Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal
Pontus Skoglund et al.
One of the main impediments for obtaining DNA sequences from ancient human skeletons is the presence of contaminating modern human DNA molecules in many fossil samples and laboratory reagents. However, DNA fragments isolated from ancient specimens show a characteristic DNA damage pattern caused by miscoding lesions that differs from present day DNA sequences. Here, we develop a framework for evaluating the likelihood of a sequence originating from a model with postmortem degradation—summarized in a postmortem degradation score—which allows the identification of DNA fragments that are unlikely to originate from present day sources. We apply this approach to a contaminated Neandertal specimen from Okladnikov Cave in Siberia to isolate its endogenous DNA from modern human contaminants and show that the reconstructed mitochondrial genome sequence is more closely related to the variation of Western Neandertals than what was discernible from previous analyses. Our method opens up the potential for genomic analysis of contaminated fossil material.
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18 comments:
Interesting. The branching pattern within the Neanderthal clade supports the idea of an orgin to the east of Europe, exactly as was proposed some time ago in one of Dienekes' posts.
What is the common root between neanderthal and denisova in the diagram?
Again, this study replicates the finding that the ancestors of modern humans mixed with heidelbergensis to produce Neanderthals.
Hi Dienekes, I was wondering if you could release an ANI/ASI calculator from your posts about using 'zombies'? Or could you analyze my 23andMe raw data to see that?
"The branching pattern within the Neanderthal clade supports the idea of an orgin to the east of Europe"
Or European "Neanderthals" like Vindija (see below) are divergent because they are actually hybrids with mesolithic modern humans, rather than 'pure' Neanderthals. The unadmixed Neanderthals would thus look ancestral.
http://dienekes.blogspot.com.au/2012/01/neandertal-shoulder-blades-and.html
IMO Vindija was not the best choice as a Neanderthal standards for modern admixture studies, as I strongly suspect (from the diagram above) it was already admixed.
"IMO Vindija was not the best choice as a Neanderthal standards for modern admixture studies, as I strongly suspect (from the diagram above) it was already admixed".
But haplogroup phylogenies can tell us nothing about possible admixture unless a particular haplogroup is discovered in an anomalous situation, such as a Neanderthal haplogroup found in an apparently modern human, or vice versa. The haplogroup is passed on from the appropriate parent independent of any admixture.
Yep. You are right. It is only going to affect the autosomal situation.
One thing the branching pattern does suggest (and German will be pleased) is that at face value the ancestral modern human mt-DNA line looks to have entered Africa from Asia before it formed. Denisovans (who may be 'Homo heidelbergensis') gave rise to what became Neanderthals, and then some early branch of Neanderthals gave rise to the 'modern human' line. That scenario is by no means impossible, or even unlikely. Y-DNA appears to be much older in Africa than does mt-DNA. In other words no equivalent to A00 (L00?) has been found.
"Denisovans (who may be 'Homo heidelbergensis') gave rise to what became Neanderthals, and then some early branch of Neanderthals gave rise to the 'modern human' line."
As shown in the figure from the paper, it would be more accurate to say that Homo heidelbergensis was ancestral both to Denisovans and also to the common ancestor of Neanderthals and AMH, and that AMH and Neanderthals shared a common ancestor. We know from autosomal DNA that AMH does not descend from Neanderthals.
The physical evidence suggests that Homo erectus originated in Africa, and that Denisovans and Neanderthals both descend from early migrations out of Africa. H. heidelbergensis was widespread in Africa, Europe and western Asia. When and where did it originate? Perhaps there was multiregional evolution in the period from 1 million to 600,000 years ago?
There is no DNA evidence that indicates AMH arose in Eurasia before 200 kya and than migrated to Africa. It might be possible, but the physical evidence suggests that AMH evolved in Africa from an H. heidelbergensis population that remained in Africa.
I think the most you can say is that there is a possibility that the common ancestor of Neanderthals and AMH arose in Eurasia, and a subsequent back migration to Africa might have given rise to AMH in Africa, but it seems highly speculative. Is there any evidence to support this.
@terryT
"One thing the branching pattern does suggest (and German will be pleased) is that at face value the ancestral modern human mt-DNA line looks to have entered Africa from Asia before it formed. Denisovans (who may be 'Homo heidelbergensis') gave rise to what became Neanderthals, and then some early branch of Neanderthals gave rise to the 'modern human' line."
