Early European Lineages

Aberdeen

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The Eurogenes Blog has a link to an abstract by researchers who were looking into early European lineages. The site containing the actual abstract is biorxiv.org/content/early/2013/12/23/001552 The Abstract states:

"Analysis of ancient DNA can reveal historical events that are difficult to discern through study of present-day individuals. To investigate European population history around the time of the agricultural transition, we sequenced complete genomes from a ~7,500 year old early farmer from the Linearbandkeramik (LBK) culture from Stuttgart in Germany and an ~8,000 year old hunter-gatherer from the Loschbour rock shelter in Luxembourg. We also generated data from seven ~8,000 year old hunter-gatherers from Motala in Sweden. We compared these genomes and published ancient DNA to new data from 2,196 samples from 185 diverse populations to show that at least three ancestral groups contributed to present-day Europeans. The first are Ancient North Eurasians (ANE), who are more closely related to Upper Paleolithic Siberians than to any present-day population. The second are West European Hunter-Gatherers (WHG), related to the Loschbour individual, who contributed to all Europeans but not to Near Easterners. The third are Early European Farmers (EEF), related to the Stuttgart individual, who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model the deep relationships of these populations and show that about ~44% of the ancestry of EEF derived from a basal Eurasian lineage that split prior to the separation of other non-Africans."

Sounds quite interesting. However, the abstract contains no details about Y DNA or mtDNA. I don't know whether they just looked at autosomal DNA or whether the actual research paper would provide information on haplotypes. Does anyone know whether it would be possible to access the actual paper?
 
The Eurogenes Blog has a link to an abstract by researchers who were looking into early European lineages. The site containing the actual abstract is biorxiv.org/content/early/2013/12/23/001552 The Abstract states:

"Analysis of ancient DNA can reveal historical events that are difficult to discern through study of present-day individuals. To investigate European population history around the time of the agricultural transition, we sequenced complete genomes from a ~7,500 year old early farmer from the Linearbandkeramik (LBK) culture from Stuttgart in Germany and an ~8,000 year old hunter-gatherer from the Loschbour rock shelter in Luxembourg. We also generated data from seven ~8,000 year old hunter-gatherers from Motala in Sweden. We compared these genomes and published ancient DNA to new data from 2,196 samples from 185 diverse populations to show that at least three ancestral groups contributed to present-day Europeans. The first are Ancient North Eurasians (ANE), who are more closely related to Upper Paleolithic Siberians than to any present-day population. The second are West European Hunter-Gatherers (WHG), related to the Loschbour individual, who contributed to all Europeans but not to Near Easterners. The third are Early European Farmers (EEF), related to the Stuttgart individual, who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model the deep relationships of these populations and show that about ~44% of the ancestry of EEF derived from a basal Eurasian lineage that split prior to the separation of other non-Africans."

Sounds quite interesting. However, the abstract contains no details about Y DNA or mtDNA. I don't know whether they just looked at autosomal DNA or whether the actual research paper would provide information on haplotypes. Does anyone know whether it would be possible to access the actual paper?

There is a preview PDF on that site that you can download. Some very interesting citations briefly here:

Stuttgart belonged to
mtDNA haplogroup T2, typical of Neolithic Europeans10, while Loschbour and all Motala
individuals belonged to haplogroups U5 and U2, typical of pre-agricultural Europeans1, 8 (SI4).
Based on the ratio of sequences aligning to chromosomes X and Y, we infer that Stuttgart was
female while Loschbour and five Motala individuals were male11 (SI5). Loschbour and four
Motala males belonged to Y-chromosome haplogroup I, showing that this was a predominant
haplogroup in pre-agricultural northern Europeans

