Who would think that the reclusive platypus would be such a trouble-maker? When the antipodean oddity made its British debut in 1799, it stirred up a ferocious debate that lasted 85 years; one that Darwin himself didn't even see the end of.

At first naturalists thought the furry creature with the webbed feet and the duck's bill was a hoax, the work of a skilful Chinese taxidermist. A specimen in London's National History Museum bears the scars of an attempt to unpick the fine 'stiches'. When none were found, the debate turned to whether this creature was really a mammal at all. Though furry, no nipples or mammary glands were visible.

Even more perplexing, dissection showed a single lower body opening like the cloaca of a bird or reptile. That earned it, and its similarly equipped cousin the echidna, a new classification amongst mammals: the 'monotremes'.

Mammary glands were located in the 1830s. But it took till 1884 for William Caldwell's famous telegram "Monotremes oviparous, ovum meroblastic," to reach the gobsmacked naturalists of the British Association for the Advancement of Science. What the young Scottish embryologist had telegraphed was: the platypus laid eggs and they were yolky. There it was: a furry, suckling, lizard-limbed, egg laying mammal. Who could resist the temptation to see it as a missing link between reptiles and mammals? Darwin, even without the egg-laying information, pronounced: "these anomalous forms may almost be called living fossils."

Now, some 209 years after the platypus first confounded the scientific community, the U.K. journal Nature has published a detailed analysis of the creature's genome; its genetic blueprint revealed in 2.3 billion letters of DNA code.

Revelations in the code

The code certainly offers revelations. "It's a key missing piece from the evolutionary puzzle that allows us to establish what the earliest common ancestors of mammals were like," says Wes Warren, whose lab at Washington University in the U.S. city of St. Louis, Missouri, carried out much of the sequencing.

But it also offers more confounding clues. "It shows the platypus method of sex determination has more in common with birds than other mammals. I'm not sure if I can make sense of this," says Des Cooper, a marsupial geneticist at the University of New South Wales in Sydney, Australia.

Let's start with the revelations that make sense and leave that confounding thing called sex till last.

There are some parts of the genome that show the platypus for what it is: a hybrid of reptilian and mammalian features. For instance the platypus' reptilian roots can be seen in the very dialect of the code. All animal genomes have stutters of repeating DNA. Some are long-lasting stanzas of thousands of letters or more; others are tiny hiccups of a few letters known as microsatellites. It turns out the platypus hiccups bear far more resemblance to those of chickens and reptiles than to those in mammals.

More evidence of the reptilian dialect is seen in a cluster of genes that control the size of the foetus. In mammals other than monotremes, these genes come imprinted with different activities: if they came from a sperm, they are highly active; if they are from an egg they are inactive. But the platypus genes from either egg or sperm have the same activity.

Andrew Pask and Marilyn Renfree at Melbourne University believe the reason the platypus genes don't bear imprints is revealed by their cleaner DNA. While the foetal growth genes of mammals are peppered with stanzas of repetitive DNA, the platypus genes are relatively free of them, as are the corresponding genes of the chicken (overall the platypus genome has about the same fraction of repetitive DNA as other mammals: 50 per cent). "Repetitive [DNA] often causes neighbouring genes to shut down and that may have been useful for establishing imprinting in the other mammals", explains Pask.

From yolk to milk

Like other mammals, around 2 per cent of the platypus genome codes for proteins – 18, 527 of them. Some provide tantalizing traces of the journey from reptile to mammal, particularly the ones that produce egg yolk and milk.

The yolk of a reptile's egg is all the nourishment the developing foetus will ever get. But a mammal nourishes its developing young continuously, first with the placenta and then with milk, which allows for the development of the big mammalian brain. But how do you go from being an egg-laying reptile to an animal with a placenta and milk production?

The platypus doesn't give all the answers but it does give us a clue. It seems the first step is to get the milk production happening; then you can afford to ease off on yolk production. Essentially the foetus gets weened from yolk to milk. That's what you see in the platypus genome. All the casein milk protein genes that other mammals have are already present. They are nestled right next to the genes for making tooth enamel proteins.

Most likely the milk protein genes evolved from those tooth enamel genes. A copying error created a second but faulty set of tooth genes that eventually turned out to be useful as milk proteins. On the other hand the platypus egg yolk genes, the vitellogenins, are on the way out. While chickens have three copies, the platypus only has one.

Venom genesis

Another feature the platypus shares with its reptilian ancestor is a potent venom it produces from a spur on its hind legs. Kathy Belov and colleagues at the University of Sydney accidentally identified the genes that produce the venom.

