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  (Source: AP)
DNA comes from sequencing of Neanderthal toe-bone found in Siberia

Three years after an international team of experts led by researchers at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany published a "draft" of the genome of Homo neanderthalensis (commonly known as the "Neanderthal"), the team has come back with a higher-quality "finished" map of the genome.

I. Getting to Know Our Neighbors, Distant Ancestors

Neanderthals are one of mankind's closest relatives.  Neanderthals and modern man (Homo sapiens) are though to have diverged from a common ancestor around 350,000 years ago.  That ancestor is thought to have evolved into humans in Africa, but into Neanderthals in Europe.  Another close relative, Denisovans, are thought to have diverged slightly earlier in Asia.

Nonetheless, humans and these relatives would eventually reunite and even have intimate sexual relationships, which led to some modern humans bearing pieces of Neanderthal/Denisovan DNA.

These "donations" from our close relatives are thought to have endowed people of European or Asian descent with hardier immune systems.

The DNA for the sequenced Neanderthal genome comes from a toe-bone found in the Denisova cave in southern Siberia.

Denisova cave
[Image Source: Current Biology/Science]

That cave is also home to preserved human and Denisovan remains; in fact the Denisovan remains are being used to carry out a similar sequencing project on that genome.

II. Contamination, Region Variance Leave Picture Only Mostly Complete

Svante Paabo, a geneticist who led the research, wrote in an email to the Associated Press, "The genome of a Neanderthal is now there in a form as accurate as that of any person walking the streets today."

Or it is for the Altal Neanderthals, at least.  Much like modern man, where people from different areas developed unique genetic makeups, Neanderthals are hypothesized to have subtle regional differences in their genomes.

As Ars Technica points out, it is misleading to suggest that the genome is a "complete" genome for the entirety of the Neanderthal population that once inhabited Europe, Asia, and the Middle East.  Rather, the Neanderthal genome represents a finished/complete picture of the Neanderthals in one region.

Family tree
Scientists think that the Altal branch of the "family tree" is complete with the finished sequencing. [Image Source: MPI]

Professor Paabo is preparing a paper on the work.  He enthuses, "We will gain insights into many aspects of the history of both Neanderthals and Denisovans, and refine our knowledge about the genetic changes that occurred in the genomes of modern humans after they parted ways with the ancestors of Neanderthals and Denisovan."

The finished genome is available here in "BAM" format, with chromosome file sizes ranging from 1.9-13 GB a piece, depending on the size, except for the small 'Y' chromosome, which is only 331 MB.

One other way that the genome is somewhat incomplete is contamination.  Analysis showed that approximately 1 percent of the DNA in the sample was contamination from the cave's later human residents.  Those gaps -- and the variations between Neanderthals in different regions -- will have to be filled in with future gene studies.

Source: MPI



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The French...
By wingless on 3/21/2013 3:13:48 PM , Rating: 3
I like how they carved out a branch specifically for the French to separate them from the rest of modern humanity.

Nicely done science!




RE: The French...
By cashkennedy on 3/21/2013 6:36:52 PM , Rating: 1
How do you know your not primarily part of the "french" group, unless your like asian or something, then I guess your in the clear.


RE: The French...
By Iketh on 3/21/2013 10:31:06 PM , Rating: 1
YOU'RE man YOU'RE


RE: The French...
By CZroe on 3/21/2013 10:55:00 PM , Rating: 2
[COMMA] man, man[.] [COMMA] man.

Also, @OP:
[COMMA] science


RE: The French...
By CZroe on 3/21/2013 10:53:22 PM , Rating: 2
you're
you're
you're


RE: The French...
By CZroe on 3/21/2013 10:56:17 PM , Rating: 2
Also, questions have question marks.


RE: The French...
By KOOLTIME on 3/21/2013 6:42:04 PM , Rating: 2
The article states clearly its by region, and the bone was found see map in that region.

Not carved out to a specific race other then how most races are set via regions.

Read more close its not a global idea, it says for the region it was located in for that time frame.


RE: The French...
By cashkennedy on 3/21/2013 6:49:28 PM , Rating: 2
He was refering to the chart of various regional varieties of each species, specifically the homo sapien side, which is not discussed at all in this article. So the article has nothing to do with his comment that the french are their own "regional" variety of homo sapien, that he saw on the chart which is based completly on the frequency of similar traits / genes.


I see your genes are as big as mine...
By DNAgent on 3/21/2013 9:17:51 AM , Rating: 2
quote:
The finished genome is available here in "BAM" format, with genes ranging from 1.9-13 GB a piece, depending on the size, except for the small 'Y' chromosome, which is only 331 MB.


Should be "chromosome sizes ranging from 1.9-13 Gb a piece"




By DNAgent on 3/21/2013 9:20:25 AM , Rating: 2
Actually, that's wrong too...the file sizes range from 331 MB to 13 GB....chromosomes have more gigabases than that.


Hey, it's alright...
By Magius on 3/22/2013 10:35:11 PM , Rating: 2
quote:
... except for the small 'Y' chromosome, which is only 331 MB.


