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Thursday, April 3, 2014

The really old Europe is mostly in Eastern Europe


A new version of the Lazaridis et al. ancient genomes preprint has just appeared at arXiv (see here). It includes several new Principal Component Analysis (PCA) maps, TreeMix graphs, a ChromoPainter/fineSTRUCTURE co-ancestry matrix, and an updated ADMIXTURE analysis. The revised text underlines the relatively close genetic relationship between indigenous European hunter-gatherers and present-day Eastern Europeans:


The co-ancestry matrix (Fig. S19.3) confirms the ability of this method to meaningfully cluster individuals. We highlight two clusters: Stuttgart joins all Sardinian individuals in cluster A and Loschbour joins a cluster B that encompasses all Belarusian, Ukrainian, Mordovian, Russian, Estonian, Finnish, and Lithuanian individuals. These results confirm Sardinia as a refuge area where ancestry related to Early European Farmers has been best preserved, and also the greater persistence of WHG-related ancestry in present-day Eastern European populations. The latter finding suggests that West European Hunter-Gatherers (so-named because of the prevalence of Loschbour and La Braña) or populations related to them have contributed to the ancestry of present-day Eastern European groups. Additional research is needed to determine the distribution of WHG-related populations in ancient Europe.


Fig. S10.5 suggests that the main axis of differentiation in Europe when the subcontinent is considered as a whole may tend to Northeastern Europe rather than SSE/NNW (8). This is consistent with our analysis of ancestry proportions in European populations (Fig. 2B, Extended Data Table 3) which indicate a cline of reduced EEF (and increasing WHG) ancestry along that direction.

Citation...

Iosif Lazaridis, Nick Patterson, Alissa Mittnik, et al., Ancient human genomes suggest three ancestral populations for present-day Europeans, arXiv, April 2, 2014, arXiv:1312.6639v2

118 comments:

barakobama said...

Motala12 seems to also have had blue eyes and dark hair, and but had rs1426654 A/A like Stuttgart and Otzi. So not all Mesolithic Europeans had G/G alleles, and A/A in Mesolithic Europeans and middle easterns(Stuttgart and modern) is probably just from early west Eurasians. Like i have said maybe a million times my opinion is that the skin color of these ancient individuals is unknown.

barakobama said...

Do you now have the raw data(or whatever) of all of the ancient individuals mentioned in this new Laz?

It would be great to get some Yamna, Catacomb, Unetice, Bell beaker, Corded Ware, and Andronovo genomes to see how WHG, EEF, and ANE they were and how they relate to each other and modern east Europeans(or just Europeans and Indo Europeans in general).

Colin Welling said...

"The really old Europe is mostly in Eastern Europe"

No. The WHG component is concentrated in Northern Europe, not Eastern Europe. (Cluster does not have the same meaning).

The populations where WHG is estimated at over 40% are all Northern: Scottish, Icelandic, Norwegian, Estonians, Latvians, and Belorussians.

The Czechs, Ukrainians, and Bulgarians all have less.

Additionally, WHG is closer to EEF than it is to ANE [p92], of which NW Europeans have more of the former and NE Europeans have more of the later. Finally, some NE populations include extra East Asian type heritage.

Hence the populations closest to WHG folks and the populations with the most WHG ancestry are both Northern Europe.

But we shouldn't get too far ahead of ourselves, we still don't know that WHG type folk are the only Mesolithic/Paleolithic inhabitants of Europe. Its still possible that ANE like people were in Eastern Europe early on or that EEF like people were in Southern Europe early on. My thinking is that ANE was in Central Asian till after the ice age. I really don't know where the EEF ancestors were at the end of the ice age.

barakobama said...

Collin, WHG is highest in northern Europe but is higher in mainland eastern Europe(e.g Poland and Ukraine) than in mainland western Europe(e.g. Germany, Netherlands, Britain) and higher in north-east Europe(e.g. Lithuania, Finland, estonia) than in north-west Europe(i.g. Sweden and Norway). It's specifically highest in north-eastern Europe. In mainland eastern Europe WHG is about as high or higher than in Swedish and Norwegian(who have the highest in north-west Europe).

Colin Welling said...

you're still saying its higher in northern Europe rather than eastern Europe, which is what I pointed out.

the other points I made are more subtle, so you might want to read it carefully.

And what do you mean by the level of WHG in Swedish, Dutch, Germans, and Polish? I don't see any of them in the above study.

barakobama said...

"you're still saying its higher in northern Europe rather than eastern Europe, which is what I pointed out."

Specifically WHG's highest in north-eastern Europe. If you exclude the Balkans from eastern Europe, WHG's highest in eastern Europe. We both mean the same thing about WHG distribution just we are getting confused on geographic terms.

"And what do you mean by the level of WHG in Swedish, Dutch, Germans, and Polish? I don't see any of them in the above study."

I am basing that statement on their results in admixtures and placements in PCA's. Alot of people knew how what is now known as WHG is distributed before Laz.

Anders Pålsen said...

Was the Finestructure analysis linked or unlinked? The former have tendency weight more on more recent ancestry.

Davidski said...

They don't say, although I'm sure they'll tell you if you e-mail them.

But I think they do make a very important point in regards to analyzing ancient samples with these sorts of methods:

"To avoid imputing alleles into sites for which data was missing in the ancient genomes, we restricted analysis to a set of 495,357 sites which were complete in all 779 included samples (777 modern West Eurasians of Fig. 1B, Loschbour, and Stuttgart). We phased the data using BEAGLE 42 with parameters phase-its=50 and impute-its=10. We phased each of chromosomes 1-22 separately, and then combined results using ChromoCombine."

Did you impute markers for the ancient genomes in your analyses? They're outside the range of modern genetic variation, so doing that might well have biased their results.

Matt said...

WHG similarity overall is highest in Eastern Europe, so it's reasonable to say that this is the most old Europe group. Some of this similarity does come from ANE-WHG similarities though, so the Baltic may be pipped out in total WHG ancestry by Icelanders and Swedes.

The ratio of WHG:ANE seems highest in Sardinia and Southwest Europe. This may be because of WHG mixture in early farmers or because early farmers in the Near East were already WHG like.

Now, isolated Southwest Europeans are the most distant Europeans on a world scale from African and East Asian populations (only slightly compared to isolated Northeast Europeans and Northwest Europeans of comparable isolation don't really exist as natural populations). This has some difficulty for the paper's concept where population distances in Europe from non-Europeans can be expressed by mixtures between WHG and ANE and a Basal Eurasian, where Basal Eurasian would be central on a world PCA (i.e. basal means = central, before divergence pushed other populations away from one another) and WHG and ANE are more distant.

