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Jean M
04-23-2013, 08:04 PM
Paul Brotherton et al, Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans (http://www.nature.com/ncomms/journal/v4/n4/full/ncomms2656.html)


Haplogroup H dominates present-day Western European mitochondrial DNA variability (>40%), yet was less common (~19%) among Early Neolithic farmers (~5450 BC) and virtually absent in Mesolithic hunter-gatherers. Here we investigate this major component of the maternal population history of modern Europeans and sequence 39 complete haplogroup H mitochondrial genomes from ancient human remains. We then compare this ‘real-time’ genetic data with cultural changes taking place between the Early Neolithic (~5450 BC) and Bronze Age (~2200 BC) in Central Europe. Our results reveal that the current diversity and distribution of haplogroup H were largely established by the Mid Neolithic (~4000 BC), but with substantial genetic contributions from subsequent pan-European cultures such as the Bell Beakers expanding out of Iberia in the Late Neolithic (~2800 BC). Dated haplogroup H genomes allow us to reconstruct the recent evolutionary history of haplogroup H and reveal a mutation rate 45% higher than current estimates for human mitochondria.

The complete consensus mt genome sequences have been deposited to NCBI GenBank under accession numbers KC553980 to KC554018. The results are also in my online table of Ancient Western Eurasian DNA (http://www.buildinghistory.org/distantpast/ancientdna.shtml).

Jean M
04-23-2013, 08:31 PM
Crucial points from the paper:

Early Neolithic (and in particular LBK) mt genomes are either rare today (H16, H23 and H26), extinct or have not yet been observed in present-day populations (H46b, H88 and H89). In sharp contrast, most of the later H sub-hgs are more common in present-day European populations (for example, hg H3, H4, H6, H7, H11 and H13)12,14–16. Of the 39 haplotypes detected, only three (within the common, basal, sub-hg H1) were shared between Early Neolithic and Middle to Late Neolithic cultures. As the later Neolithic haplotypes are on different sub-hg branches from the Early Neolithic haplotypes, these patterns combined show minimal local genetic continuity over this time period.

LBK and Bell Beaker samples were not related to present-day Germans. Although all three ancient groups were sampled from the same Central European location only the Middle Neolithic group genetically resembles present-day populations from this region.

Mittelelbe-Saale’s earliest farmers (LBK) cluster with present-day Caucasus, Near Eastern and Anatolian populations. Mitochondrial genomes
from Bell Beaker individuals in Mittelelbe-Saale display close genetic affinities to present-day Iberian populations. This is largely based on high frequencies of sub-hgs H1 and H3, which are thought to have spread from a glacial Iberian refugium. [I have my doubts.]

The calibrated ‘Neolithic’ rate infers a considerably younger coalescence date for hg H (10.9–19.1 kya) than those previously reported.

GailT
04-24-2013, 02:21 AM
Thanks, Jean. It's an excellent paper, and I'm busy comparing their ancient samples to the FTDNA projects now to see if we can say anything more about current distributions of the rare subclades.


The calibrated ‘Neolithic’ rate infers a considerably younger coalescence date for hg H (10.9–19.1 kya) than those previously reported.

The midpoint 15 kya is only slightly older than the Behar et al. 2012 estimate of about 13 kya for haplogroup H, but given the uncertainty range, this is quite consistent. So their estimate and also the Behar et al estimate are both considerably younger than previous estimates for H that were much older.

This paper is the nail in the coffin for the "H1 and H3 glacial Iberian refugium" theory, which was never based on good science, but rather a very early, naive form of phylogeography. They pound that nail a couple of time in the paper, including in the end of the Discussion section.



Overall, our results suggest that the broad foundations of the Central European mtDNA pool, here approximated via hg H, were formed during the Neolithic rather than the post-glacial
period. ENE hg H mt lineages brought in from the Near East by Central Europe’s first farmers do not appear to have contributed significantly to present-day Central Europe’s hg H diversity,
instead being largely superseded during the MNE and LNE (with the process starting around 4000 BC), after which there appears to have been substantial genetic continuity to the present-day in Central Europe.

In conclusion, demographic changes across the MNE, followed by the widespread Bell Beaker cultural phenomenon, are likely to have been the key factors in the expansion of hg H across
Western Europe and the eventual rise of hg H to become the predominant mtDNA hg.

Jean M
04-24-2013, 07:55 AM
Curiously they still stick to the idea that H1 and H3 spread from Iberia. I doubt it.

