700,000-Year-Old Horse Becomes Oldest Creature With Sequenced Genome

sciencehabit writes "Scientists have sequenced the oldest genome to date—and shaken up the horse family tree in the process. Ancient DNA derived from a horse fossil that's between 560,000 and 780,000 years old suggests that all living equids—members of the family that includes horses, donkeys, and zebras—shared a common ancestor that lived at least 4 million years ago, approximately 2 million years earlier than most previous estimates. The discovery offers new insights into equine evolution and raises the prospect of recovering and exploring older DNA than previously thought possible."

Comments

Re:Bible is truth not false science

[hkroger]

No, horses were created 6 thousand years ago by God. Just like the Bible says. People are willingly ingorant of the worldwide flood. "For this they willingly are ignorant of, that by the word of God the heavens were of old, and the earth standing out of the water and in the water: Whereby the world that then was, being overflowed with water, perished: But the heavens and the earth, which are now, by the same word are kept in store, reserved unto fire against the day of judgment and perdition of ungodly men. II Peter 2

Damn, I was going to joke about God and stuff, but this guy got here first. +1 Funny

Re:Bible is truth not false science

[Anonymous Coward]

> No, horses were created 6 thousand years ago by God.

The problem is that God (monotheism) was only created 4 thousand years ago. (by humans)

Re:Bible is truth not false science

[Anonymous Coward]

So is this voted up for laughs? or are people on slashdot with mod points actually that wilfully deluded?
I guess I should not ask....... having a book that tells you what is right and wrong, makes the world black and white in clear code, gives you an illusion of the understanding of everything and a way to "win" is just too attractive to give up, even for pesky reality.
see
http://www.youtube.com/playlist?list=PL126AFB53A6F002CC
for some of the better refutation

Welcome to Pliocene Park

[plover]

We may never get a dinosaur theme park, but we've got a decent shot at a carousel full of ancient horses, saber-tooth tigers, and wooly mammoths. What could possibly go wrong?

Re:Welcome to Pliocene Park

[cold fjord]

Quite.

Bears, tigers, lions and wolves escape from Ohio zoo

Re:Welcome to Pliocene Park

[PolygamousRanchKid]

What could possibly go wrong?

Oh, that horsey DNA will end up in our frozen lasagne, here in scenic, and quite rainy, Europe . . .

Re:Welcome to Pliocene Park

[jd2112]

Lions and Tigers and Bears (and Wolves), Oh My!

Re:Welcome to Pliocene Park

[eriqk]

Quite.

Bears, tigers, lions and wolves escape from Ohio zoo

We did it!

Re:Bible is truth not false science

[b4dc0d3r]

Jesus Christ, it's like the science idiots were right all along.

What've we left? Buggery? Geocentrism? Non man made global warming? Jesus Mary and Joseph cooked into toast?

  Have we at the least found the fecking ark?

World's Oldest and First Ass

[danbert8]

I'm glad we now understand the genetic base of the jackass. Maybe with this knowledge medical science can remove those genes from human DNA.

Re:World's Oldest and First Ass

[Anonymous Coward]

What? And leave an empty shell?

Re:World's Oldest and First Ass

[Anonymous Coward]

This is an opportune moment to mention one of my favorite scientific paper titles ever.

Re:World's Oldest and First Ass

[Anonymous Coward]

Say what you want about his social graces, but that guy was a real stud.

Re:World's Oldest and First Ass

[Anonymous Coward]

Damn you, you made me laugh.

Is the science repeatable?

[cold fjord]

I've read some articles on attempts to extract and sequence old DNA in this sort of range, and I'm surprised they've been able to do this given the half-life of DNA.

I wonder how many other researchers are making claims of extracting DNA this old? It seems improbable, but maybe the state of the art has greatly improved.

DNA has a 521-year half-life

The team predicts that even in a bone at an ideal preservation temperature of 5 C, effectively every bond would be destroyed after a maximum of 6.8 million years. The DNA would cease to be readable much earlier — perhaps after roughly 1.5 million years, when the remaining strands would be too short to give meaningful information.

Re:Is the science repeatable?

