easily.

The same researchers previously noted that the reduced activity of duplicated genes is self-perpetuating. Now that gene expression has returned to a normal level, the cell can no longer afford to lose either copy. The spare tires have made themselves essential again. Using methylated DNA to keep duplicated genes in check therefore seems to be a very temporary solution to a long-term problem.

The scenario sketched by the researchers does explain why the genomes from different species, from yeast to man, still contain genetic siblings that both carry out the same jobs in the cell. These are not young genes: some of them have been duplicated million of years ago. This appears to be the other face of duplicated genes. Instead of driving evolution, they can also introduce needless complexity and dependence, in an already crowded genome.

Images:
Metaphase by Roy van Heesbeen.

References:
Ying-Fei Chang A, & Liao BY (2011). DNA methylation rebalances gene dosage after mammalian gene duplications. Molecular biology and evolution PMID: 21821837

These berries are called 'miracle fruit': after consumption, they make sour taste sweet.

Three years ago, a friend and I were eating a slice of lime. If we had had any normal sense of taste, the sour fruit would have made us squint our eyes and twist our faces. Instead, we just sucked the juice from the fruit without twitching a muscle. To mock sourness some more, we had a sip of vinegar. My friend and I were ‘taste tripping’.

Moments before, we had let a tablet dissolve in our mouths. The tablet itself had no taste, but it did form a thin layer of film on our tongues. The packaging said that the active ingredient was a mysterious protein called miraculin. The effects of this protein were miraculous indeed: for more than an hour, sour tasted sweet.

Miraculin was first extracted in 1968, from a berry that grows in West Africa. The local population knew about the effects of the berry for much longer. They chewed on the pulp of the fruit to make stale and sour maize bread more tasty, for example. At the time, scientists didn’t know exactly how miraculin worked, but they did have a hunch. “It is believed that the protein binds to receptors of the taste buds and modifies their function”, is what they wrote. Now, forty years after the initial isolation of miraculin, researchers from Japan and France have proved them right.

The research team discovered that miraculin binds to the human sweet taste receptor (hT1R2-hT1R3). Most molecules that bind the sweet taste receptor, such as sugar and aspartame, induce a sweet sensation, but this is not the case for miraculin. Miraculin only activates the sweet taste receptor in a sour environment. This explains why vinegar tastes as sweet as syrup once your entire tongue is covered with miraculin. In a neutral environment the sweet taste receptor doesn’t respond to miraculin at all.

Miraculin only activates the sweet taste receptor in a sour environment.

Miraculin is different from other sweeteners in this regard. Aspartame always activates the sweet taste receptor for example, no matter how acidic or neutral the environment is.

The researchers found that in some cases, miraculin competes with these sweeteners. They first exposed the receptors to miraculin and then applied aspartame in a neutral environment. The receptors remained silent. However, something strange happened when the researchers made the environment a bit more sour. As soon as the researchers added aspartame, the receptor’s response skyrocketed, increasing to levels way beyond a normal aspartame response.

This is speculation on my part, but this means it should be interesting to try some goat’s milk in combination with miraculin. According to this table, goat’s milk is slightly acidic, so during a taste trip, it should taste sweeter than it normally does.

The team also determined to which part of the receptor miraculin binds. For these experiments they exploited the fact that miraculin has no effect on the sweet taste receptors of mice. By swapping and mixing pieces of human and mouse receptor, they found that a small part of the human T1R2 protein was all it took for miraculin to activate the receptor. This region is different from where most sweeteners bind the receptor, so it’s unlikely that miraculin directly competes with them.

Instead, the researchers think that when miraculin binds the sweet taste receptor, it changes its shape in such a way that it becomes impossible for other sweeteners to bind. Then, when the environment becomes more sour, miraculin changes shape itself, reactivating the receptor. Two amino acids in the miraculin protein are particularly important for shapeshifting. They are histidines, which gain protons in acidic conditions. This changes the overall charge of miraculin, which could lead to a change of shape.

Miraculin binds the T1R2 part of the sweet taste receptor.

This is not the entire story of what miraculin does to our sense of taste. In addition to making sour taste sweet, it also seems to neutralize any eye-twitching sourness. Keiko Abe, one of the main authors of the study, said: “Miraculin weakens sourness, so it is likely that miraculin blocks the function of some sour taste receptor.” They are currently investigating whether this is the case.

It is easy to take the way we perceive our environment for granted, but even small protein like miraculin can turn our senses on their head. This all goes to show how much we depend on the proteins that form our cells and the molecules that cross our way. Indeed, cats and rodents have a mutation in their T1R2 gene, which makes it impossible for them to taste sweetness at all. So just remember: when life turns sour, just apply some miracle proteins. They will sweeten your day.

Note: Ed Yong from the excellent Not Exactly Rocket Science has also written about miraculin. Check out his take on the story here.

The Blackfooted Penguin is the only African penguin.

The history of penguins in Africa is a history of false starts. The first penguin pioneers that settled Africa millions of years ago all went extinct. But the penguins didn’t give up. They came back, swept there by ocean currents, and repopulated the African coasts. That’s what the palaeontologists Daniel Ksepka and Daniel Thomas conclude in a paper that was published last week.