"Hey! Size is not everything, alright? Not like it caused our extinction. Darn modern humans...*poor neanderthal goes to cry in the corner*

Bad jokes aside, this is pretty cool. Now we just need to fill in those holes with frog DNA and, what? It's been done already?




Hmmm...
By geronimo2013 on 3/23/2013 11:07:13 PM , Rating: 2
Are we not men? We are...




Lies!
By Skywalker123 on 3/21/13, Rating: -1
RE: Lies!
By Asetha on 3/21/2013 3:38:45 PM , Rating: 4
Idiotic comment. Yes, I realize it's sarcasm. Still idiotic.


RE: Lies!
By talikarni on 3/21/2013 4:49:33 PM , Rating: 1
That is part of the stereotypical poor education about most religions, especially Christianity. There is nothing saying that Adam and Eve weren't neanderthals, just as theres nothing to say they were made exactly like upright homo-sapiens of today.


RE: Lies!
By retrospooty on 3/21/2013 5:24:26 PM , Rating: 2
Yup... The book is filled with a whole lot of non-specific crap that could be taken many different ways, from Catholics, to protestants, to many different cults, to the Nazi's. All in the name of the bible. Same with the Islamic end of it. It can be taken anywhere from extremely pacifist, to suicide bomber.

It's all written by primitive uneducated men... Unless of course God really wants us to be confused and killing each other ;)


RE: Lies!
By CZroe on 3/22/2013 3:24:18 AM , Rating: 2
The Nazi Party is a Judeo-Christian sect influenced by Biblical interpretation? I mean, I've heard that higher-ups were into The Occult, but that's the first time I've ever heard someone imply the exact opposite.


RE: Lies!
By retrospooty on 3/22/2013 7:42:11 AM , Rating: 2
The "Occult" thing is a way Christians try to distance themselves from the Nazi's crimes. They may have been interested, or dabbled in the Occult, but the fact is Hitler was Christian, as were most Germans in the time period.

Or were you just being sarcastic ?


RE: Lies!
RE: Lies!
By Reclaimer77 on 3/22/2013 8:20:45 AM , Rating: 2
quote:
but the fact is Hitler was Christian, as were most Germans in the time period.


Well they might have CALLED themselves Christians. But someone correct me if I'm wrong, but you kinda have to at least attempt to follow the teachings of Christ to be a "Christian" I thought?

I can call myself a Vegan, sure, but last night I ate a steak and this morning had bacon and eggs and washed it down with a glass of milk. /shrug


RE: Lies!
By retrospooty on 3/22/2013 5:51:03 PM , Rating: 2
No Christian that I have ever met does that.

“I like your Christ, I do not like your Christians. Your Christians are so unlike your Christ.”

? Gandhi


What kind of idiotic file format...
By Shadowmaster625 on 3/21/13, Rating: -1
By retrospooty on 3/21/2013 10:09:24 AM , Rating: 2
RE: What kind of idiotic file format...
By freeagle on 3/21/2013 11:06:43 AM , Rating: 2
An expert on DNA indexing has spoken...

A binary seach tree, where each leaf would represent one base pair, would contain (3.2e9 - 1) vertices (roughly, the - 1 is there just to draw the relationship between vertices and leafs in general). Each vertex needs to somehow point to both of its children. Each such pointer requires at least 4 bytes, so thats 8 bytes per vertex, times 3.2e9 is 25.6e9 bytes, so 23.84 GB. Granted, you could compress such a data structure when storing into a file, but I assume you need more metadata for each vertex than just pointers to its children...

I'm not saying this is what they use to index the the bases, I'm no DNA data indexing export either, but it certainly is not "just a couple extra megabytes"


RE: What kind of idiotic file format...
By TheEinstein on 3/21/2013 1:06:28 PM , Rating: 2
3.2 billion base pairs is actually 3.2 billion bits.

Since effectively the data is RAND compression is highly unlikely to save many bits

3.2 /8 = 400 million bytes. He was correct in his 400mb size file.

Unless there is 'empty pairs' of sorts. There is no need for vertexes if you run sequential.

Now given if there is variable count per specie (I am no genetitsist (sp?)) then the solution is simply count til finished

You only need to run a tree if there is a variable placement based upon previous results and then only if the system is not self indexing.


By cashkennedy on 3/21/2013 6:40:18 PM , Rating: 2
I would imagine there is a bunch of extra information to allow the data to be accessed / searched faster, such as what proteins various sections lead to , and possibly a index column that says what numerical position each base pair is in. Im no expert on databases though, but there are plenty of retarded ways to make databases, and although text files of pure data are nice and small they take forever to search.


By MantisLion on 3/22/2013 2:10:38 AM , Rating: 1
Just so you know, .BAM files are alignment files, that is, they are stacks of individual DNA sequences from a sequencing machine aligned together to form a final sequence. This is done to ensure that each base is sequenced multiple times for maximum accuracy, as next-generation sequencing techniques sacrifice some quality of base call for quantity of sequencing. It's not just the raw end sequence they have there, otherwise you would be correct in your 400MB figure.

I've worked with .BAM files that have been >30GB, but only covering approximately 50 megabases worth of actual sequence data, simply because the coverage (sequencing depth) of each base was on average 250x.


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