August 07, 2008

Complete Neanderthal mtDNA sequence

Public release:
Analysis of the new sequence confirms that the mitochondria of Neandertal's falls outside the variation found in humans today, offering no evidence of admixture between the two lineages although it remains a possibility. It also shows that the last common ancestor of Neandertals and humans lived about 660,000 years ago, give or take 140,000 years.
Cell, Vol 134, 416-426, 08 August 2008

A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing

Richard E. Green,1, Anna-Sapfo Malaspinas,2 Johannes Krause,1 Adrian W. Briggs,1 Philip L.F. Johnson,3 Caroline Uhler,4 Matthias Meyer,1 Jeffrey M. Good,1 Tomislav Maricic,1 Udo Stenzel,1 Kay Prüfer,1 Michael Siebauer,1 Hernán A. Burbano,1 Michael Ronan,5 Jonathan M. Rothberg,6 Michael Egholm,5 Pavao Rudan,7 Dejana Brajković,8 Željko Kućan,7 Ivan Gušić,7 Mårten Wikström,9 Liisa Laakkonen,10 Janet Kelso,1 Montgomery Slatkin,2 and Svante Pääbo1

Summary

A complete mitochondrial (mt) genome sequence was reconstructed from a 38,000 year-old Neandertal individual with 8341 mtDNA sequences identified among 4.8 Gb of DNA generated from ∼0.3 g of bone. Analysis of the assembled sequence unequivocally establishes that the Neandertal mtDNA falls outside the variation of extant human mtDNAs, and allows an estimate of the divergence date between the two mtDNA lineages of 660,000 ± 140,000 years. Of the 13 proteins encoded in the mtDNA, subunit 2 of cytochrome c oxidase of the mitochondrial electron transport chain has experienced the largest number of amino acid substitutions in human ancestors since the separation from Neandertals. There is evidence that purifying selection in the Neandertal mtDNA was reduced compared with other primate lineages, suggesting that the effective population size of Neandertals was small.

Link

10 comments:

Crimson Guard said...

Wonder why Eric Trinkaus still so adamantly supports the intermixture theory for, despite lack of physical and genetic evidence to the contrary.

terryt said...

Not so fast Crimson Guard. There have been any number of posts here proving haplogroups are very loosely associated with particular modern physical and genetic types, so I'm sure we can assume this was so in more ancient times.

On another note I see the authors suggest "that the effective population size of Neandertals was small" at the time, 38,000 years ago. This fits with other evidence, and may indicate why Neanderthals were ultimately replaced. We'd certainly expect them to be very inbred by 38,000 years ago.

Dragon Horse said...

"There have been any number of posts here proving haplogroups are very loosely associated with particular modern physical and genetic types, so I'm sure we can assume this was so in more ancient times.
"

Really. WOuld it make sense that the further you go back in history, the smaller and more isolated human populations where (into hunter-gather clans) the less true what you say is?

Antigonos said...

"Wonder why Eric Trinkaus still so adamantly supports the intermixture theory for, despite lack of physical and genetic evidence to the contrary?"

Trinkaus supports the Neanderthalian admixture because he has found skeletons and bone material that show this!
It is silly Crimson to say that Neanderthals and Early Moderns did not mingle just because the mtDNA of ONLY ONE Neanderthal was studied!
Neanderthals vary in their substance greatly. There are Neanderthals that have for example the FOXP2 gene and others that don't!
Also mtDNA is highly affected by natural selection.
We should wait until the full DNA of the Neanderthals is fully recovered and then we will have evidence in our hands to come to a verdict.

Crimson Guard said...

All evidence available thus far, including genetic, do not show intermixture. The supposed hybrid skulls, were actually Cromagnon(modern man) with certain archaic features(ala browridge).

terryt said...

Dragon Horse asked, "WOuld it make sense that the further you go back in history, the smaller and more isolated human populations where (into hunter-gather clans) the less true what you say is?"

Certainly that might be so, but even then that pre-supposes the idea of a single out of Africa origin and that there was no admixture with pre-existing more ancient types.

Regarding survival of ancient non-African genes Mathilda has posted this:

http://mathildasanthropologyblog.wordpress.com/2008/08/03/ancient-dna-in-asians-casts-doubt-on-the-out-of-africa-theory/

Admiitedly from a 2004 paper.

At another post she has pondered the reason why the recent single out of Africa theory has become the received standard orthodoxy:

http://mathildasanthropologyblog.wordpress.com/2008/08/04/so-all-anthropologists-support-the-out-of-africa-theory-do-they/

In the comments Milford Wolpoff has listed ten papers supporting the idea of admixture and, of course, I have put my two cents' worth in too.

Antigonos said...

Dear Crimson

The modern human autosomal DNA does show archaic features on the contrary with Y-DNA or mtDNA that do not.
The problem is that the latter are very much affected by natural selection and can't be used as a rigid indication.
Only after the autosomal DNA of at least a handsome of Neanderthals is retrieved we might be able to come to a final verdict.
Finally the skulls you mention are not Cro-magnon.
Hybrid individuals like Es Skhul, Quafzeh, some of the Predmost fossils, Oase and finally the Lapedo Child DO SHOW NEANDERTHALIAN FEATURES.

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

Maju said...

I am with Crimson Guard.

Nevertheless, mtDNA alone cannot disprove some minor ammount of admixture. The same team are working to sequence the full Neanderthal genome and that should clear everything, at least to a much higher extent.

What is clear already is that our maternal lineage at least is not Neanderthal at all. There have been several partial sequencings pre-dating this one and al have placed Neanderthal mtDNA quite distant from the range of H. sapiens.

Antigonos said...

If Neanderthalian mtDNA sequences have been wiped out by natural selection or some other evolutionary process from our DNA how can we tell?
Our mtDNA doesn't show Neanderthalian admixture probably because it is not there anymore!
It has been eliminated.
Anyway as Maju said things will clear to a satisfactory level when we will have the autosomal DNA of one Neanderthal. It is not much and by no means it is conclusive since Neanderthals did vary a lot (like in the case of FOXP2 gene) and one autosomal sample doesn't say a lot but at least it is something indicative.

Maju said...

MtDNA is haploid. It cannot show any admixture because it is not affected by recombination, specially as we already knew that H. sapiens mtDNA is all descendant of a single woman, the so-called Mitochondrial Eve, who was not obviously Neanderthal. Same for Y-DNA.

Neither of them can exclude small levels of admixture that would be only detectable in the diploid part of the genome. But what the great distance of Neanderthal mtDNA re. ours does indicate is that they were clearly a distinct species and that our two species were pretty different when they came into contact. This may have hindered admixture not just because of pure biological reasons but also maybe for psycho-cultural ones.

But even the smallest level of admixture may have caused, if Neanderthals had some genes that were fitter than ours for certain conditions, a good deal of introgression. All this is anyhow very speculative at the moment. We must wait till Neanderthal genome is fully sequenced.