Africa has always been the most penguin-free continent of the Southern Hemisphere. The first penguins only came to Africa 30 million years after they had first spread to Australia, Antarctica and South America. Today, only the Blackfooted Penguin lives in Africa. But African penguin diversity wasn’t always this low. Palaeontologists have unearthed the fossil remains of four more species of penguin over the past few decades. All of these ancient penguins are extinct today.

A Blackfooted Penguin and a reconstruction of his distant, smaller cousin Inguza predemersus.

There are two possible explanations for the presence of ancient and modern penguins in Africa. Either different species of penguin migrated to Africa on separate occasions, or they all descend from a single group of penguins that arrived in Africa a long time ago.

Biologist call this last scenario an endemic or adaptive radiation. Radiations often happen when a single species colonizes an island or continent. The descendants of this species adapt to different niches and diverge into new lineages. Famous examples of adaptive radiations are Darwin’s finches that colonized the Galapagos and evolved beaks of different shapes, or the lemurs of Madagascar that evolved into creatures the size of mice and gorillas.

Which explanation is closest to actual penguin history, depends on the shape of the penguin family tree. For example, if all African penguins are closer related to each other than they are to other penguins, this would be evidence for an endemic radiation. If, on the other hand, the closest relatives of African penguins all live outside of Africa, it is more likely that they settled Africa multiple times.

Kspeka and Thomas reconstructed the family tree of African penguins by comparing their bones. Of the extinct African penguins, only the skeletons of the large Nucleornis insolitus and smaller Inguza demersus were complete enough to be included in this analysis. Small differences in their bones lead Ksepka and Thomas to conclude that the Blackfooted Penguin, Inguza and Nucleornis are not closely related to each other, indicating that these three penguin species colonized Africa on their own.

But how did they get there? Ksepka and Thomas point out that there are two ocean currents in the South Atlantic that could have swept penguins from South America to the African coast. On his blog, Ksepka aptly describes the currents as a ‘penguin conveyor belt’.

Ocean currents flowing from South America to Africa have brought penguins to Africa at least thrice.

Ocean currents also explain why penguins were unable to spread further north and why they never reached Madagascar (there are exceptions, of course). Both east and west, ocean currents have limited penguin expansion.

Inguza and Nucleornis in Africa arrived in Africa after the current ocean current system was reorganized, 20 million years ago. This would explain why penguins came to Africa as late as they did: the ocean streams that make up the penguin corridor to Africa only opened up relatively recently.

The presence of Blackfooted Penguins in Africa is more recent than that of Inguza and Nucleornis. The oldest fossils of this species are around 300 thousand years old. Few fossils have preserved from the intervening years, so nobody really knows how long Inguza, Nucleornis and the other ancient penguins endured. Ksepka thinks that sea level change played a role in their extinction:

South Africa appears to have had a better environment for penguins in the past than today, because diversity drops from four species 5 million years ago to one today. One possible cause is sea level change. Penguins like to breed in places where land predators can’t reach their eggs, so small rocky islands are ideal. The sea level has dropped over the past few million years in South Africa, and many islands that existed five million years ago are now connected to the mainland. Those areas may have been lost as nesting sites.
-Daniel Ksepka

The Blackfooted Penguin has made itself quite at home in Africa, despite the low sea levels of today. Yet the future doesn’t look bright for this latest arrival. Commercial fishers and fur seals compete with the Blackfooted Penguin for food. Today, the charismatic flippered bird has been listed as an endangered species. If history teaches us anything, it is that African penguins have been vulnerable to perturbations in the past. We should cherish this lone survivor.

These rare, strange ticks were rediscovered this month.

The most precious fluid in the world isn’t black. It’s red. According to some estimates, there are over 14,000 species of insects and other crawlers that feed on blood. Every class and order seems to have its own blood loving family member. The most famous blood sucking arachnids, eight-legged animals such as mites, spiders and scorpions, are the ticks. This month, South African researchers announced in PLoS ONE the rediscovery of a rare tick. This strange creature has the potential to answer some of the evolutionary questions that still surround these parasitic blood suckers.

Ticks come in two varieties. There are soft ticks (Argasidae) and hard ticks (Ixodidae). Hard ticks get their name from the large and tough shield that they carry on their backs. Soft ticks lack this shield and have a leathery ‘skin’ instead. Another difference between soft and hard ticks is the location of their mouth parts. Hard ticks have their mouth parts on the front their body, giving the impression of a ‘head’, while soft ticks carry their mouth parts on their belly.

Hard (left) and soft (right) ticks have a different anatomy

While these differences are enough to warrant a separation of ticks into two distinct families, there are still many uncertainties about how and when these families evolved. Some researchers argue that ticks evolved from mite-like creatures as much as 400 million years ago, in the Devonian. These dawn ticks could perhaps have parasitized the first amphibians. Others suggest a much later date for the evolution of ticks, around 100 million years ago, in the Cretaceous. It isn’t even clear whether blood-feeding evolved once, in the common ancestor of all ticks, or twice, in hard and soft ticks independently.

How to solve this tick conundrum? Enter a third family of ticks, the Nuttalliellidae. The only species of tick in this family, Nuttalliella namaqua, is a strange creature that combines features of both soft and hard ticks. It carries a small pseudo-shield and has its ‘head’ on the front like hard ticks do, but it has the same leathery skin as soft ticks. The hybrid nature of this ‘soft hard tick’ makes it perfect for illuminating the some of the dark corners in the evolutionary history of ticks, were it not for one problem: it was last seen in 1981, in South Africa.