Moreover, the greater distinction of Early European Farmers from all world populations seems to have been present from their origin, see Figure S10.1 -

http://i.imgur.com/cvYvu6H.png

It'll be interesting to see what mechanisms this is reconciled by (the theoretical centrality of basal eurasian vs the not actual centrality of more basal eurasian populations). These are large scale trends so don't seem like they could just reduce to high local drift in Southwest Europe, but must be underpinned by a large scale phenomenon.

Eastern Europe is the really old Europe, but not really the really European Europe, today. (and the Old Europeans don't even seem to have been the most phenotypically European, based on current analysis of their genotypes, weird as this may seem to us today).
Fig S10.5 is an interesting but unusual looking PCA. However, it is not clear that it really is the most useful reflection of intra-European present day genetic diversity compared to one of the more conventional "geographic" PCA of Europe, such as from Wang et al 2012. -

http://www.molecularecologist.com/wp-content/uploads/2012/09/journal.pgen_.1002886.g002.png.

As the authors say

"It is clear from the comparison of Table S10.2 that our study has a qualitatively very different distribution of samples compared to Novembre et al. (2008). In particular, in the combination of Central Europe (C), Western (W) and Northwestern (NW) Europe, our study has 11.2% of samples compared with 51.3% in Novembre et al. (2008).

Conversely, in Eastern (E) and Northeastern Europe(NE) our study has 23.3% of samples compared with 4.5% in Novembre et al. (2008).

Our results highlight the fact that the correspondence between the map of Europe and the first two principal components depends on the composition of the included samples. Unfortunately, the lack of coverage of C and opposite balance of W/NW and E/NE in the two studies does not allow us to “mimic” the distribution of Novembre et al. (2008) and to test if the genetic-geographic correspondence might emerge in our dataset. An interesting avenue for future research is to study the conditions under which sample selection may lead to a correspondence between PCA and geography.

... Importantly, the cline of ancestry proportions that we detect in this study does not depend on the relative sampling representation of different regions (as does PCA) as is evident when individual European populations are either fit to a formal model (SI14) or to an algebraic procedure (SI17). "


Working out the "right" amount of samples from each subregion to use is difficult - the optimal PCA should reproduce a FST distance matrix the closest when its dimensions are summed and deviate least when "walking down" its PCA.

Davidski said...

Matt,

Insightful comments as always.

Let me just say though, that there's no need to work out the "right" amount of samples from each subregion to get a high correlation with geography for European and West Eurasian PCA. The best thing to do is to pack the PCA with as many samples from as many subregions as possible. If there's no correlation with geography after that, then the dataset is too limited.

My latest PCA maps of Europe and West Eurasia look like geographic maps, and I don't pick the samples, but basically throw in everyone except close relatives. I'll post a PCA of Europe when I get more computer time.

Shaikorth said...

"Now, isolated Southwest Europeans are the most distant Europeans on a world scale from African and East Asian populations"

While this is true for Sardinians regarding East Eurasians and Amerindians, they are in fact closer to Africans than most Europeans. This is visible in IBS sharing and even in the Africa - Eurasia dimension of some PCA's.

Levels of ANE are fairly standard in Northern Europe. Norway and Lithuania have the same estimate, Scots have more ANE than Ukrainians and Belarusians, and Hungarians beat most Northeast and Northwest Europeans on average values. So I think it's really doubtful that ANE increases WHG similarity in Eastern Europe more than it does in the Northwest.

DarthVadent2 said...

I have a hypothesis regarding Basal Eurasian, I think one of the earliest populations that carried this component in high frequencies were the Natufians of the Levant. Brace and other anthropologists described them morphologically as having Sub-Saharan African affinities, and they even clustered with African populations, but they didn't conclude that there was any genetic continuity between modern Middle Easterners and the Natufians, but I'm starting to think that they may have been wrong. Both the EEF and Basal Eurasian components exhibit SSA affinities, and Basal Eurasian itself may have been a Northeast African component. So I'm thinking maybe the Natufians, being a pre-agricultural harvesting society, were one of the first carriers of this Basal Eurasian component.

This would also explain the relative African-shift of many Middle Easterners and even some Southern European populations, compared to the more hunter-gatherer influenced WHG+ANE admixed populations of Europe. Even Caucasians, with their high ANE are much closer to Africans than most European populations. Namely because they're mostly descended from Middle Easterners.

Here's what I think, I think there was probably an Ancestral West Eurasian population that was collaterally related to WHG, ANE and the ancestral Non-Basal Eurasian ancestor of EEF. Europeans are basically a mixture of WHG+ANE, while Middle Easterners are a mixture of a population may have been distantly related to WHG and ANE and Basal Eurasian.

Anders Pålsen said...

Davidski,

No I do not impute the markers for the ancient individuals, only for the modern individuals. All ancient genome markers in my analaysis are observed ones.

Anders Pålsen said...

I see by the way in the material that it seem to be linked model used in Chromopainter-Finestructure.

You may get different results using linked and unlinked model. I found for example that the La Braña 1 appears to be closer in geneology to the Basque and Sardinians as the linked model found more shared haplotypes with them in terms of recombination and mutational distance, but in the unlinked model appeared similar to modern Saamis and Finns as similarity in allele frequences. it make sense that the La Braña 1 find its closest haplotypes among the modern locals in the Iberian area.

I see this in modern population relationship as well. In the linked model Vologda Russians and Mordovians cluster with Eastern European populations but in the unlinked model cluster with Saamis and Finns. The more recent admixture with Eastern Europeans appears to weight in.

Also Saamis and Finns cluster different. In the linked model Saamis and Finns cluster, but in the unlinked model Saamis cluster with Volgda Russians and Mordovians. This probably also due to more recent admixture between Saamis and Finns.

Shaikorth said...

If La Braña clusters with Basques in chromopainter/fineSTRUCTURE linked mode, shouldn't Loschbour, a very similar hunter-gatherer type, have done the same if the Lazardis run was also linked?

Davidski said...

Not necessarily, as Loschbour comes from Luxembourg, which is basically the North European Plain. Also, check out the I2 that he has; its closest match is in Kargopol, Northwestern Russia.

In other words, the regional WHG groups that Loschbour and La Brana-1 belonged to might have contributed segments to very different populations.

Davidski said...

Colin,

Populations from Eastern Europe always show higher indigenous European hunter-gatherer ancestry than populations from Western Europe from more or less the same latitude.

Therefore, the statement that the really old Europe is mostly in Eastern Europe (as opposed to Western Europe) is true.

Moreover, please note the following passage from the new version of the preprint that is also relevant to your earlier reservations about the "Hunter" ancestral population in this paper being a genetic one.

"Thus, Europeans appear to be a mixture of one element related to Early European Farmers and one related to both MA1 and Loschbour, consistent with our model (Fig. 2A) that derives them from a “Hunter” population that had both Loschbour- and MA1-related ancestry (SI14)." Supp info, page 76.

