German researchers publish full Neanderthal genome

Mar 19, 2013

(Phys.org) —The Max Planck Institute for Evolutionary Anthropology, in Leipzig, Germany, hascompleted the genome sequence of a Neandertal and makes the entire sequence available to the scientific community today.

In 2010, Dr. Svante Pääbo and his colleagues presented the first draft version of the from data collected from three bones found in a cave in Croatia. They have now used a toe bone excavated in 2010 in Denisova Cave in southern Siberia to generate a high-quality genome from a single Neandertal individual.

The Leipzig team has used sensitive techniques they have developed over the past two years to sequence every position in the genome about 50 times over, using DNA extracted from 0.038 grams of the toe bone. The analysis of the genome together with partial genome sequences from other Neandertals, and the genome from a small finger bone discovered in the same cave, shows that the individual is closely related to other Neandertals in Europe and western Russia (see Figure). Remarkably, Neandertals and their relatives, Denisovans, were both present in this unique cave in the Altai Mountains on the border between Russia, China, Mongolia and Kazakhstan.

In the 2010 draft version of the Neandertal genome, each position was determined, on average, once. In the now-completed version of the genome every position was determined on average 50 times over. This allows even the small differences between the copies of genes that this Neandertal individual inherited from its mother and father to be distinguished. Today, the Leipzig group makes the entire Neandertal genome sequence available for the scientific community over the internet.

"The genome is of very high quality", says Dr. Kay Prüfer, who coordinates the analyses of the genome in Leipzig. "It matches the quality of the Denisovan genome, presented last year, and is as good as or even better than the multiple present-day human genomes available to date."

"We are in the process of comparing this Neandertal genome to the Denisovan genome as well as to the draft genomes of other Neandertals. We will gain insights into many aspects of the history of both Neandertals 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 and Denisovans" says Pääbo. The group will present a paper describing the later this year. "But we make the freely available now to allow other scientists to profit from it even before it is published" says Pääbo.

The project is made possible by financing from the Max Planck Society and is part of efforts since almost 30 years by Dr. Pääbo's group to study ancient DNA. The toe bone was discovered by Professor Anatoly Derevianko and Professor Michael Shunkov from the Russian Academy of Sciences in 2010 during their excavations at Denisova Cave, a unique archaeological site which contains cultural layers indicating that human occupation at the site started up to 280,000 years ago.

Explore further: The origin of the language of life

More information: Neanderthal genome: www.eva.mpg.de/neandertal/

Related Stories

Entire genome of extinct human decoded from fossil

Feb 07, 2012

(PhysOrg.com) -- In 2010, Svante Pääbo and his colleagues presented a draft version of the genome from a small fragment of a human finger bone discovered in Denisova Cave in southern Siberia. The ...

Dating encounters between modern humans and Neandertals

Oct 04, 2012

To discover why Neandertals are most closely related to people outside Africa, Harvard and Max Planck Institute scientists have estimated the date when Neandertals and modern Europeans last shared ancestors. The research, ...

Draft version of the Neanderthal genome completed

Feb 12, 2009

In a development which could reveal the links between modern humans and their prehistoric cousins, scientists said Thursday they have mapped a first draft of the Neanderthal genome. Researchers used DNA fragments ...

Recommended for you

The origin of the language of life

Dec 19, 2014

The genetic code is the universal language of life. It describes how information is encoded in the genetic material and is the same for all organisms from simple bacteria to animals to humans. However, the ...

Quest to unravel mysteries of our gene network

Dec 18, 2014

There are roughly 27,000 genes in the human body, all but a relative few of them connected through an intricate and complex network that plays a dominant role in shaping our physiological structure and functions.

EU court clears stem cell patenting

Dec 18, 2014

A human egg used to produce stem cells but unable to develop into a viable embryo can be patented, the European Court of Justice ruled on Thursday.

User comments : 13

Adjust slider to filter visible comments by rank

Display comments: newest first

Qshadow
3 / 5 (1) Mar 19, 2013
"German researchers publish full Neanderthal genome"
Maybe this is silly question, but:
How do they know it is really FULL and nothing is missing?
after all they had a very old and degraded sample.
Claudius
2.7 / 5 (7) Mar 19, 2013
They compared it with Chuck Norris' genome. :)
antialias_physorg
4.2 / 5 (9) Mar 19, 2013
How do they know it is really FULL and nothing is missing?

Because we know how long the genome is (how many base pairs).We know how many chromosomes there are - and what they look like at the ends (the telomeres) - so you can always tell whether you have a full chromosome or something is missing.

And as noted in the article: They had enough to, on average, sequence every part of it 50 times over.
Lurker2358
1 / 5 (15) Mar 19, 2013
How do they know it is really FULL and nothing is missing?

Because we know how long the genome is (how many base pairs).We know how many chromosomes there are - and what they look like at the ends (the telomeres) - so you can always tell whether you have a full chromosome or something is missing.


