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Natural Science Forum / Biology / Paleontology / November 2006



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Paper: Analysis of one million base pairs of Neanderthal DNA

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Robert Karl Stonjek - 15 Nov 2006 22:03 GMT
Nature 444, 330-336 (16 November 2006) | doi:10.1038/nature05336; Received 14 July 2006; Accepted 11 October 2006

Analysis of one million base pairs of Neanderthal DNA
Richard E. Green1, Johannes Krause1, Susan E. Ptak1, Adrian W. Briggs1, Michael T. Ronan2, Jan F. Simons2, Lei Du2, Michael Egholm2, Jonathan M. Rothberg2, Maja Paunovic3,4 and Svante Pääbo1

Abstract
Neanderthals are the extinct hominid group most closely related to contemporary humans, so their genome offers a unique opportunity to identify genetic changes specific to anatomically fully modern humans. We have identified a 38,000-year-old Neanderthal fossil that is exceptionally free of contamination from modern human DNA. Direct high-throughput sequencing of a DNA extract from this fossil has thus far yielded over one million base pairs of hominoid nuclear DNA sequences. Comparison with the human and chimpanzee genomes reveals that modern human and Neanderthal DNA sequences diverged on average about 500,000 years ago. Existing technology and fossil resources are now sufficient to initiate a Neanderthal genome-sequencing effort.

 1.. Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany
 2.. 454 Life Sciences, 20 Commercial Street, Branford, Connecticut 06405, USA
 3.. Institute of Quaternary Paleontology and Geology, Croatian Academy of Sciences and Arts, A. Kovacica 5/II, HR-10 000 Zagreb, Croatia
 4.. Deceased.
Source: Nature
http://www.nature.com/nature/journal/v444/n7117/abs/nature05336.html

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Posted by
Robert Karl Stonjek

John Harshman - 16 Nov 2006 00:16 GMT
> Nature 444, 330-336 (16 November 2006) | doi:10.1038/nature05336;
> Received 14 July 2006; Accepted 11 October 2006
[quoted text clipped - 18 lines]
> 500,000 years ago. Existing technology and fossil resources are now
> sufficient to initiate a Neanderthal genome-sequencing effort.

> Source: Nature
> http://www.nature.com/nature/journal/v444/n7117/abs/nature05336.html

This makes it now very, very unlikely that any significant interbreeding
between H. neanderthalensis and H. sapiens ever occurred. Big
confirmation for the mitochondrial result.
John Roth - 16 Nov 2006 13:22 GMT
> > Nature 444, 330-336 (16 November 2006) | doi:10.1038/nature05336;
> > Received 14 July 2006; Accepted 11 October 2006
[quoted text clipped - 25 lines]
> between H. neanderthalensis and H. sapiens ever occurred. Big
> confirmation for the mitochondrial result.

How do you get this? The paper says that they found no
evidence, but left the possibility open.

>From the article, p335, end of paragraph beginning 2nd column:

--------------------------------------------------

Nevertheless, this high level of derived alleles in the
Neanderthal is incompatible with the simple population split model
estimated in the previous section, given split times inferred from the
fossil record. This may suggest gene flow between modern humans
and Neanderthals. Given that the Neanderthal X chromosome shows
a higher level of divergence than the autosomes (R.E.G., unpublished
observation), gene flow may have occurred predominantly from
modern human males into Neanderthals. More extensive sequencing
of the Neanderthal genome is necessary to address this possibility.

-----------------------------------------------------------------

John Roth
John Harshman - 16 Nov 2006 17:06 GMT
>>>Nature 444, 330-336 (16 November 2006) | doi:10.1038/nature05336;
>>>Received 14 July 2006; Accepted 11 October 2006
[quoted text clipped - 28 lines]
> How do you get this? The paper says that they found no
> evidence, but left the possibility open.

I haven't read the paper, and have no access to it, so I can say
anything I like. However...

>>From the article, p335, end of paragraph beginning 2nd column:
>
[quoted text clipped - 5 lines]
> fossil record. This may suggest gene flow between modern humans
> and Neanderthals.

Sorry, but how does a high level of derived alleles suggest gene flow?
What does this mean?