...
ADMIXTURE
...
We projected onto the PCs genetic data from ancient individuals2, 19, 20, which
reveals that European hunter-gatherers like Loschbour and Motala fall outside the variation of
West Eurasians in the direction of European differentiation from the Near East. This pattern is
suggestive of present-day Europeans being admixed between ancient European hunter-gatherers
and ancient Near Easterners
, an inference that we confirm below. Loschbour clusters with
~7,000 year old hunter-gatherers from Spain20, allowing us to propose a “West European Hunter-
Gatherer” (WHG) meta-population. The Motala individuals cluster with ~5,000 year old
Neolithic hunter-gatherers2 from the Pitted Ware Culture (PWC) in Sweden, suggesting a
“Scandinavian Hunter-Gatherer” (SHG) meta-population that maintained biological continuity
across the Neolithic transition. Stuttgart clusters with two early farmers—the ~5,300 year old
Tyrolean Iceman and a ~5,000 year old southern Swedish farmer2 from the Funnel Beaker
Culture—suggesting an “Early European Farmer” (EEF) meta-population similar to present-day

Sardinians. Two Upper Paleolithic Siberian samples project beyond the variation of Europeans
on the second PC (Fig. 2A), suggesting that they may be derive from the Ancient North Eurasian
(ANE) population previously shown to have contributed to Europeans
 
So, three basal european meta-populations:

1. An indigenous Western European group with y-dna "I" that is isolated from Middle-Eastern/West Asian populations.

2. A Northern European group with a Siberian connection (maybe R1 and descended from Mammoth hunters?)

3. A Middle-Eastern/West Asian group probably arriving with agriculture and ushering in the Neolithic (Maybe haplogroups G, E, J, etc?).

Very interesting but not entirely unexpected. Finding haplogroup "I" in Mesolithic Northern Europe cements that as the dominant y-dna group in Paleolithic Europe, I would think. Interesting too that Ancient West Europeans and the Northern Siberian Hunters shared mtdna. It seems they were closely related, but distant enough to form distinct populations.
 
Very interesting paper.
So it means that 4th wave of population, the Indo Europeans, didn't bring much of autosomal change. If not their strong paternal Y influence and the language, we wouldn't be able to guess from autosomal DNA correlation and comparison. Or perhaps they were already strongly mixed with ANE in West Asia and East Europe and with EEF of Anatolia, and lacking their unique autosomal signal?
 
Very interesting paper.
So it means that 4th wave of population, the Indo Europeans, didn't bring much of autosomal change. If not their strong paternal Y influence and the language, we wouldn't be able to guess from autosomal DNA correlation and comparison. Or perhaps they were already strongly mixed with ANE in West Asia and East Europe and with EEF of Anatolia, and lacking their unique autosomal signal?

I've always wondered if the Indo-Europeans originated simply from the Eastern fringes of this basic Central European population blend of ANE, WHG, and EEF. Maybe even the low-level West Asian signal in Indo-Europeans comes from the earlier LBK culture in Central Europe and not from Anatolia proper.
 
I've always wondered if the Indo-Europeans originated simply from the Eastern fringes of this basic Central European population blend of ANE, WHG, and EEF. Maybe even the low-level West Asian signal in Indo-Europeans comes from the earlier LBK culture in Central Europe and not from Anatolia proper.

That's what i would have thought. Might have had a massive impact in terms of ancestry that what be very difficult to detect through autosomal genetics due to their similarities.

I wonder if this ancestral Siberian component is somehow related to that Amerindian-shift in many Europeans, perhaps.
 
This is great. Looks like we can get a lot of info out of the Supplemental. Check out Supplemental Information 5 in particular.

The Loschbour sample is I2a1b* L178+, which seems to be a now-extinct (or super rare?) branch related to I2a-Din, I2a-Disles, and I2a-Isles. Motala12 is also I2a1b, and although I2a-Isles wasn't technically ruled out, I2a1b* looks possible as well.

Motala2, Motala3, and Motala9 weren't tested very well, but all are probably I2 of some sort, with a few subclades ruled out here and there. Interestingly, all could be I2a1b* too.