Searching for this little parasite was difficult because no one knew on what kind of animal it fed. Up till now, biologists had collected a mere 21 specimens. These were found under rocks, in dusty meerkat skins in museums and inside the nests of the striped swallow. Mammals and birds thus seemed likely hosts, but attempts to let these ticks feed on pigeons, rabbits and rodents all failed.

Study author Daniel de Klerk found Nuttalliella namaqua hiding in a rock crevice.

It’s not that biologists didn’t try to find Nuttalliella. Daniel de Klerk, one of the co-authors of the PLoS ONE study, has been searching for it for almost thirty years. He even lost a finger tip due to a snake bite during one of his expeditions. This month, he and colleagues from the University of Pretoria were finally rewarded for their perseverance. They discovered thirty ticks, including many living ones, not far from where were this species was first found in 1930. Ben Mans, lead author of the study, describes the find:

“We found them by pure luck. We were driving along a dirt road and I saw a patch of green grass and just stopped. Daniel started to pick at rocks in a crevice, looked through them with a magnifying glass, and suddenly he called out that he found something. And that was it. It felt quite amazing to know that we have found a tick that we had little chance of finding. It was one of those moments that makes science really worthwhile.”

The team soon knew that these ticks were Nuttalliella:

“They are really small and blend in well with their environment, so they can be quite difficult to see. However, their legs are distinctly reddish in color and their pseudo-scutum [pseudo-shield] was clearly visible when you zoomed in with a camera. So we knew that these were probably the correct ticks. Later in the day we identified them using a stereo microscope and our hunch was confirmed.”

Some of the females had recently fed and still carried the blood of their previous hosts within their guts. After dissecting the tick and removing her guts, the team saw that the blood cells of the tick’s victims had a nucleus, indicating that the blood came from a reptile or a bird (mammals have blood cells without a nucleus). DNA analysis of the blood revealed that the blood came from several species of lizards, including some species of girdled lizards. Live feeding experiments later confirmed that Nuttalliella happily feeds on lizards, solving the mystery of the missing host. However, Mans says that few ticks feed on lizards exclusively, and it is quite possible that Nuttalliella is a generalist.

Nuttalliella feeding on a lizard

Even more interesting than the identity of its host, was the nature of this little tick itself. The old museum specimens of Nuttalliella are too old for DNA extraction, but isolating DNA from fresh ticks is no problem. Based on this DNA, Mans and his colleagues found that Nuttalliella belong at the base of the family tree of ticks. This means that hard and soft ticks share a more recent ancestor than all the three families do together. Such a placement is ideal for inferring what properties the ancestral tick must have had. For example, since all three families of ticks feed on blood, the ancestral tick probably did so too.

Since Nuttalliella only occurs in South Africa, Mans suggests that the origin of ticks also lies in this region, around 270 million years ago. At this time Africa was still part of the supercontinent Gondwanaland, which Antarctica, South America and Australia. As Mans writes in his paper, these were turbulent times. Many ancient lineages, such as those that would lead up to modern lizards, mammals and birds were founded in this time. Vertebrate evolution was in full swing. And then disaster struck. Around 250 million years ago, most species on this earth went extinct. Never before and never since did so many species die out.

This upheaval must have affected these ancient ticks. Many of their hosts went extinct, after all. The soft ticks and hard ticks eventually spread over the world and diversified into many different species, perhaps as vertebrate life recovered from ‘the Great Dying’. The ancestor of Nuttalliella straggled along in Africa however, without spawning a large family. Perhaps this ancestor had difficulty switching hosts after the Permian extinction, but this is speculation. Mans says that “nobody has yet seriously considered why species richness differs between various tick lineages.” And considering the difficulty with which Nutalliella was found, it remains to be seen whether this lineage was really unlucky, or whether more family members are hiding under rocks, somewhere in Africa.

Images:
Tick anatomy from ticktexas.com
Other pictures from reference.

References:
Mans BJ, de Klerk D, Pienaar R, & Latif AA (2011). Nuttalliella namaqua: A Living Fossil and Closest Relative to the Ancestral Tick Lineage: Implications for the Evolution of Blood-Feeding in Ticks. PloS one, 6 (8) PMID: 21858204

Milk comes from cows. Most of us know that. More urban readers are forgiven for thinking milk comes from supermarkets. But the the question where milk comes from has the potential to reach beyond dairy farms and breakfast tables. It could be about the origins of milk itself, millions of years ago. “Where does milk come from?” becomes “how did milk evolve?”

Milk is essential for the survival of pups, cubs and calves around the world. Young mammals can gain weight and grow on a diet of milk alone because it is rich in proteins, vitamins, calcium and saturated fats. But milk has not always been this nutritious.

Our mammalian ancestors started giving milk when they were still laying yolky eggs. The shells of these eggs weren’t hard and calcified like the eggs of birds. They were soft and had a parchment-like eggshell instead, much like the eggs of lizards and snakes. If you would study such eggshells under a microscope, you would see that their surface is covered with millions of narrow pores. If it is too hot or dry, water evaporates through these pores, putting the eggs at risk of drying out.

A hatching corn snake. Notice the leathery texture of the egg shell.