DMXX
04-24-2013, 06:00 PM
Curiously they still stick to the idea that H1 and H3 spread from Iberia. I doubt it.

Is there any genetic proof of any expansions out of the Iberian peninsula into Europe, or is it all conjecture?

Jean M
04-24-2013, 06:40 PM
Is there any genetic proof of any expansions out of the Iberian peninsula into Europe, or is it all conjecture?

The idea was originally based on high density in Iberia, plus the knowledge that Cantabria was an Ice Age refuge, just the same as the conjecture that R1b spread from Iberia. Once people wean themselves from the ideas that density = origin point, and that nobody moved in Europe after the Mesolithic, what is left?

As they say themselves, H seems to have spread into Europe from the Near East with farmers.

J Man
04-24-2013, 07:34 PM
What about the H samples from Upper Paleolithic Iberia and Mesolithic Karelia? Maybe some H in Europe is of pre-Neolithic origin?

Jean M
04-24-2013, 08:17 PM
Could be, J Man, but every time we get a new date calculated for H, it gets earlier. Behar 2012 worked it out at 12,846 years ago = 10,000 BC. He has H1 at 9,888 years ago = 7,888 BC and H3 at 8,919 years ago = 6,919 BC. Such estimates are not infallible, but it is telling that H-type mtDNAs from Europe have on average six differences in their coding region, while U-type mtDNAs have on average 18 differences. That suggests a much older population expansion in U than in H. See Fu, Q., Rudan, P., Pääbo, S. and Krause, J. 2012. Complete mitochondrial genomes reveal Neolithic expansion into Europe (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0032473), PLoS ONE, 7 (3), e32473., which showed a dramatic growth spurt around 9,000 years ago (7000 BC) for H with the spread of farming into Europe.

So claims of H in aDNA at an earlier date now get a sceptical eye from me. They really need to provide a full mtDNA genome and proof of measures taken to avoid contamination, including replication of results in two different labs.

J Man
04-24-2013, 08:20 PM
Could be, J Man, but every time we get a new date calculated for H, it gets earlier. Behar 2012 worked it out at 12,846 years ago = 10,000 BC. He has H1 at 9,888 years ago = 7,888 BC and H3 at 8,919 years ago = 6,919 BC. Such estimates are not infallible, but it is telling that H-type mtDNAs from Europe have on average six differences in their coding region, while U-type mtDNAs have on average 18 differences. That suggests a much older population expansion in U than in H. See Fu, Q., Rudan, P., Pääbo, S. and Krause, J. 2012. Complete mitochondrial genomes reveal Neolithic expansion into Europe (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0032473), PLoS ONE, 7 (3), e32473., which showed a dramatic growth spurt around 9,000 years ago (7000 BC) for H with the spread of farming into Europe.

Maybe the case is that a few subclades of H were present in Upper Paleolithic and Mesolithic Europe but the majority arrived during the Neolithic with farming. What do you think about that?

Jean M
04-24-2013, 08:39 PM
The odds on that scenario don't look good from where I'm sitting. I wouldn't bet on it.

J Man
04-24-2013, 08:42 PM
The odds on that scenario don't look good from where I'm sitting. I wouldn't bet on it.

Do you think then that pretty much all H in Europe today came from early Neolithic farmers spreading out of the Near East originally?

Jean M
04-24-2013, 09:07 PM
That's what I'm saying. And it is what this paper is saying.

J Man
04-24-2013, 09:26 PM
That's what I'm saying. And it is what this paper is saying.

Didn't the Der Sarkissian study which showed one sample of H from Mesolithic Karelia use mtDNA full sequences or genomes? Or did they not?

Jean M
04-24-2013, 09:46 PM
You mean Uznyi Oleni Ostrov, Russia [UZOO 77] 7500 BP = 5500 BC. The culture was Mesolithic, but this is within the period after Neolithic farmers entered Europe. So mixture with farmers somewhere en route might account for that one. So I put it in my table as reported (H), though the full mtDNA genome was not tested. HVR-I (16056–16409) and 22 haplogroup-diagnostic single nucleotide polymorphisms (SNPs) in the coding-region were tested. Strict criteria were followed to authenticate aDNA data and detect contamination by exogenous DNA or artefactual mutations caused by post-mortem DNA damage.

