Neolithic mtDNA haplogroup H (Haak et al)


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PostPosted: Wed Feb 20, 2013 11:45 pm
Paper to be read at the 2013 meeting of the American Association of Physical Anthropologists 9-13 April 2013 in Knoxville, Tennessee.

Wolfgang Haak et al. including the Genographic Consortium, Neolithic human mitochondrial haplogroup H genomes and the genetic origins of Europeans.

Haplogroup (hg) H dominates present-day Western European mitochondrial (mt) DNA variability (>40%), yet was less prevalent amongst early Neolithic farmers (~19%) and virtually absent in Mesolithic hunter-gatherers. To investigate this haplogroup’s significance in the maternal population history of Europeans we employed novel techniques such as DNA immortalization and hybridization-enrichment to sequence 39 hg H mt genomes from ancient human remains across a transect through time in Neolithic Central Europe. The results of our population genetic analyses reveal that the current patterns of diversity and distribution of hg H were largely established during the Mid-Neolithic, but with substantial genetic contributions from subsequent pan-European cultures such as the Bell Beakers, which expanded out of Iberia in the Late Neolithic (~2800 BC). Using a strict diachronic approach allowed us to reconcile ‘real-time’ genetic data from the most common European mtDNA hg with cultural changes that took place between the Early Neolithic (~5450 BC) and Bronze Age (~2200 BC) in Central Europe. This revealed the Late Neolithic (2800-2200 BC) as a dynamic period that profoundly shaped the genetic landscape of modern-day Europeans. Furthermore, linking ancient hg H genome sequences to specific points in time by using radiocarbon dates as tip calibrations allowed us to reconstruct a precise lineage history of hg H and to calculate a mutation rate 45% higher than traditional estimates based on the human/chimp split.

http://physanth.org/annual-meeting/82nd ... ogram-2013

Thanks to Dienekes for pointing it out.
Last edited by JeanM on Sat Feb 23, 2013 11:59 pm, edited 1 time in total.

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PostPosted: Thu Feb 21, 2013 1:59 am
Furthermore, linking ancient hg H genome sequences to specific points in time by using radiocarbon dates as tip calibrations allowed us to reconstruct a precise lineage history of hg H and to calculate a mutation rate 45% higher than traditional estimates based on the human/chimp split.


They must have sequenced the full genome if they are using the results to calibrate the mutation rate, so it will be very interesting to see the paper. The small number of ancient mtDNA full sequences that are currently available seem to be generally consistent with the Soares mutation rate (although the sample size is small), so it's interesting that they have a faster mutation rate. If anything, I was expecting to see a slower mutation rate.

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PostPosted: Thu Feb 21, 2013 7:02 am
Upcoming papers like this on the phylogeography of mtDNA H and Y-DNA R1a and R1b in Europe will be the death knell of archeology being thought of as a useful method of learning about ancient migrations.

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PostPosted: Thu Feb 21, 2013 9:35 am
Wishful thinking David. This is a study of ancient DNA. Such studies enable us to tie haplogroups to particular cultures. It is phylogeography using only modern DNA that is being superseded.

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PostPosted: Thu Feb 21, 2013 9:46 am
Gail - This will be a key paper in several ways. At last we are in sight of a resolution of the mutation rate wars. One paper won't resolve the issue, but it shows the way forward. The methodology of fitting aDNA to radiocarbon dates is the most reliable.

It also makes clear the dynamism of the Copper Age. People had been thinking about that possibility for a couple of years and this clearly set out to test it. Full authors list: W. Haak, P. Brotherton, J. Templeton, G. Brandt, J. Soubrier, C.J. Adler, S.M. Richards, C.S. Der Sarkissian, R. Ganslmeier, S. Friederich, V. Dresely, M. Van Oven, J. Korlach, S.Y. Ho, L. Quintana-Murci, D.M. Behar, H. Meller, K.W. Alt, A. Cooper, the Genographic Consortium.

So we are liable to see this thinking in the new edition of Spencer Wells, Deep Ancestry.