Snakes and lizards prevent this from happening by laying their eggs in a moist soil. But early mammals solved this problem in a different way, Olav Oftendal thinks. He suggests that lactation didn’t evolve to nourish, but to drench. Fluids secreted through the skin of ancestral mammals could have protected the eggs from drought and desiccation. If true, the first ‘milk’ was not that milky at all: think twice before mixing Triassic milk with your cornflakes.

The eggshell pores forced the ancient mammals to look for answers. When these answers were found, the advantages of an passable eggshell could begin to be exploited. Through the pores, extra nutrients added to the moistening fluid reached the developing hatchling inside the egg. New opportunities awaited in this twilight zone between moist and milk. Eggs could grow smaller, because the yolk no longer need to provide every single nutrient the embryo needed. Young animals could delay their development, since they no longer needed to hatch as miniature adults.

But that’s running ahead of the story. There are genes that can tell us more about how our ancestors switched from yolk to milk.

Electron microscope picture of a milk micelle.

Caseins
Caseins are the most abundant proteins in milk. They come in two forms. One type binds calcium, the other one is insensitive to calcium. When you bring thousands of these caseins together, they self-assemble into a soluble micelle. Micelles look a bit like little balls of hair. The ‘hairs’ are really the tails of caseins that are sticking outwards. The calcium-insensitive caseins stabilize the micelle, but it is thanks to the calcium-binding caseins that micelles are loaded with calcium. If milk contained the same concentration of calcium without the micelles, the calcium wouldn’t remain soluble and precipitate.

From cows to kangaroos, all mammals have casein genes. And in every mammalian genome, the caseins are surrounded by closely related genes. The technical name for this family of genes is ‘secretory calcium-binding phosphoprotein family’. Or SCPP family, for friends. As the family name implies – most of the SCPP family members can bind calcium. The SCPP family is old. One of its oldest family members, SPARCL1, uses calcium to mineralize our bones. It evolved more than 400 million years ago and can be found in all creatures with a calcified skeleton, such as bony fish, reptiles, birds and mammals.

The SPARCL1 gene was duplicated again and again. These carbon copies of SPARCL1 were free to evolve new functions. Some copies now mineralize other tissues, such as the enamel of our teeth. Kazuhiko Kawasaki and his colleagues from Penn State University have shown that milk caseins evolved from such tooth mineralizing SCPPs. One of the recent reconstructions by Kawasaki revealed that the different types of caseins also evolved from different types of tooth mineralizing SCPPs.

The evolution of the SCPP proteins, from the earliest tetrapods to the almost-mammalian synapsids. The SCPP family has been evolving fast: genes were duplicated and lost many times. The calcium-binding caseins are CSN1/2, the calcium-insensitive casein is CSN 3.

Vitellogenins
When something is gained, something else is lost. A recurring pattern in evolution. While caseins were born from tooth genes, the vitellogenin family became extinct.

Vitellogenins are the defining proteins of egg yolk. In all species that lay eggs (from insects to amphibians), vitellogenins provide the nourishment that developing embryos inside an egg need. Ancient mammals were no exception to this rule. They had three different vitellogenin genes, like modern birds and reptiles do.

But as milk became more nutritious, the egg yolk of pre-mammalian eggs became less and less important. When they were no longer needed, the vitellogenin genes were inactivated one by one. The remnants of these vitellogenins can still be found in our genomes today. They are the broken relics of a time when our distant ancestors still laid eggs. Still recognizable, but without a function for many millions of years.

While the birth and death of families of genes make for good dramatic narrative, it is important to realize that milk evolved gradually. There is no single point in time when milk, or mammals for that matter, sprung into existence. From pelycosaurs, to therapsids, to cynodonts: mammal-like creatures have around for millions of years.

Hatching corn snake by Jonathan Crowe.
Micelle picture from second reference.
SCPP evolution from third reference.

Oftedal OT (2002). The origin of lactation as a water source for parchment-shelled eggs. Journal of mammary gland biology and neoplasia, 7 (3), 253-66 PMID: 12751890

DALGLEISH, D. (2004). A possible structure of the casein micelle based on high-resolution field-emission scanning electron microscopy International Dairy Journal, 14 (12), 1025-1031 DOI: 10.1016/j.idairyj.2004.04.008

Kawasaki K, Lafont AG, & Sire JY (2011). The evolution of milk casein genes from tooth genes before the origin of mammals. Molecular biology and evolution PMID: 21245413

Brawand D, Wahli W, & Kaessmann H (2008). Loss of egg yolk genes in mammals and the origin of lactation and placentation. PLoS biology, 6 (3) PMID: 18351802

Sea lettuce that washed upon the shore of Maryland.

Charles Darwin described life as an eternal struggle for existence. Species compete for a limited amount of space and resources, so only those varieties that are best adapted to their niche will survive. The logic behind this reasoning is sound, yet it doesn’t apply to microbes living on sea lettuce. This humble seaweed picks bacteria on a basis of first-come, first-served, no competition involved. Not the fittest, but the luckiest shall survive.

That’s what Catherine Burke and her colleagues conclude after studying the microbial ecosystems that live on the leaves of sea lettuces from intertidal pools. The team extracted and sequenced the DNA of these microbes directly, without first culturing them in the lab. Such a genetic census, the method is called metagenomics, presumably gives an unbiased reflection of all the microbes that live in a certain environment.

