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Thursday, November 21, 2013

First genome of an Upper Paleolithic human


The highly anticipated paper on the genome of the 24,000 year-old Siberian known as Mal'ta boy or MA-1 is now out at Nature. Here's the abstract:

The origins of the First Americans remain contentious. Although Native Americans seem to be genetically most closely related to east Asians1, 2, 3, there is no consensus with regard to which specific Old World populations they are closest to 4, 5, 6, 7, 8. Here we sequence the draft genome of an approximately 24,000-year-old individual (MA-1), from Mal’ta in south-central Siberia9, to an average depth of 1×. To our knowledge this is the oldest anatomically modern human genome reported to date. The MA-1 mitochondrial genome belongs to haplogroup U, which has also been found at high frequency among Upper Palaeolithic and Mesolithic European hunter-gatherers10, 11, 12, and the Y chromosome of MA-1 is basal to modern-day western Eurasians and near the root of most Native American lineages5. Similarly, we find autosomal evidence that MA-1 is basal to modern-day western Eurasians and genetically closely related to modern-day Native Americans, with no close affinity to east Asians. This suggests that populations related to contemporary western Eurasians had a more north-easterly distribution 24,000 years ago than commonly thought. Furthermore, we estimate that 14 to 38% of Native American ancestry may originate through gene flow from this ancient population. This is likely to have occurred after the divergence of Native American ancestors from east Asian ancestors, but before the diversification of Native American populations in the New World. Gene flow from the MA-1 lineage into Native American ancestors could explain why several crania from the First Americans have been reported as bearing morphological characteristics that do not resemble those of east Asians2, 13. Sequencing of another south-central Siberian, Afontova Gora-2 dating to approximately 17,000 years ago14, revealed similar autosomal genetic signatures as MA-1, suggesting that the region was continuously occupied by humans throughout the Last Glacial Maximum. Our findings reveal that western Eurasian genetic signatures in modern-day Native Americans derive not only from post-Columbian admixture, as commonly thought, but also from a mixed ancestry of the First Americans.


Indeed, MA-1 looks like he could be an early ancestor of West Eurasians, including and especially Europeans. Mitochondrial haplogroup U was almost fixed in Upper Paleolithic and Mesolithic Europe (see here), while R1a and R1b are, after all, the most common and widespread Y-chromosome haplogroups in Europe today.

Below is the bar graph from the K=9 (nine ancestral populations assumed) ADMIXTURE analysis, which turned out to be the optimal run. Note that the Mal'ta sample appears mostly South Asian (37%), European (34%), and Amerindian (26%), but also with minor Oceanian ancestry (4%). Interestingly, among the Europeans, it's the groups from Northern and Eastern Europe that carry the highest levels of these components. This is probably a reflection, at least in large part, of their elevated indigenous European hunter-gatherer ancestry (for instance, see here).


At K = 9, MA-1 is composed of five genetic components of which the two major ones make up ca. 70% of the total. The most prominent component is shown in green and is otherwise prevalent in South Asia but does also appear in the Caucasus, Near East or even Europe. The other major genetic component (dark blue) in MA-1 is the one dominant in contemporary European populations, especially among northern and northeastern Europeans. The co-presence of the European-blue and South Asian green in MA-1 can be interpreted as admixture of the two in MA-1 or, alternatively, MA-1 could represent a proto-western Eurasian prior to the split of Europeans and South Asians. This analysis cannot differentiate between these two scenarios. Most of the remaining nearly one third of the MA-1 genome is comprised of the two genetic components that make up the Native American gene pool (orange and light pink). Importantly, MA-1 completely lacks the genetic components prevalent in extant East Asians and Siberians (shown in dark and light yellow, respectively). Based on this result, it is likely that the current Siberian genetic landscape, dominated by the genetic components depicted in light and dark yellow (Figure SI 6), was formed by secondary wave(s) of immigrants from East Asia.

Here's a figure showing the levels of shared genetic drift between MA-1 and 147 present-day non-African populations. Among the Europeans it's the Lithuanians, Northwestern Russians and Baltic and Volga Finns who are most similar to the ancient sample. It's also interesting to note the relatively high position on the list of the Kalash from South Central Asia and Lezgins from the North Caucasus. At the bottom are Bedouins and Palestinians, mainly because of their non-trivial Sub-Saharan admixture, followed by Oceanians, East Asians, and South Indians, probably due to deep differentiation between their main ancestral clades and that of MA-1.


Rumor has it that the same team of scientists is now trying to sequence genomes from Upper Paleolithic sites west of Mal'ta. I wonder how far west? I see that the authors mention the Sungir site from near Moscow a couple of times in the paper, in relation to its similarity to the Mal'ta site. Perhaps they're working on a Sungir genome right now? If so, what's the bet that the Y-DNA turns out to be another basal R?

For more on the Mal'ta genome, including some lengthy discussions on the topic with a few regular readers, click on the links below...

Ancient European admixture in the Americas, or ancient Amerindian admixture in Europe?

Surprising aDNA results from Paleolithic Siberia (including Y-DNA R)

Citation...