> Given that the Neanderthal X chromosome shows
> a higher level of divergence than the autosomes (R.E.G., unpublished
> observation), gene flow may have occurred predominantly from
> modern human males into Neanderthals. More extensive sequencing
> of the Neanderthal genome is necessary to address this possibility.

I really don't see how a bigger sample than one million bases could be
necessary, unless it were somehow targeted at, say, the Y chromosome.
How significant is the difference between X and autosomes?
John Roth - 17 Nov 2006 18:14 GMT
> >>>Nature 444, 330-336 (16 November 2006) | doi:10.1038/nature05336;
> >>>Received 14 July 2006; Accepted 11 October 2006
[quoted text clipped - 54 lines]
> necessary, unless it were somehow targeted at, say, the Y chromosome.
> How significant is the difference between X and autosomes?

Without access to the actual paper (and the background to understand
what it's saying) the best thing is to look at John Hawk's blog and
at Razib's two blogs. There are other interesting sites and blogs, but
those two are
exemplary, and they link to just about everything else you need to
know. Hawks, by the way, is not only a professor at the U
of Wisconsin / Madison, he's in the middle of a lot of
paleoanthropology
himself, with a paper on Neanderthals in press that he's been dropping
hints about. He's been a long time supporter of multi-regionalism, in
one version or other.

http://johnhawks.net/weblog

Razib is a grad student who seems to be quite well regarded by
the pros. "Chet Snicker" is Razib, and I have no idea what the
deal is behind the nom-de-plum. Nor do I want to know.

http://www.gnxp.com/MT2/
http://www.scienceblogs.com/gnxp/

Note that you don't get on scienceblogs except by invitation,
which I suppose says something.

John Roth
John Harshman - 17 Nov 2006 19:39 GMT
>>>>>Nature 444, 330-336 (16 November 2006) | doi:10.1038/nature05336;
>>>>>Received 14 July 2006; Accepted 11 October 2006
[quoted text clipped - 44 lines]
>>Sorry, but how does a high level of derived alleles suggest gene flow?
>>What does this mean?

What it apparently means is a high level of *shared* derived alleles,
mostly referring to SNPs. Given the long coalescence times of human
neutral sequences, it may be hard to distinguish gene flow from no gene
flow. I bigger sample of individuals might be necessary. Easy for modern
humans, hard for Neanderthals.

>>>Given that the Neanderthal X chromosome shows
>>>a higher level of divergence than the autosomes (R.E.G., unpublished
[quoted text clipped - 5 lines]
>>necessary, unless it were somehow targeted at, say, the Y chromosome.
>>How significant is the difference between X and autosomes?

I doubt they need a bigger sample of bases. What they need is a bigger
sample of individuals. Unfortunately, they can't control what sequences
they get, so would have to do a great amount of sequencing on other
individuals to get any reasonable sample overlap.

> Without access to the actual paper (and the background to understand
> what it's saying)

Background I got. But I found the blog useful.

> the best thing is to look at John Hawk's blog and
> at Razib's two blogs. There are other interesting sites and blogs, but
[quoted text clipped - 20 lines]
>
> John Roth
spiznet - 16 Nov 2006 13:26 GMT
> > Nature 444, 330-336 (16 November 2006) | doi:10.1038/nature05336;
> > Received 14 July 2006; Accepted 11 October 2006
[quoted text clipped - 25 lines]
> between H. neanderthalensis and H. sapiens ever occurred. Big
> confirmation for the mitochondrial result.

Where does it say anything to this effect in the abstract? I don't see
it there? Is it in the article, or are you just pulling this out of the
air?
-Spiznet
Lee Olsen - 16 Nov 2006 16:55 GMT
> > > Nature 444, 330-336 (16 November 2006) | doi:10.1038/nature05336;
> > > Received 14 July 2006; Accepted 11 October 2006
[quoted text clipped - 29 lines]
> it there? Is it in the article, or are you just pulling this out of the
> air?