J Man
04-24-2013, 10:10 PM
You mean Uznyi Oleni Ostrov, Russia [UZOO 77] 7500 BP = 5500 BC. The culture was Mesolithic, but this is within the period after Neolithic farmers entered Europe. So mixture with farmers somewhere en route might account for that one. So I put it in my table as reported (H), though the full mtDNA genome was not tested. HVR-I (16056–16409) and 22 haplogroup-diagnostic single nucleotide polymorphisms (SNPs) in the coding-region were tested. Strict criteria were followed to authenticate aDNA data and detect contamination by exogenous DNA or artefactual mutations caused by post-mortem DNA damage.

Yes I suppose admixture with incoming farmers could explain that one. Do you think that the fact the only that one sample of H was found at Uznyi Oleni Ostrov, Russia at 7,500 BP may lend credence to that H sample coming from admixture with early European Neolithic farmers?

Jean M
04-24-2013, 10:38 PM
I prefer not to get into the numbers game with a sample from one site. I prefer to look at larger samples over a wide range of sites, which is what we now have for the European Mesolithic. You can see for yourself in my online table that U5 and U4 predominate almost to exclusivity across a good range of Europe. That pattern is dramatically different from that of the Early Neolithic. What this particular study does is take the story further, showing a discontinuity between the LBK and the Later Neolithic and Bronze Age. The LBK mtDNA H lineages are mainly not found in modern populations.

J Man
04-24-2013, 10:59 PM
I prefer not to get into the numbers game with a sample from one site. I prefer to look at larger samples over a wide range of sites, which is what we now have for the European Mesolithic. You can see for yourself in my online table that U5 and U4 predominate almost to exclusivity across a good range of Europe. That pattern is dramatically different from that of the Early Neolithic. What this particular study does is take the story further, showing a discontinuity between the LBK and the Later Neolithic and Bronze Age. The LBK mtDNA H lineages are mainly not found in modern populations.

So it is the Bell Beaker H types that are mainly found in modern Europeans correct?

lgmayka
04-25-2013, 03:23 PM
Maybe the case is that a few subclades of H were present in Upper Paleolithic and Mesolithic Europe but the majority arrived during the Neolithic with farming.
Perhaps part of the difficulty is with the definition of the term Neolithic. Perhaps you, like me, were taught in school to associate Neolithic with crop-growing. But others use the term more generally to embrace animal husbandry, which is really an entirely different activity requiring an entirely different set of tools and skills, is to some extent an alternative to crop-growing, and may have spread across Europe along a different path. Take a look at this Wikipedia article on agriculture in Lithuania (http://en.wikipedia.org/wiki/Agriculture_in_Lithuania):
---
Agriculture in Lithuania dates to the Neolithic period, about 3,000 to 1,000 BC. It has been one of Lithuania's most important occupations for many centuries.
...
The use of domestic animals, first seen during the Bronze Age, had become widespread during the Iron Age.
Wheat cultivation in the area has been dated to the 1st century BC; the first evidence of widespread cultivation of rye has been dated to the 1st century AD. Barley probably appeared in the 2nd century BC, while potatoes did not gain popularity until the late 18th century.
---

The article blithely claims that Lithuania entered the Neolithic as early as 3000 BC, yet cannot cite a single crop grown in the country earlier than 200 BC!

My hypothesis is that Lithuania never experienced any significant influx of so-called Middle Eastern agriculturalists (crop-growers). Perhaps that is why Lithuania reports only 1.7% mtDNA H1 even though its total mtDNA H is 33% (http://onlinelibrary.wiley.com/doi/10.1046/j.1529-8817.2003.00119.x/full).

Jean M
04-25-2013, 10:11 PM
My hypothesis is that Lithuania never experienced any significant influx of so-called Middle Eastern agriculturalists (crop-growers).

I agree entirely.


The article blithely claims that Lithuania entered the Neolithic as early as 3000 BC, yet cannot cite a single crop grown in the country earlier than 200 BC!

Marek Zvelebil and Robin Dennell (eds.), Harvesting the Sea, Farming the Forest: The Emergence of Neolithic Societies in the Baltic Region (1998) gives plenty of detail, including this map. Much of Lithuania falls north of the 2000 BC line (for the arrival of agriculture) it seems.