Raghavan et al., Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans, Nature, (2013), Published online 20 November 2013, doi:10.1038/nature12736


76 comments:

barakobama said...

"Europeans. Mitochondrial haplogroup U was almost fixed in Upper Paleolithic and Mesolithic Europe (see here), while R1a and R1b are, after all, the most common and widespread Y-chromosome haplogroups in Europe today."

Davidski you also know about the very recent spread of y DNA R1a and R1b in Europe. You agreed that R1b L11 in west Europe spread mainly in the bronze age and arrived just 5,000 years ago. R1a Z283 is connected with Indo European Corded ware culture it would have spread probably mainly 4,000-5,000 years ago. R1a Z93 Is also connected with Indo Europeans especially in Asia with Indo Iranians and Tocharian's and would have spread mainly 3,000-4,000 years ago.

Why using MA-10 Y DNA R to connect him with modern Europeans? Just 8,000 years ago R1b would have only existed in parts of the middle east and possibly central Africa with R1b V88, R1a would have probably only existed around Ukraine and Russia or possibly other parts of Europe and Asia , R2 would have only existed around south asia.

There is no evidence Y DNA R is basal for west Eurasians aka Europeans, middle easterns, and NOTH AFRICANS, I don't think west Eurasian is a good name because north Africans are included. If you went back 10,000 years the vast majority or all of Europeans male ancestors would not have Y DNA R. We cant base everything on modern distribution!!

barakobama said...

"Mitochondrial haplogroup U was almost fixed in Upper Paleolithic and Mesolithic Europe (see here),"

That is true but it is also true that we don't have any Palaeolithic or Mesolithic y DNA from anywhere else in west Eurasia. And there is a very small amount from Europe anyways.

German Dziebel says that the study should MA-10 was apart of a U lineage that hasn't been found in any modern people. He wasn't apart of U5, U4, U2, and U8 which are the subclades which have been found in Palaeolithic and Mesolithic Europeans. His U lineage may have also come from the middle east. I don't understand why people only connect him to Europe.

Davidski said...

Look, there was Y-DNA R at Mal'ta, so there's a very good chance that there also was Y-DNA R in Europe at sites like Sungir in Russia, which were very similar to Mal'ta.

But this doesn't mean that R1b didn't enter, or even re-enter, Europe from nearby well after the Ice Age.

Davidski said...

Ancient Northern and Eastern Europe are connected to Siberia by archeology, anthropology and genetics.

The ancient Middle East and even Mediterranean Europe are more connected to Africa than to Siberia.

Davidski said...

Oh, by the way, note that Mal'ta boy doesn't have a drop of Middle Eastern admixture.

barakobama said...

Wow Davidski it seems MA-10 may have been part South Asian 37%, European(pre Neolithic) 34%, Native American 16%, Oceania 4%, and Na Dene 1%.

I know nothing about the science of autosomal DNA. The dark blue seems very connected to North European like ancestry in Europeans which we know through ancient DNA probably is straight from Palaeolithic Europe. The light blue seems to be maybe connected with west Asian, southwest Asian, or med like ancestry or just non Norh Euro related west Eurasian ancestry. MA-10 had 34% dark blue and no light blue. The green seems to obviously show south Asian like ancestry in MA-10 and he had 37%. The orange seems very Native American and MA-10 had 16%. The pink seems connected with NA dene and some Siberian people and MA-10 has 1%. The Purple is definitely connected with Oceania people and MA-10 has 4%.

Northeast Europeans had a pretty good amount of pale yellow which shows probably Siberian ancestry and looks nearly 100% in Nganasan's who speak a Uralic language. Which makes me think that very popular originally east Asian y DNA N1c1 was spread in northeast Europe maybe with Uralic languages. There is also some Green south Asian? and pink NA Dene/Siberian? in mainly northeast Europeans or east Europeans. The south Asian, Na Dene, Siberian in Europe seem connected.

It is similar to Dodecade autosomal DNA results. More northern Indo Aryan Indians have much more middle eastern(light blue) than southern Dravidian Indians. Both though have mainly south Asian(green) and it is extremely high in Dravidians. All south Asians show some east Asian ancestry like in Dodecade. Dravidians have a lot more purple(Oceania) though. All South Asians also show some possibly Siberian and Na Dene like ancestry.

MA-10 maybe had mainly south Asian and European ancestry. Is there any research on his skull shape which would probably be very Caucasoid. I have heard there are unique Y DNA P lineages in south Asia and that R2 probably originated there. Is it possibly MA-10 y DNA R is a direct paternal line from a south Asian? I wish there was some autosomal and Y DNA from Palaeolithic middle east, Europe, south Asia, and north Africa to compare to MA-10.

Na dene and Siberians show a pretty good amount of dark blue(pre Neolithic European?). I was always surprised to see North European in really remote Siberian tribes in Dodecade globe13.

spagetiMeatball said...

He doesn't, but we know that some native american groups (Na-Dene) I think have quite high frequencies of mtDNA X, which today is also very frequent in the druze, so we can't completely rule out contact between ancient siberia and the near east, or maybe more probably continuous gene flow from siberia into warmer parts of eurasia, as people were trying to escape the cold.

barakobama said...