After matching the DNA sequences to species, Burke found that each lettuce harbours a unique community of microbes. Between the six algal samples, only 15% of the microbial species were shared. This suggests that microbes colonize sea lettuce more or less randomly. It doesn’t matter who these bacteria are. As long as they can grow on sea lettuce and get there soon enough, they will become part of the lettuce’s microbial ecosystem. Ecologists recognize this scenario as the lottery model: whichever species arrives first, wins the lottery.

This lottery hypothesis was first proposed by Peter Sale in 1976. Sale didn’t have microbes and sea lettuce in mind when he described his theory, but fish and coral reefs. Given two similar species of fish and a vacant reef, the species that colonizes the coral reef first will be able to defend it against further intruders. Philip Munday later provided experimental evidence for this lottery effect. He showed that when a reef fish colonized a reef with a head start of 8 hours, a competing species couldn’t displace the resident later. When both fish were introduced together, each species won half of the times.

Gobiodon histrio, or the Green coral goby, was one of the species used in the lottery study by Munday.

A lottery can only be fair and random if each species has a similar chance of winning. This is only possible if competing species resemble each other. For animals this is almost synonymous to being closely related, such as the gobies that Munday used in his experiments. When two animals are only distantly related, one will always have an advantage over the other, by virtue of being bigger, smarter or sneakier. But relatedness isn’t really an issue for bacteria. They can share genes across species boundaries with relative ease, after all.

Although the sea lettuce lottery was won by different bacteria every time, Burke discovered that each microbial community has a similar core set of genes that differed from the genes that were present in the surrounding sea water. An impressive 70% of the genes in the different communities have similar functions. Many of these genes make community life on a mass of floating algae possible. Take the genes that produce adhesion proteins. These proteins make microbes stick to surfaces and each other, forming biofilms. Other examples include proteins that convert the sugars that algae produce, or genes that make bacteria switch from a mobile to a sessile lifestyle.

This conservation of genes across different communities could mean that there are only so many ways of colonizing see lettuce. The genes are like lottery tickets that many different bacteria buy to enter the sweepstakes. The species that win the lottery might be random, but their genes are not.

These insights mirror findings elsewhere. Earlier this year, researchers from Heidelberg discovered that each person has one of three different types of bacterial ecosystems in their gut. These ecosystems didn’t correlate with the diet, sex, weight, age or health of their test subjects. For all we know, they could arise from random colonizations of microbes when we are young, just like the microbes that live on sea lettuce.

Metagenomics is a young field, but it has already revealed many hidden aspects of microbial community life. Teasing apart the random and non-random forces that shape these communities should keep microbial ecologists busy for years to come.

Images:
Sea lettuce by Eutrophication&hypoxia.
Green coral goby by WonderKris.

References:
C Burke, P Steinberg, D Rusch, S Kjelleberg, & T Thomas (2011). Bacterial community assembly based on functional genes rather than species Proceedings of the National Academy of Sciences : doi/10.1073/pnas.1101591108
Munday, P. (2004). Competetive coexistence of coral-dwelling fishes: the lottery hypothesis revisited Ecology, 85 (3), 623-628 DOI: 10.1890/03-3100

Coconut palms on the Southern Maalhosmadulu Atoll in the Pacific.

On January 9 in 1878, the Spanish brig Providencia was en route from Cuba to Spain, but would never arrive at this destination. Although the weather was clear that day, the ship wrecked off the shores of Florida. Its cargo, 20.000 coconuts harvested on the Caribbean island of Trinidad, was scattered along the coast¹.

The settlers of Florida knew an opportunity when they saw one and planted some of the stranded coconuts around their homes. The coconut palms and groves that grew from these seeds later gave Palm Beach County its name. Fifty years after the Providencia sank, a reporter of the Palm Beach Post wrote:

“From that wreck has grown the palms that line the streets and parks of Palm Beaches. [..] 20.000 coconuts provided the beginning of trees not indigenous to the area, but quite at home, nevertheless.”
~ Palm Beach Post, Nov 20 1938

Not indigenous, but quite at home. This description not only fits the palms that sprang from Providencia‘s wreck, it’s true for coconut palms around the world. Although coconut palms now adorn the coasts of tropical beaches everywhere, from the Caribbean to Madagascar and Hawaii, the tree is not a native species there. All these palms, like the palms of Palm Beach, were introduced by humans.

Coconut palms can be found on every tropical coast, although they are not native there.

Humans have always been eager to bring coconuts along on their travels, and for good reasons. Coconuts are not only a source of both food and water, different parts of the coconut palm can also be used for other purposes. Alcohol and sugar can be extracted from its sap, and cocos oil from the nut itself, for example. Today, they grow on both sides of the Atlantic and Pacific ocean. But where did this useful crop first come from?

Since coconut palms have been crossed, cultivated and transported for thousands of years, retracing the coconut’s path through archaeological sources alone is difficult. The coconut’s collective history has been preserved far better inside its DNA. By mapping the relatedness of coconut palms around the globe, it is possible to reconstruct the tale of their expansion. Last month, Kenneth Olsen and colleagues published a thorough analysis of coconut DNA in PLoS ONE from 1322 coconut palms around the world.