[Anonymous Coward]

If that research states that DNA can be possibly be recovered if it is less than 6.8 million years old, why is 10% of that time a surprise? Moreover, what you quoted did not specify the sample size. Assuming their DNA half-life is correct, larger sample sizes will be able to produce meaningful information at dramatically older ages. 6.8 million years ago may only be relevant for a specific amount of genetic material from a specific source. What if there are more strands in each cell, More cells per gram, or simply a bigger chunk of bone? That is not at all accounted for. The larger the sample size, the higher the likelihood that meaningful information can be derived simply due to the sheer volume of outliers likely to be present.

Re:Is the science repeatable?

[cold fjord]

You have to not only recover it, but to read it as well. And the fine article from the post indicates they were able to actually conduct genetic analysis on it. That pulls the maximum viability date in quite a bit. The jump in age over previous finds in which they've been able to extract viable information is pretty significant, going from 130,000 years to between 560,000 and 780,000. And note that the figures I show from the story I quoted were under ideal preservation. Maybe it is all correct, but it seems a bit of a longshot to pull that information from such an old bone. I suppose they could just have been lucky.

Re:Is the science repeatable?

[csirac]

To cut a long story short, at "6.8 mllion years old" I assume they mean "the longest read (maximum number of consecutive GATC 'letters' in a row) you're possibly going to get is one". Imagine having a pile of letters which were once arranged into the collective works of William Shakespeare: could you re-assemble the original work? No. But what if you had 4-letter fragments? You might be able to learn something about the english language, indirectly, but you probably won't be able to reverse-engineer the complete original work. Now what if you had slightly longer fragments? That would help. What if the garbled pile of letters/fragments actually consisted of multiple, similarly (randomly!) shredded copies of Shakespeare? Well, as long as they're randomly fragmented in different ways - you can imagine that where we guess two fragments might join each other, if we have a fragment from that same region from another copy wich spans that join - we can become more and more confident about forming a plausible assembly. So we can take advantage of this redundancy and randomized fragmentation to attempt recovery of the original work.

In other words, the more degraded the DNA, the shorter the fragments and the harder it is to come up with an assembly. At some point the fragmentation might be so bad that the only way you can attempt to achieve anything is to try to use a relevant, well understood reference sequence from a modern day specimen/consensus for comparison (or clues, or to fill-in-the-blanks)... if one exists. I'm no geneticist, but I think in those circumstances the confidence in the results start to go from "hey, that's cool!" to "interesting" to, eventually, an artist's rendition of what an ancient genome might have looked like - drawing from long lost cousins which are still alive today.

Happily, re-assembling short, fragmented DNA happens to be how commodoty high-speed, high-throughput, low-cost sequencing works these days - DNA is split into small lengths, Eg. 500-ish basepairs, and then depending on the experiment/purpose/targets etc. it's all (or partially) re-assembled by finding enough overlapping bits (hopefully beginning and ending with proprietary markers used in the splitting process) with statistical tricks to qualify if the data is sufficient, which areas are problematic in coverage/confidence etc... and it helps enormously if you're working on an organism that's already been sequenced to death for comparison.

So there are many well advanced tools for coming up with contiguous DNA from a pile of short reads.

IIRC, the other trick with ancient DNA is - first of all, extracting enough useful material to begin with, without damage. As reads get shorter, increased redundancy helps - more randomly overlapping regions can ease the task of re-assembly - but very short reads might mean that a number of different assemblages are possible. Not to mention delicate amplification methods which might increase the noise as well as the signal...

Re:Is the science repeatable?

[ledow]

Kind of like the way that one photo of Jupiter through a telescope will be blurry and useless.

But take 10,000, choose the best 5%, layer them over each other, centre them, then form an overlaid image, and you can get some STUNNING results from even a blurry, horrible, 10,000 image source.

(For reference - google "Registax").

I'd go for that. It doesn't seem implausible at all, and DNA is much more simple in construction than you might think - which gives fewer combinations but more tricky fitting together. Get enough fragments, though, and you can throw it through a computer and get something useful out of the other end.

Re:Is the science repeatable?

[julesh]

You have to not only recover it, but to read it as well. And the fine article from the post indicates they were able to actually conduct genetic analysis on it. That pulls the maximum viability date in quite a bit.

