Comparisons of Neandertal mtDNA with modern humans and modern chimpanzees

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Percy before I go and see if he can get it in appropriate format....this is a wonderful example of why academic publishing that is not free access is really crap ..all the BMC journals and PLoS are open access and you can access all figures and data...without paying..the author pays to publish instead.

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Thanks for the effort, and I totally agree with you. Like I said earlier, I could use my journal account at work but this would be a little unethical since this is non-work related. Also, some journals charge both the authors and the subscribers, or charge for online access. They get you coming and going.

Hi Loudmouth,
I'll send a copy of the article snail mail to you when I get back from the conference where I am presenting and my subsequent trying to sit still on a beach in southern France cheers,
M

...and the ball is still rolling...just saw this..Mol. Biol. Evol. 21(6):1081-1084. 2004
NUMTs in Sequenced Eukaryotic Genomes
Erik Richly and Dario Leister
Max-Planck-Institut fr Zchtungsforschung, Kln, GermanyCorrespondence: E-mail: leister@mpiz-koeln.mpg.de.Mitochondrial DNA sequences are frequently transferred to the nucleus giving rise to the so-called nuclear mitochondrial DNA (NUMT). Analysis of 13 eukaryotic species with sequenced mitochondrial and nuclear genomes reveals a large interspecific variation of NUMT number and size. Copy number ranges from none or few copies in Anopheles, Caenorhabditis, Plasmodium, Drosophila, and Fugu to more than 500 in human, rice, and Arabidopsis. The average size is between 62 (baker's yeast) and 647 bps (Neurospora), respectively. A correlation between the abundance of NUMTs and the size of the nuclear or the mitochondrial genomes, or of the nuclear gene density, is not evident. Other factors, such as the number and/or stability of mitochondria in the germline, or species-specific mechanisms controlling accumulation/loss of nuclear DNA, might be responsible for the interspecific diversity in NUMT accumulation.Key Words: duplication gene transfer genome evolution mitochondria NUMT pseudogene

interesting -- did not know that: is that what causes some pages with pictures to take longer loading?filed for future use on posting original pictures, but hard to avoid when using pictures from other sites ps - I notice that my e-mail reply notifications are not coming anymore?

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we are limited in our ability to understand
by our ability to understand RebelAAmerican.Zen[Deist
{{{Buddha walks off laughing with joy}}}

Not coming at all? Or taking 3 or 4 hours to arrive?Our server has been experiencing email delays for a couple weeks, and I'm working the issue with our webhosting company. The delay can be as long as 3 or 4 hours, or at least that's the worst I've experienced myself. It would be helpful to know if there are also email dropouts. Is anyone else experiencing either of these problems, either delays or dropouts of email notifications?

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--	Percy
	EvC Forum Administrator

I have changed my preferences to turn it off and then to turn it on again to see if that clears it. As yet I have not had a single message since the software change. I have only today verified that there have been replies (been busy). (ps -- isn't this offtopic of an offtopic post???)

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we are limited in our ability to understand
by our ability to understand RebelAAmerican.Zen[Deist
{{{Buddha walks off laughing with joy}}}

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Hi Loudmouth,
I'll send a copy of the article snail mail to you when I get back from the conference where I am presenting and my subsequent trying to sit still on a beach in southern France

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email: thebread05@yahoo.comNothing better than going to meetings on the lab's dime, especially to the Frech Riviera. Last trip for me was on Cape Cod near Martha's Vineyard. I didn't even have to present anything, which let me enjoy the conference even more. Enjoy.

just got notification for this one

Can you give an explaination for a non scientist.rickrose

After a little thought I deleted my reply.
rickroseThis message has been edited by Rick Rose, 05-13-2004 11:09 AM