These coconuts are being dried to make copra, from which cocos oil is made

The team discovered that despite the coconut’s complicated history, the underlying genetic structure of coconut populations is simple. Most coconuts belonged to one of two genetically distinct groups. One population traces back its ancestry to palms on the coasts of India, the other group descended from palms in Southeast Asia. Even palms that now grow on the other side of the world are still members of one of these two groups. Palms in Middle America are mostly of the Pacific variety, whereas Caribbean palms belong to the Indian group, for example.

Since the genetic differences between the Indian and Pacific varieties are so numerous and clear, the two lineages must have been evolving in separate directions for a long time. For this reason, Olsen’s team concluded that the coconut palm was not domesticated once, but twice: in India and on the Malay Peninsula. Following the Pacific domestication, settlers would have brought the coconut to the Polynesian islands. Austronesian seafarers from the Philippines later introduced the coconut to the Pacific coast of Middle America. The coconut palms that were domesticated in India spread westwards. After they had been introduced in East Africa, Europeans brought the coconut to the Atlantic coast of Africa and later to South America.

The two lineages not only differ genetically, there are also biological differences. The fruit of the Indo-Atlantic palms are more elongated and angular compared to the rounder, Pacific fruits. In earlier theories about coconut evolution, palms bearing elongated fruits were seen as wilder plant, whereas the trees with rounder fruits were supposed to be ‘more domesticated’. Since the two types of palm arose from independent domestications, this theory no longer holds. Rounder fruit did not evolve from angular fruit in a linear fashion.

These coconut fruits are of the rounder ('niu vai') type.

Of course, the evolutionary history of coconut palms is not just a matter of Indian versus Pacific coconuts. Evolution never deals in black and white. The genetic differences between both varieties are not absolute. Some coconut trees, like those on Madagascar, are genetic mixtures of the Pacific and Indian varieties. At some point the two groups must have interbred and produced offspring on the African island.

Since Madagascar is an island in the Indian Ocean, so the Indo-Atlantic heritage of Madagcasar’s palms is no surprise. The Pacific ancestry is more confusing though. Coconut palms on the Seychelles, an island group just north of Madagascar, contain few traces of Pacific ancestry So how did Pacific coconuts get to Madagascar?

The answer, again, involves human migration and trade. The people of Madagascar themselves partly descend from Southeast Asian ancestors. To explain this genetic mixing of people and coconuts, geneticists and anthropologists suggest that seafarers from the Malay archipelago frequented Madagascar on their trade routes to East Africa. Perhaps some of these traders and their coconuts eventually settled in Madagascar. Arab traders could also have played a role in the dispersal of Pacific coconuts. Arabic influences on East Africa are evidenced by the spread of Islam and introduction of Asian crops in this region. The Seychelles were never part of the Malay and Arabian trade routes, which explains why these palms have no Pacific heritage.

Next time you see a coconut palm, I hope you’ll realize that is more than just a fancy tree with tasty seeds on a tropical beach. The coconut’s evolutionary history is intertwined with the complex history of human migration, trade and colonization. That’s not bad, for a humble seed far from home, but quite at home nevertheless.

The genetic composition and spread of coconut palms around the world

Images:
Coconut palm by Sykez
Coconut distribution by Niklas Jonsson.
Drying coconuts by Dan Iserman
Golden coconut fruit by DeusXFlorida
Spread of coconuts around the world from second reference.
References:
Oyer H (2001), The wreck of the Providencia in 1878 and the naming of Palm Beach County, Vol. 29, South Florida History
Gunn BF, Baudouin L, & Olsen KM (2011). Independent Origins of Cultivated Coconut (Cocos nucifera L.) in the Old World Tropics. PloS one, 6 (6) PMID: 21731660

Random mutations in proteins have similar effects, except that they introduce molecular errors, rather than grammatical ones. A random amino acid that takes the place of an established one (amino acids are the building blocks of proteins, just like words are the building blocks of sentences) often distorts its local surroundings. Sometimes these small, local changes ripple through the protein, destabilizing its entire structure.

This doesn’t mean that a mutated protein is lost beyond hope, however. In a recent paper, Joe Thornton and two colleagues describe an ancient, destabilizing mutation that paved the way for the evolution of a protein with new function. Some proteins first have to be broken, before they can be fixed.

The proteins that Thornton and his team studied were the glucocorticoid receptor and the mineralocorticoid receptor (GR and MR). Both these proteins are activated by steroid hormones and can switch other genes on or off. Their effects on the body are different, however. MR is responsible for maintaining the balance of water and salt in the body, while GR orchestrates the stress response. Amongst other things, activation of GR eventually leads to an increase in blood sugar and repression of the immune system. The two receptors also differ in their sensitivity to hormones. MR can be activated by a variety of different hormones at low doses, whereas GR only responds to high concentrations of the stress hormone cortisol.

GR and MR both evolved from the single ancestral gene AncCR (for ‘Ancestral Corticosteroid Receptor’). This gene was duplicated 450 million years ago in the common ancestor of cartilaginous fish and bony vertebrates. Thornton reconstructed this extinct AncCR earlier and found that it was sensitive to a variety of steroid hormones, just like the modern MR. He concluded that after the initial duplication, MR was the gene that retained AncCR’s original properties while GR was free to evolve a new function.

GRs in cartilaginous fish, such as the little skate depicted here, respond to multiple steroid hormones. They are not specific for cortisol, like our GRs are.