383

Black Taylor
04-30-2013, 12:10 AM
Does anyone here know if someone has compiled contoured or clinal frequency maps of the various types of H? The maps I see either usually lump H into useless monolithic blocks (i.e. all H are lumped together and are simply called H), or provide those irritating clusters of pie charts that are hard to assimilate at a glance. I started thinking about this the other day when I realized that out of 900-odd relatives at 23andme I didn't have many other H* like myself; most of the other H's were part of designated sub-branches. This talk of BB migrating H versus Balkan H versus Mesolithic H makes me want to see a properly contoured map I can scratch my head over.

J Man
04-30-2013, 12:19 AM
Perhaps part of the difficulty is with the definition of the term Neolithic. Perhaps you, like me, were taught in school to associate Neolithic with crop-growing. But others use the term more generally to embrace animal husbandry, which is really an entirely different activity requiring an entirely different set of tools and skills, is to some extent an alternative to crop-growing, and may have spread across Europe along a different path. Take a look at this Wikipedia article on agriculture in Lithuania (http://en.wikipedia.org/wiki/Agriculture_in_Lithuania):
---
Agriculture in Lithuania dates to the Neolithic period, about 3,000 to 1,000 BC. It has been one of Lithuania's most important occupations for many centuries.
...
The use of domestic animals, first seen during the Bronze Age, had become widespread during the Iron Age.
Wheat cultivation in the area has been dated to the 1st century BC; the first evidence of widespread cultivation of rye has been dated to the 1st century AD. Barley probably appeared in the 2nd century BC, while potatoes did not gain popularity until the late 18th century.
---

The article blithely claims that Lithuania entered the Neolithic as early as 3000 BC, yet cannot cite a single crop grown in the country earlier than 200 BC!

My hypothesis is that Lithuania never experienced any significant influx of so-called Middle Eastern agriculturalists (crop-growers). Perhaps that is why Lithuania reports only 1.7% mtDNA H1 even though its total mtDNA H is 33% (http://onlinelibrary.wiley.com/doi/10.1046/j.1529-8817.2003.00119.x/full).

Bramanti tested ancient samples from the Kunda and Narva cultures from pre-farming Lithuania. Three of the these ancient samples turned out to be U5b and one was U4.

alan
05-01-2013, 05:45 PM
I wonder if there is any possibility that the movement of western H eastwards was linked to the movement of R1b west and could have been linked to high status marriage networks. I tend to fancy, if a copper age model is correct, to see R1b moving west through the Alps reaching Liguria by 3000BC. Perhaps the spread of H east commenced in the pre-beaker copper age as R1b spread west. H may be the reciprical part of sought after marriage alliances by groups who wanted the new wave of metallurgists to enter their territory (I am generally a believer that this was invited rather than down to conquest). For example, late Neolithic Iberian chiefs may have married their daughter into a Ligurian metalworking group as an alliance move that then allowed R1b metallurgical groups to move into Iberia. Perhaps the earliest maritime beaker spreading east along the Med. was simply INITIALLY moving along with the H females from the west. I realise that the movement of copper working into Iberia is shortly pre-beaker but this process of alliance, movement of specialists, trading etc could have continued in two directions along the Med. with the maritime beaker pot simply being one of the west-east perhaps female driven aspects of this network once established.

There is little doubt to me that metallurgical groups and mining of the post-Carpatho-Balkan collapse period are due to an east-west spread that first passed through the Alps (especially clear in Italy) c. 3300BC (maybe a century or so earlier) and apparently reached Liguria about 3000BC and presumably Iberia very soon after. So, if the mtDNA H group looks like a west-east spread it is equally true that metallurgical groups are an east-west spread as would the spread of R1b have been. In this kind of alliance making tradition of political marriages it is possible that the mtDNA flow may have been in a reverse trajectory to the yDNA flow. Perhaps the same is even true of maritime beaker. Maybe initially at least it the physical traces of the reciprocal reverse flow of of male lineages from further east. This of course could have quickly been muddied if these women's pottery preferences and perhaps other cultural preferences were quickly absorbed into the societies to the east around SE France and northern Italy.