Which is why the article you cited goes on to state "[t]he DNA would cease to be readable much earlier — perhaps after roughly 1.5 million years, when the remaining strands would be too short to give meaningful information." Given that 1.5Myear figure, why is 700Kyear surprising? It's not like they're expecting a technological breakthrough to make that 1.5My figure possible: we can already sequence pretty-much any single DNA strand we want, and reconstruction from short fragments is also an existing and thoroughly-developed technology.

Re:Is the science repeatable?

[only_human]

It looks like it was a difficult accomplishment:
They also combined DNA sequencing techniques to get maximum DNA coverage — using routine next-generation sequencing with single-molecule sequencing in which a machine directly reads the DNA without the need to amplify it up which can lose some DNA sequences. [1]
Such genetic puzzle assembly generally includes multiple samples from each part of the genome, sometimes as many as five or 10. In this case, the so-called coverage was just 1.12. [2]
"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." [3]
[1]http://www.nature.com/news/first-horses-arose-4-million-years-ago-1.13261
[2]http://www.latimes.com/news/science/la-sci-ancient-horse-genome-20130627,0,2514595.story
[3]http://news.nationalgeographic.com/news/2013/06/130626-ancient-dna-oldest-sequenced-horse-paleontology-science/

Re:Is the science repeatable?

[csirac]

I'd go for that. It doesn't seem implausible at all, and DNA is much more simple in construction than you might think - which gives fewer combinations but more tricky fitting together. Get enough fragments, though, and you can throw it through a computer and get something useful out of the other end.

But that's the whole problem! Doesn't matter if you image a lonely letter 'A' on a shred of paper in 72dpi, 300dpi, 60000dpi - it's still a letter A, and you're never going to know what its neighbours were :-) Imagine those 10,000 image sources you mentioned, imagine they're 10,000px each. But instead of working from whole frames neatly arranged into 10000 frames of 100x100 pixels, all you have are 100000000 apparently random, individual pixels. How would you begin the task of assembling them into a single picture? You can imagine that as you grow the fragment size into 2x2, 4x4, 10x10 etc etc. squares which randomly cover random different pieces of the subject, you can eventually come up with a single compelling assemblage with a strong consenus that "this is what the subject must have looked like". But if these fragments get too small, especially without any idea of what the subject should look like... you suddenly get a worthlessly large number of equally valid contigs.

Re:Is the science repeatable?

[csirac]

Not to mention - imaging a planet doesn't affect the planet. Extracting DNA, without contamination is a huge challenge for ancient DNA. It's hilarious how many NCBI sequences of mammal specimens turn out to matches for fish or insects (lab assistant's lunch? Did a fly get smooshed into a vial?) etc. Even if you do successfully extract, isolate and amplify some ancient DNA, how do you know you amplified actual DNA of the specimen and not something living in it (nematode etc)? In any case, I was just speculating that the "6.8M" year figure was perhaps the limit for the stability of the basic chemicals making up the GATCs under ideal conditions. IIRC they very quickly loose their structure and loose context from their neighbours much more quickly than that though. Disclaimer: not a scientist :-)

Re:Is the science repeatable?

[ledow]

Yes, it's a little closer to, say, reassembling a shredded document. If you shred it enough, of course it's just a bundle of characters that are really hard to piece together.

But if DNA really takes as long as stated to decompose even under ideal conditions, we are basically one half of the time required for it to decompose under those conditions to the point where it's probably not capable of reassembly. So we aren't stuffed, even without ideal conditions. And tying in with what we know of horse DNA, we're even less stuffed.

And putting huge amount of computation and DNA from the same animal through it, and we're even less stuffed. Seems to me to be a pretty damn useful technique, overall, even if it's only "statistically" correct.

And contamination? Sure it's possible. But the chances of modern DNA contamination are vanishingly small (that's why we have all those labs and things, and how you know your cancer result is yours and not that of the fly that flew into the hospital where you were being tested), and the ancient contaminations - unless they form the majority of the sample - will be pushed out by sheer probability and statistics.

Nobody is saying that this is 100% the exact DNA of this animal (and why would you WANT that? It might be a complete throw-back and have a one-off DNA coding that no other animal of its type has ever had). But it's so close to dammit, on average, that it's more than useful for scientific enquiry.

If you gather enough of a material, and it's in good enough condition, and you try hard enough to piece it all together, and get enough "overlaps" (which is the equivalent of a "fit" in terms of jigaws, shredded paper, etc.), then you can be pretty damn confident that this DNA is similar to that of the original animal. That's got implications, even if it's only 80% accurate, for everything from forensics to archaeology.

