Apathy, weary sighs, and fatigue: these are the symptoms of the psychological malaise that Carl Zimmer calls Yet Another Genome Syndrome. It is caused by the fast-flowing stream of publications, announcing the sequencing of another complete genome.

News reports about such publications tend to follow the same pattern. Scientists have deciphered the full genome of Animal X, which is known for Traits Y and Z, which could include commercial importance, social behaviour, being closely related to us, or just being exceptionally weird. By understanding X’s collection of As, Gs, Cs and Ts, we may gain insights into the genetic basis of Y and Z, which will be terribly important and there will be parties and cake.

Note the future tense. The value in sequencing yet another genome is almost never in the act itself, but in enabling an entire line of subsequent research. It’s the harbinger of news; it’s rarely news itself.

But there are exceptions. This week, there’s a paper about a new animal genome that goes the extra mile. It includes not just one full sequence, but twenty-one. It doesn’t just spell out the creature’s DNA, but also uses it to address some big questions in evolutionary biology. And its protagonist is a small, unassuming fish – the three-spined stickleback.

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In a cauldron of boiling, acidic water, kneeling at the foot of a Russian volcano, one species of microbe is on the cusp of becoming two.

Sulfolobus islandicus is an archaeon – one of many single-celled microbes that thrive in extreme environments. Mutnovsky volcano is certainly one such place. Found at the far eastern end of Russia, it’s full of churning, scalding springs that are nonetheless teeming with microscopic life. S.islandicus thrives in these springs, feasting on the sulphur within the water.

Now, Rachel Whitaker from the University of Illinois has found that the species has pretty much split into two separate lineages. Both share the same water, and they can trade genes with one another, but they have started to part ways and are becoming increasingly distant. In this hot, hostile and acidic world, the origin of the species is playing out before our eyes.

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The Nile crocodile is a truly iconic animal. Or, more accurately, two iconic animals. As I’ve just written over at Nature News:

The iconic Nile crocodile actually comprises two different species — and they are only distantly related. The large east African Nile crocodile (Crocodylus niloticus) is in fact more closely related to four species of Caribbean crocodile than to its small west African neighbour, which has been named (Crocodylus suchus).

Evon Hekkala of Fordham University in New York and her colleagues revealed evidence for the existence of the second species by sequencing the genes of 123 living Nile crocodiles and 57 museum specimens, including several 2,000-year-old crocodile mummies.

The results resolve a centuries-old debate about the classification of the Nile crocodile, and have important implications for the conservation of both species.

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In a lab in Kansas, Aracely Lutes has created a new species of all-female lizard that reproduces by cloning itself. There wasn’t any genetic engineering involved; Lutes did it with just a single round of breeding.

This feat stands in stark contrast to the slow pace at which species usually arise. Here’s the typical story: different populations become separated in some way, whether by space, time, predators, sexual preferences, or an inability to understand one another. Differences gradually build up between them, until they can no longer produce fit and fertile offspring. Voila – where there was once one species, there are now two.

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The rivers and lakes of Africa are filled with conversations that you cannot hear or take part in. These chats are conducted by fishes called mormyrids or elephantfishes, which can produce and sense electric fields. They use their abilities to navigate through murky waters, hunt their prey, and talk to one another. It’s clearly a successful lifestyle, for there are over 200 species of mormyrid alive today.

Bruce Carlson from Washington University in St Louis thinks that the origin of these diverse species lay in the diversity of their electric songs. Different species of mormyrid communicate with different electric signals, which work as badges of identity. When they’re ready to mate, they find partners of their own kind by listening out for their preferred electric dialect.

The evolution of these diverse signals hinged in turn on changes in the mormyrids’ brains and sense organs. These allowed them to pick up subtler differences in their electric signals and talk to each other in more varied ways. This opened up a world of communication, but it was also the mormyrid equivalent of the Tower of Babel. By gaining the ability to communicate in different dialects, the species of mormyrid grew apart.

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In the novel Dr. No, the titular villain explains to James Bond that he once survived an assassination attempt because his heart was in the wrong place. The good doctor had a condition called situs inversus – his organs were mirror images of their normal versions, found on the opposite side of his body. His heart, being on the right, was unharmed when his would-be murderer stabbed the left side of his chest. Having a mirror-image body can be useful when someone’s out to kill you and while that’s true for criminal masterminds, it also applies to snails.

In Japan, Satsuma snails have shells that mostly coil in the same direction. If you put your finger in the shell’s centre and follow the spiral outwards, you would probably move in a clockwise circle. And Iwasaki’s snail-eating snake knows it.

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Imagine taking a course of antibiotics and suddenly finding that your sexual preferences have changed. Individuals who you once found attractive no longer have that special allure. That may sound far-fetched, but some fruit flies at Tel Aviv University have just gone through that very experience. They’re part of some fascinating experiments by Gil Sharon, who has shown that the bacteria inside the flies’ guts can actually shape their sexual choices.

The guts of all kinds of animals, from flies to humans, are laden with bacteria and other microscopic passengers. This ‘microbiome’ acts as a hidden organ. It includes trillions of genes that outnumber those of their hosts by hundreds of times. They affect our health, influencing the risk of obesity and chronic diseases. They affect our digestion, by breaking down chemicals in our food that we wouldn’t normally be able to process. And, at least in flies, they can alter sexual preferences, perhaps even contributing to the rise of new species.

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This is an old article, reposted from the original WordPress incarnation of Not Exactly Rocket Science. I’m on holiday for the moment, but you can expect a few new pieces here and there (as well as some exciting news…)

Certain groups of animals show a remarkable capacity for quickly evolving into new species to seize control of unexploited niches in the environment. And among these ecological opportunists, there are few better examples than the cichlids, a group of freshwater fishes that are one of the most varied group of back-boned animals on the planet.

In the words of Edward O. Wilson, the entire lineage seems “poised to expand.” The Great Lakes of Africa – Tanganyika, Malawi and Victoria – swarm with a multitude of different species; Lake Malawi alone houses over 500 that live nowhere else in the world. All of these forms arose from a common ancestor in a remarkably short span of time. Now, a new study suggests that this explosive burst of diversity has been partly fuelled by rivalry between hostile males.

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On the western coast of America, a combination of cool fog and salty sea spray keeps the soil moist all year round. In these wet conditions, you’ll find an unassuming plant called the yellow monkeyflower. Drive further inland, and the climate changes considerably. It’s hotter and drier, and every summer brings a harsh drought. But here too, the yellow monkeyflower blooms but its lifespan is shorter and its leaves are less luscious. Despite their different habitats and lifestyles, both groups of monkeyflowers are members of the same species. But that might eventually change.

David Lowry from Duke University discovered the secret of the monkeyflower’s dual identities lies in a flipped chunk of DNA. A large chunk of the plant’s genome, containing around 360 genes, has been flipped upside-down, effectively giving it two genomes for the price of one.

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What happens if you cross a fish that has white spots on a black body with another fish that has black spots on a white body? You might think that you’d get a fish with a single uniform colour, or one with both types of spots. But the hybrid’s skins are very different and far more beautiful. It does not inherit its parents’ palettes, overlaid on top of each other; instead, it gets a mesmeric swirl of black and white that looks like a maze on its skin.

To understand where these hybrid patterns come from, you need to look at how fish decorate their skins in the first place. These patterns can be very complicated, as even the briefest swim through a coral reef will tell you, but they also vary from individual to individual – one trout will have a slightly different array of spots to another. These differences tell us that intricate patterns aren’t stamped onto a fish’s skin according to a genetically encoded blueprint. They’re living patterns, generated through a lively dance between a handful of molecules.

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