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PostPosted: Thu Feb 21, 2013 9:58 am
JeanM wrote:Wishful thinking David. This is a study of ancient DNA. Such studies enable us to tie haplogroups to particular cultures. It is phylogeography using only modern DNA that is being superseded.


You mean the phylogeography of certain Slavic mtDNA markers based on modern samples that we recently discussed? The same one that showed expansions from Central Europe to Eastern Europe?

Where's the conflict with the ancient mtDNA H data discussed above? I'm seeing the same thing again...

Near East and/or Southern Europe > Central/Western Europe > Eastern Europe

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PostPosted: Thu Feb 21, 2013 10:14 am
Since I haven't seen the full paper, I can't say that it definitely does not talk about directions of movement of mtDNA H, but the only movement actually specified in the abstract is that of Bell Beaker pottery, as one example of the shifts taking place in the Copper Age. As far as I can tell this is a study of layers through time in one region - Central Europe - to see when the current patterns of diversity and distribution of hg H in Europe were established. H is common all over Europe today, so just testing one central region should give us an idea of the chronology. That is what they are after.

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PostPosted: Thu Feb 21, 2013 10:47 am
JeanM wrote:Since I haven't seen the full paper, I can't say that it definitely does not talk about directions of movement of mtDNA H, but the only movement actually specified in the abstract is that of Bell Beaker pottery, as one example of the shifts taking place in the Copper Age. As far as I can tell this is a study of layers through time in one region - Central Europe - to see when the current patterns of diversity and distribution of hg H in Europe were established. H is common all over Europe today, so just testing one central region should give us an idea of the chronology. That is what they are after.


The abstract says that the patterns of mtDNA H diversity seen in Central Europe today were already largely present there during the mid-Neolithic. So that tells us very clearly there was no replacement in Central Europe after the mid-Neolithic of natives mostly lacking H by invaders from the east rich in H. Indeed, the abstract goes on to say that these patterns of diversity were added to by population movements from the west.

Not only that, but the theory of high frequencies of the European lactase persistence allele being introduced into Europe from the steppe now looks redundant. The rise of this mutation was an in-situ process, much like the spread of mtDNA H across Europe.

So your last hope is that R1a and R1b will buckle the trend and turn out to be latecomers from the east who took over harems of mtDNA H and LP rich Western and Central European women.

But I don't like your chances.

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PostPosted: Thu Feb 21, 2013 12:20 pm
Tomatoes wrote:The abstract says that the patterns of mtDNA H diversity seen in Central Europe today were already largely present there during the mid-Neolithic. So that tells us very clearly there was no replacement in Central Europe after the mid-Neolithic of natives mostly lacking H by invaders from the east rich in H.


I had already concluded that. At one time I did wonder if Indo-Europeans were carrying rather more H than the average Neolithic band, since the level of it overall seems to rise in Europe between the Neolithic and the present. You are perhaps recalling that? Perhaps that idea was still present in my text when I took it down last June? I can't recall. Final text on this point reads:

The levels of mtDNA H in early Neolithic aDNA so far discovered in Europe are distinctly lower than in modern Europeans, where H represents about 45% of the population. Levels of H appear closer to modern in late Neolithic to Early Bronze Age Europeans. The cause of this is unclear. MtDNA H5a seems to have dispersed partly with the Indo-Europeans. Yet that would not wholly account for the dominance of H today. One possibility is that natural selection has been at work, since persons carrying mtDNA H recover better after sepsis.


The picture may turn out more complex, with more H coming in up the Danube with dairy farmers in the Late Neolithic before another swirl of the gene pool with the widespread BB and Corded Ware dispersals. I wouldn't get too excited by the direction of BB pottery movement. That was just part of a to-and-fro between the Carpathian Basin and Iberia.

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PostPosted: Sat Apr 13, 2013 12:37 am
The paper was presented today - has anyone heard any news about it? I hope we don't have to wait for publication to get a better preview of the results.

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