Thread: Neanderthal DNA sequenced

From a 38,000 year old bone. The studies have sown that the Neanderthal DNA variance is outside the normal variance of humans today, suggesting that the 2 human species did not mate, although this is still not conclusive from thsi data.

Article

Technically there wasn't a single nucleotide of the neanderthal genome sequenced, since the article concerned mitochondrial DNA.

precisely why I did not mention anything about nucleotides, and that it suggests that there was no mating between the species and that it was inconclusive.

The first part of your reply concerning nucleotides has me gotten me thoroughly confused.

As in, I don't see the connection between not mentioning nucleotides and the difference between mitochodrial and proper genome.

that is because I was not even referring to nucleotides in my paraphrased OP, but nevermind.

Back on topic - a question I have related to the topic of the article, can someone explain how:

1. DNA (mitochondrial or whatever) can be retrieved from a bone taht old and
2. Does this study suggest that Neanderthal and Sapiens were more divergent?
3. (I probably will get flamed for this one) what is the difference between mitochondrial and 'real' DNA? - what implications does this pose for the conclusions suggested?

Note: although I am a physicist and a teacher of physics, I am not a biologist and far from a geneticist, so please do not flame me (not that I am accusing the respondee to my OP as some may assume).

2. the study suggests a certain timeline of divergence of neanderthal and sapiens lineage.

they put it now at 660,000 ± 140,000 years.

Of course mitochondria are only passed on by females, so it could technically be the case that sapiens males have mated with neanderthal females for longer, but not the other way around.

But that would be very speculative and probably unlikely.

OKay, I agree, the odds of the scenario that sapiens males mated with neanderthal females for longer than the opposite does sound a bit off.

There probably was indeed some 'cross pollination' going on, but it is unlikely that this would have affected sapiens evolution?

[Please remember, I am not strong in genetics]

Apparently the application of High-throughput 454 sequencing techniques made it possible to do the full sequencing.

That kind of technique relating to neaderthals was first reported in Nature in 2006 for the use in Neanderthal DNA

http://www.nature.com/nature/journal...ture05336.html

In this technology, single-stranded libraries, flanked by common adapters, are created from the DNA sample and individual library molecules are amplified through bead-based emulsion PCR, resulting in beads carrying millions of clonal copies of the DNA fragments from the samples. These are subsequently sequenced by pyrosequencing on the GS20 454 sequencing system.

if you wonder what 454 stands for; it's a company. It's a kind of shotgun sequencing method and to be honest, I don't have a clue about the details. It's just that the people discovered it is extremely well suited for sequencing of ancient DNA.

It circumvents some of the problems that arise with the standard methods such as loss of templates and competition of templates.

The method was originally published in 2005
http://www.nature.com/nature/journal...ture03959.html


It is possible to also find regular DNA, but MtDNA just seems to be more robust in this respect and is preserved better.

Originally Posted by southern_firestorm

OKay, I agree, the odds of the scenario that sapiens males mated with neanderthal females for longer than the opposite does sound a bit off.

There probably was indeed some 'cross pollination' going on, but it is unlikely that this would have affected sapiens evolution?

[Please remember, I am not strong in genetics]

The essence is I guess (if the data is correct and reliable) that there hadn't been any crossbreeding between the two populations for a very very long time. Despite they were living basically next to each other and were in many respects very similar.

To be honest, I don't know what they exactly know about the genomic DNA of neaderthals at the moment. Maybe they couldn't even crossbreed? What if they had different amount of chromosomes?

I will scan the Cell paper (the one the news report is based on) quickly and see if they say something.

That does make sense regarding the cross breeding.

I would appreciate your views on the paper, and thank you for your patience in answering my questions.

some general points from the Cell paper.

The paper has lots of controls and such for contamination. Contamination with human MtDNA is of course a big problem in these kind of studies.

The common ancestor of neanderthal and homo sapiens lineage lived about 600,000 years ago. The last common ancestor of us living humans (according to the mitochondrial definition) lived about 200,000 years ago. (the last human we all are related too lived only a few thousands years ago in Asia).

The protein evolution (the DNA sequence translated into a protein sequence) showed that the Neanderthals probably had a rather small population size compared to humans over time.

A really strange find was that according to the sequences the Neanderthal lineage should be shorter than the human one and this cannot be fully explained by the fact that the fossils are 38,000 years old, and the human MtDNA is from extant humans. They don't give a proper explanation other than refer to the statistical nature of making such phylogenies; "a large stochastic component to phylogenetic branch length".

And lastly they speculate that it should be possible to actually sequence the nuclear genome of Neanderthals with this method.

That would be very interesting.

original paper:
http://www.cell.com/content/article/...92867408007733

So chimps have 46 chromosomes and humans have 48. That's already a major reason why they are not crossbreeding.


I guess we have to wait till they sequence more of the nuclear genome of the Neanderthal to get a better picture.

That might take a while. Mitochondrial DNA is rather small compared to nuclear DNA.

3. (I probably will get flamed for this one) what is the difference between mitochondrial and 'real' DNA? - what implications does this pose for the conclusions suggested?


The difference between nuclear and mitochondrial DNA can better be answered by wikipedia. Forgive me for just giving links.

http://en.wikipedia.org/wiki/Nuclear_DNA

http://en.wikipedia.org/wiki/Mitochondrial_DNA

oh...they actually expect the have the nuclear genome sequence within a year. (!!!)

http://www.nature.com/news/2008/0808...2008.1026.html

The research, published in Cell1, is a taster for the unveiling later this year of the complete Neanderthal nuclear genome sequence — which many hope will reveal the key genetic changes that propelled the evolution of human behaviour.

that's quite amazing.

Very interesting stuff!