If so then after an initial Iberian female driven spread east along the Med. early beaker ideas could have then been adopted and then driven by male lineages further east in SE France and nearby who spread them further. This kind of idea is useful as it makes some sense of how a clearly east-west movement of R1b and metallurgy can be squared with a roughly contemporary west-east movement of western H lineages and beaker pottery. An early process like that could have led to the peculiar melding of a western mt lineage with an eastern yDNA lineages and this early process would have given them both distinctive y and mt DNA characteristics which, once established could have spread out by both male movement and outgoing marriage alliances into non beaker areas.

alan
05-01-2013, 05:53 PM
One thing to bear in mind in this theory is that a great deal of the full beaker package and traditions was unknown or rare in the earliest beaker period and only became a feature later when beaker had spread to central Europe. A great deal of the earliest beaker culture other than metallurgy was routed in the traditions of south-west Europe. However, metallurgy had only been spread to Iberia from aloing the Med. to the east shortly before beaker pottery may have spread the other way. So, the spread of metallurgy east was not required.

alan
05-02-2013, 01:14 PM
OF course the only way to prove that western H moving east with earliest beaker was a reciprocal reverse direction alliance marriage thing would be if it could be shown that the earliest beaker burials outside Iberia were female. However that could have been a very narrow window and very hard to distinguise from 2nd generation. I suppose we would need to look at the earliest female beaker burials in Iberia and look at the gender and grave goods of the very earliest beaker burials outside Iberia in southern France for example. As far as i recall the female part of the beaker package was maritime pots, copper awls, v-perforated buttons and necklaces and (with odd exceptions) didnt include bracers, arrows, copper knives etc. The other problem is the classic central European north-south orientated inhumations with the female head to the south on her rights side looking east is very rare in the earliest beaker burials in Iberia, southern France etc. They instead tended to use (often old) megalithic tombs and collective burial. Reuse and disturbance of these obvious monuments tends to jumble the bones and artefacts making interpretation very hard. I

t is also a complex scenario where the east-west spread of pre-beaker copper working was fairly quickly followed up by the west-east spread of beaker material and marriage alliance could have gone in multiple directions. It seems extremely unlikely to me that (other than DF27) that this out of Iberia beaker phase had anything to do with the European spread of R1b. R1b is clearly at its root an east-west spread while beaker and perhaps the rise of mtDNA H is a west-east thing. In a patrilocal society the female would move. One scenario I could see is the movement of Iberian high status women east along the Med. as a kind of alliance/hostage type situation to ensure safety of metallurgical lineages moving into Iberia. Another process known among the Celts at much later times was actual hostage giving or fosterage of high status children to another elite group. This obviously aided alliance and kind of acted as a hostage too. It also is a little-explored (in this hobby) way that ideas, tastes and even languages can move when a royal child who was brought up fosterage to another external royal family returns to his birth parents/territory in adulthood.

Táltos
12-16-2013, 05:18 AM
Crucial points from the paper:

Early Neolithic (and in particular LBK) mt genomes are either rare today (H16, H23 and H26), extinct or have not yet been observed in present-day populations (H46b, H88 and H89). In sharp contrast, most of the later H sub-hgs are more common in present-day European populations (for example, hg H3, H4, H6, H7, H11 and H13)12,14–16. Of the 39 haplotypes detected, only three (within the common, basal, sub-hg H1) were shared between Early Neolithic and Middle to Late Neolithic cultures. As the later Neolithic haplotypes are on different sub-hg branches from the Early Neolithic haplotypes, these patterns combined show minimal local genetic continuity over this time period.

LBK and Bell Beaker samples were not related to present-day Germans. Although all three ancient groups were sampled from the same Central European location only the Middle Neolithic group genetically resembles present-day populations from this region.

Mittelelbe-Saale’s earliest farmers (LBK) cluster with present-day Caucasus, Near Eastern and Anatolian populations. Mitochondrial genomes
from Bell Beaker individuals in Mittelelbe-Saale display close genetic affinities to present-day Iberian populations. This is largely based on high frequencies of sub-hgs H1 and H3, which are thought to have spread from a glacial Iberian refugium. [I have my doubts.]

The calibrated ‘Neolithic’ rate infers a considerably younger coalescence date for hg H (10.9–19.1 kya) than those previously reported.
Jean M, I appreciate your thoughtful insights into these findings as it involves my own mtDNA. It helps me to understand why there is not much out there about it. I wonder if some of the administrators of the Haplogroup H project at FTDNA would adapt some of this in a way to show a breakdown of the many subclades of H in the project?

Jenny
12-16-2013, 04:21 PM
East of the Caucasus is my favorite origin, especially for H1b. Agree, disagree?

newtoboard
12-16-2013, 04:45 PM
East of the Caucasus is my favorite origin, especially for H1b. Agree, disagree?

On what basis? Just asking because I am not that knowledgeable on the distribution of mtdna H1b.