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World's Oldest Genome Sequenced From 700,000-Year-Old Horse DNA
National Geographic ^ | June 26, 2013 | Jane J. Lee

Posted on 06/28/2013 8:13:52 AM PDT by null and void

Well-preserved specimen pushes back the timing of modern horse evolution.

A group of Przewalski's horses, once considered extinct in the wild.


Photograph by Michael Nichols, National Geographic


Photograph courtesy D.G. Froese via Nature

DNA shines a light back into the past, showing us things that fossils can't. But how far back can that light extend?

Some of the oldest DNA sequences come from mastodon and polar bear fossils about 50,000 and 110,000 years old, respectively. But a new study published online today in the journal Nature reports the latest in the push for recovering ever more ancient DNA sequences. Samples from a horse leg bone more than 700,000 years old have yielded the oldest full genome known to date.

"We knew that sequencing ancient genomes as old as 70,000 to 80,000 years old was possible," said Ludovic Orlando, an evolutionary geneticist with the Natural History Museum of Denmark at the University of Copenhagen. "So we said, why not try even further back in time?"

The Pleistocene horse genome Orlando and colleagues pieced together helped them determine that the ancestor to the Equus lineage—the group that gave rise to modern horses, zebras, and donkeys—arose 4 to 4.5 million years ago, or about two million years earlier than previously thought. (Learn more about the evolution of horses.)

The ancient horse genome also allowed the team to determine the evolutionary relationship between modern domestic horses and the endangered Przewalski's horse, a native to the Mongolian steppes that represents the last living breed of wild horse.

The team found that Przewalski's horses were an offshoot of the lineage that gave rise to domestic horses. The two groups diverged around 50,000 years ago.

Once considered extinct in the wild, Przewalski's horse was re-introduced into the wild from a captive population of only a few dozen. While this number suggests that the genetic diversity of the species might be too small to support, the study shows that Przewalski's horses are in fact more genetically diverse than domestic breeds such as Arabian and Icelandic horses.

"We think that there's enough genetic diversity within the Przewalski's horse to keep conservation efforts viable," Orlando said.

Cold Storage

Extracting ancient genomes from long-dead samples is labor intensive, and there is a limit to how far back one can go.

Studies on the half-life of DNA suggest that even under ideal circumstances, DNA sequences older than 1.5 million years will be too short to be readable. So it's highly unlikely that DNA will be recovered from dinosaurs, since they disappeared 65 million years ago, except for the lineage leading to modern birds.

But the preservation environment of an ancient sample can help extend the amount of time DNA has before it degrades past the point of being recoverable.

"Cold is good," said Orlando. Frozen is even better, because liquid water isn't present to degrade DNA molecules.

The six-inch (15-centimeter) horse leg bone the team analyzed originated in the Yukon Territory of western Canada. Permafrost kept the remains in a kind of cold storage for about 735,000 years until scientists dug it out in 2003.

To determine whether there might be any biological molecules left in the sample, Orlando and colleagues first looked to see if they could spot amino acids from collagen—a protein found in bone—in the specimen.

Once they identified and successfully sequenced those proteins, the researchers moved on to trying to extract DNA from the ancient leg bone.

As is the case with the majority of ancient fossils, most of the DNA they found was from bacteria that had populated the bone after the horse died. Using DNA from modern horses as a reference, the team was able to identify "endogenous" DNA that belonged to the ancient horse itself.

"We sequenced 12 billion DNA molecules, of which 40 million [were of] horse origin," said Orlando. "There was a bit of horse DNA in an ocean of microbial DNA."

A New World

The recovery of a genome almost an order of magnitude older than any previous genomic information opens up a wide range of new targets for studying fossils at the genetic level, possibly including ancient human species, if they lived in cooler environments.

"You name it—what are your favorite Pleistocene beasts?" wrote Hendrik Poinar, an evolutionary geneticist at McMaster University in Ontario, Canada, in an email.

Poinar, who was not involved in the current study, would like to see this applied to elephant evolution. "This should address issues related to the origin of hair and size plasticity and how they adapted to very different ecologies."

He was not surprised that researchers were able to sequence a complete genome from 700,000 years ago. It just takes time and money, Poinar said.

But he also points out that sequencing ancient genomes is more about preservation in various environments than the age of a specimen. "I am sure there will be older genomes soon enough."


