Platypus genetics revealed! As weird as you'd expect.

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Platypus genetics revealed! As weird as you'd expect.

Post by SylasGaunt »

Platypus Genetic Code Unravelled
Scientists have deciphered the genetic blueprint of the duck-billed platypus, one of the oddest creatures on Earth.

The animal comes from an early branch of the mammal family, and like mammals it is covered in fur and produces milk. However, it lays eggs like a reptile.

Researchers say this unique mixture of features is reflected in its DNA.

The genome sequence, which is published in the journal Nature, holds clues to how humans and other mammals first evolved, they add.

The platypus (Ornithorhynchus anatinus) is the latest in a string of mammals, including the mouse, rat, sheep, horse and dog, to have its genome decoded.

But it is the only member of the monotremes (egg laying mammals) for which we have a genetic blueprint.

Dr Chris Ponting, of the MRC Functional Genetics Unit at the University of Oxford, UK, is one of more than 100 researchers from the US, UK and Australia, who took part in the study. He said the platypus was chosen because of its unusual features.

The platypus is so strange that it was considered a hoax when sent from Australia to European researchers in the 19th Century.

"It has a very weird appearance because it's a mishmash of the bill of a duck, the eyes of a mole, the eggs of a lizard and the tail of a beaver," Dr Ponting told BBC News.

"It was one of several (mammals) we could have chosen, but it was certainly the one that everyone seemed to wish to sequence because of its unusual features."

Dr Ponting said the genome sequence enabled scientists to look back in time to see what an early mammal would have been like.

He said: "It's wonderful to see all of the different mishmash of features that the platypus exhibits; to see those features reflected in the DNA, in the genes of this creature, which has held mysteries for the scientists and the general population ever since it was discovered 200 years ago."

The DNA came from a female, nicknamed Glennie, which was captured in the wild in New South Wales, Australia.

The sequence was then compared with stretches of DNA from about 100 platypuses living in the wild.

Dr Mark Batzer, from Louisiana State University in Baton Rouge, who also worked on the study, said the data would help in conservation efforts by allowing scientists to investigate population size, structure and breeding habits.

"In the case of the platypus, clearly we learned a lot about a unique organism that has relevance in terms of its endangered status and conservation biology," he said.

"One big surprise was the patchwork nature of the genome with avian, reptilian and mammalian features," he added.

The platypus and the small spiny mammal known as the echidna are the only existing species of monotremes in the world. All other mammals give birth to live young.

The platypus is widespread in the eastern states of Australia, living in and around streams and rivers.

They have acute sight, but only open their eyes above water.

Underwater, they rely on touch and a special sense called electro-reception that allows them to detect tiny changes in the electrical field generated by their prey.
So they've deciphered the little guy's gene patterns and... they're just as weird as expected. Well hello there common ancestry! (though granted everything has a common ancestor if you go back far enough).

Though I have this image in my head of a snake, a beaver, a duck, and a lot of tequila.
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Re: Platypus genetics revealed! As weird as you'd expect.

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"One big surprise was the patchwork nature of the genome with avian, reptilian and mammalian features," he added.
What's that about avian-like genes? I thought the "bill" was just a flattened mouth with thick, rubbery skin, not a keratin structure jutting beyond the jaw. I wouldn't think the beast would have any genes that are more bird-like than reptilian. Both are so far derived from their purely reptilian common ancestor (although I understand birds are now classified as reptiles, why really I don't know). Unless maybe there are some early genes that were preserved in birds and monotremes but not lizards or crocodiles.

I also wonder about the genetic connection between having one orifice and laying eggs. As a layman, I wouldn't immediately assume that the two must necessarily go together, yet is it coincidence that the only mammals that lay eggs also have one hole? Obviously both are basal characteristics, but why must both be preserved or discarded together?
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Post by Wyrm »

The platypus bill is nothing like a duck's bill. Nothing. It's got shit that a duck bill doesn't have (electroreceptors), and doesn't have shit that a duck's bill does have (horny outer layer).

There are no avian-like features to the platypus that isn't shared with other mammals — that didn't come directly from the fact that we're decended from mammal-like reptiles.
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Post by SylasGaunt »

Indeed the article doesn't mention what the avian features are. If I remember right it's egg-laying is closer to reptilian than anything else (leathery shell and all). Looking around I noticed another article that mentions they've got a gene on their X5 chromosome that matches up with one from birds though they don't know if it does the same thing. Maybe it's the spurs? I'll have to see if I can find something more detailed.