Now we are talking! And to take it one step further: Amerindians have shown a special proximity to Neandertals in a number of studies across different genetic systems.
"it would be more accurate to say that Homo heidelbergensis was ancestral both to Denisovans and also to the common ancestor of Neanderthals and AMH"
But we don't really know what Homo heidelbergensis was. Denisova could well represent the 'species'. I did say 'some early branch of Neanderthals' which is much the same as 'AMH and Neanderthals shared a common ancestor'.
"The physical evidence suggests that Homo erectus originated in Africa, and that Denisovans and Neanderthals both descend from early migrations out of Africa. H. heidelbergensis was widespread in Africa, Europe and western Asia. When and where did it originate? Perhaps there was multiregional evolution in the period from 1 million to 600,000 years ago?"
I agree with all of that, especially 'Perhaps there was multiregional evolution in the period from 1 million to 600,000 years ago'.
"There is no DNA evidence that indicates AMH arose in Eurasia before 200 kya and than migrated to Africa".
Unlike German I am not suggesting AMH originated in Eurasia. But the tree does suggest that the ancestor of AMH (the mt-DNA line anyway) did not originate from an African H. erectus but most likely entered that continent from Eurasia (perhaps in the form of H. heidelbergensis).
"physical evidence suggests that AMH evolved in Africa from an H. heidelbergensis population that remained in Africa".
I don't think we have any evidence as to whether H. heidelbergensis evolved in Africa or moved into that continet from Eurasia.
"the most you can say is that there is a possibility that the common ancestor of Neanderthals and AMH arose in Eurasia, and a subsequent back migration to Africa might have given rise to AMH in Africa, but it seems highly speculative. Is there any evidence to support this".
The mitochondrial DNA tree in the article certainly suggests that scenario.
Sorry. Another comment re. Denisovans and H. heidelbergensis. Did you see this post:
http://dienekes.blogspot.co.nz/2013/12/400-thousand-year-old-human-mtdna-from.html
It seems we can only consider the Sima de los Huesos individual as being H. heidelbergensis yet it has Denisova mt-DNA. That suggests the two were one and the same. As Eurologist said at the time 'I am happy to see that heidelbergensis is again more widely seen as the main solution to this problem -- as I have suggested for a long, long time'.
Perhaps there was multiregional evolution in the period from 1 million to 600,000 years ago?
Gail and Terry,
I of course agree with this, but would put the lower limit to some time after 400,000 ya for climate reasons.
As I have stated before, I think the most straightforward explanation of the tree is an ooA migration just at the beginning of the heidelbergensis -> Neanderthal transformation in Europe, which had left the population extremely small (due to climate), while of course that of Africa was huge, in comparison.
"I think the most straightforward explanation of the tree is an ooA migration just at the beginning of the heidelbergensis -> Neanderthal transformation in Europe, which had left the population extremely small (due to climate)"
The more I think about it the more convinced I am that 'Denisova' is none other than 'Homo heidelbergensis'. I agree heidelbergensis' origins may lie in Africa but the 'Denisova' branch is certainly Eurasian. The tree suggests that such an early OoA included the ancestors of modern humans. They are at the tip of a tree whose earlier branches both definitely lived outside Africa. Therefore I would include 'modern humans' in your transformation scenario. A modern human ancestry from African H. heidelbergensis doesn't fit the tree at all.
I somewhat disagree with your last comment regarding the population size. H. heidelbergensis was quite widespread, although interestingly never present in SE Asia and only doubtfully present anywhere in East Asia. We are left with the conclusion that the DNA from the Denisova cave represents the last inbred remnant of a once widespread human population. That population had given rise to Neanderthals, who were to replace heidelbergensis through Europe and Central Asia, and also to modern humans, who may have developed from a heidelbergensis population who had entered Africa after separating from the ancestors of Neanderthals.
Terry - copying and pasting from two of yours comments:
But the tree does suggest that the ancestor of AMH (the mt-DNA line anyway) did not originate from an African H. erectus but most likely entered that continent from Eurasia (perhaps in the form of H. heidelbergensis)
The tree suggests that such an early OoA included the ancestors of modern humans. They are at the tip of a tree whose earlier branches both definitely lived outside Africa. Therefore I would include 'modern humans' in your transformation scenario. A modern human ancestry from African H. heidelbergensis doesn't fit the tree at all.
Your logic seems to assume that H. heidelbergensis existed only outside of Africa, i.e., that AMH mtDNA must descend from a Eurasian H. heidelbergensis. Or am I missing something in your theory?