Her main interest had been to find out how the platypus protects its young from the grotty environment they live in. When born, they have no functioning immune system – no spleen, no thymus, no T or B cells, no antibody-making cells. The belief was that mother's milk carried some anti-microbial compounds. Belov found the antimicrobial gene cathelicidin, seven copies of it in fact. Humans only carry one.

As many studies of animal genomes are showing, duplicating genes is a quick way to evolve new traits. But Belov's code scan also picked up a gene that vaguely resembles another anti-microbial gene known as defensin. It turned out this gene was not employed against microbes but against larger adversaries: it was the major component of the venom.

Reptile venom, it turns out has also evolved from the defensin gene. But according to Belov's analysis, the co-opting of defensin in platypus and in reptile venom were independent events.

Serious smelling power

The platypus may have held on to many ancestral characteristics but its adaptation to its watery world is awe-inspiring. It spends most of its time underwater, blind and deaf, relying on electro sensors on its bill to detect the electric impulses of prey.

A big surprise from reading the genome is that it may also be adept at detecting water-borne odorants. Tsviya Olender and Doron Lancet at the Weizmann Institute in Rehovot, Israel, analysed the platypus code for clues to its system of odour detection.

As Lancet puts it, "animals have two noses". One, which depends on olfactory sensors, can only detect air-borne compounds. The other is the vomeronasal organ (humans probably don't have one). Vomeronasal receptors are like nasal taste buds, able to detect non-volatile compounds.

For instance dogs taste pheromones in urine by touching their tongue to the vomeronasal organ in their upper palate. The platypus turns out to be superbly endowed with vomeronasal receptors. "A typical mammal has a couple of hundred of them; the platypus has 1,000", says Lancet. Since the platypus spends 90 per cent of its time in water, he speculates the platypus uses these receptors for detecting water-soluble odorants.

Which brings us finally to sex and the platypus. Specifically the sex chromosomes of the platypus.

Platypus sex

For most mammals, their chromosomes look pretty similar, all fairly large and about 50 of them. Reptiles and birds are very different though; they tend to have lots of tiny chromosomes that early cytologists referred to as 'chromosome dust'. Shockingly to the first cell biologists who peered down the microscope and saw them, the platypus chromosomes resemble those of birds and lizards. They are a mess of 46 tiny chromosomes and 6 big ones.

But it's not just the outward appearance of the chromosomes that bears a resemblance to birds. Mammals like us (eutherians) or kangaroos (marsupials) all determine sex by having different sets of sex chromosomes. Getting a pair of the two big X's makes a female. An X and a little Y, makes a male. Birds on the other hand have an opposite system. Two copies of a big Z chromosome make you a male, while a Z plus a little w, makes you a female.

But not all animals have different sex chromosomes. In many species of reptile for instance, males and females have the same chromosomes. Their sex is determined by temperature.

If you're a turtle egg, in cool conditions you're a male; if it warms up you're female. So the thinking is that a couple of hundred million years ago, some animals stopped relying on temperature and put their own failsafe sex switch onto one of the chromosomes. At that point the chromosome pair had to stay different, and so they drifted further and further apart, till the point that you have the almost unrecognisable pairs of X and Y or Z and W.

So what do we see in the platypus? For starters, they have ten sex chromosomes! Females have five pairs of X and males have five X and five Y. None of the platypus sex chromosomes are even vaguely related to ours. Searching for the remains of our X chromosome, locates it on a regular chromosome, autosome number six. It's a finding that nicely aligns with the theory that sex chromosomes evolved from ordinary ones.

Weird mammals, weird results

If the platypus sex chromosomes are not similar to ours, then what are they like? To use the words of the eminent geneticist Jenny Graves at Australian National University in Canberra. When it to comes to sex determination "platypus do it like a chook".

She says that because work from her lab and others at ANU, has revealed that the platypus sex chromosome is very much like the big sex chromosome of the bird – the Z. "In the past we identified a handful of genes that were the same; now its clear that the platypus X-5 and the chcken Z, share hundreds of genes; they're virtually the same [chromosome]."

For many researchers this is totally confounding. Birds and platypus are on very different branches of the evolutionary tree.

But Graves suspects their common ancestor may well have had both systems of sex determination: XY and ZW, and that their offspring may have opted for one way or the other, or even both. It was she says, "not supposed to be able to happen". But the Japanese frog Rana rugosa, shows it can happen. Some populations are XY; others are ZW.

"When you work on weird Australian mammals you get weird results, and these sometimes have tremendous consequences," says Graves.

It seems, two hundred years on, the platypus is still causing upheavals. But only the first few pages of the ancient platypus text have yet been decoded. With scientists around the world immersing themselves in this and other animal genomes, they hope that the the long-buried secrets of mammalian evolution will gradually emerge.

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