Also apparently the Platypus (what the hell is the plural of that anyway? Platypuses? Platypi?) has 10 sex determining chromosomes. Go figure.
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Post by Fire Fly »

Science

A more detailed account of the platypus genome.
Science 9 May 2008:
Vol. 320. no. 5877, p. 730
DOI: 10.1126/science.320.5877.730

News of the Week
GENOMICS:
Genome Speaks to Transitional Nature of Monotremes
Elizabeth Finkel*

Zoologists have always thought that the platypus was a missing link in the chain between reptiles and mammals. The furry beaverlike mammal lays small, round, leathery eggs from a reptilelike cloaca, and the hatchlings slurp milk from modified sweat glands off the mother's stomach. Now an analysis of the genome reveals how platypus DNA is also an amalgam of mammalian and reptilian features. Wes Warren of the Genome Sequencing Center at Washington University in St. Louis, Missouri, and 100 authors describe these features in the 8 May issue of Nature.

Mammals divide into three groups. Most--from whales to shrews--are eutherians with highly developed placentas. Some are marsupials, which, like kangaroos and opossums, give birth to and then provide milk for immature young outside the womb. The platypus and its cousins, the echidnas, are all that remains of the monotremes, which branched from the marsupials and eutherians some 166 million years ago. "If there is something between reptiles and mammals, it's monotremes," says Stephen O'Brien of the U.S. National Cancer Institute in Frederick, Maryland.

The new genome sequence confirms the ancient split between monotremes and other mammals. "It's a missing part of the big evolutionary genetics puzzle," O'Brien adds.

The clearest traces of the journey from reptile to mammal come from tracking the yolk and milk genes. Chickens have three vitellogenin egg yolk genes; the platypus has just one left. But the casein milk protein genes that mammals have but reptiles don't are all there. And just as in other mammals, in platypus, they are clustered next to the tooth enamel genes from which they are thought to have evolved, the researchers report.

The story of the platypus' march away from the reptilian world is also told in the sex chromosomes. According to Jenny Graves of the Australian National University in Canberra, sex chromosome-wise, "they do it like a chicken." Typically, male mammals have X and Y sex chromosomes, with the Y chromosome carrying a male sex-determining gene called SRY. Male birds have two Z chromosomes, which carry a gene called DMRT1 that is involved in male gender determination in fruit flies, humans (although it's not on the Y chromosome), and, most likely, birds. At first, cytologists thought the platypus was like the mammal: It had X and Y chromosomes, albeit five pairs of them, and it was thought that they were essentially humanlike. Then in 2004, Graves's lab discovered that one of these "X" chromosomes carried DMRT1. The genome sequence now shows that one of the platypus X chromosomes (X5) has more than just that one bird gene: It's almost entirely equivalent to the chicken Z chromosome. "We suspect DMRT1 is involved in the platypus sex determination," says Frank Grützner, Graves's former postdoc, who now heads a lab at the University of Adelaide in Australia.

Gene regulation also seems to be more primitive, as platypus genes do not show parental imprinting. In marsupials and eutherians, imprinted genes are dialed to different settings and sometimes shut down altogether, depending on whether they originated from the male's sperm or the female's egg. According to Andrew Pask and Marilyn Renfree of the University of Melbourne, the distribution of repetitive DNA elements in this monotreme may explain the difference. As in other mammals, about 50% of the platypus genome is comprised of repetitive DNA. But although these repeats pepper imprinted genes in marsupials and man, they are largely absent from the equivalent genes in platypus. "Repetitive elements may have been useful for establishing imprinting in the other mammals," Pask suggests.

Another feature the platypus shares with reptiles is that it makes venom, which it delivers from a hind leg spur. The genome analysis indicates that, like snake and lizard venom, platypus venom appears to have evolved from antimicrobial genes known as defensins. However, according to Kathy Belov of the University of Sydney, the platypus genes evolved independently.

A big surprise is the platypus's large endowment of a particular class of vomeronasal receptor genes--about 1000 of them--based on the analysis by Doron Lancet and Tsviya Olender of the Weizmann Institute in Rehovot, Israel. "A typical mammal has a couple of hundred of them," says Lancet. Unlike olfactory receptors, which detect only airborne compounds, these receptors are more like nasal taste buds, able to detect nonvolatile compounds. For instance, dogs taste pheromones in urine by touching their tongue to the vomeronasal organ in their upper palate. Because the platypus spends 90% of its time in water, Lancet speculates that the platypus uses these receptors for detecting water-soluble odorants.

"Looking at the venom, egg, and milk genes is really interesting, but as with comparisons between opossum, mouse, and human genomes, the protein-coding sequences don't explain the interesting developmental transitions," notes John Mattick of the University of Queensland in Brisbane, Australia. Differences in gene regulation, most likely, provide the answer. And in this respect, the platypus researchers still have their work cut out for them, he adds: "[Gene regulation] information is there but is not yet understood."
I don't know much about platypuses but the bit about them having venom surprised me. I wasn't aware until now there existed mammals who have venomous mechanisms.
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Post by CaptainChewbacca »

Platypus is (I believe) the ONLY venomous mammal in the world, and I won a trivia contest by knowing that :P
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Post by Oskuro »

The fucking platypus has electroreceptors?! And is venomous?!