Thank you for the posting and responding.The color graph thing seems to show MA-10 had mainly North European(pre Neolithic European) like ancestry and south Asian. So I would agree he might have something to do with Europe and south asia. That could mean Europeans and south Asians migrated to Siberia and mixed with Native American, Siberian-Na Dene, and Oceania like people. Or that back then there were many extremely mixed tribes in a lot of Eurasia. which I doubt.

It is definitely possible a mainly Y DNA R people existed in Europe during the Palaeolithic but that is not where R1b M269(mainly L11) and probably R1a M417(mainly Z283) in Europeans today descends from. It is definitely possible though that R1a originated in Europe so R1 may have existed in Europe 24,000 years ago and today has modern direct male descendants.

But I think saying R1a and R1b are popular in Europe today is not evidence that MA-10 gets his west Eurasian or north European like ancestry partly from his Y DNA R male line. He may have gotten the Y DNA R from south asia or even Siberia. Since Y DNA R is so closely related to dominate Y DNA haplogroups in east Asia, America's, and Oceania I think it is possibly it originated in eastern Asia. The age estimates for Y DNA P are to young to be from the common ancestor population of modern day native Americans and west Eurasians. MA-10 is evidence he was very mixed not from common ancestor root. mtDNA shows a clear cut between west Eurasians and east Eurasians going back over 60,000 years.

barakobama said...

Your right that there was mixing between Mesolithic east Europeans and Mongoloids at least 8,000 years ago. And all the other stuff about archeology and anthropology is also true. I agree it is possibly eastern Europeans 24,000 years ago where somehow connected with Siberia. Iran-Pakistan though is pretty close to Siberia. MA-10 probably south Asian ancestry is also evidence people in that area where somewhat connected to Siberia 24,000 years ago.

The dark blue though also exists in the middle east and south Asia and all might not be European inter marriage. The MA-10 results were extremely unexpected by most people. Why couldn't it be possibly his dark blue did not originate in what is called Europe. I do think he probably does have ancestry going back to Europe though. All I am doing is looking at the colors and trying to connect them with certain people a second grader could do that. I am sure there are many explanations for MA-10 results that we need an expert with autosomal DNA to explain the possibilities.

I think MA-10 is more important in learning about European's and south Asian's ancestry than Native American. He was much more European and south Asian like than Native American.

German Dziebel said...

"study should MA-1 was apart of a U lineage that hasn't been found in any modern people. He wasn't apart of U5, U4, U2, and U8 which are the subclades which have been found in Palaeolithic and Mesolithic Europeans."

This seems to be the situation. Unlike Dolni Vestonice, which tied back to U5, MA-1 is on its own, which is consistent with its extreme easternmost location.

"some native american groups (Na-Dene) I think have quite high frequencies of mtDNA X, which today is also very frequent in the druze, so we can't completely rule out contact between ancient siberia and the near east."

The pink component in the ADMIXTURE run may be depicting this very connection, although Na-Dene are not the population known for mtDNA hg X. It's only found in Southern Athabascans.

barakobama said...

I know that's very important. The light blue and dark blue are definitely west Eurasian aka Caucasian. The dark blue seems connected with North Euro like ancestry. The light blue may just show non North Euro Caucasian ancestry. MA-10 had 34% dark blue with no light blue. I would assume that means he has some type of north European aka pre Neolithic European like ancestry. MA-10 results are evidence that those Mesolithic and Neolithic Europeans already tested can trace almost all of their ancestry to Europe over 30,000 years ago.

I ignored this originally as meaning nothing. But Gotland hunter gatherers from 2,000-2,800bc in globe13 Ajv52 had south Asian: 6.6%, Palaeo African: 2.9%, Amerindian: 1.1%,
Ajv70 had Australasian: 3.5%, west African: 1.7%, Amerindian: 3.1%

Otzie 5,300 year old early copper age farmer from the alps. Australasian: 1.3%, east Asian: 1.3%. La Brana 7,000 year old Mesolithic farmer from Spain. had 3.2% Palaeo African.

In K7b La Brana had 9.3% African, Ajv had 4.33%, Otzie had 0.8%. Ajv52 also had 8.1% south Asian.

In K12 Ajv52 had Sub Saharan: 4.3%, Ajv70 had 1.3%, LA Brana had 1%. LA Brana also had 10.3% east African, Gok4(funnel beaker culture Neolithic farmer Sweden) had 0.7%, Otzie had 2.4%. Otzie also had 2% southeast Asian and 5.7% northwest African. AJv70 also had 1.6% Siberian.

Those surprising results except for maybe northwest African in Otzie. Might actually be for real. There could have been some very crazy mixing that happened. I doubt they mean anything though.

MfA said...

I guess South Asian here is the so called SouthWestAsia/Gedrosia/ANI for West Asian populations.. I think it is same case for Mal'ta boy too.. Here's extrapolated numbers..

Pathan 56,3
Brahui 55,1
Burusho 54,4
Balochi 54,4
Mal'ta 37,0
Tajik 33,2
Iran 29,4
Lezgins 26,8
Georgia 22,7
Armenia 19,6
Druze 13,6

barakobama said...