Motala6 couldn't be typed.
 
I've always wondered if the Indo-Europeans originated simply from the Eastern fringes of this basic Central European population blend of ANE, WHG, and EEF.
You might be totally right, they were in vicinity anyway, and even EEF reached them already. They came to Europe as warriors/farmers.
Having said that, I don't think that their numbers were equal to existing European population. Most likely as small as 5-10% of total. Regardless of their numbers, it looks like they didn't kill all existing European men and took their wives (as some of us expected) but instead mixed heavily with existing populations.
It would be great to get DNA of early Romans and see who they resembled the most, or if they had an unique signature.
 
BTW, Thanks for the links Aberdeen.

Additional points to the citations which I think are essential I list here (my comments are in brackets):

- ANE (Ancien North Eurasians) contributed also to native-american ancestry (That's why I still expect to find one Y-HG Q in some european hunter gatherer eventually).

- WHG (Loschbour) came from a very small population size (very isolated or even inbred? This could explain their isolated situation in the PCA plot.)

- neither Loschbour (hunter-gatherer) nor Stuttgart (farmer) could digest milk.

- both, Loschbour h-g and Stuttgart farmer had almost certainly dark hair (possible link to the Saami who are also significantly much darker haired than the neighbouring nations?)

- Loschbour h-g probably had darker skin than Stuttgart farmer (I find this very surprising! Perhaps non-euro admixture?)

- Loschbour h-g had a chance (> 50%) to have had blue eyes, whereas Stuttgart farmer hat almost certainly brown eyes.

- the one autosomal PCA for europe stretches from Sardinia to the Baltic (this again confirms K12b and Globe 13!)

- all european hunter-gatherers have the least near-eastern admixture compared to all west eurasian populations (not surprising).

- european hunter-gatherers appear autosomally more distant to each-other than farmers and most contemporary europeans, such that the authors decided to make separate clusters for them: WHG, SHG, ANE (I think it is also possible that these clusters are distant merely because
of different admixtures, for instance WHG=SHG+southern[+non-european?]; ANE=SHG+Siberian; this would make SHG the true hunter-gatherer component, but this is a quick & dirty hypothesis only!)

- Farmers, Ötzi, Funnel Beakers and Sardinians are very similar (no surprise)

- contemporary europeans seem to be a mix of Hunter-Gatherers and Near-Easteners, but the authors rejected this assumtion due to additional f3 statistics and too low resolution of PCA analysis, thus assuming 3 ancestral main populations ANE, WHG, EEF (Could ANE partially come from Indo-europeans perhaps? Maybe, since Sardinia-Baltic cline is confirmed and both contain non-IE speakers (i.e. old-Sardinian and Finnish)).

- neolithic farmers stem from ancient near-easteners, but contemporary near-easteners have become altered by other admixtures (I remember saying this before)

- neolithic farmers probably were already admixed with hunter-gatherers, although not sure whether WHG or ANE.

- lowest farmer ancestry is in baltic countries, highest in mediterranean (again K12b and Globe 13 are confirmed)

- Europeans are approx. 40% WHG and 20% ANE.

- Finns, Mordovians, Russians, Chuvash, and Saami experienced some additional Siberian admixture later, possibly indicated by Y-HG N (not surprising).



I hope I made no mistakes. Good night!
 
I've always wondered if the Indo-Europeans originated simply from the Eastern fringes of this basic Central European population blend of ANE, WHG, and EEF. Maybe even the low-level West Asian signal in Indo-Europeans comes from the earlier LBK culture in Central Europe and not from Anatolia proper.

Yeah, I think in particular many Indo-Europeans brought even more ANE to europe, besides west asian. This would explain why almost all europeans are closer to ANE today than to WHG in the PCA map. Ironically, some Finno-Ugric peoples would be autosomally closer to the some original Indo-Europeans too. Loschbourg looks suspiciously isolated in PCA plot, even more than La Brana.
 