No, he is correct, the keyword being "significant"

> -Spiznet
John Harshman - 16 Nov 2006 17:09 GMT
>>>Nature 444, 330-336 (16 November 2006) | doi:10.1038/nature05336;
>>>Received 14 July 2006; Accepted 11 October 2006
[quoted text clipped - 30 lines]
> air?
> -Spiznet

If there were significant interbreeding, we would expect some of the
sequences to be anomalously similar between H. sapiens and the
neanderthal sample. The abstract doesn't mention any, and I would be
very surprised if anything so significant had failed make it into the
abstract. What the abstract doesn't say can be as informational as what
it does say.
johnwl4@aol.com - 18 Nov 2006 23:06 GMT
> >>>Nature 444, 330-336 (16 November 2006) | doi:10.1038/nature05336;
> >>>Received 14 July 2006; Accepted 11 October 2006
[quoted text clipped - 37 lines]
> abstract. What the abstract doesn't say can be as informational as what
> it does say.

   The two studies came to somewhat different conclusions, because
they were considering different selections of single nucleotide
polymorphisms, or SNP's.   One group looked at SNP's derived after the
split from Pan, and found 30, which was too many for the time of split
between Homo s,,  and Neandertals.   This group concluded some
interbreeding.  The other looked at rare ones, IIRC, and  concluded
only  a little, if any.
    Another scientist thought that both were reasoning beyone their
data, and Lalueza was dubious (I remember his name, because he has
instituted a practise of treating a dig like a crime scene - rubber
gloves, gowns, masks, sterile tools, and freezing specimens.)
     Me - I don't know enough to have an opinion.    Just a
non-innocent bystander.
       Regards
         John GW
johnwl4@aol.com - 18 Nov 2006 23:52 GMT
> > Nature 444, 330-336 (16 November 2006) | doi:10.1038/nature05336;
> > Received 14 July 2006; Accepted 11 October 2006
[quoted text clipped - 25 lines]
> between H. neanderthalensis and H. sapiens ever occurred. Big
> confirmation for the mitochondrial result.

   BTW, have you read what John Hawks says about this on his site?  I
get confused easily
over who has said what.
   Hawks quotes from the Green paper:
 "We analysed the DNA sequences generated from a contemporary human
using the same sequencing protocol as was used for the Neanderthal.
Although ancient DNA is degraded and damaged, this comparison controls
for many of the aspects of the analysis including sequencing and
alignment methodology. In this case, 7.1% of the divergence along the
human lineage is assigned to the time subsequent to the divergence of
the two human sequences. The average divergence time between alleles
within humans is thus 459,000 years with a 95% confidence interval
between 419,000 and 498,000 years. As expected, this estimate of the
average human diversity is less than the divergence seen between the
human and the Neanderthal sequences, but constitutes a large fraction
of it because much of the human sequence diversity is expected to
predate the human-Neanderthal split. Neanderthal genetic differences to
humans must therefore be interpreted within the context of human
diversity."
   and, since that is under copyright, I'd better add the source,
Nature 444: 330-336.

  I find the excerpt a little confusing, since Green, et. al., are
comparing this modern human with some other genome, the standard one, I
suppose, but Hawks discusses this, and concludes that Hn may   have
varied from the standard very little more than some modern humans.   By
standard, I mean merely the genome listed as a type.   I guess the
correct term is not standard, but Congress something or other.
     Regards
      John GW
deowll - 22 Nov 2006 04:23 GMT
>> Nature 444, 330-336 (16 November 2006) | doi:10.1038/nature05336;
>> Received 14 July 2006; Accepted 11 October 2006
[quoted text clipped - 25 lines]
> between H. neanderthalensis and H. sapiens ever occurred. Big
> confirmation for the mitochondrial result.

It confirms Jack. The only thing you can hope to learn by studying
mitochondria is about mitochondria including the history of that line of
mitochondria. It isn't linked to anything else. Thus it can't tell you about
anything else.

According to Mitochondria at least one blue eyed blond is a Native American.

The bottom line is you are going to have to look at every bleeping
separately heritable hunk of DNA and try to figure out where it most likely
entered the modern gene pool. Then you will have some idea of the history of
that hunk of DNA which is all you can know by studying it.
John Harshman - 23 Nov 2006 18:46 GMT
>>>Nature 444, 330-336 (16 November 2006) | doi:10.1038/nature05336;
>>>Received 14 July 2006; Accepted 11 October 2006
[quoted text clipped - 30 lines]
> mitochondria. It isn't linked to anything else. Thus it can't tell you about
> anything else.