"fANovember 21, 2013 at 10:24 AM

I guess South Asian here is the so called SouthWestAsia/Gedrosia/ANI for West Asian populations.. I think it is same case for Mal'ta boy too.. Here's extrapolated numbers..

Pathan 56,3
Brahui 55,1
Burusho 54,4
Balochi 54,4
Mal'ta 37,0
Tajik 33,2
Iran 29,4
Lezgins 26,8
Georgia 22,7
Armenia 19,6
Druze 13,6"

Are you getting this from the K=9 bar graph?

MfA said...

Yep, It is from K9..

Davidski said...

The reason for these surprising results is that there aren't enough ancient genomes yet to create ancient clusters. When these ancient clusters start appearing, the hunter-gatherers will stop looking like mixtures of modern clusters, and modern genomes will start looking like mixtures of ancient clusters. I explained this in my other blog entry.

“Indeed, perhaps this is also why when the Mal'ta individual is forced into modern genome-wide genetic clusters, he appears West Eurasian, South Asian and Amerindian? However, eventually, when enough Mammoth Steppe genomes are sequenced, we're likely to see a new cluster emerge that is modal in these samples.”

http://eurogenes.blogspot.com.au/2013/10/ancient-european-admixture-in-americas.html

barakobama said...

So are you saying the Green which is most popular in south Asia. "is the so called SouthWestAsia/Gedrosia/ANI for West Asian populations". Meaning that Mal'ta may have some ancestry from the middle east?

Davidski said...

Obviously not, since the light blue component is a major feature of the West Asian samples, but missing entirely from the Mal'ta genome.

MfA said...

I didn't imply West Asian influence.. SouthCentralAsia is more like a Caucasus' sister branch in old Central Asia, later pushed towards West Asia-SouthAsia..
@Davidski What do you think about Armenians score 20% South Asia? It is also clear MA-1 scores similar Baloch and Lezgin segments in NGSadmix graph..

MfA said...

Oh, I see where the west asia thing come out, I meant South Central Asia in my first post, not SWA, though Gedrosia/ANI thing should have gave you the clue.. Sorry for typo..

barakobama said...

So Mal'ta was forced into modern clusters and might not actually have European, native American, and south Asian like ancestry. How are the clusters found through SNP's in austome chromosomes? Do you try to find 5 clusters in some tests or 10 in others? Can you please try to explain the science behind this to me?

barakobama said...

The Y DNA tree says Ma-1 is ancestral to haplogroup R. There is also a red circle on the root of R1 and R2.

Davidski said...

Some of the South Asian component among the Armenians is actually from South Asia, but most of it is probably the result of shared Upper Paleolithic ancestry with South Asians, which got to West Asia when the hunter-gatherers from the mammoth steppe were forced south by the Ice Age.

So I can see either or both of these scenarios being true:

a) South Asians are more drifted than West Asians and Europeans, so some of the ancestry they share with these groups gets lumped into a South Asian-specific cluster which has nothing to do with the component we know as Ancestral South Asian (ASI).

b) The Y-DNA R ancestors of the mammoth steppe foragers came from South Central Asia.

In any case, this is all very interesting, because it suggests that the South Asian-specific and West Asian-specific components we see in various analyses might indicate Upper Paleolithic European ancestry among extant Europeans, to a large degree anyway.

barakobama said...

Ancient Eurasian DNA just updated some results. Of course Mal'ta who Jean Manco says genes show had dark skin, dark brown hair, and brown eyes. Show also just added pigmentation to Otzi the ice man saying he had brown eyes, brown hair, and fair skin. Where did she get this info it is was I expected. But I think she may just be going off of the leak which said Mal'ta was much darker than Otzie and we already know Otzie had brown eyes and hair.

There is also a update on mtDNA from Lokomotiv, Irkutsk Russia dating to 6125–4885 BC. Here is a link on google maps of Lokomotiv, Irkutsk Russia.

https://www.google.com/maps/preview#!q=Lokomotiv%2C+Irkutsk+Russia+&data=!4m15!1m14!4m8!1m3!1d26184711!2d106.6510473!3d58.6319736!3m2!1i931!2i591!4f13.1!10b1!26m3!1e12!1e13!1e3


You can see at is at the coast of Lake Baikal just like Mal'ta. Here are the results.

U5a=2, F=2, D=2, A=2, G2a=1.

This shows by this time Mongoloid mtDNA had arrived in this region. Also that there was some European influence on at least the maternal side. There is a 7,800bc U5a from Chekalino, Russia, and 8,000-7,000bc U5a1 from Lebyazhinka, Russia, You can see on a map they are right at the border with Kazakhstan, very far eastern Europe.

Here is a link to more important ancient mtDNA from Russia showing inter marriage between east European hunter gathers and east Asians.

http://anthropogenesis.kinshipstudies.org/2012/11/yuzhnyi-olenii-ostrov-ancient-mtdna-evidence-for-amerindian-admixture-in-europe/

Even more ancient mtDNA showing mixing between east European hunter gathers and east Asians. Is from Ust Tartus culture in Sopka, Russia from 4,000-3,000bc.