Re:Is the science repeatable?

[Gr8Apes]

I read your link - I don't know why you're surprised. The article itself states 500K years as the oldest known successful extraction and reading of DNA.

Furthermore, all the assumptions and theories are based on the analysis of 3000-8000 year old bird bones. The most significant factors in DNA degradation are stated to be exposure to water, followed by oxygen and micro-organism activity. Enzymes will only take you so far, and are listed as the starting point. I'd say that this particular theory will undergo quite a bit scrutiny in the coming years, and will at best be a rule of thumb since there are far more variables to account for than they have so far.

Re:Is the science repeatable?

[csirac]

I only mention the contamination issue because, at one of the seminars run by the Ancience Centre for DNA in Adelaide - it was highlighted as a significant problem early on in their research which resulted in detailed and rigorous sampling and processing protocols to get any worthwhile results at all. I seem to recall that early ancient DNA efforts had several false success which later turned out to be contamination - it's non-trivial. Even the act of using bare hands to wash an old bone in water overwhelms any tiny amount of useful, amplifiable ancient DNA.

The ACAD lab looked more like a semiconductor cleanroom compared to the more traditional labs near where I was working (plant DNA).

Re:Is the science repeatable?

[csirac]

And putting huge amount of computation and DNA from the same animal through it, and we're even less stuffed. Seems to me to be a pretty damn useful technique, overall, even if it's only "statistically" correct.

Which technique are we discussing? Next-gen contig/alignment is quite mature, as is the understanding of the limitations. Older, slower, more expensive tech is still in use in some lesser-studied critters which, for want of a better word, aren't entirely validated on the next-gen stuff and some experiments are just plain easier to do.

If we're talking about the tech in TFA, yes it certainly describes the most delicate way one could conceive of for treating precious single strands of ancient DNA molecules - a kind of almost-in-situ imaging (versus the much more traumatic chemical techniques I'm more familiar with). Hence the 10-20x-ish increase in reach back in time - they've substantially lowered the minimum DNA quality/quantity required to get interesting sequence data out.

I guess I just wanted to convey something along the lines of "garbage in, garbage out". If you've got garbage in, no amount of CPU power is going to fix that. Denying this, as you know, is like yelling "enhance!" at bad images/videos on sci-fi or crime movies. Fitting data to models might yield some interesting stuff, or it might just yield whatever you want it to yield. I've seen geologists play tricks on each other with seismic interp, tuning filters to create convincing structures out of white noise!

And, as you said, even if they can get good data over just a few genes, even that's useful to evolutionary biologists - they can talk all day about rate of change in those genese and have arguments about calibrating genetic clocks with fossil records (unless that's just a plant biologist thing...)

all living equids—members of the family tha

[Selur]

!! The centaur !! :D The Chimp centaur (http://www.freakingnews.com/Chimp-centaur-Pictures-5092.asp) ruled the earth :D

Joan Rivers

[Anonymous Coward]

So Joan Rivers went on 'Who do you think you are?' then.

So....

[Anonymous Coward]

When do i get my unicorn that spews rainbows?

Re:Bible is truth not false science

[Anonymous Coward]

Polite.... how can I know who is who among ACs or what people are thinking? You don't have to be stupid to be a creationist unfortunately
http://rationalwiki.org/wiki/Salem_Hypothesis
seen enough of this in real life and on slashdot before, some people just want an engineering manual for life.

At that age

[Anonymous Coward]

At 700,00 years old, I'd guess he has a long face.

There is truth to the saying...

[JRHelgeson]

You can't beat a dead horse.

Re:There is truth to the saying...

[maxwell demon]

You can't beat a dead horse.

Of course you can beat it. It just doesn't make much sense.

Re:There is truth to the saying...

[GodfatherofSoul]

Correct, nuthin' beats a dead horse. -- Ben Dover

Re:There is truth to the saying...

[Barsteward]

you can but you can't beat a good wank

Source material

[antifoidulus]

So they sequenced a 700,000 year old horse? In other words, a Tesco hamburger?*rimshot*

Re:Source material

[Anonymous Coward]

I disagree and moderated you as such. "Rimshot"? Seriously? Grow up idiot.