This just isn't true. Mitochondria aren't linked to nuclear genes, but
there are limits on just how different the history of mitochondria can
be from the history of pieces of the nuclear genome. It's possible that
the divergence of neanderthals and modern humans are recent enough to be
close to that limit, but it doesn't look like that to me. Now if
introgression is entirely one-way, i.e. without any contribution by
neanderthal females to the modern human lineage, the mt data might be
biased. But that would run counter to Haldane's rule, so seems less
likely than alternatives.

> According to Mitochondria at least one blue eyed blond is a Native American.

Is there something wrong with that idea? How do you define "Native
American"?

> The bottom line is you are going to have to look at every bleeping
> separately heritable hunk of DNA and try to figure out where it most likely
> entered the modern gene pool. Then you will have some idea of the history of
> that hunk of DNA which is all you can know by studying it.

Apparently statistical sampling is a technique you reject?
deowll - 23 Nov 2006 23:44 GMT
>>>>Nature 444, 330-336 (16 November 2006) | doi:10.1038/nature05336;
>>>>Received 14 July 2006; Accepted 11 October 2006
[quoted text clipped - 47 lines]
> Is there something wrong with that idea? How do you define "Native
> American"?

Somebody whose ancestors, most of them anyway, were here at least three
thousand years ago. This woman almost certainly only had native American
mitochondria. As a means of figuring out the source of her nuclear DNA
looking at her mitochondria would be the mother all of mistakes. This sample
of one would lead to a very wrong conclusion.

>> The bottom line is you are going to have to look at every bleeping
>> separately heritable hunk of DNA and try to figure out where it most
[quoted text clipped - 4 lines]
>
> Apparently statistical sampling is a technique you reject?

It won't give you the total picture. Counting on it may leave you looking
foolish.

Two examples. We have at least some Asian DNA from out of Africa about
2,000,000 yrs back. That kicks a lot of theories in the head. That may be
one of the oldest but not only ouch out there. If you check around there are
already a lot of known ouches out there. Simple facts that do not fit many a
theory.

We have an X chromosome that was picked up from chimps a long time after the
rest of our DNA seems to have split from the chimp line. That means the LCA
of humans and chimps occurred twice.

DNA is being reworked by selection all the time. At best what you find in
the modern gene pool is not going to give you a complete family tree. It
does not work that way. You do not carry unique genetic markers off all your
ancestors and until you've actually read the entire book you don't know the
story.

As one man said, "I had the family tree all worked out until I read
grandma's secret diary. It turned out she had a thing for traveling
salesmen."  Of course he only learned what happened with one grandma. What
went on with the other grandma's farther back is obscure.

Even after we get the current edition of the DNA book read, data coming out
of fossils is going to still be causing a lot of ouches and even that won't
be the total story.

Data sampling needs to include a lot more data than we now have. Some
checking a few years back made me certain that a lot of people are over
looking a lot of data already known because they don't want to deal with it
or haven't bothered to look.

My last thought on this is that if I can find it then its not that hard to
find.
John Harshman - 24 Nov 2006 04:48 GMT
>>>>>Nature 444, 330-336 (16 November 2006) | doi:10.1038/nature05336;
>>>>>Received 14 July 2006; Accepted 11 October 2006
[quoted text clipped - 53 lines]
> looking at her mitochondria would be the mother all of mistakes. This sample
> of one would lead to a very wrong conclusion.

Your idea is silly. You have no idea where her mitochondria came from.
And statistically speaking, if she had, say, only a full-blooded Native
American maternal grandmother, her nuclear genome would also be 1/4
Native American too. Apparently eye and hair color were not in that part
of the genome. Mind you, genetic differences among populations are small
compared to those within populations.

>>>The bottom line is you are going to have to look at every bleeping
>>>separately heritable hunk of DNA and try to figure out where it most
[quoted text clipped - 7 lines]
> It won't give you the total picture. Counting on it may leave you looking
> foolish.

So you do reject statistical sampling. In order to say anything reliable
about genetic variation, we need to know the complete genomes of all
individuals in the population. Well, it's one way to go.