BTW, Thanks for the links Aberdeen.

Additional points to the citations which I think are essential I list here (my comments are in brackets):

- ANE (Ancien North Eurasians) contributed also to native-american ancestry (That's why I still expect to find one Y-HG Q in some european hunter gatherer eventually).

- WHG (Loschbour) came from a very small population size (very isolated or even inbred? This could explain their isolated situation in the PCA plot.)

- neither Loschbour (hunter-gatherer) nor Stuttgart (farmer) could digest milk.

- both, Loschbour h-g and Stuttgart farmer had almost certainly dark hair (possible link to the Saami who are also significantly much darker haired than the neighbouring nations?)

- Loschbour h-g probably had darker skin than Stuttgart farmer (I find this very surprising! Perhaps african admixture?)

- Loschbour h-g had a chance (> 50%) to have had blue eyes, whereas Stuttgart farmer hat almost certainly brown eyes.

- the one autosomal PCA for europe stretches from Sardinia to the Baltic (this again confirms K12b and Globe 13!)

- all european hunter-gatherers have the least near-eastern admixture compared to all west eurasian populations (not surprising).

- european hunter-gatherers appear autosomally more distant to each-other than farmers and most contemporary europeans, such that the authors decided to make separate clusters for them: WHG, SHG, ANE (I think it is also possible that these clusters are distant merely because
of different admixtures, for instance WHG=SHG+southern[+non-european?]; ANE=SHG+Siberian; this would make SHG the true hunter-gatherer component, but this is a quick & dirty hypothesis only!)

- Farmers, Ötzi, Funnel Beakers and Sardinians are very similar (no surprise)

- contemporary europeans seem to be a mix of Hunter-Gatherers and Near-Easteners, but the authors rejected this assumtion due to additional f3 statistics and too low resolution of PCA analysis, thus assuming 3 ancestral main populations ANE, WHG, EEF (Could ANE partially come from Indo-europeans perhaps? Maybe, since Sardinia-Baltic cline is confirmed and both contain non-IE speakers (i.e. old-Sardinian and Finnish)).

- neolithic farmers stem from ancient near-easteners, but contemporary near-easteners have become altered by other admixtures (I remember saying this before)

- neolithic farmers probably were already admixed with hunter-gatherers, although not sure whether WHG or ANE.

- lowest farmer ancestry is in baltic countries, highest in mediterranean (again K12b and Globe 13 are confirmed)

- Europeans are approx. 40% WHG and 20% ANE.

- Finns, Mordovians, Russians, Chuvash, and Saami experienced some additional Siberian admixture later, possibly indicated by Y-HG N (not surprising).



I hope I made no mistakes. Good night!

One of the Loschbour males couldn't be assigned a haplogroup, but initially it appeared he was Q1 until there was a contradiction. So, almost but not quite yet i guess.
This is from the supplementery information, but taken from a quote by Jean M at Anthrogenica:

Motala6 was L55+ (19413335 G>A), placing it in Y-haplogroup Q1a2a, but L232-, which contradicts the hypothesis that it belongs to haplogroup Q1. These two observations are phylogenetically inconsistent, and we are unable to assign a haplogroup to this individual.
 
Interesting note from page 30:

Figure S5.1: Phylogenetic position of Loschbour Y chromosome within present-day haplogroup I.
The highlighted branch (yellow) displays the Loschbour individual and its closest relative for the Y
chromosome in the dataset, a present-day Russian.
 