Re:Source material

[Anonymous Coward]

Maybe studying the genome will help them figure out how this horse has managed to live so long.

Re:Source material

[Barsteward]

"Grow up idiot" says the Anonymous Coward

Re:Source material

[Anonymous Coward]

OH SNAP! You found the one flaw in his statement! It's such a powerful statement that you posted it without using any punctuation, too!

Beat that son of a bitch!

[UltraZelda64]

Is it dead yet?

SO SLOW YOU GOTTA BEAT A DEAD HORSE !!

[Anonymous Coward]

Pah-Theh-Tick !!

Re:Bible is truth not false science

[Barsteward]

"having a book that tells you what is right and wrong"

Now what book would that be? Harry Potter? The little book of hugs? Mein Kampf?

Re:Bible is truth not false science

[Barsteward]

" You don't have to be stupid to be a creationist unfortunately"

You do....

Re:Bible is truth not false science

[Anonymous Coward]

Nowhere in the Bible does it state the Earth is 6,000 years old.

Re: all living equids—members of the family

[Barsteward]

:o) almost as good as the crocaduck from Banana Man and his cohort the twat actor

Re:Bible is truth not false science

[Joce640k]

... makes the world black and white in clear code...

This word "clear", I don't think it means what you think it means.

Ancient DNA NOT derived from a horse fossil?

[K. S. Kyosuke]

If there's DNA inside, how can that be a fossil? I always thought that this would make it a subfossil, by definition.

Re:Ancient DNA NOT derived from a horse fossil?

[julesh]

You clearly haven't learned media-science-speak, in which "fossil" means "any remnants of something that lived more than a handful of thousands of years ago, no matter how it has been preserved".

Re:Ancient DNA NOT derived from a horse fossil?

[IndustrialComplex]

Do you really care if someone calls Pluto a planet instead of the more precise term dwarf planet?

Nature doesn't have to organize itself into neat little boxes for easy categorization. If the message is understood, even with non-precise language, the message is still understood.

Also with regard to your concern for definition:

http://science.howstuffworks.com/environmental/earth/geology/soft-tissue-dinosaur-fossil.htm

Re:Bible is truth not false science

[Barsteward]

i know, i was just asking which book he was quoting (or trying to)

Look at my horse

[cadeon]

My horse is amazing.
http://www.youtube.com/watch?v=etm3kN6VBv8

Re:Look at my horse

[karnal]

Beaten to the punch, I wanted to post this. Even better - the original flash:

Weebl's Stuff - Amazing Horse

So _that's_ what happened to Celestia's dad

[Anonymous Coward]

It took a lot to bring that guy down: pyroclastic flow and a glacier.

Re:Bible is truth not false science

[Anonymous Coward]

Depends on what you mean by "creationist." Most Christians accept evolution, the 13 billion year age of the universe, but still believe that God created it all using evolution as one of his tools.

2/3rds of the world's population are either Christian or Muslim. You just called 2/3s of all people stupid, which is a just an incredibly fucking stupid thing to do.

Re:Bible is truth not false science

[Barsteward]

"You just called 2/3s of all people stupid, which is a just an incredibly fucking stupid thing to do." - bollox. only small (but vocal) minority are creationists.

This might be hard for you to understand but just because a large number of people believe something stupid, doesn't make it true.

Klink

[Anonymous Coward]

Of course if the horse were in fact as old as you say there would be no DNA. Instead what we see is the entire global fossil record is a result of a catastrophic global flood as recorded by many cultures including the Bible. The constant reports / baseless claims about bazzillions of years amounts to nothing more than propaganda; your pagan religion.

No: Welcome to PLEISTOCENE Park

[Dr La]

Pleistocene Park, not Pliocene Park.

The Plio-Pleistocene boundary is at 2.6 million years ago. With 700 000 yrs, this Horse is Middle Pleistocene (the Lower-Middle Pleistocene boundar is at 780 000 yrs ago).

Re:No: Welcome to PLEISTOCENE Park

[plover]

Philistine.

Hogan!

[Anonymous Coward]

At least Klink could spell "bazillions," you illiterate rhubarb-sucking mook.

Q: What do the Jedi Mind Trick and religion have in common?

A: They both work on weak-minded fools.