Rick Rose,Mammuthus is a little busy lately, so I'll try and fill in for the time being. He may come back and correct me on a few points if I get them wrong.In our discussions (Mammuthus and I) we have been talking about the Neandertal mitochondrial DNA data. The studies seem to indicate that there are enough differences between neandertal and human mitochondrial DNA is enough to conclude that humans and neandertal's were separate species. This does not rule out the ability to interbreed, but if interbreeding were a common occurence then the mitochondrial DNA's should be more alike.However, Mammuthus has brought up some very good points that cast doubt on the reliability of the neandertal mitochondrial DNA (mitDNA here after). Mitochondria are organelles that carry their own DNA separate from human genomic DNA. It has been hypothesized that mitochondria are actually trapped bacteria that the cell uses for energy production. However, once in a while the mitDNA can be inserted into the human genome (nuclear mitochondrial DNA, numt hereafter). Numt's are then susceptible to mutation, and those mutations will differ from the mutations accruing in the mitDNA. Therefore, the numt and mitDNA will have different DNA sequences. Also, it is hard for scientists to differentiate between mitDNA and numt's when they are amplifying certain sequences.So the problem then becomes this. Are the differences between neandertal and human mitDNA due to the fact that we are amplifying neandertal numt's. That is, are we comparing apples and oranges. Could it be that the neandertal true mitDNA is very close to human mitDNA in sequence, but numt interference is blinding us to the truth. The post that you replied to is a species to species comparison of the occurence of numt's. In apes and humans, the numt insertion rate is very high compared to other species. We would expect neandertals to also have a high number of numt sequences in their genomic DNA.What I feel is a solid control for this proposed problem is the sequencing of mitDNA from anatomically modern humans (amh) that lived close to the same time as neandertal's. If the age of the mitDNA and genomic DNA is leading to the the sequencing of numt's instead of true mitDNA, then this same problem should be seen in amh's as well. The data shows that ancient amh and neandertal mitDNA differ by the same amount as current human mitDNA. Also, amh mitDNA fits nicely within the normal distribution of current human mitDNA. That is, anatomically modern humans 20,000 years ago had the same mitDNA sequences as we humans do today.Mammuthus's other criticism is this. If amh mitDNA sequence showed signifigant differences from current human mitDNA, it might be thrown out in favor of sequences that are closer to current humans. The same thing may not happen with neandertal mitDNA, the differences might be more easily accepted as being real when in fact it might be due to numt.Well, I hope this helps you understand the predicament surrounding the sequencing of ancient hominid mitDNA. Just as a side note, mitDNA is used for sequencing since there are 1,000's of copies of mitDNA compared to genomic DNA. This is because there are numerous mitochondria, each with their own genome, per human cell. It is thought that you will have better chances of amplifying mitDNA since there are a lot more sequences floating around in the organic remains of ancient species.

I grasp your expo. Thanks. Very interesting subject.Do you know if it has been verified that modern humans have genetic material from a known source other than Neanderthal? -- homo erectus or other? Just a brief answer. I don't want to cause drift.rickrose

Hi Loudmouth (and hello Rick)
I can only briefly reply as I am on a low bandwidth connection and don't have much time.Loudmouth's summary is good but my objection to the overall conclusions of the neandertal work are slightly different. I do not think the neandertal sequence (at least that of Krings et al.) represent Numts. They designed primers specific for the neandertal sequence and screened modern human DNA and from over 30 samples (if memory serves) of different ethnic origin, the nea sequence never turned up. Also, thousands of humans have been sequenced for mtDNA sequences and the nea sequence has never turned up.My problem is the following, if you have a neandertal bone (or Cro-magnon), and you do all the proper controls and get a human sequence, is it authentic (i.e. endogenous sequence), is it a Numt? can one accept it? According to Paabo and Cooper, no. If you get human sequences from Cro Magnon or neandertals, there is no way to discern whether you have obtained a contaminant from an endogenous authentic sequence. Thus, my objection is that if you cannot accept a modern human (or similar to modern human) sequences from neandertals or Cro-Magnon as authentic, then you cannot scientifically test their relationship to modern humans. By discarding sequences that are similar to modern human DNA, you a priori assume that neandertals were different from humans...and assuming your conclusions and discarding evidence against it sounds like creationism..not like science. Alternatively, it just may be that with current methodologies one cannot address the question of human-neandertal realtionships.

Got the picture. As of yet, comparisons may not be possible as you explained. Are there other methods of comparison that could preclude the contamination issues? Just a short answer when you have time.rickrose

Not yet.

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Aslan is not a Tame Lion