Here are the results. U=6(U2e=3, U5a1=2, U4=1), Z=4, C=4, A=1, D=1

It seems Russian far eastern European hunter gatherers west Eurasian mtDNA haplogroups fell almost entirely under U5a(probably mainly or all U5a1), U4, and U2e. All are about 35% in Bronze and Iron age, Indo Iranian?, Y DNA R1a1, mainly light haired and eyed people in Asia. This shows they were not the first migrations of Europeans into Siberia and central Asia.

terryt said...

"When these ancient clusters start appearing, the hunter-gatherers will stop looking like mixtures of modern clusters, and modern genomes will start looking like mixtures of ancient clusters".

Exactly. That's why we keep seeing such ridiculous comments as 'Native Americans are proto-Mongoloid'. All populations, including South Asians, are the result of periodic admixture. Razib makes an interesting observation on the subject:

http://blogs.discovermagazine.com/gnxp/2013/11/long-first-age-mankind/#.Uo0eOcSkrIU

Quote:

"Reticulation. Graphs. Admixture. These words all point to the reality that rather than being the culmination of deep rooted regional populations which date back to the depths of the Pleistocene, most modern humans are recombinations of ancient lineages. On the grandest scale this is illustrated by the evidence of ‘archaic’ ancestry in modern humans. But even more pervasively we see evidence of widespread admixture between distinct lineages which are major world populations which we think of as archetypes".

DOD879 said...

he green peaks in the sakili, which is a south Indian population. Not Balochi.

DOD879 said...

What I was trying to say is that his South Asian+Papuan admixture shows more "ASI like" affinity than ANI.

Davidski said...

ASI ancestry among the Indian samples in this study is represented by the South Asian, Oceanian and East Asian components. But these three components make up 90-100% of the genetic structure of the Indians. This leaves almost no room for ANI, unless a large part of the South Asian component shared by the Indian samples is in fact ANI.

What this suggests is that the Mal'ta South Asian component is 100% ANI, of the same type that is seen in West Asia and Europe today. This makes sense considering that archeologically the Mal'ta site shows links to European sites where ASI was unlikely to have been present before the Ice Age, and where it's not present today.

Onur said...

David, why not test the Mal'ta boy yourself before deciding on what his "South Asian" component must represent?

DOD879 said...

David,
I do think that all Indians have significant ANI admixture, or that ASI and ANI were not that different from each other except for the papuan like admixture in the ASI. The ASI signature in today's populations seems to be a ("South India/Asian" + "Papuan") signature, which Malt'a boy has.
If you look at the HarappaWorld results, the Papuan (>2%) seems to show up only in those populations that one would associate with ASI or Malenesia.

andrew said...

FWIW, there are multiple lines of evidence to suggest that R1b-V88 is intrusive into Africa sometime in the mid-Holocene. Among them are the strong demarkation between R1b-V88 carrying populations and geographicaly nearby populations, and Y-DNA mutation dating, and where R1b-V88 fits on the phylogenetic tree of R1b which can be correlated to archaeology likely associated with fairly basal R1b elsewhere.

Davidski said...

I don't know about HarappaWorld, but in this analysis the minor Oceanian admixture shown by the Mal'ta sample also shows up among Europeans and West Asians.

The Mal'ta population had archeological and genetic ties with people who were the ancestors of present day Europeans and West Asians, and they passed on their South Asian-like and Oceanian-like admixture to them. So if this is ASI, it's not the same ASI as in South Asia today.

Nirjhar007 said...

On-a
ASI is south Indian ANI is north Indian and the reason of the Neolithic Development there which legacy is still on both in culture and materials of daily life from the Neolithic.....
on-b
Well i mostly agree here only i think the European component we show is as archaic as the Amerindian Component in Europeans....

jackson_montgomery_devoni said...

Davidski,

Have you ever thought about creating an ADMIXTURE calculator at a low level K like Dienekes globe4 one to possibly capture Amerindian like ancestral signals in Europeans? I think it would be interesting and fun for us to play around with. I ask this because if you created one it would probably be more informative than Dienekes because your calculators do not suffer from the calculator effect.

Eduardo Pinto said...

Hey David, here are their genomes

http://www.cbs.dtu.dk/suppl/malta/

Davidski said...

Yeah, I know, but the Mal'ta genome isn't in a PLINK ped file. It's not even in a VCF file.

First I'd have to call the SNPs and make a VCF file, and then convert the VCF file into a PLINK ped file. That would take days, if not a couple of weeks.

I might do it. Maybe.

Eduardo Pinto said...

If that kooky guy Genetiker can do it, you can also do it!
Come on David you don't want to be lagging behind Dienekes, Verenich or even kooky Genetiker.

Davidski said...

He might be kooky, but he's obviously got the bandwidth. However, what's the guarantee that he got it right?

Anyway, I'll see what I can do.

About Time said...

It's in plink format at http://www.evolutsioon.ut.ee/MAIT/public_data/malta/

Davidski said...

I've got that dataset. The Mal'ta genome isn't there.

Helgenes50 said...

@ Davidski

First of all, thank you for all your work.

What do you think of the Sardinians ? from the last results, they have a high percentage of dark blue. that certainly means that they have an Ancestry in common with the hunter gatherers.