The evolutionary path that the GRs took after this duplication is unclear, although some circumstantial clues illuminate the way. In cartilaginous fish, GR still responds to the same broad set of hormones as MR and AncCR, although it is not as sensitive to them. Based on this finding Thornton reasoned that GR evolved in two distinct and independent steps: GR first became insensitive to hormones (in the common ancestor of bony animals and cartilaginous fish), before it evolved the specific response to cortisol (in the ancestor of bony vertebrates).

To test this scenario, Thornton and his team ‘resurrected’ the ancestral GR (AncGR) from the sequences of hundreds of GRs in modern animals. The activity of this reconstructed AncGR was similar to that of to the modern GR of cartilaginous fish: they both respond to the same hormones as AncCR, but only when they are present in high concentrations. This observation is in line with the two-step hypothesis.

Both MRs and GRs evolved after a single ancestral gene (AncCr) was duplicated. GR first became insensitive to most hormones (single rectangle) before becoming specific for cortisol in bony vertebrates (double rectangle).

The sequence of the reconstructed AncGR gave a clue as to how this reduced sensitivity evolved. Thornton and colleagues saw that AncGR had acquired 36 different mutations since it first parted ways with AncMR. To study how these mutations affected AncGR’s sensitivity to hormones, the researchers engineered some of these mutations back into the original AncCR. Two mutations had particular dramatic effects. They decreased hormone sensitivity more than 100 times when they were introduced by themselves, and 10,000 times when they were present together.

The structure of AncGR revealed that these mutations didn’t mess up the part of the protein that binds hormones, as you might expect. Instead, they destabilized the entire protein. One mutation (V43A) carved a hole in the otherwise tightly packed protein, whereas the other (R116H) disrupted molecular interactions that were present in the original protein. These changes are far from subtle. They degraded the original structure and function of the entire protein, much like the glaring grammatical error that destroys the meaning of a sentence. That AncGR remained functional at all was due to a different mutation (C71S), that partly buffered the effects of the other two.

While these two mutations are harmful at first glance, in hindsight you could say that they opened up a new evolutionary opportunity. After all, it was only because GR became insensitive to hormones that it could find a distinct niche for itself. It remains to be seen how common this ‘bad mutation turns good’-scenario really is. After all, a mutation that had impaired GR too much would have eliminated all function, dooming the protein to decay over time. The balance between creation and destruction is a delicate one indeed.

Images:
Little skate by Andy Martinez
GR phylogeny from reference.

References:
Carroll SM, Ortlund EA, & Thornton JW (2011). Mechanisms for the evolution of a derived function in the ancestral glucocorticoid receptor. PLoS genetics, 7 (6) PMID: 21698144

For a species on which so many knowledgeable women and men have written, it is surprising how much is still unclear about its evolutionary history. E. coli‘s general place in the tree of life has been well resolved, but when scientists take a closer look at the E. coli family, relationships blur and become uncertain. Part of the problem is that different strains of E. coli seem to be evolving into different directions. If true, this “could reflect the end of E. coli as a species”, researchers wrote in BMC Evolutionary Biology last month.

Scientists have long known that E. coli is not a single entity. Some strains are benign inhabitants of our guts, some make us deadly ill and some only live in laboratories. Most E. coli belong to one of of five different groups: A, B1, B2, D and E. These groups correlate with some of the biological aspects of the bacteria that belong to it. E. coli from group B2 often cause diseases, for example (although groups A, B1 and D also have their share of pathogenic bugs).

The evolutionary relationships between these different groups are hazy however. In 2009 scientists published a tentative family tree of E. coli  in PLoS Genetics, based on comparisons of almost 2000 genes of 20 different strains of E. coli. Despite the large scale of this research, the published tree far from the definite truth. In some cases only 11% of the analyzed genes supported a certain branch.

The family relationships of E. Coli change, depending on the DNA you analyze.

To get some grip on the slippery E. coli, Shana Leopold and her colleagues decided to focus on their  ’backbone DNA’ – long stretches of DNA with few differences between the different strains. The problem of comparing all the E. coli genes – like in the 2009 paper –  is that you also include the genes that are  often shuttled between different strains. These mobile elements have different evolutionary histories than their hosts, and thus are of limited use for resolving their family relationships.

But even with these stable stretches of DNA, Leopold could not solve the evolutionary puzzle that is the E. coli family. She ended up with a different family tree depending on the segment of DNA that she analyzed. Sometimes group E appeared as an offshoot of group A for example, whereas it was located on one the main branches in other trees.

This is counter-intuitive for someone who believes stable species and strains. The only way to resolve this scenario is to accept that the strains of E. coli have mixed and matched (recombined) different portions their DNA in the past. Suppose that at some point, group A transferred some of its DNA to group E. Today, this piece of DNA will give the impression that group A and E are closer related to each other than the piece of DNA adjacent to it.

The complicated family ties suggest that recombination happened often and regularly in E. coli‘s past. Does it still happen as much today? The answer is no. Leopold saw that DNA is often shared by strains within the same group, and rarely between strains in different groups.

What has changed for E. coli, so that modern recombination is rare? Maybe it became more difficult to accept foreign DNA for the different strains, as they adapted to specific niches over time. If  genetic transfer is slowing down, and maybe even coming to a halt, E. coli is becoming many species, instead of one.