Form same paper:
DiscussionOur finding that Loschbour and all four Motala males whose haplogroups we could determine belong
to Y-haplogroup I is not entirely unexpected, as this clade of the human Y-chromosome phylogeny is
found almost exclusively in Europe6
, with much rarer occurrences elsewhere. Its sister clade
(haplogroup J) is thought to have a Near Eastern origin7
. It has been hypothesized that I was common
in pre-agricultural Europeans8
, and our study confirms this directly as it documents its presence in two
European hunter-gatherer groups from the period immediately antedating the Neolithic transition.
We cannot, at present, determine when Y chromosome haplogroup I entered Europe, although its
occurrence in two Mesolithic European hunter-gatherer populations (Loschbour and Motala) suggest
an old origin, potentially entering Europe during the Upper Paleolithic around 40,000 years ago.
It is tempting to speculate that haplogroup I might be the dominant European Y chromosome
haplogroup in Palaeolithic Europe, as the male counterpart of maternally inherited mitochondrial
haplogroup U (SI4). Y chromsome haplogroup I9 as well as mitochondrial haplogroup U were also
identified in Neolithic Europeans, and are found throughout Europe in present-day populations. Thus,
both maternally- and paternally-inherited genetic components of present-day Europeans may reflect a
history of major admixture: genetic contribution from both the hunter-gatherers and early farmers of
Europe. We further note that Y chromosome haplogroup I is scarce in the Near East today, with only
sporadic occurrences of this haplogroup in the North Caucasus (~3% in frequency)10, consistent with
very limited gene flow from Europe into this area.
The present-day frequency of haplogroup I in Europe is variable, with local maxima in Scandinavia2
and the western Balkans which might reflect more recent expansions. Our finding that Loschbour, a
Mesolithic west European, was M423+ contrasts with a previous suggestion11 that this lineage
diffused during the Neolithic from south-eastern Europe.
The absence of Y-haplogroup R1b in our two sample locations is striking given that it is, at present,
the major west European lineage. Importantly, however, it has not yet been found in ancient European
contexts prior to a Bell Beaker burial from Germany (2,800-2,000BC)12, while the related R1a lineage
has a first known occurrence in a Corded Ware burial also from Germany (2,600BC)13. This casts
doubt on early suggestions associating these haplogroups with Paleolithic Europeans14, and is more
consistent with their Neolithic entry into Europe at least in the case of R1b15, 16. More research is
needed to document the time and place of their earliest occurrence in Europe. Interestingly, the Mal’ta
boy belonged17 to haplogroup R* and we tentatively suggest that some haplogroup R bearers may be
responsible for the wider dissemination of Ancient North Eurasian ancestry into Europe, as their
haplogroup Q relatives may have plausibly done into the Americas17.
This work provides a first glimpse into the the pre-Neolithic Y chromosomes of Europe. Despite the
fact that our sample is limited to two locations and five male individuals, the results in this section are
consistent with haplogroup I representing a major pre-Neolithic European clade, and hint at
subsequent events during and after the Neolithic transition as important contributors to the Y
chromosomal variation of living Europeans.
 
One of the Loschbour males couldn't be assigned a haplogroup, but initially it appeared he was Q1 until there was a contradiction. So, almost but not quite yet i guess.
This is from the supplementery information, but taken from a quote by Jean M at Anthrogenica:

Motala6 was L55+ (19413335 G>A), placing it in Y-haplogroup Q1a2a, but L232-, which contradicts the hypothesis that it belongs to haplogroup Q1. These two observations are phylogenetically inconsistent, and we are unable to assign a haplogroup to this individual.

Thanks, very interesting! So there is truly a chance of paleolithic Q in europe as I expected some time ago. According to the eupedia map, Scandinavia is the european hotspot of Q1a2b1, and there is also some Q1a2a1a2 and some also in Britain. So it would match the hypothesis for Motala, if true.
 
Neither of the ancient modern humans
carried the derived alleles at three loci associated with alcohol metabolism (ALDH2, ADH1Ba and
ADH1Bb)
If I understood this right it means that they were not acquainted with alcohol well yet. Looks like alcohol came with farmers.
 