Davidski said...

Yes, they do, but it's difficult to say how much exactly, because the dark blue component also appears in the Near East.

Based on the abstract below, we already know that Scandinavians are just over 50% hunter-gatherer, so most Europeans, except those around the Baltic, would be much less than that.

http://www.diva-portal.org/smash/record.jsf?pid=diva2:645429

spagetiMeatball said...

David, can we construct any accurate forensic portraits yet of the distinct prehistoric european groups, like hunter-gatherers and farmers, or are there not enough skeletons? Would be interesting to see what the two unadmixed groups looked like. I'm guessing the HG's were all blondes?

Davidski said...

I suppose we'll soon find out when the genomes of the Gotland hunter-gatherers are published.

Mal'ta boy was in all likelihood very dark, and you can see those results in the supplemental PDF. The Siberian Kurgan mummies were about 60% fair haired and blue/green eyed, but they were basically modern Europeans rather than Mesolithic hunter-gatherers.

barakobama said...

I kind of agree with SpagetiMeatball there was probably a lot of blonde hair in the hunter gatherers because of who their closest modern relatives are. When you rank it the more hunter gatherer related in autosomal DNA the more blonde(except Sami). It would be cool to know what hair color La Brana, Gok4, St. Forvar, and Gotland hunter gatherers had.

It was not just the Siberians but also hair and eye color from related people in Kazakhstan. Possible all Indo Iranian and Tocharian speakers in central asia and Siberia during bronze and iron age. They had probably vast majority Y DNA R1a1a1b2 Z93. Also so far it seems very different mtDNA haplogroup percentages than any modern Europeans. With a notably high amount of U5a, U4, and U2e possibly over 30%, and T1a at over 10%.

I do agree though since they were farmers and bronze age people. They definitely didn't have the exact same genetic makeup as hunter gatherers.

I think pigmentation genes from pre historic remains can be used as Genetic information especially for Europeans. If somehow there is pigmentation genes taken from Palaeolithic Europeans and they all have pale skin with diverse hair and eye colors. You know pretty much as a fact they are the main ancestors of modern Europeans.

barakobama said...

"Our results also demonstrate that while Middle Eastern populations are not the most similar to Neolithic farmers, this observation can be explained by African-related admixture in more recent times for Middle Eastern groups, which, once accounted for, reveals that the other major component of their ancestry resembles Neolithic farmers."

I really don't understand this. I know the people who wrote that abstract are extremely smart. But is there really any evidence of recent African(what type north or south) admixture in the near east, Do they think west Asian and southwest Asian in globe13 originated in Africa? I think they are just trying to make the European farmers like modern near easterns, Which they definitely are not in mtDNA, autosomal DNA, and pigmentation. It is just a fact and we will have to try to explain it somehow.

"Based on the abstract below, we already know that Scandinavians are just over 50% hunter-gatherer, so most Europeans, except those around the Baltic, would be much less than that."

Davidski do you know how reliable what they said on the abstract is? How can they get just over 50% how can they really know? It would make sense to me. Because in mtDNA the vast majority of Europeans maternal lineages are from the farmers not hunter gatherers. I think what spagetiMeatball said about HG's being all blonde's might be even more true now. Because Otzi a farmer had pale skin which all the farmers probably did. So hunter gatherer ancestry wont effect skin color in a major way. But Europeans who have just over 50% hunter gatherer ancestry like Scandinavians have majority blonde hair. I wonder what hair color percentages of a 100% hunter gatherer population would be. That makes it hard to believe the farmers wouldn't mix with the hunter gatherers. With all of the blonde hunter gatherer women.

Davidski said...

Take a closer look at the bar graph from the Mal'ta study. The Bedouin, Palestinians, Druze and even Iranians have Sub-Saharan admix that Europeans lack.

http://img43.imageshack.us/img43/2810/hhx4.png

So that quote makes sense. There are probably other differences between the Swedish Neolithic farmers and most modern Near Eastern groups, but these aren't as obvious as the Sub-Saharan admixture.

Onur said...

Populations of Anatolia, the Armenian Highlands, Transcaucasia and northern Mesopotamia lack the African components. This is clear from all the ADMIXTURE analyses of them. It seems that whatever Sub-Saharan genetic influence there is in West Asia has not passed beyond the lands of the Arabic speakers and some southern parts of Iran.

barakobama said...

"Take a closer look at the bar graph from the Mal'ta study. The Bedouin, Palestinians, Druze and even Iranians have Sub-Saharan admix that Europeans lack.

http://img43.imageshack.us/img43/2810/hhx4.png

So that quote makes sense. There are probably other differences between the Swedish Neolithic farmers and most modern Near Eastern groups, but these aren't as obvious as the Sub-Saharan admixture."

The southwest Asian and west Asian in globe13 that Otzi and Swedish farmers have very little of. there is no way both came to the near east from Africa in the last 9,000 years or so. The European farmers are not very Near eastern their mainly I guess Meditreaen. mtDNA haplogroup subclades tells the same story they are that similar to modern Near easterns.