Now, are you positing that most of this "Hunter" ancestry in Eastern Europe is of post-Neolithic Central Asian origin? That's unlikely to be true because the ChromoPainter/fineSTRUCTURE results referred to above actually show genealogical links via shared segments, rather than just broad genetic affinities. Thus, Eastern Europeans like Ukrainians and Belarusians are indeed comparatively closely related to old Europeans like Loschbour, rather than just to similar populations from somewhere else.

Also, if you're wandering about Poles and Germans I do have an entry about them that looks at this issue at my other blog:

http://polishgenes.blogspot.com.au/2014/01/poles-more-indigenous-to-europe-than.html

Thank you, come again. :)

Colin Welling said...

" Populations from Eastern Europe always show higher indigenous European hunter-gatherer ancestry than populations from Western Europe from more or less the same latitude."

So you're factoring out latitude while making a geographic statement... I rest my case.

If you want to say WHG ancestry peaks in Northeast Europe (which may or may not be true as Matt said), fine. But the next logical addition (especially when you say most) to Northeast Europe is Northwest Europe, not Eastern Europe with Ukrainians, Czechs, and Bulgarians. That is to say, the natural statement is Northern Europe.

I was just pointing out the more correct way of looking at things and probably a bit of bias.

"Thank you, come again. :)"

oh I did, I did...

barakobama said...

Colin forget about the whole east or north Europe thing. The last thing i will say is that WHG is higher in for example Ukraine and Poland than in north-west Europe and around the same or a little higher than in Sweden-Norway, even though they are more southern than Ireland and Sweden-Norway. There is no law that says the more north the more WHG. In the Neolithic farmers in Sweden were hardly any differnt than Stuttgart and Otzi, it has not been discovered yet why WHG is so much higher in the north. I tend towards saying Indo Europeans and Uralics are responsible, but mainly native Mesolithic ancestry+new Mesolithic east European ancestry in north-west Europe does make some sense.

Colin Welling said...

Now, are you positing that most of this "Hunter" ancestry in Eastern Europe is of post-Neolithic Central Asian origin?"

No, I definitely did not say that. I said that ANE probably came to Europe after the ice age, from Central Asia.

Does page 76 really go against that?

I think you misinterpreted my post. I realize the WHG labeled component in Ukrainians is indeed valid and relatively high.

The uncertainty I have is whether or not meso/ paleo Europeans were only WHG like.

The last thing i will say is that WHG is higher in for example Ukraine and Poland than in north-west Europe and around the same or a little higher than in Sweden-Norway, even though they are more southern than Ireland and Sweden-Norway.

This statement contradicts the paper... Scots, Norwegians, and Icelandic all have more WHG than Ukraine.

Colin forget about the whole east or north Europe thing.

Agreed, we aren't learning much this way.

Colin Welling said...

WOW, look at the ANE peak in Northern Spanish, 16.3.

I am pretty convinced that the people who brought ANE to Western Europe also carried and probably introduced r1b to that region. Of course I'm assuming ANE came to Western Europe in the bronze age.

Ben Overboord said...

@barackobama

Motala12 seems to also have had blue eyes and dark hair, and but had rs1426654 A/A like Stuttgart and Otzi. So not all Mesolithic Europeans had G/G alleles, and A/A in Mesolithic Europeans and middle easterns(Stuttgart and modern) is probably just from early west Eurasians. Like i have said maybe a million times my opinion is that the skin color of these ancient individuals is unknown.

The odd thing is that the higher you get in latitudes the lighter these samples seem to get. Just like nowadays, only the lightness is just higher in latitude.

barakobama said...

"Moreover, please note the following passage from the new version of the preprint that is also relevant to your earlier reservations about the "Hunter" ancestral population in this paper being a genetic one.
"

I could not find anywhere in the preprint where they make it very clear MA1 is more related to European hunter gatherers than to non WHG and ANE west Eurasian ancestry in Stuttgart and modern near easterns.

In Supplementary Information 14, they "investigat(ed)" "some simple relationships" of the ancient samples(La brana-1, Loschbour, Motala12, MA1, Stuttgart) with each other "using f4-statistics".

Loschbour and La Brana-1 are closer to Stuttgart than to MA1, which i think is because Stuttgart had around 20-30%(my guess) WHG that was probably closely related to western European WHG. Motala12 though is closer to MA1 than to Stuttgart, which could be because of ANE ancestry but he is closer to European hunters than to MA1 and he is estimated to only have around 19% so i think it's partly because WHG is very close to ANE.

Also look at this quote from pg.122

"An interesting detail of Fig. S14.20 is that the Near_East is modeled as a mixture of basal_Eurasian and a node Y which forms a clade with Loschbour. Present-day Near Eastern populations are indeed more closely related to European hunter-gatherers than to MA1 despite having some MA1-related ancestry. This can be easily seen in Extended Data Fig. 6C where the range of the statistic f4(Test, Chimp; MA1, Loschbour) is negative for all West Eurasian populations including all Near Eastern ones, suggesting that they share more drift with Loschbour than with MA1 (the statistic is Z<-4 for all West Eurasian populations except the Lezgin where it is Z=-3.6)."


The PCA's seem to say exactly what yours do and that MA1 is closely related to Mesolithic Europeans. I think it may be more complicated though than them being brothers. Possibly the non ANE west Eurasian form native to the middle east is more closely related to Mesolithic Europeans than MA-1 is.

barakobama said...

They seem to suggest that Stuttgart was basal Eurasian+WHG, then how would they explain non ANE ancestry in the middle east today that is closely related to WHG?

pg.137"When we allow three migrations (Figure S16.4), we observe an extra Basal Eurasian migration edge
into LaBrana (17%) as well as MA1 admixture into Karitiana (39%) and Basal Eurasian admixture
into Stuttgart (52%) with the remainder (48%) from the (Loschbour, LaBrana) common ancestor.
"

barakobama said...

Ben, in my opinion pigmentation difference between modern Europeans is because of differnt ancestors not latitude. Most of the ancestors of modern Scandnavians, Irish, and Finnish arrived in where they live now during the bronze age.

There was almost no difference in ancestry between Motala12, Loschbour, and La Brana-1 besides that Motala12 had some ANE and La brana-1 had some EEF. Plus Motala12's ancestors had been in Scandinavia for 2,000-3,000 years at the most, but there is a low chance he was purely from the first people to settle there.

I don't know what the skin color was of Motala12, Loschbour, and La Brana-1 it could have been anything from deep brown to snow white. It is a pretty amazing find though that they all had light eyes and dark hair(probably black) since today light hair-eyes are connected. It really complicates things when you try to find the origin of that stuff.

Shaikorth said...