I'd suggest that H. heidelbergensis was widespread, in Africa and Eurasia, and that AMH could have evolved from a population that remained in Africa, while Neandertals evolved from a population that had exited from Africa. Denisovans could represent an earlier OoA migrations. I suggest this possibility because we have physical evidence of early AMH in Africa but not in Eurasia.
Of course this is very speculative, I don't think we can reach any certain conclusions based on the limited mtDNA that we have, one sample at 400 kya, which could be considered at the very end or after the period in which H. heidelbergensis thrived.
"Your logic seems to assume that H. heidelbergensis existed only outside of Africa, i.e., that AMH mtDNA must descend from a Eurasian H. heidelbergensis. Or am I missing something in your theory?"
Yes, you are missing something. I'm fully aware 'that H. heidelbergensis was widespread, in Africa and Eurasia'. However the diagram shows the Neanderthal/AMH line descends from a population that includes the 400,000 year old Sima de los Huesos individual and the 40,000 year old Denisova individuals. Therefore we can be reasonably sure it descends from a European line. What we don't know is how closely related any African H. heidelbergensis lines were to this European line, although we would expect the mt-DNAs in the two regions to diverge over time.
"AMH could have evolved from a population that remained in Africa, while Neandertals evolved from a population that had exited from Africa".
Not likely, because we know from the diagram that Neanderthals and AMHs share a common ancestor, descended from what looks almost certainly to be a European H. heidelbergensis population. I'm certainly prepared to accept the Neanderthal/AMH split is the result of some members of the ancestral population entering Africa and forming the AMH line there.
"Denisovans could represent an earlier OoA migrations".
Almost certainly do. But that is concerned with the base of the diagram and not represented on it. It remains a possibilty that H. heidelbergensis evolved from an H. erectus population outside Africa and some moved back in.
"we have physical evidence of early AMH in Africa but not in Eurasia".
It is extremely doubtful that at the Neanderthal/AMH split the latter line instantly became 'modern humans'.
"one sample at 400 kya, which could be considered at the very end or after the period in which H. heidelbergensis thrived".
That is not quite correct. We have two members of the same line who had survived at Denisova until 40,000 years ago. As I said yesterday, 'the Denisova cave represents the last inbred remnant of a once widespread human population'. European nevertheless.
"we know from the diagram that Neanderthals and AMHs share a common ancestor, descended from what looks almost certainly to be a European H. heidelbergensis population".
Embarrassing mistake. My excuse (and it's a poor one) is that I was confusing aDNA and mt-DNA. The Neanderthal/AMH line split from the Denisova/Sima line around 1 million years ago, not half a million. It is therefore quite possible that the Neanderthal/AMH line remained in Africa. However it is just as possible that both lines formed in Eurasia. The nearly 2 million years old Dmanisi population seems reasonably basal and is possibly ancestral to both H. erectus and H. ergaster. It seems that Homo rhodesiensis is only some 300,000 years old and is presumably Neanderthal's relation and AMH's ancestor.
@ German:
German is running into problems under any scheme he may propose for an out of America theory. He has elsewhere claimed some African lineages such as Y-DNA A00 and mt-DNAs L0 and L1 are the products of introgression from pre-modern humans. But any such 'pre-modern' humans must still be part of the AMH(xNeanderthal) line. And we don't need to reconstruct the phylogenies if we are intent on seeing such a dichotomy.
The problem we have is: where do we draw the line between 'archaic' and 'modern'? It is actually impossible to draw such a line. Darwin's idea of 'gradual change' has been unjustifiably overthrown by the idea of 'punctuated equilibrium', rapid change over a short period. But 'punctuated equilibrium' is just 'gradual change' sped up for a time. The change is never 'sudden'. In fact it is doubtful if it has ever been 'sudden' since before humans and chimps parted ways.
I'm fully aware 'that H. heidelbergensis was widespread, in Africa and Eurasia'. However the diagram shows the Neanderthal/AMH line descends from a population that includes the 400,000 year old Sima de los Huesos individual and the 40,000 year old Denisova individuals. Therefore we can be reasonably sure it descends from a European line.
Neanderthal/AMH and Sima de los Huesos share a common ancestor who lived much earlier than 400 kya, so the location of Sima de los Huesos does not tell us anything about where that common ancestor lived. We will need many more samples and at much greater age before we can do any sort of phylogeographic analysis of H. heidelbergensis and its descendants.
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