That's not even true.

One of the contributing factors to neuromuscular diseases is that the human genome actually has a natural variation from person to person in the number of copies of certain genes, and their base pairs. There is a range for normalcy, and if the person is above or below that their chance of showing disease is higher. That's just one example.

The funding for this "research" should be spent on broad spectrum research on living humans to help identify and treat potential disease markers before they cause damage.

Instead, they waste all this money on twiddling around with the bones of people who died ages ago.
PaulLev
1 / 5 (2) Mar 19, 2013
for more on Neanderthals and their genes, see The Silk Code
C_elegans
5 / 5 (11) Mar 19, 2013
It is quite true.

Genomes are assembled by producing thousands of 200-300 base pair patches of DNA (called contigs). Having so many of them allows you to stitch them together in a continuous fashion.

contig1------__________________
-----contig2-------_______________________
--------- contig3-------____________________

And we can learn a lot from Neanderthals. In one example, the sequence of the Neanderthal genome can be compared to ours to recognize conserved pieces of DNA between our species, such as regulatory elements in non-coding DNA sequences, bits of DNA that control whether the following gene is on or off. Also, we could identify the genes that make us different, potentially explaining why our species was successful and theirs was not. Finally, this first genome acts as a framework for future sequences to be easily compared to.

But I'm glad Lurker is here to tell everyone how to do their jobs. He seems to have it all figured out already.
antialias_physorg
5 / 5 (11) Mar 19, 2013
That's not even true. One of the contributing factors to neuromuscular diseases is that the human genome actually has a natural variation from person to person in the number of copies of certain genes

Which is rare - and would not show up as a 50 fold cover. They were trying to sequence the full Neanderthal genome - not every possible pathological variation.

Instead, they waste all this money on twiddling around with the bones of people who died ages ago.

You have so little imagination. Genome changes can tell us about adaptations to certain environments - which in turn may help us either cure diseases or see weakpoints in our current genome, or even help us with genetic engineering isues when we wish to adapt to other environments (e.g. off-world).

Any knowledge is useful. Only short-sighted people think that researching the next iPad is the most useful thing to do long term.
Lurker2358
1 / 5 (9) Mar 19, 2013
I'm glad Lurker is here to tell everyone how to do their jobs. He seems to have it all figured out already.


Nothing about telling others how to do their jobs.

Some inaccurate statements were made.

Only short-sighted people think that researching the next iPad is the most useful thing to do long term.


Come now, surely you aren't comparing me to such a crow?

You must know my history, eh? I want the maximum ethical advancement in all fields.

Smartphones have a lot more potential than what is being done with them, but they are a toy compared to the tech I hope to see accomplished.

The real problem I have with it is we haven't even learned how to properly identify genetic diseases in living life forms, where you can test it in a lab or in human trials, except the most obvious cases, so how can you expect to detect that in an extinct one?

Think of that swine disease the chinese just had (other article). Figure that out first. Save food and resources.
C_elegans
5 / 5 (3) Mar 20, 2013

The real problem I have with it is we haven't even learned how to properly identify genetic diseases in living life forms, where you can test it in a lab or in human trials, except the most obvious cases, so how can you expect to detect that in an extinct one?


To what exactly are you referring to? We have identified thousands of genetically inherited diseases by sequencing thousands of diseased families. Not all diseases are caused by a single genetic polymorphism, so we generally can't 'sequence' your diabetes or Ahlzheimer's. Furthermore, pathogens live covertly alongside billions of unique bacteria on each person, so how would we 'sequence swine disease'? Sequencing is not generally used for pathogens, maybe you're thinking of swine cancer???

roedy_green
5 / 5 (3) Mar 20, 2013
With the genome, what can we deduce about Neatherthal biochemistry, physiolgy, frailties etc.?
DarkHorse66
3 / 5 (2) Mar 20, 2013
I do follow articles such as these with quite some fascination, but like anyone who might be tempted to look up background or supporting material, the following might present a problem (unless I have missed something):
"In 2010, Dr. Svante Pääbo and his colleagues presented the first draft version of the Neandertal genome from data collected from three bones found in a cave in Croatia."
I'm presuming that the draft version that the author of the article is referring to, is actually this one, that is sitting in my 'related stories' section and has the date 'Feb 12, 2009'?
http://phys.org/n...tml#nRlv
Cheers,DH66
Sinister1811
2.5 / 5 (8) Mar 20, 2013
This is interesting, because they can compare the Neanderthal genome to the modern human genome and find differences and similarities between the species. This can also shed more light on our own evolutionary tree.
philw1776
3.3 / 5 (3) Mar 20, 2013
So were many Neanderthals red heads as some have claimed?
This is fascinating research. Kudos to all involved. I'm certain there will be serendipitous discoveries that will help us understanding homo sapiens' genome better, et. al.

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.