This would not be the first time E. coli parted ways with its brothers. Almost 140 million years ago, Escherichia and Salmonella became two different species. What this single number hides is that there’s a period of 70 million years before the two species truly became two. The oldest genes were separated 180 million years ago, whereas the youngest were still shared until 100 million years ago!

The niche-specific genes of Salmonella and Escherichia were the first to become locked in in their respective genomes. These genes could simply not be shared because they fulfilled a specific role in Escherichia or Salmonella. More general genes could still be recombined between the two strains/species however. It took millions of years before these sequences had diverged enough.

Nowadays the distinction between Salmonella and Escherichia is clear, but for millions of years this wasn’t the case. The situation might be the same for E. coli now. Species diverge into strains, who might become species again. We just don’t know it yet.

Becoming two species took 70 million years for Salmonella and Escherichia.

Images:
E. Coli with flagellum by E.H. White (Creative Commons licence)
Phylogenetic trees from publication 1.
Divergence of Escherichia and Salmonella genes from publication 3.

References:
Leopold SR, Sawyer SA, Whittam TS, & Tarr PI (2011). Obscured Phylogeny and Recombinational Dormancy in Escherichia coli. BMC evolutionary biology, 11 (1) PMID: 21708031
Touchon M, Hoede C, Tenaillon O, Barbe V, Baeriswyl S, Bidet P, Bingen E, Bonacorsi S, Bouchier C, Bouvet O, Calteau A, Chiapello H, Clermont O, Cruveiller S, Danchin A, Diard M, Dossat C, Karoui ME, Frapy E, Garry L, Ghigo JM, Gilles AM, Johnson J, Le Bouguénec C, Lescat M, Mangenot S, Martinez-Jéhanne V, Matic I, Nassif X, Oztas S, Petit MA, Pichon C, Rouy Z, Ruf CS, Schneider D, Tourret J, Vacherie B, Vallenet D, Médigue C, Rocha EP, & Denamur E (2009). Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS genetics, 5 (1) PMID: 19165319
Retchless, A., & Lawrence, J. (2007). Temporal Fragmentation of Speciation in Bacteria Science, 317 (5841), 1093-1096 DOI: 10.1126/science.1144876

Do you want to know more?

I interviewed Shane Leopold and Phillip Tarr the BMC paper before writing this blogpost. Their joint reply sadly came in to late to incorporate into the post itself, but I still want to share them with you. Here are my questions and their replies.

Since some modern groups of E. coli did share DNA in the recent past, the authors also sketch a second future scenario, in which some groups of E. coli fuse (coalesce) into new groups.

In the introduction you write ‘this [...] could reflect the end of E. coli as a species, or herald the coalescence of E. coli groups into new species’. Wouldn’t a coalescence of different groups as nascent species also mean that E. coli as a descriptor for the entire species is invalid?

You raise a fascinating question. Take company X with five divisions A, B1, B2, D and E. Divisions A, B1, and E have similar or complementary product lines, use similar technologies, collaborate often, and share customers, and B2 and D also share between themselves to the same extent, but the product lines, technologies and customers have no overlap with those of divisions A, B1, and E. Company X then splits (coalesces its total) into two independent subsidiaries (A-B1-E and B2-D). The A-B1-E and B2-D subsidiaries continue not to work together; they make different products, and have different corporate structure and cultures. However, each has ‘inherited’ staff and equipment and customers from company X. Well, in this case, does company X exist in these new incarnations, or not? This is the coalescence scenario.

Or, if company X is composed of five divisions A, B1, B2, D and E. Divisions A, B1, and E have similar or complementary product lines, use similar technologies, collaborate often, and share customers, and B2 and D also share between themselves to the same extent. However, as time goes on, these interactions between A, B1 and E and between B2 and D diminish (as interactions between A, B1, E, B2 and D seem to have diminished in the past), and then interactions even within the divisions diminish. In that case, there is minimal interaction (recombination) seen for any of these employees (organisms) and there is scant fulfillment of the requisites of being a company (species). That is the pre-senescence scenario.

This question touches on the definition of a species, and how it is defined. There has been debate about that within the scientific community. Is a species a group of interacting organisms (freely exchanging DNA), or is it based upon genomic relatedness (70% DNA-DNA hybridization, or more recently, >95% nucleotide similarity). How do you define two groups of organisms that are highly similar but do not exchange DNA?

Do bacterial species exist at all?
It appears that E. coli have functioned as a species to the extent they freely exchanged DNA in the past. But, recently, maybe they haven’t. The applicability of the species concept has been questioned for bacteria, and we hope our data add to the debate. We also hope to introduce the possibility that a set of organisms that we define as a species is constantly evolving, and thus altering the cohesiveness of the group, maybe even changing so much that they no longer fit within the parameters of our species definition.

Will we ever be able to resolve our inability to ‘foresee future evolution’? Could we have predicted 140 million years ago that salmonella and escherichia would become different species?
Fascinating question you ask: by delineating where sets of bacteria have been (phylogenetically), and localizing where these organisms are in the present, can we predict where these organisms will go in the future? Maybe yes – if we could define with experimental evolution models the frequency and kinds of chromosomal accommodation, and if we could then predict the selective pressures and bottlenecks that will occur, we might be able to formulate predictive models of future evolution. You and I will probably not be around to see if the models are validated in the wild, however.