"They seem to suggest that Stuttgart was basal Eurasian+WHG, then how would they explain non ANE ancestry in the middle east today that is closely related to WHG?"

Regarding Middle Easterners and their relation to Loschbour, Saudis and Bedouins aren't that close and presumably a pure "Basal Eurasian" would be even less so. Stuttgart is much closer to Loschbour than modern Middle Easterners because it basically is half WHG.

This is a rough estimate, but assuming the ratio of Basal Eurasian/WHG in Stuttgart is roughly 50/50, a pure "Basal Eurasian" would be twice as Sub-Saharan shifted in comparison to Loschbour as Stuttgart is, and have a position on dimension 1 of the study's global PCA (SSA-nonSSA) that is equivalent to that of Bedouins. Thus the Bedouins seem to be as good a proxy to Basal Eurasians as we can get among modern populations. Basal Eurasians actually might be nothing more than some kind of African-admixed Middle Eastern population, just with with no ANE so they'd cluster even further from amerindians than Bedouins.

barakobama said...

Matt, west and east Eurasian are more related to each other than basal Eurasian, right? So why would basal Eurasian be in a neutral center position in PCA's? I would expect them to hide in a corner away from all other Eurasians.

It seems that is what Basal Eurasian ancestry does in some of Davidski's PCA's.

http://eurogenes.blogspot.com/2014/02/pca-of-five-ancient-genomes.html

MA-1 and La Brana-1 seem to be closer to Siberians than modern west Eurasians, when really it may be basal Eurasian ancestry which is making modern west Eurasians more separate from ancient west Eurasians and modern Siberians. In this new preprint they say la brana-1 had some basal Eurasian ancestry which is probably why he is pulled more to the left than MA-1 is.

There are many good candidates of basal Eurasian mtDNA and Y DNA in Neolithic Europeans and modern west Eurasians, which is exciting.

"Eastern Europe is the really old Europe, but not really the really European Europe, today. (and the Old Europeans don't even seem to have been the most phenotypically European, based on current analysis of their genotypes, weird as this may seem to us today)."

What do you mean by not really European today? European in my opinion is people who are admixed in a similar way to modern Europeans, so east Europeans totally qualify.

My guess is that Mesolithic Europeans had distinctly north European facial and body build traitsX2. If we went back in time in would probably be hard to see their facial and body build differences. All we know about pigmentation is that they had mainly dark hair, light eyes, and according to current knowledge dark skin.

I think the combination a robust wide face, stocky body build, pitch black head hair and beard, dirty dark skin, shocking blue eyes, animal skins as clothing, and a spear would look very bad ass in person. I don't care if they looked foreign to us modern Europeans, i am proud to have ancestor who looked like that.

https://www.google.com/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&cad=rja&uact=8&docid=c9hKwhi4EicyhM&tbnid=UjrAkq-wKTMVKM:&ved=0CAUQjRw&url=http%3A%2F%2Fwww.focus.it%2Fscienza%2Focchi-azzurri-pelle-e-capelli-scuri-come-eravamo-7-mila-anni-fa_C12.aspx&ei=Dx8_U--aNcOlsASGz4CQAw&bvm=bv.64125504,d.aWc&psig=AFQjCNFkCFZGA0GiLrFT4IFODMZxBleA_Q&ust=1396732002233113

When i leave high school and am allowed to grow facial hair i am going try to look like a ginger La brana-1.

barakobama said...

Shai, Laz seems to make it pretty clear that basal Eurasian in Stuttgart split before the common ancestor of west and west Eurasians. If it was really just a middle eastern-African mix they would be able to tell. Plus there hasn't been one mtDNA L(M and N-) sample found in Neolithic Europe expect for Iberia. There are some L2a1's from Neolithic Syria though. I don't see evidence of African ancestry via Stuttgart like farmers in modern Europeans.

I think Stuttgart may have had basal Eurasian ancestry from the near east but most of her near eastern ancestry was probably closely related to WHG and ANE, then she also had something like 20-30% WHG.

Shaikorth said...

"Laz seems to make it pretty clear that basal Eurasian in Stuttgart split before the common ancestor of west and west Eurasians. If it was really just a middle eastern-African mix they would be able to tell."

They haven't actually even decided if "Basal Eurasian" existed if you read the supplementary information. Basically it's a theoretical construct, but importantly it behaves identically to Middle Eastern with some sort of African (in a way similar to Bedouins) - causes African shifts in plots, decreases similarity to Eurasians furthest from Africans and so on. In the Lazaridis admixture test at k9-k17 Stuttgart looks 40-45% "Loschbour" and the rest is a component that peaks in Bedouins and contains SSA alleles (you can notice this by looking at the difference in Bedouins' SSA component at K8 and K9).

I expect that the African affinities in "Basal Eurasian" will be explored more once the genome bloggers get their hands on Stuttgart.

barakobama said...

I just made a simple map of Mesolithic DNA given in Jean Manco's site. I think it's useful.

https://mapsengine.google.com/map/edit?mid=zpAcd_2YNln8.kYMnaPX2WqH0

I did not include samples that had uncertain haplogroups(e.g. Portugal). There were some were i dis agreed with the reported haplogrouop, for example one of the Pitted ware samples was reported as U4d but it had all of the defining HVR1 mutations of K1a, and none of U4(expect for deepsubclades but it had defining mutations of many deep U). subclades). I put what it was reported as anyways, though.

I listed the likely hair and eye color of La Brana-1, Loschbour, and Motala12 not every little SNP associated with pigmentation. I did not list probable skin color because there are a lot of possibilities, and there are a bunch of SNP's associated with skin color and it would take up to much space.

Grey said...

I think a lot of the argument on this stems mainly from the labels chosen.

EEF is 1/2 WHG and 1/2 "Basal Eurasian."

Basal Eurasian isn't basal. It's Afro-Asiatic.

If EEF is 1/2 WHG and 1/2 Afro-Asiatic and Afro-Asiatic came from the south then WHG is more likely *southern* than western.

If WHG is actually SHG (i.e. the LGM's southern forest zone from Iberia to Anatolia) then ANE is more likely NHG (i.e. the mammoth steppe from France to Siberia).

The obvious LGM demarcation would be

So LGM

ANE = NHG = mammoth steppe

WHG = SHG = southern forest zone

Basal Eurasian = Afro-Asiatic (Nile / Fertile Crescent)

Post LGM

1. SHG + NHG re-expand north.

2. Afro-Asiatics mix with SHG somewhere (Thessaly? Anatolia? Levant?) to create EEF.

3. EEF displace the ANE/WHG of western Europe and push them to the western and northern periphery.

4. EEF/LBK collapse leads to inward folding of the western, northern and eastern peripheries to refill the center.

#

Hence north and northeast Europe having the highest surviving *unmixed* SHG (aka WHG).