You might be totally right, they were in vicinity anyway, and even EEF reached them already. They came to Europe as warriors/farmers.
Having said that, I don't think that their numbers were equal to existing European population. Most likely as small as 5-10% of total. Regardless of their numbers, it looks like they didn't kill all existing European men and took their wives (as some of us expected) but instead mixed heavily with existing populations.
It would be great to get DNA of early Romans and see who they resembled the most, or if they had an unique signature.

I've always wondered whether the small amount of R1a found throughout western Europe were enough to represent the IE signature just by itself. Although I realize that idea could get me burned for heresy around here.
 
If I understood this right it means that they were not acquainted with alcohol well yet. Looks like alcohol came with farmers.

That idea would make a lot of sense, IMO. Without much technology, attempts to make wine from wild berries are more likely to produce vinegar. Beer is easier to make, I think.
 
BTW, thanks for finding the link to the PDF that I missed ElHorsto. This is interesting stuff. And it turns out that the PDF was on the same website as the east Asian stuff that I posted today under Y haplotypes that Dienekes mentioned in his blog.
 
I'm having a tough time squaring these autosomal admixtures with the y-dna that we see through most of Europe today (dominance of the R1b lines). Nice find on the article, but it sure does raise a few questions.
 
BTW, Thanks for the links Aberdeen.

Additional points to the citations which I think are essential I list here (my comments are in brackets):

- ANE (Ancien North Eurasians) contributed also to native-american ancestry (That's why I still expect to find one Y-HG Q in some european hunter gatherer eventually).

- WHG (Loschbour) came from a very small population size (very isolated or even inbred? This could explain their isolated situation in the PCA plot.)

- neither Loschbour (hunter-gatherer) nor Stuttgart (farmer) could digest milk.

- both, Loschbour h-g and Stuttgart farmer had almost certainly dark hair (possible link to the Saami who are also significantly much darker haired than the neighbouring nations?)

- Loschbour h-g probably had darker skin than Stuttgart farmer (I find this very surprising! Perhaps non-euro admixture?)

- Loschbour h-g had a chance (> 50%) to have had blue eyes, whereas Stuttgart farmer hat almost certainly brown eyes.

- the one autosomal PCA for europe stretches from Sardinia to the Baltic (this again confirms K12b and Globe 13!)

- all european hunter-gatherers have the least near-eastern admixture compared to all west eurasian populations (not surprising).

- european hunter-gatherers appear autosomally more distant to each-other than farmers and most contemporary europeans, such that the authors decided to make separate clusters for them: WHG, SHG, ANE (I think it is also possible that these clusters are distant merely because
of different admixtures, for instance WHG=SHG+southern[+non-european?]; ANE=SHG+Siberian; this would make SHG the true hunter-gatherer component, but this is a quick & dirty hypothesis only!)

- Farmers, Ötzi, Funnel Beakers and Sardinians are very similar (no surprise)

- contemporary europeans seem to be a mix of Hunter-Gatherers and Near-Easteners, but the authors rejected this assumtion due to additional f3 statistics and too low resolution of PCA analysis, thus assuming 3 ancestral main populations ANE, WHG, EEF (Could ANE partially come from Indo-europeans perhaps? Maybe, since Sardinia-Baltic cline is confirmed and both contain non-IE speakers (i.e. old-Sardinian and Finnish)).

- neolithic farmers stem from ancient near-easteners, but contemporary near-easteners have become altered by other admixtures (I remember saying this before)

- neolithic farmers probably were already admixed with hunter-gatherers, although not sure whether WHG or ANE.

- lowest farmer ancestry is in baltic countries, highest in mediterranean (again K12b and Globe 13 are confirmed)

- Europeans are approx. 40% WHG and 20% ANE.

- Finns, Mordovians, Russians, Chuvash, and Saami experienced some additional Siberian admixture later, possibly indicated by Y-HG N (not surprising).



I hope I made no mistakes. Good night!

What time would this later be? Include the Balts also. Just reminding you that Uralic and Indo-European are connected.
 

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