> Two examples. We have at least some Asian DNA from out of Africa about
> 2,000,000 yrs back. That kicks a lot of theories in the head. That may be
> one of the oldest but not only ouch out there. If you check around there are
> already a lot of known ouches out there. Simple facts that do not fit many a
> theory.

No idea what that meant. What's your source for this 2 million yeara old
Asian DNA?

> We have an X chromosome that was picked up from chimps a long time after the
> rest of our DNA seems to have split from the chimp line. That means the LCA
> of humans and chimps occurred twice.

No, if it's really valid, it just means that there was some
introgression between chimps and human lineages a bit later than the
time most gene flow ended.

> DNA is being reworked by selection all the time. At best what you find in
> the modern gene pool is not going to give you a complete family tree. It
> does not work that way. You do not carry unique genetic markers off all your
> ancestors and until you've actually read the entire book you don't know the
> story.

OK, might as well not bother then, because we'll never be able to
sequence everyone's entire genome, not to mention all the dead people.

> As one man said, "I had the family tree all worked out until I read
> grandma's secret diary. It turned out she had a thing for traveling
[quoted text clipped - 12 lines]
> My last thought on this is that if I can find it then its not that hard to
> find.

Out of curiosity, what are you talkign about?
deowll - 29 Nov 2006 02:04 GMT
>>>>>>Nature 444, 330-336 (16 November 2006) | doi:10.1038/nature05336;
>>>>>>Received 14 July 2006; Accepted 11 October 2006
[quoted text clipped - 60 lines]
>
> Your idea is silly. You have no idea where her mitochondria came from.

It's not that uncommon to know who your ancestors are for a good many
generations back and at least in the maternal line you can be fairly certain
about the fact.

> And statistically speaking, if she had, say, only a full-blooded Native
> American maternal grandmother, her nuclear genome would also be 1/4
> Native American too. Apparently eye and hair color were not in that part
> of the genome. Mind you, genetic differences among populations are small
> compared to those within populations.

When it comes to who gets what genes from several generations back
statistically speaking you can only consider the answer to be meaningful in
you are talking about groups rather than individuals. The answer is yes or
no. Not some sort of average.

>>>>The bottom line is you are going to have to look at every bleeping
>>>>separately heritable hunk of DNA and try to figure out where it most
[quoted text clipped - 12 lines]
> about genetic variation, we need to know the complete genomes of all
> individuals in the population. Well, it's one way to go.

Works for finding oil in the ground too.

>> Two examples. We have at least some Asian DNA from out of Africa about
>> 2,000,000 yrs back. That kicks a lot of theories in the head. That may be
[quoted text clipped - 6 lines]
> No idea what that meant. What's your source for this 2 million yeara old
> Asian DNA?

It was in paleo anthro and I followed the links given. Look it up. It'll
take about four years to get published in a book.

>> We have an X chromosome that was picked up from chimps a long time after
>> the
[quoted text clipped - 5 lines]
> introgression between chimps and human lineages a bit later than the
> time most gene flow ended.

A lot later and that was the real LCA unless you want to write a new
defination.

>> DNA is being reworked by selection all the time. At best what you find in
>> the modern gene pool is not going to give you a complete family tree. It
[quoted text clipped - 6 lines]
> OK, might as well not bother then, because we'll never be able to
> sequence everyone's entire genome, not to mention all the dead people.

They are working on being able to do the first one. The data suggests they
can bring the price down to a $1,000 in the life span of some of the people
now alive at which time they want to stick a copy in everybody's medical
records.

>> As one man said, "I had the family tree all worked out until I read
>> grandma's secret diary. It turned out she had a thing for traveling
[quoted text clipped - 19 lines]
>
> Out of curiosity, what are you talkign about?

What I said. I decided a few summers ago to take a few days and find out how
much data was available. There was a mountain. A lot of it meant either you
and the people like you aren't as well informed as you think or a lot of
people are lying about what they've found.

Some of it actually dates back to methods predating cheap DNA testing but
proteins come from somewhere. The last I heard it was genes. If you look at
what got published a few years back things go one way. Shift through this
stuff and you don't think much of a lot of what many people said.