This is separate from the half of EEF which is also SHG (aka WHG) so strictly speaking to calculate the total SHG (aka WHG) in a population you'd add half their EEF percentage to their unmixed SHG percentage.

Davidski said...

It's not certain how much WHG-like ancestry EEF had. But based on this quote, I don't think they were half European.

"The amount of Near Eastern admixture estimated for Stuttgart can be seen in Table S13.2 and ranges between 55-100% with estimates increasing as the amount of estimated African admixture in BedouinB increases. Estimates using Dinka or Ju_hoan_North as an African outgroup are similar. There are reasons to doubt both the lower estimates (near 55%), since ALDER provides only a lower bound on African ancestry, but also the higher estimates (near 100%) since there is direct evidence that Stuttgart has European hunter-gatherer ancestry (Fig. 1B and Table S13.1). Determining the precise levels of Near Eastern admixture in Stuttgart must await further ancient DNA studies from both Europe and the Near East, but we can at least reasonably suggest that most of the sample’s ancestry was Near Eastern, consistent with the mtDNA evidence for the Linearbandkeramik, which demonstrated a strong Near Eastern influence."

Shaikorth said...

Using She, Ju_hoan_North and 7.3 % estimated African the amount of Near Eastern in Stuttgart in fact exceeds 100%. We should definitely discount the 7.3% estimates.

The 4.2% and 5.1% estimates are also fully consistent in ranking the relation of East Eurasians to Near Eastern component both when Dinka and Ju_hoan_North are used.

Ranking from most distant to least distant:

Eskimo
Ulchi
Chukchi
She
Ami
Onge
Han
Kharia

Among the non-Siberian/Eskimo populations, She seem to be less Near Eastern than the Austronesian-speaking Taiwanese aborigines, Onge and especially Han for whom some West Eurasian admixture seems clear.

James said...

EEF and Basal Eurasian don't exhibit SSA affinities. Stuttgart is pure blue until K=10, unlike the Bedouins and other MENAs, who have a lot of orange and red SSA admixture that's no doubt recent. Because of that, none of them are good proxies for ancient populations.

Davidski said...

James,

What makes you think that the ADMIXTURE results can actually tell us anything useful in this context?

Lots of populations come out pure whatever color in ADMIXTURE runs, and yet we know for a fact that they're mixed.

Shaikorth said...

In the Lazaridis admixture test issues appear as early as K2, because African component forms around Khoisan they appear unmixed and all Pygmy groups appear to carry significant Eurasian.

To further demonstrate limitations of formal admixture tests, the K2 division can even be between East Eurasian and non-East Eurasian, with Yemenite Jews appearing less East Eurasian than Mbuti or Yoruba - obviously not really the case.
http://www.nature.com/nature/journal/v466/n7303/extref/nature09103-s2.pdf

Davidski, in that PCA a good sequence of Motala would likely be even better than Loschbour or La Braña to account for ANE in Europe.

James said...

ADMIXTURE has no problem showing the SSA in MENAs and the Asiatic in MA1, Motala and Loschbour. Stuttgart has no such admixture.

K=2 is never the best run to use. But by K=4 everything is set straight. Even better at 5 and 6.

Shaikorth said...

I thought about the Lazaridis model a bit. For Europeans specifically the PCA equivalent should perhaps have a line from Stuttgart to the point between Loschbour and MA-1 (when they're on the same plot using maximum overlapping SNP's?). The location of the point corresponds to the ANE/WHG ratio of the fitting population for which it was highest.

The ENA end of the related dimension should be occupied by Ami (maybe She?) or Onge.

Shaikorth said...

K4 is just as flawed as K2, most poignantly seen in the relationship of Karitiana and MA-1.

The amount of Bedouin component containing Sub-Saharan alleles in Stuttgart is somewhat informative of the African shift - the same Bedouin component also appears in Sardinians in slightly smaller amount because they have more WHG than Stuttgart. PCA's are even more informative (SSA shift compared to, for example, Basques and all Northern Europeans is also visible in Sardinians to a lesser degree than in Stuttgart), and I have no doubt IBS sharing comparisons will tell the same story. Basal Eurasian theory has nothing that can't be explained with a SSA-shifted Middle Eastern component.

Davidski said...

James,

Loschbour, Motala and especially MA-1 are outside the range of modern genetic variation, so they'll often show exotic signals as the algorithm tries to make sense of their genetic structure.

On the other hand, Stuttgart is a pretty good match for modern Sardinians. You can see that in the ADMIXTURE analysis because the pink cluster from K=17 peaks among Stuttgart and the Sardinian samples. This masks their admixtures.

In fact, Stuttgart and the Sardinians share the pink cluster with the Bedouins from K=10 to K=16, and we know that Bedouins have considerable Sub-Saharan admixture, only some of which shows up in ADMIXTURE analyses.

So it's not as simple as you're trying to make it out. There's a lot of East African-related ancestry all over the Near East and well into Europe, but most of it is cryptic.

Shaikorth said...

There is a revised version of their admixture run, where the Bedouin component persists in Stuttgart and Sardinians until K=19.

http://biorxiv.org/content/biorxiv/suppl/2014/04/02/001552.DC2/001552-2.pdf

The highest K values seem to be getting less informative as all hunter-gatherers look progressively more like Loschbour, eventually becoming identical.

anthrospain said...

It's obvious that this admixture of SSA in Bedouins and Near-Easters is more recent than the Farmer expansion, since farmers don't show as much SSA, if any at all.

Davidski said...

Yes, I think the more recent SSA admix among the Bedouin is likely to show up, while the more ancient stuff often won't. This is probably due to genetic drift since the ancient admixture events.

Colin Welling said...

Basal Eurasian theory has nothing that can't be explained with a SSA-shifted Middle Eastern component.

The authors seemed to be open to either. Tell me if I'm wrong, but aren't there two types of Basal Eurasian, as ironic ad that is? In that case basal should be "real", right?

DarthVadent2 said...

"EEF and Basal Eurasian don't exhibit SSA affinities. Stuttgart is pure blue until K=10, unlike the Bedouins and other MENAs, who have a lot of orange and red SSA admixture that's no doubt recent. Because of that, none of them are good proxies for ancient populations."

You're making the mistake of assuming that these ADMIXTURE clusters illustrate "pure" proxies of ancient populations. The fact of the matter is, these are ancestral components are composed of composites of alleles, some of those alleles are subsumed at higher Ks. For example, I'll use this Pagani et al K2 to K10 spreadsheet.

https://docs.google.com/spreadsheet/lv?key=0AqWOT2m6btAGdEpjTExTRG1NU1NKRnJfd3hOeWkwdkE&type=view&gid=2&f=true&sortcolid=-1&sortasc=true&page=2&rowsperpage=250

Notice how Middle Eastern populations register African admixture at K=4, which decreases or in the case of Iraqi Jews, disappears at K=5 and K=6 and is moved into the Red Sea/Arabian.