What else? They'll find out the thing has Autobot ancestry?
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Post by weemadando »

CaptainChewbacca wrote:Platypus is (I believe) the ONLY venomous mammal in the world, and I won a trivia contest by knowing that :P
The echidna also has the spurs but the venom gland isn't fully developed so it's not venomous. But, to counter, it does have a FOUR HEADED PENIS. Yes. I'm serious.
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Re: Platypus genetics revealed! As weird as you'd expect.

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"It has a very weird appearance because it's a mishmash of the bill of a duck
As already mentioned, the resemblance is superficial at best - structurally it is NOTHING like a duck's bill.
He said: "It's wonderful to see all of the different mishmash of features that the platypus exhibits; to see those features reflected in the DNA, in the genes of this creature, which has held mysteries for the scientists and the general population ever since it was discovered 200 years ago."
Actually, I'm pretty sure the native Australians noticed them a LOT longer ago than a mere 200 years....
The platypus and the small spiny mammal known as the echidna are the only existing species of monotremes in the world. All other mammals give birth to live young.
Stating "the" echidna is a bit misleading - there are actually four species of echidna. And before anyone asks, yes, all male echidnas regardless of species really do have a four-headed penis, but during intercourse they apparently use only half of it at a time.
I also wonder about the genetic connection between having one orifice and laying eggs. As a layman, I wouldn't immediately assume that the two must necessarily go together, yet is it coincidence that the only mammals that lay eggs also have one hole? Obviously both are basal characteristics, but why must both be preserved or discarded together?
Everything that lays eggs does everything - shit, fuck, lay eggs - through one hole, the cloaca. For that matter, some live-bearing critters like guppies and some species of sharks give birth through their cloacas as well. Non-monotreme mammals are the oddballs for dividing the sewer from the playground. Back when European scientists weren't sure if monotremes were a kind of marsupial or actual egg-layers the existence of a cloaca instead of distinct vagina and asshole in the females was used as an argument in favor of egg-laying, although as I pointed out there are live-bearing animals that do just fine with that same arrangement, although none of those are mammals.
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Post by hongi »

I'm surprised there hasn't been the comment about "God must have a sense of humour!' that always seems to accompany platypi articles.
"[Gene regulation] information is there but is not yet understood."
I keep up to date with evolutionary biology which is at the intersection between genetics and applied biology, so it's quite interesting to see the whole field abuzz with gene regulation research. Evolutionary developmental biology is the latest exciting field (the greatest thing since sliced bread if you ask its adherents) and gene regulation is a huge part of that. If you're going to get into biology in the next 20 years, you should aim for this. It's not how many genes you have, it's how they're used that counts.
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Post by Drooling Iguana »

LordOskuro wrote:The fucking platypus has electroreceptors?! And is venomous?!

What else? They'll find out the thing has Autobot ancestry?
Well we never found out what happened to most of the stasis pods after the Beast Wars. These things could be fuzors.
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Post by darthbob88 »

CaptainChewbacca wrote:Platypus is (I believe) the ONLY venomous mammal in the world, and I won a trivia contest by knowing that :P
Actually, there are a few other venomous mammals.
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Post by FA Xerrik »

I'm no expert on monotreme fossil history, but a cursory look through wikipedia suggests that no fossils have been found outside of Australia. If monotremes really do represent the link between reptiles and mammals, would it be viable to postulate that mammals, at least as we know them today, may well have first evolved in what is now Australia?
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Post by Mayabird »

The only way one can talk about "avian" genes is if the genes in both the platypus and birds are holdovers from reptilian ancestry way back when. And I mean way back when, as the line that produced mammals may have split off over 300 million years ago. It's just silly at that point.

But it's not silly to compare genes and gene regulation of animals that have had over a hundred million years to evolve in isolation from other mammalian lines. I'm wondering if they'd gained features like venom and electroreceptors or just kept them over that time.
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Post by weemadando »

darthbob88 wrote:
CaptainChewbacca wrote:Platypus is (I believe) the ONLY venomous mammal in the world, and I won a trivia contest by knowing that :P
Actually, there are a few other venomous mammals.
It is however the only venomous monotreme. But hey, like that's hard.