I think it is dumb to assume that the Near eastern farmers that spread across Europe had to genetically be just like modern Near eastern people. There could have been a very Autosomally Meditreaen people in the Near east 10,000 years ago that for some reason went extinct later. The mtDNA haplogroup subclades from Neolithic Europeans fits with modern Europeans not Near easterns. For example they had vast majority J1c under J like modern Europeans and unlike modern near easterns who have mainly J1b. I could give many more examples.

The mtDNA from pre Pottery early Neolithic Syria was actually kind of similar to Neolithic Europeans.

Pre Pottery Neolithic B Syria Total mtDNA=16
K=5 31.25%(K?=2), T2b=3 18.75%, H=2 12.5%(H5=1), L2a1=2 12.5%, H or K=2 12.5%, C1=1 6.25%, R?=1 6.25%
Dja’de el Mughara
7,400-6,700BC mtDNA=1: T2b=1
Tell Halula
6,800-5,750BC mtDNA=10 : T2b=2, H or K=2, L2a1=2 K?=2, H5=1, R?=1
Tell Ramad
6,000-5,750BC mtDNA=5: K=3, H=1, C1=1

T2b today is mainly European. Out of 114 LBK samples 22.8% had T and all that show a subclade under T were T2. And 12 out of 17 under T2 had T2b. T2b has also already been found in early Neolithic Iberia. I am just saying it is possible that if we get autosomal DNA from some of the earliest farmers in the Near east. They might be very similar to Otzi and Gok4, extremely Meditreaen like.

Otzi and Gok4's farmer ancestors even though they had been in Europe for already over 2,000-3,000 years had very little inter marriage with hunter gatherers. It is possibly they rarely inter married with outsiders while still in the Near east.

The vast majority of modern European maternal lineages are from the farmers not hunter gatherers. Like you said before Davidski all Europeans except Scandinavians and Baltic's probably trace most of their ancestry to the farmers. This would mean most Europeans ancestors 12,000 years ago were in a hot and sandy Near east. I wish I could take a autosomal DNA test to get an idea how much farmer and hunter gatherer ancestry I probably have. My Dad in Geno 2.0 got 40% Meditreaen and 35% North European. I am probably a lot more Near eastern farmer than I originally thought. Many Europeans may be similar to Hispanics as being mixed from native population and invades. Hispanic's are very mixed between mainly Iberian and Native American. Europeans are mainly a mix between native hunter gatherer's and near eastern farmer.

Davidski said...

Many modern samples from the southern Levant and Arabia lack West Asian influence. Half of the Bedouins here lack the South Asian component, which I think is in part a proxy for the usual West Asian component.

http://img43.imageshack.us/img43/2810/hhx4.png

So the Mediterranean farmers of Neolithic Europe might have come from more southerly areas which at that time lacked both West Asian/South Asian and Sub-Saharan admix.

spagetiMeatball said...

What is the south asian component exactly? It's not the frequently-mentioned "ASI" is it?

Davidski said...

It's a composite created by the South Asian samples, probably because they're the most drifted. Some of it is ASI, but ASI doesn’t exist in Europe.

About Time said...

Are white whales related to white wolves? Convergent evolution is part of the game in nature.

Malta boy was probably dark and lived in similar time and environment as paleo euros and he was somehow related to Europeans.

You are for some reason making assumptions. Maybe they had some or many pale individuals, maybe not. Show me the genes.

Nirjhar007 said...

ASI = Ancestral South Indian
Thats the correct one but some use it joining with ANI= Ancestral North Indian component which is mostly made of Baloch+SW Asian component with some NE Euro+Caucasian+N asian and some minimum ones....
The South Indian Component started to mix with ANI when Harappans Shifted East and South from~2000 BC so it is perfectly natural that Europeans don't have the South Indian Component!

barakobama said...

About Time....

Mal'ta was definitely very mixed and had mainly non European like ancestry. It is debatable if Europeans ancestors were pale skinned at that time anyways. I am not saying we should base everything on pigmentation genes. I am saying that it can be used to help see who they may be more related to today.

I really don't understand why there is nothing on the autosomal DNA of the bronze and iron age Kurgen people in mainly Siberia. I would guess they are most related to modern Baltic's, Russians, and Scandinavians. Based on their hair and eye color and that they are suppose to descend from Yamna culture in far eastern Europe.They may be more related to hunter gatherer samples than any modern people because of their high amount of U5, U2e, and U4

barakobama said...

"So the Mediterranean farmers of Neolithic Europe might have come from more southerly areas which at that time lacked both West Asian/South Asian and Sub-Saharan admix."

Are you saying the green which seems very south Asian is also very west Asian? There are some Bedouins who lack the green completely. The light blue is very popular in more farmer descended Europeans like Sardinians. So I don't know maybe it is some how common ancestor between Near easterns and European farmers.

I made the point it is not just autosomal DNA. Neolithic European farmers are totally different from the hunter gatherers and also very different from all modern Near easterns. They could have been apart of a people in the Near east that has now become extinct or blended in as a small minority with other Near easterns.

Davidski said...

I've added another figure from the study to the blog entry, to better explain the Mal'ta boy's genetic affinities.

Davidski said...