That African admixture didn't vanish, it's being masked by the Red Sea/Arabian component.

Matt said...

Shaikorth - While this is true for Sardinians regarding East Eurasians and Amerindians, they are in fact closer to Africans than most Europeans. This is visible in IBS sharing and even in the Africa - Eurasia dimension of some PCA's.

Oh yeah, totally, although from what I remember of FST numbers compared to Northeast European isolates, the Sardinians and Basques are slightly further from the Oceanians and their kindred ENA clusters (East Eurasian and Onge), more than they are closer to any of the Africans (particularly West Africans who appear to be the least likely to have had any sort of Near Eastern admixture).

Barak - west and east Eurasian are more related to each other than basal Eurasian, right? So why would basal Eurasian be in a neutral center position in PCA's? I would expect them to hide in a corner away from all other Eurasians.

The East Eurasian and WHG/ANE are only closer (more related) to one another by the statistic used in the paper which adjusts for the amount of drift by each from Africans (the outgroup).

If you don't adjust for the drift, as PCA naturally wouldn't do, then a Basal Eurasian as included in their models should be central simply by having less drift.

Imagine you had three boats which went out to sea together. One of them stops while the other two move off together for a little bit, then these two go off in completely opposite directions.

Eventually, once they have been driving long enough the boat which stopped will be closer to each of the other two than they are to one another, even though it broke away first.

If the drift were close to equal in the Basal Eurasian branch, then it would be as you say (basal Eurasian populations off in the corner). But that doesn't fit their models don't have drift like that....

Shaikorth said...

"Oh yeah, totally, although from what I remember of FST numbers compared to Northeast European isolates, the Sardinians and Basques are slightly further from the Oceanians and their kindred ENA clusters (East Eurasian and Onge), more than they are closer to any of the Africans (particularly West Africans who appear to be the least likely to have had any sort of Near Eastern admixture"

Fst distances are generally distorted in isolates. There was one study about Italian isolates where this was especially well demonstrated, though I can't find it atm.

The Sardinian SSA-shift is more visible in IBS sharing and their placing in a global PCA's Mbuti/San/Yoruba vs others dimension (tends to be dimension 1). Basques are more in line with Central Europeans in that regard, which fits their much greater hunter-gatherer ancestry.

About Time said...

@Grey, interesting thoughts. Didn't La Brana register a little but if SSA in admixture? Maybe WHG-SHG were trampsing around in the Sahara or Mediterranean in general.

Also goes to the fish diet of Paleo-Britons (if I'm remembering this correctly). Maritime cultures, fishermen.

There were big lakes in N Africa even in Iron Age - Greeks (Herodotus?) said one was Lake Tritonis and Athena had links to there. Also Odysseus/Ulysses and Aeneas. Not to say some literary figure was real, but shows the routes were at least in the cultural lexicon.

Makes me wonder if some of the SHG "went native" and ended up speaking a version of Afro-Asiatic at times.

Davidski said...

I've changed the links above to the v2 version of this preprint at arXiv, because over there everything comes as a single PDF, and the links actually work.

http://arxiv.org/abs/1312.6639v2

About Time,

Nope, the complete La Brana genome doesn't show any Sub-Saharan admixture.

Davidski said...

By the way, has anyone noticed that the new version includes the complete La Brana-1 genome as opposed to just the partial sequence?

About Time said...

@Davidski, hmm good to know. Then Basal is still possibly not a branch of SHG that mixed with SSA, but rather a branch that stayed near origin when others intensified adaptations for mobility and hunting large game (with all necessary cognitive + cultural changes that entailed). That's my "Basal conscientious objector" model to explain incipient sedentism in absence of full agriculture.

Anders Pålsen said...

Davidski wrote "Nope, the complete La Brana genome doesn't show any Sub-Saharan admixture."

This was seen in some early analysis by genome bloggers (including myself) where there had not been done proper contamination filtering.

James said...

You guys are just ignoring the evidence and making up your own. Many recent studies have found Eastern mixture in hunter gatherers, but not SSA in farmers. This one is the same, and the ADMIXTURE results are consistent with the other results.

K=3 reveals a West Eurasian ancestry component. The ancient samples appear to be mostly West Eurasian in their ancestry, although the hunter gatherers are also inferred to have greater or lesser extents of an eastern non-African (ENA) component lacking in Stuttgart. This is consistent with the positive f4(ENA, Chimp; Hunter Gatherer, Stuttgart) statistic reported in SI12, which we interpret there as showing that ENA populations are closer to European Hunter-Gatherers than to Stuttgart.

They even say that to use Bedouins as a proxy for the NE farmers that contributed to Stuttgart, they had to subtract the SSA admixture.

_Admixture proportions for Stuttgart in the absence of a Near Eastern ancient genome_
We used Loschbour and BedouinB as surrogates for “Unknown hunter-gatherer” and Near Eastern (NE) farmer populations that contributed to Stuttgart (SI13). Ancient Near Eastern ancestry in Stuttgart is estimated by the f4-ratio f4(Outgroup, X; Loschbour, Stuttgart) / f4(Outgroup, X; Loschbour, NE). A complication is that BedouinB is a mixture of NE and African ancestry. We therefore subtracted the effects of African ancestry using estimates of the BedouinB African admixture proportion from ADMIXTURE (SI9) or ALDER.

Davidski said...

James,

Read this carefully and try to understand it. From page 103 of the supplement info:

"The model of Fig. S14.6 proposes that MA1 is unadmixed, but it was argued that MA1 may have basal East Asian (basal eastern non-African in our terminology) admixture based on the evidence that MA1 shares more alleles than Sardinians with either Oceanians or East Asians. This was a reasonable suggestion because of the sample’s provenance, but statistics of the form f4(ENA, Chimp; Loschbour, MA1) appear symmetric for any eastern non African (ENA) population from the set (Ami, Atayal, Han, Naxi, She, Papuan, Bougainville, Onge) with |Z|<0.3. If MA1 had more basal East Asian admixture than Loschbour, these statistics should be negative. It is possible that both Loschbour and MA1 experienced eastern non-African gene flow, but it is not parsimonious (under the model of eastern non-African gene flow) that two samples from widely separated geographical locations (Western Europe and Siberia) and times (8-24 thousand years ago) would experience such gene flow in amounts that precisely cancel themselves out to produce perfectly symmetric statistics of the given form.