Oh and shrews for the win, angry venomous rats? YES!
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Post by hongi »

FA Xerrik wrote:I'm no expert on monotreme fossil history, but a cursory look through wikipedia suggests that no fossils have been found outside of Australia.
Platypus fossils have been found in South America. They were all connected up in Gondwana remember.
FA Xerrik wrote:If monotremes really do represent the link between reptiles and mammals
Monotremes don't represent the link between reptiles and mammals. I'll explain down below.
FA Xerrik wrote:would it be viable to postulate that mammals, at least as we know them today, may well have first evolved in what is now Australia?
Maybe?

I've found the Science article to be more confusing (that may just be me) than the BBC article:
Science wrote:Zoologists have always thought that the platypus was a missing link in the chain between reptiles and mammals
Let me say definitively that the monotremes are NOT a link between reptiles and mammals. Monotremes are the descendants of a split between prototherians (egg-laying mammals such as monotremes) and other mammals (therians, including placentals and marsupials). A split between mammals and mammals.

Reptiles and mammals split some 300 million years before this split between prototherians and therians. So I'll repeat that again. Monotremes are not the link between reptiles and mammals. The article should have come out immediately after the opening sentence with a firm denial of the veracity of that statement.
Science wrote:...Now an analysis of the genome reveals how platypus DNA is also an amalgam of mammalian and reptilian features.
Reptiles and mammals split off some 300 million years ago from a common amniote ancestor.

This means mammals (including platypi) cannot have reptilian traits. The two are separate lineages. You can say that mammals have traits that are reminiscent of their cousins the reptiles.

But even this is unnecessarily confusing. Simply state that mammals have ancestral amniotic traits, the same ancestor that reptiles share. This amniotic ancestor explains the seemingly reptile traits that platypi have.

For example, reptiles got their egg-laying trait from the amniote ancestor. Mammals also got this egg-laying trait from the amniote ancestor. This trait is not reptilian, it is amniotic. Some of these ancestral amniotic traits like egg-laying have been lost in the therian mammals (placentals/marsupials).

Only a little while later, they get it right:
The new genome sequence confirms the ancient split between monotremes and other mammals. "It's a missing part of the big evolutionary genetics puzzle," O'Brien adds.
And this article is one of the better ones. Many of the popular press articles are way off the mark. Why couldn't they have asked a researcher to check it for basic errors?
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Post by hongi »

Mayabird wrote:But it's not silly to compare genes and gene regulation of animals that have had over a hundred million years to evolve in isolation from other mammalian lines. I'm wondering if they'd gained features like venom and electroreceptors or just kept them over that time.
Apparently platypi invented venom and the bill separately in their own lineage.

I found a picture on a science blog that helps.
Johonebesus wrote:(although I understand birds are now classified as reptiles, why really I don't know).
Because birds descended from reptiles, they're counted as reptiles the same as we're counted as apes because we descended from apes. Scientists classify on the basis of ancestry, which is why I have a dinosaur outside my window right at this moment!
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Post by Drooling Iguana »

But mammals are also descended from reptiles, but aren't classified as reptiles. Why don't birds get their own group? I mean, the warm-bloodedness alone divides them rather sharply from modern reptiles.
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Post by hongi »

But mammals are also descended from reptiles, but aren't classified as reptiles.
Have a look at the picture again. Mammals are not descended from reptiles. Mammals descended from an amniotic common ancestor that also gave rise to the reptiles.
Why don't birds get their own group? I mean, the warm-bloodedness alone divides them rather sharply from modern reptiles.
No matter what bizarre trait you develop, you will always belong to the same ancestral clade/group. That is why we and most other organisms that are visible to the naked eye are all modified eukaryotes, even though we don't look anything like a microscopic micro-organism.

To put it another way, snakes are tetrapods (four-limbed organisms). But snakes don't have four limbs. They descend from ancestors who did. They are still classified as tetrapods.

It's been relatively recently understood that biological classification reflects evolutionary relationships. It isn't arbitrary. It amazes me to this day, that the positions of animals on the 'tree of life' are accurate (or somewhat accurate) representations of the evolution of life. Linnaeus started the classification thing off, Darwin brought it to everyone's attention.
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Post by Drooling Iguana »

Ah. I hadn't actually looked at the picture.
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Post by hongi »

Damn it, I apologise for the double posting. But I see the problem with the picture. The term 'mammal-like reptile' is confusing and inaccurate, as Wikipedia explains:
Therapsids are an order of synapsids (Class Synapsida). Traditionally, synapsids were referred to as reptiles and were known as the "mammal-like reptiles". However, they are now classified as a sister-group to the reptiles, and are phylogenetically closer to the mammals.
The correct term is mammal-like synapsid.
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Post by FA Xerrik »

Ah, thanks for the clarification. The synapsid distinction had me confused, I thought that they represented a separate lineage (the reptomammals) that had died out in the past, replaced by a new mammalian lineage derived from reptiles. You learn something new every day.
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