Yes, the green component is a complex mix of South Asian, West Asian and Eastern European components. So it doesn't mean the same thing in all the samples.

spagetiMeatball said...

It looks like amerindians carry more genes from MA-1 than other populations, right?

Davidski said...

Yes, it looks that way, and it also seems as if they share much more recent ancestry with MA-1. Next up are some Siberians and Eastern and Northern Europeans. It's interesting how far down the list are Armenians, even though they don't have any Sub-Saharan ancestry.

spagetiMeatball said...

How could the MA-1 dudes make it down to south and west asia? I though those genes made it there only much later with migrating indo-aryans who had a lot of MA-1 ancestry.

Davidski said...

The mammoth-steppe populations probably moved to Southern Europe, the Caucasus and South Central Asia during the Ice Age. Then they expanded north again after the glaciers melted. A few thousand years after that, R1a Kurgan populations from Eastern Europe migrated to Siberia and then to South Asia.

spagetiMeatball said...

So are you still working with this old model: http://bga101.blogspot.ae/2012/03/northwest-eurasians-southwest-eurasians.html ?

Europeans = near eastern farmers + ancient siberians ?

Also, despite all the admixture in Europe, it seems that 4/5 of the main Y-DNA lineages are R1a or R1b, so paternally directly descended from the mammoth-hunters. So it was always these dudes and other women: They weren't joking around! Yikes...

Davidski said...

Yeah, I think that model is still relevant. But I was wrong in one important aspect; I thought that the Northwest Eurasians were mostly Neolithic farmers from Anatolia or Iran, but it now seems they were mostly hunter-gatherers from the arch that runs from Europe to India across Central Asia.

Onur said...

Barak,

Gok4 (the Swedish Neolithic farmer) and Oetzi are too high in the "Atlantic Baltic" component of the K7b, the "Atlantic Med" component of the K12b, the "Atlantic Baltic" component of the world9, and the "Northwestern" and "Southwestern" components of the euro7 ADMIXTURE analyses to be relatively unmixed descendants of West Asian Neolithic farmers. So they, just like Sardinians, have significant levels of European hunter-gatherer ancestry. Gok4, in line with her geographical location, has more European hunter-gatherer ancestry than Oetzi, but Oetzi's level of European hunter-gatherer ancestry is no less important, especially considering his geographical location.

Onur said...

Forgot to mention. Oetzi and especially Gok4, just like Sardinians, are too high in the "North European" and "Mediterranean" components of the globe13 ADMIXTURE analysis to be relatively unmixed descendants of West Asian Neolithic farmers.

Davidski said...

How do you know the first farmers moving west across the Mediterranean from the Levant weren't 100% "Mediterranean"? The genetic structure of the populations that remained in the Levant might have shifted after they left.

Take a look at some of the Bedouins here. If they lacked the Sub-Saharan admix they'd be purely Near Eastern, but not West Asian. Add a bit of European hunter-gatherer admix and you've got early West Mediterranean farmers IMO.

http://img43.imageshack.us/img43/2810/hhx4.png

Onur said...

David,

Your scenario is possible, but not probable. The genetic shift you and Barak propose for West Asia is too huge for the post-Neolithic times. Of course, much more sampling is required from ancient West Eurasia, especially from the undersampled West Asian and Balkan parts, and especially from the pre-Neolithic times, to fully clarify the issue.

Davidski said...

You can see these shifts on the West Eurasian PCA. Modern Near Eastern populations are pulling towards the West Asian highlands from the non-West Asian-like Bedouins and Saudis, who, apart from their relatively high Sub-Saharan admix, probably best represent the original southern Levant populations prior to the major expansions from the West Asian highlands during and well after the Neolithic.

http://eurogenes.blogspot.com.au/2013/08/principal-component-analysis-pca-of.html

It's likely that Sardinians, Northwest Africans and even Basques are all in large part derived from these ancient non-West Asian populations from the Levant.

Onur said...

Do you mean that the West Asian Neolithic migrants to Europe came directly from the Levant rather than Anatolia, i.e., maritime colonization during the entry to Europe?

Davidski said...

They came from all over the Fertile Crescent, and entered Europe via two main routes; Anatolia and the sea. I'd say some were totally Mediterranean, while others significantly West Asian.

Onur said...

Which, do you think, were the genetically significantly "West Asian" ones, the land-based West Asian farmer migrants to Europe from Anatolia, whose descendants reached as far as Central Europe and perhaps beyond by way of the Balkans?

Then there are the maritime West Asian farmer migrants to Europe directly from the Levant, whose descendants migrated through all over maritime Southern Europe and likely beyond. Maybe they are the only ones genetically so highly "Mediterranean". Are Gok4, Oetzi and the recently-sampled farmer from what is now Burgos, Spain, descended from the maritime (Levantine) Neolithic wave to Europe?

Davidski said...

See here...

http://eurogenes.blogspot.com.au/2013/05/modern-european-admixture-components.html

Onur said...

So, your answer is yes to both of my questions?

Davidski said...

Yes.

Czesław Opolski said...

Green eyes belong to brown, grey to blue isn't it?

Davidski said...

Light eyes like blue, green and grey are produced by most of the same alleles.