TOPICS: Miscellaneous
KEYWORDS: dna; evolution; evolutionterritory; genome; godsgravesglyphs; helixmakemineadouble; horse; horsedna; przewalskishorse
Only 100 times further back and we could yet see Cretaceous Park...
1 posted on 06/28/2013 8:13:52 AM PDT by null and void
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To: null and void

This post should be tagged for “evolution” territory.


2 posted on 06/28/2013 8:23:47 AM PDT by OldNavyVet
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To: OldNavyVet

Always feel free to add any keyword you deem appropriate.


3 posted on 06/28/2013 8:26:15 AM PDT by null and void (Republicans create the tools of oppression, and the democrats gleefully use them!)
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To: null and void
Unless this type of study can prove that ancient horses had five fingers and five toes, or were adept at basket weaving ... I see no point in the research other than curiosity.

If, after studying all of this, they admit that there is not much variation or difference in the two horses ... stop the funding and go find YETI

4 posted on 06/28/2013 8:32:36 AM PDT by knarf (I say things that are true ... I have no proof, but they're true.)
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To: knarf

“... I see no point in the research other than curiosity.”

Exactly. Much government-funded research is playground stuff. Scientists having fun with other people’s money, but realizing no tangible benefit to society.


5 posted on 06/28/2013 8:35:04 AM PDT by BlueStateRightist
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To: knarf
Unless this type of study can prove that ancient horses had five fingers and five toes,
Eohippus (meaning "dawn horse") was the earliest-known horse ...

This primitive horse had 4 hoofed toes on the front feet and 3 hoofed toes on each hind foot.

I assume 4 in the front and 3 in the back doesn't meet your high standards.
6 posted on 06/28/2013 8:45:27 AM PDT by null and void (Republicans create the tools of oppression, and the democrats gleefully use them!)
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To: BlueStateRightist

People said the same thing when a few people started playing with radium containing rocks in the 1800’s


7 posted on 06/28/2013 8:47:18 AM PDT by null and void (Republicans create the tools of oppression, and the democrats gleefully use them!)
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To: BlueStateRightist

Well, this research was not done here, it was Denmark. This type of research is not necessarily “playground” stuff either. This could lead to extraction and characterization of extremely ancient human DNA as well. Being able to track, characterize and understand changes and mutations in a species genome across the span of history can lead to insights that could identify reasons for certain diseases and lethal mutations in humans today and possibly provide a path for correcting those problems and/or curing some diseases. Basic research is the groundwork for more specific and useful research and breakthroughs.


8 posted on 06/28/2013 8:47:23 AM PDT by RJS1950 (The democrats are the "enemies foreign and domestic" cited in the federal oath)
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To: RJS1950

“Basic research is the groundwork for more specific and useful research and breakthroughs.”

Understand your thoughts, fully. I have a basic science PhD in molecular biology, and an MD. But it’s impossible to refute your argument except to say one can always claim every seemingly trivial or esoteric discovery could change the world. But 99% won’t. Your argument cannot justify unlimited funding for very average ideas and scientists. There has to be a limit.


9 posted on 06/28/2013 8:53:41 AM PDT by BlueStateRightist
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To: null and void

I would if I could, but ... can’t seem to do it. Moderator might do it for us.


10 posted on 06/28/2013 9:04:08 AM PDT by OldNavyVet
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To: null and void

11 posted on 06/28/2013 9:09:49 AM PDT by Jeff Chandler (Harriet Meiers is looking pretty good right about now.)
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To: null and void
Didn't read the article (if that information was in it) and I never studied that stuff .. if it wasn't.

If indeed horse DEvolved from 4 to one toe ... and it's ANY indication of anything ... I'd get on my knees and ask Jesus to save me before I lost my mind.

12 posted on 06/28/2013 9:16:55 AM PDT by knarf (I say things that are true ... I have no proof, but they're true.)
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To: null and void

and what does radium do today ???


13 posted on 06/28/2013 9:17:49 AM PDT by knarf (I say things that are true ... I have no proof, but they're true.)
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To: RJS1950

Could, maybe, might ... what makes anyone think we’re going to be around the hundreds of years (from now) when it all MAY come to fruition ?


14 posted on 06/28/2013 9:19:22 AM PDT by knarf (I say things that are true ... I have no proof, but they're true.)
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To: BlueStateRightist; RJS1950
Recommemded reading: "Darwin's Ghost" by Steve Jones.