Our model provides a simpler alternative explanation for the asymmetry between MA1/Sardinians with respect to ENA: not through admixture into MA1 but instead through basal Eurasian admixture into Neolithic farmers. This scenario accounts for both the fact that ENA share more alleles with MA1 than with Stuttgart (because Stuttgart has basal Eurasian admixture), and for the fact that Loschbour and MA1 are symmetrically related to ENA (because they both lack Neolithic Near Eastern ancestry)."

Shaikorth said...

"You guys are just ignoring the evidence and making up your own. Many recent studies have found Eastern mixture in hunter gatherers, but not SSA in farmers. This one is the same, and the ADMIXTURE results are consistent with the other results."

No, the Sub-Saharan is very visible in PCA's and even the admixture run at certain levels (look what alleles the Bedouin component absorbs when it forms).

The flaws of admixture runs are well documented, as is their resulting in effects like showing mixed samples (Karitiana, or Stuttgart) as "pure" and something like Mal'ta which is actually the source of Karitiana's admixture as mixed.

"They even say that to use Bedouins as a proxy for the NE farmers that contributed to Stuttgart, they had to subtract the SSA admixture."

They subtracted a part of it. Bedouins have ancient and recent SSA, in total they have more than just 4 or 5 percent, and the seven percent reduction was already too much as it showed the WHG-admixed Stuttgart as almost (or over 100%) Middle Eastern. They note this too.

"The amount of Near Eastern admixture estimated for Stuttgart can be seen in Table S13.2 and ranges
between 55-100% with estimates increasing as the amount of estimated African admixture [the admixture they reduced] in
BedouinB increases. Estimates using Dinka or Ju_hoan_North as an African outgroup are similar.
There are reasons to doubt both the lower estimates (near 55%), since ALDER provides only a lower
bound on African ancestry, but also the higher estimates (near 100%) since there is direct evidence
that Stuttgart has European hunter-gatherer ancestry (Fig. 1B and Table S13.1)."

In any case, Sardinians' SSA is detectable using PCA's or IBS, or Chromopainter/FINESTRUCTURE and they have less of the SSA-shifted Middle Eastern ancestry than Stuttgart. I have full confidence that Stuttgart genome will show an African shift using the same methods, and more so than Sardinians - who are among the most SSA-shifted European populations. Theorized "Basal Eurasian" is not functionally separate from SSA-shifted Middle Eastern components formed by modern populations like Bedouins.

About Time said...

Maybe people are thinking Basal=Natufian and assuming some SSA admixture because the morphological studies of Natufians showed SSA features.

But we don't really know how ancient SSA populations really are. They are not well attested in the fossil record because damp conditions don't favor preservation of bones. You'd have to dig around Lake Chad maybe to find relevant skeletons contemporary with EMH like Ust-Ishim.

Maybe morphological similarity between Natufians and SSA is because SSA were actually Basal+(other unknown pops).

Thus Basal was really "Sui generis" that passed on genes for anatomical/behavioral modernity of a less "hunter band" type and more "forager-horticulturalist" type. Just a guess.

Key here is that Africa is the only place megafauna were not hunted to extinction - because hunter adapted cultures didn't evolve there and only lived at the fringes there. Africans that are less scared of lions etc (like Maasai) all have Mideast (Neanderthalized?) ancestry to some extent.

Shaikorth said...

"Maybe people are thinking Basal=Natufian and assuming some SSA admixture because the morphological studies of Natufians showed SSA features."

Maybe. I'm not really assuming anything because of physical anthropology. Basal Eurasian causes effects on PCAs and shared drift that are identical to effects caused by SSA-shifted Middle-Eastern ancestry, and is represented by a SSA-mixed Bedouin component at certain K values on ADMIXTURE.

We don't have a FINESTRUCTURE or IBS comparison to confirm Stuttgart's SSA affinity in comparison to modern Europeans yet, but as soon as the Stuttgart genome is made public, that will no doubt change.

Matt said...

I had a quick attempt at seeing if the distance matrix for one of their models could be reproduced by modelling Stuttgart as a mix of their African (R) and "West Eurasian" components without any Basal Eurasian.

If you model Stuttgart as a mix of around 95% West Eurasian plus some drift and 5% African, then the distances from ENA and Africans are about right, but Stuttgart is far too close to WHG.

If you model Stuttgart as a mix of around 80% West Eurasian plus some drift and 20% African, then you can get the right distance from African but the distance from all Eurasians is too high (also true if the drift is in the African branch).

Trying to model Stuttgart with combinations of the higher level nodes and Africans has similar fail results.

In order to reproduce the distances their model results in (assuming they are correct), for the terminal nodes which we actually have samples for, it seems you need a population which is quite separated from Africans and Eurasians, is more separated from Africans than Eurasians and which has an equal separation to all Eurasians to make a contribution (plus drift and the WHG/West Eurasian part).

This appears to be only really satisfied by a "Basal Eurasian".

I'm pretty sure this is why they haven't considered African mixing models in place of Basal Eurasian, it would be useful if they had an explicit note about why these models fail. Looking through the new PDF it seems most other topics that were discussed on blogs seem to have been acknowledged and made more explicit.

(On a related note, looking at the models has also made it clear to me why the authors in their models in S14 have preferred to put extra drift into Stuttgart's West Eurasian branch rather than its Basal Eurasian branch, which wasn't clear to me before. As the Basal Eurasian progenitor contributes less to Stuttgart, it would need higher drift to recreate the same distances, which is less parsimonious, so dispreferred... unless and until we find "Basal Eurasian" type samples with this state....)

barakobama said...

Matt,

Thanks for the analogy it helps alot. Why would basal Eurasian not have it's own drift? I could not find anywhere in the preprint that says basal Eurasians had no drift. If they do say so in the preprint, please give me a quote. I don't understand pretty much all of what they did so i probably just missed it.

Shaikorth said...

The "basal eurasian-as-Middle Eastern" would have had its drift after mixture. They can model Stuttgart's admix as Bedouin with some, but not all, of its African removed. Basal Eurasian, like Middle Eastern, doesn't have an equal distance to all Eurasians either, but the distance increases when moving to north and east - just like African.

This is why Stuttgart, although it's projected, exhibits more SSA shift in their global PCA than Sardinians who have the same components as Stuttgart (Middle East and WHG) but in slightly different amounts - but enough to make them one of the more SSA-shifted Europeans. I think they missed an opportunity to explore the relationship of Stuttgart and Africans using various methods in the paper. These would include global PCA's without projecting, Chromopainter/FINESTRUCTURE and IBS similarity comparisons.

There is also no need for Basal Eurasian, whatever it is, in modeling, they fo have two different succesful models without it in the paper.

About Time said...

Throwing something out there that is not (as yet) immediately testable - but might become testable if/when Basal genomes are better understood:

What if Basals started agriculture for medicinal purposes? Or to to get high even to alleviate pain.