One of the most painful realizations was the bottle neck as presented
amounted to picking one option that would fit the numbers and ignoring other
options that would fit the numbers. There was a fair amount of group think
but even so the date of the supposed bottle neck and Homo sapians sapians
moving out of Afirca got moved all over the place.

You have fun now.
johnwl4@aol.com - 29 Nov 2006 17:17 GMT
>>>>> (snip). Well, it's one way to go.
>
[quoted text clipped - 6 lines]
> No idea what that meant. What's your source for this 2 million yeara old
> Asian DNA?

   Believe it worked this way subject to someone more knowledgeable
correcting me..  Samples were compared from several groups around the
world.  Some DNA was found in the Asian sample, and not in  the others.
An examination of the SNP'S, or whatever, showed a number of changes
from other groups that were consistent with the 200 million year
difference in time.   Genetic clock, in other words.
I'll see if I can find the name of the researchers.
     Regards
       John GW
Roger Bagula - 16 Nov 2006 19:52 GMT
> /Nature/ *444*, 330-336 (16 November 2006) | doi:10.1038/nature05336;
> Received 14 July 2006; Accepted 11 October 2006
[quoted text clipped - 32 lines]
> http://www.nature.com/nature/journal/v444/n7117/abs/nature05336.html
>  

The other paper seems to have had better reproduction of dna sequences :
not just identification:

> In another paper published in Science, Professor Rubin's team used a
> different approach called metagenomics, where the fragments of
> Neanderthal genetic material were incorporated into bacteria which
> then copied themselves, generating a living "library" of DNA
> sequences. This method resulted in the recovery of 65,250 base pairs
> of Neanderthal DNA.

http://www.latimes.com/news/nationworld/nation/la-sci-neanderthal16nov16,1,75554
32.story?coll=la-headlines-nation

Hey American Moron! - 23 Nov 2006 09:45 GMT
got it the first time, dingdong.

>> Nature 444, 330-336 (16 November 2006) | doi:10.1038/nature05336;
>> Received 14 July 2006; Accepted 11 October 2006
[quoted text clipped - 48 lines]
> http://www.lat
> mes.com/news/nationworld/nation/la-sci-neanderthal16nov16,1,7555432.story?coll=la-headlines-nation
Roger Bagula - 16 Nov 2006 20:38 GMT
> /Nature/ *444*, 330-336 (16 November 2006) | doi:10.1038/nature05336;
> Received 14 July 2006; Accepted 11 October 2006
[quoted text clipped - 32 lines]
> http://www.nature.com/nature/journal/v444/n7117/abs/nature05336.html
>  

Real World and not fantasy news?
My opinion is that this ( both the German and the American effort)  is a
"government" lab project headed by political types
and the actual science ( if any) is only a side project to the publicity
machine...
Since only government sponsored labs can probably afford the sequencing
equipment, technicians
and software needed to do this kind of  work,
it doesn't really tell us very much?!
There actually might be some real scientists who will work for underpaid
GS rating pay?
Most of the real DNA people work for private DNA sequencing companies
who charge an arm and leg for
even basic genome scans.
This work is a very long way from being able to clone a Neanderthal.
It looks like a media circus...
Roger Bagula - 17 Nov 2006 16:41 GMT
> Real World and not fantasy news?
> My opinion is that this ( both the German and the American effort) is
[quoted text clipped - 12 lines]
> This work is a very long way from being able to clone a Neanderthal.
> It looks like a media circus...