From Jones' "Introduction" we have ...

"For the past two decades the nation has lived through an episode that has, with extraordinary speed, laid bare the argument of The Origin of Species. The organism involved was unknown in the ninteenth century, but is now familiar. It is the AIDS virus."

The rest of the book is a modern update of every chapter in Darwin's "Origin."

15 posted on 06/28/2013 9:30:25 AM PDT by OldNavyVet
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To: OldNavyVet

Hmmmm. I simply clicked on “Click to Add Keyword” and typed it in.

I didn’t see any particular need to attract the “but but but the entire universe is only 6016 years, 6 months, 22 days and 37 minutes old” crowd.

They and their anti-science/Luddite ilk seem to have no difficulty finding these threads without any additional help.


16 posted on 06/28/2013 9:37:25 AM PDT by null and void (Republicans create the tools of oppression, and the democrats gleefully use them!)
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To: knarf
Didn't read the article

That's a surprise.

If indeed horse DEvolved from 4 to one toe

It did.

... and it's ANY indication of anything ...

It is.

I'd get on my knees and ask Jesus to save me before I lost my mind.

No comment.

17 posted on 06/28/2013 9:40:11 AM PDT by null and void (Republicans create the tools of oppression, and the democrats gleefully use them!)
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To: knarf
and what does radium do today ???

The study of radium containing rocks lead to a few useful things.

I bet you don't know of a single one, do you?

18 posted on 06/28/2013 9:42:16 AM PDT by null and void (Republicans create the tools of oppression, and the democrats gleefully use them!)
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To: knarf
Could, maybe, might ... what makes anyone think we’re going to be around the hundreds of years (from now) when it all MAY come to fruition ?

An old man should never plant a tree.

The fruits won't appear until he is dead.

Useful lumber won't be available until his children are old.

No point. No point at all.

19 posted on 06/28/2013 9:45:10 AM PDT by null and void (Republicans create the tools of oppression, and the democrats gleefully use them!)
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To: null and void

False alarm. It’s just Hillary. All that horse manure fooled us.


20 posted on 06/28/2013 9:48:03 AM PDT by DPMD
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To: knarf

Radiate?


21 posted on 06/28/2013 9:48:50 AM PDT by DPMD
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To: null and void
“but but but the entire universe is only 6016 years, 6 months, 22 days and 37 minutes old” crowd.

That was last week. They've evolved since then.

22 posted on 06/28/2013 9:58:42 AM PDT by tacticalogic ("Oh, bother!" said Pooh, as he chambered his last round.)
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To: null and void

Nope ... I only knew about radium watch dials that were found to be dangerous and it was stopped.


23 posted on 06/28/2013 10:01:40 AM PDT by knarf (I say things that are true ... I have no proof, but they're true.)
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To: BlueStateRightist

If basic research adds to our stock of knowledge it is worthwhile. That’s why you do basic reserch even if the knowlege doesn’t make a whit of practical difference.

I really shouldn’t have to explain that to a PhD in molecular biology.


24 posted on 06/28/2013 10:11:56 AM PDT by DManA
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To: knarf

So you’ve never had a broken bone x-rayed, never needed radiation therapy, never had a radio iodine uptake test, or a thallium heart scan, never been on an airplane whose critical turbine parts were inspected with x-rays, never used a single watt generated in a nuclear power plant, never been defended by a nuclear powered submarine, know no-one descended from a serviceman who would have died on the Japanese mainland had they not surrendered?

Each of those is a direct result of a useless, purely academic 19th century study of radium.

And radium itself? It still sees some use in treating metastasized bone cancer.


25 posted on 06/28/2013 10:15:12 AM PDT by null and void (Republicans create the tools of oppression, and the democrats gleefully use them!)
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To: tacticalogic

Nonsense!

Last week it was:

“but but but the entire universe is only 6016 years, 6 months, 15 days 1 hour and 16 minutes old”


26 posted on 06/28/2013 10:16:45 AM PDT by null and void (Republicans create the tools of oppression, and the democrats gleefully use them!)
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To: null and void

When I was born 59 years ago I had a birth mark on by one of my knees. I’ve been told they put radium needles on the site to, well, I’m not sure what they were thinking.

I have a small scar there now. No adverse consequences yet that I know of.


27 posted on 06/28/2013 10:18:39 AM PDT by DManA
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To: null and void
Last week it was:

“but but but the entire universe is only 6016 years, 6 months, 15 days 1 hour and 16 minutes old”

How can you be sure it was last week? All dating methods have been proven to be unreliable.

28 posted on 06/28/2013 10:20:48 AM PDT by tacticalogic ("Oh, bother!" said Pooh, as he chambered his last round.)
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To: tacticalogic

Except Primate of All Ireland Ussher, of course...


29 posted on 06/28/2013 10:24:45 AM PDT by null and void (Republicans create the tools of oppression, and the democrats gleefully use them!)
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To: null and void
Except Primate of All Ireland Ussher, of course...

:)

30 posted on 06/28/2013 10:38:16 AM PDT by tacticalogic ("Oh, bother!" said Pooh, as he chambered his last round.)
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To: tacticalogic

Obviously a sober and studious man...


31 posted on 06/28/2013 10:40:06 AM PDT by null and void (Republicans create the tools of oppression, and the democrats gleefully use them!)
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To: null and void

Well, it is business hours.....


32 posted on 06/28/2013 10:49:27 AM PDT by tacticalogic ("Oh, bother!" said Pooh, as he chambered his last round.)
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To: tacticalogic

Not in Ireland, unless your business is a pub...


33 posted on 06/28/2013 11:01:54 AM PDT by null and void (Republicans create the tools of oppression, and the democrats gleefully use them!)
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To: null and void

Unfortunately, I’m not, and it isn’t, so back to my studies I go.


34 posted on 06/28/2013 11:14:00 AM PDT by tacticalogic ("Oh, bother!" said Pooh, as he chambered his last round.)
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To: DManA

“If basic research adds to our stock of knowledge it is worthwhile. That’s why you do basic reserch even if the knowlege doesn’t make a whit of practical difference. I really shouldn’t have to explain that to a PhD in molecular biology.”

Of course many great discoveries resulted from trivial investigations. But, there is enormous waste in academic research. Very few within these disciplines are willing to state this. Resource allocation is an important issue in an era of limited resources. We simply cannot study anything and everything for the sake of adding to our “stock of knowledge”. If you don’t agree then you sanction departments of women’s and Africana studies, or BS investigations into environmental studies that are more political then scientific. Even basic molecular biology is laden with silly and unimaginative projects.


35 posted on 06/28/2013 12:12:18 PM PDT by BlueStateRightist
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To: null and void
Pretty sarcastic reply, eh bucko.

'COURSE I've had an x-ray ... but as far as I know, none of the rest.

I have no idea (nor do you) WHERE my electricity comes from .. and you somehow think I'm an enemy of research?

This all started with the genomes of ancient horses and you've got me denegrating WW2 vets and their offspring?

GFY, n&v.

36 posted on 06/28/2013 2:52:43 PM PDT by knarf (I say things that are true ... I have no proof, but they're true.)
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To: BlueStateRightist
The thread topic is physical science. Our side discussion is about the merits of physical science. I have do idea why you drag woman's studies into it except maybe to be augmentative.

Any hard science research that adds to our understanding of the physical world has merit. None of it is silly. How you evaluate any piece of research in the scheme of things depends on your intests.

And even if you insist on judging research by what useful technology it spawns, you can never tell. A seemingly insignificant finding might be the first link in a long chain that ends in a world changing finding. Or a piece of research might sit on a shelf for a century until some new discovery makes it vital.

In mathematics (not physical but a hard science) boolean logic was a pure abstract concept with no practical use in the real world. Any layman looking at Boole's work would have called it silly, a waste of time. Until people started thinking about automatic computing. Then it became core of the technology that civilization is built on.

No, no hard science research is silly.

37 posted on 06/28/2013 3:10:09 PM PDT by DManA
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To: knarf

About what I’d expect from someone who boasts that they didn’t read the article.

You did manage to read quite a few things that were not in my reply, and attribute what you read into it as my malice.

Have a nice day.

(s) offspring of a WWII vet, Pacific theater, Okinawa, Semper Fi!...


38 posted on 06/28/2013 3:15:13 PM PDT by null and void (Republicans create the tools of oppression, and the democrats gleefully use them!)
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Note: this topic was posted 6/28/2013. Thanks null and void.

39 posted on 06/12/2014 5:58:41 PM PDT by SunkenCiv (https://secure.freerepublic.com/donate/)
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