http://www.nature.com/nature/journal/v425/n6958/full/425550a.html

In a "24/7 nanolecture", geneticist Eric Lander summarized the Human
Genome Project in 24 seconds —
"The genome cost US$3 billion and gave us three billion letters: one
dollar a letter. Such a deal!"—
and then, rather more successfully, in seven words: "Genome. Bought the
book. Hard to read."
Jois - 18 Nov 2006 00:00 GMT
Nature 444, 330-336 (16 November 2006) | doi:10.1038/nature05336; Received
14 July 2006; Accepted 11 October 2006
Analysis of one million base pairs of Neanderthal DNA
Richard E. Green1, Johannes Krause1, Susan E. Ptak1, Adrian W. Briggs1,
Michael T. Ronan2, Jan F. Simons2, Lei Du2, Michael Egholm2, Jonathan M.
Rothberg2, Maja Paunovic3,4 and Svante Pääbo1
Abstract
Neanderthals are the extinct hominid group most closely related to
contemporary humans, so their genome offers a unique opportunity to identify
genetic changes specific to anatomically fully modern humans. We have
identified a 38,000-year-old Neanderthal fossil that is exceptionally free
of contamination from modern human DNA. Direct high-throughput sequencing of
a DNA extract from this fossil has thus far yielded over one million base
pairs of hominoid nuclear DNA sequences. Comparison with the human and
chimpanzee genomes reveals that modern human and Neanderthal DNA sequences
diverged on average about 500,000 years ago. Existing technology and fossil
resources are now sufficient to initiate a Neanderthal genome-sequencing
effort.
Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6,
D-04103 Leipzig, Germany
454 Life Sciences, 20 Commercial Street, Branford, Connecticut 06405, USA
Institute of Quaternary Paleontology and Geology, Croatian Academy of
Sciences and Arts, A. Kovacica 5/II, HR-10 000 Zagreb, Croatia
Deceased.
Source: Nature
http://www.nature.com/nature/journal/v444/n7117/abs/nature05336.html

Posted by
Robert Karl Stonjek

--------------------------------------------------

Here's what Nature calls the editor's summary:

Editor's Summary
16 November 2006
Neanderthal Genomics

Neanderthal traits appear in the human fossil record of Europe and western
Asia about 400,000 years ago and vanish about 30,000 years ago. The
Neanderthals are our closest extinct relatives, so as DNA technology
advances the tantalizing prospect of identifying genetic changes
characteristic of fully modern humans comes closer. A 38,000-year-old
Neanderthal bone of sufficiently high quality to allow the extraction of
more than a million base pairs has now been identified: it was originally
found Vindija cave in Croatia (pictured on the cover) in 1980. Comparison of
its DNA with the chimp and human genomes reveals that Neanderthal and human
ancestors - like humans but unlike apes - had a small effective population
size. The technology used in this work offers the prospect of a draft
Neanderthal genome within two years.
Can ya'll tell me what difference "effective population size" makes?
TIA,
Jois
John Harshman - 18 Nov 2006 01:08 GMT
> Nature 444, 330-336 (16 November 2006) | doi:10.1038/nature05336; Received
> 14 July 2006; Accepted 11 October 2006
[quoted text clipped - 47 lines]
> Neanderthal genome within two years.
> Can ya'll tell me what difference "effective population size" makes?

It has effects on two important things: the amount of neutral
polymorphism in a population, and the length of time it takes these
polymorphisms to become fixed after interbreeding stops.
Hey American Moron! - 23 Nov 2006 09:45 GMT
are WE and We and WE repeating ourselves, infinitesimallymally mallyz?

> Nature 444, 330-336 (16 November 2006) | doi:10.1038/nature05336; Received
> 14 July 2006; Accepted 11 October 2006
[quoted text clipped - 49 lines]
> TIA,
> Jois
Hey American Moron! - 23 Nov 2006 09:50 GMT
Inevitably, everyone will throw themselves off cliffs like lemmings
to interpret FIRST!

I suggest we stand back and let the research work, then allow the
authors and significant others to comment ........... before all the
APE-sh.ts HERE throw a neandrum and go extinct!.

Sheesh!  Stop the tail gating and piling on!

> Nature 444, 330-336 (16 November 2006) | doi:10.1038/nature05336;
> Received 14 July 2006; Accepted 11 October 2006
[quoted text clipped - 34 lines]
> Posted by
> Robert Karl Stonjek
Spanish Paranoia - 24 Nov 2006 12:00 GMT
> Inevitably, everyone will throw themselves off cliffs like lemmings
> to interpret FIRST!
[quoted text clipped - 4 lines]
>
> Sheesh!  Stop the tail gating and piling on!
That's all you can do moron, sit back and believe every idiocy they
show you on TV.
Have you been told already about Noah's Ark?

moron ...

> > Nature 444, 330-336 (16 November 2006) | doi:10.1038/nature05336;
> > Received 14 July 2006; Accepted 11 October 2006
[quoted text clipped - 114 lines]
>
> --------------9032EFD0930A2260175646FB--
 
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