Sounds odd, but we know that early farmers in Europe were pretty sickly. Maybe from inbreeding or initial conditions that disfavored aggression/physical health (as in - these were people who stayed behind when EMH started on a "wolf like" evolutionary trajectory that we can see even in surviving Amerind hunter societies).

This kind of apparently adverse evolutionary circumstance could basically force Basals to get smarter about finding herbs and cultivating plants, not to mention caring for each other.

Like a "leper colony" in the medieval sense that came into its own and was forced to adapt in new ways. Or again, self selected "conscientious objectors" who didn't like hunting and preferred to stay behind when others went chasing big dangerous megafauna.

Other side effect is that (given a few thousand years of hunters roaming far and wide and acquiring some archaic Eurasian admixture) Basals would avoid evolutionary costs of semi-dysfunctional molecular pathways caused by archaic introgression (unlike hunters).

Sounds silly now, but in a few years you can start looking at genes for medical problems and selection on things like brain development, aggression, etc.

barakobama said...

What Sub Saharan-like effect does basal Eurasian have on the PCA's?

It is obvious in this PCA that middle easterns, Europeans(only represented by Basque and Sardinians), and early European farmers are pulled down away from fellow west Eurasians Mesolithic Europeans and Upper Palaeolithic north Eurasians.

http://4.bp.blogspot.com/-43t2J5JB4wI/U0E3V9B8oCI/AAAAAAAACe4/YdQUgTXvmDg/s1600/PCA+global.png

I don't see an obvious shift towards Africa though like in Bedouin and Mozabites. Stuttgart is kind of pulled towards Africa in dimension 1 but Skoglund farmer is farther away from Africans in dimension 1 than any of the European hunter gatherers and some modern eastern non Africans. So if anything that PCA is saying that there is something in middle eastern blood(therefore it's in early European farmers and modern Europeans) that's basal Eurasian.

Plus not one mtDNA L(M-, N-) has been found in Neolithic Europe outside of Iberia, and it is extremely rare in Europeans today.

The preprint makes it clear that they think there were close relatives of Europeans(Loschbour, La Brana-1) in the near east(closer than Europeans were to MA1). Using f4-statistic(don't fully understand what it is) they found that Loschbour and La Brana-1 are closer to Stuttgart than they are to MA1.

"The fact that Loschbour and Stuttgart are closer to each other
than either one is to MA1 is accounted for by their descent from the “Western Eurasian” node, thus sharing the west Eurasian drift."

I remember part of the preprint which said that modern near easterns share more drift with loschbour than with MA-1. I don;t have time to find it now. What was MA-1, was he basal west Eurasian? Possibly the closeness of MA-1 and La Brana-1 in Davidski's PCAs is just because they were the only pure west Eurasians in the PCAs. Also is there any evidence of conatct between Europe and west asia between 24,000-8,000BP. There are two U5 samples in Europe that are 31,155 years old and even a U5 from Solutreans so it seems WHG is very ancient in Europe.

Davidski said...

Yes, MA-1 and La Brana-1 are probably close on my PCA plots because the former lacks any sort of Neolithic Near Eastern admixture, while the latter seems to have only a minimal amount.

I think it's important to keep in mind how old and isolated MA-1 is. It's no wonder that Stuttgart, La Brana-1 and Loschbour are all closer to each other than they are to MA-1, because they're much younger than MA-1, and Stuttgart clearly has some indigenous European ancestry.

But if we consider the clades they came from, then that changes things. The clades that gave rise to MA-1 on one hand, and La Brana-1 and Loschbour on the other, are much closer to each other than they are to the theorized Basal Eurasian clade that Stuttgart appears to be partly derived from.

Davidski said...

Hey Matt, I've got confirmation that the authors are checking the comments at bioRxiv, and adding things to the paper to clarify issues based on these comments.

Shaikorth said...

"I don't see an obvious shift towards Africa though like in Bedouin and Mozabites. Stuttgart is kind of pulled towards Africa in dimension 1 but Skoglund farmer is farther away from Africans in dimension 1 than any of the European hunter gatherers and some modern eastern non Africans."

Stuttgart is pulled towards Africa a bit more than most African-shifted Europeans, the effect is small but visible. Having considerable WHG admixture limits the shift compared to a "pure" farmer. It is a projection, but the matter is testable.

Skoglund farmer is where it is due to a) having less SNP's which throws things off as it did for lod La Braña sequence b) being projected onto the PCA. Part of the reason why they project those into PCA's might also explain why La Braña and MA-1 are so close in Davidski's West Eurasia PCA - limited amount of SNP's overlapping. Loschbour should be somewhat further from MA-1 if I'm right here.

James said...

The PCA you're discussing is also consistent with the ADMIXTURE results. MA1 is around half Eastern and hunter gatherers somewhat less. Stuttgart has no SSA, or perhaps some undetectable level under 1 %.

Davidski said...

James, you need to start thinking out of the box here.

MA-1 is not around half eastern because he's not admixed. It's the people you're comparing him to who are admixed.

Shaikorth said...

Sardinians have more than 1% (how much exactly is unclear, but clearly more than Basques or Central Europeans), and Stuttgart is slightly more SSA-shifted than Sardinians.

I finally managed to find a global Chromopainter/FINESTRUCTURE run with Sardinians, done by Anders Pålsen:

https://sites.google.com/site/fennobga/CCAggrWorld240413.png

Sardinians have one of the greatest affinities to the Sub-Saharan group of Mandenka, Yoruba, Pygmies and San among Europeans - and clearly highest affinity to Ethiopians, Mozabite Berbers and Moroccans among Europeans (stronger than Spanish have despite Lazaridis study's ALDER test detecting more than 12% Mozabite admixture in them) - supporting the idea of East African signature in Basal Eurasian. Stuttgart, since it has less WHG admixture, should show even more of both.

Colin Welling said...

I think it's important to keep in mind how old and isolated MA-1 is. It's no wonder that Stuttgart, La Brana-1 and Loschbour are all closer to each other than they are to MA-1, because they're much younger than MA-1, and Stuttgart clearly has some indigenous European ancestry.

This is misleading. Populations evolve away from each other (especially two living populations) unless there is admixture. In the case of EEF there is likely direct WHG ancestry, along with WHG-like ancestry and Basal Eurasian ancestry. If you want to imagine each {ancestral clade of EEF} relative to WHG and MA, by order of their relatedness to WHG you get the following.

WHG, {WHG}, {WHG-Like}, MA, {Basal Eurasian}

But overall, the global tend has been increasing differentiation. Maybe until recent times that is...

Colin Welling said...

Does anybody have any ideas on why the island Iceland has more WHG than Norway and Scotland, two progenitors of the country?

Is it that: the Norwegians settling Iceland had more WHG than the Norwegians used in this study (Bergen?).

That the Irish have more WHG than the Norse?

That isolation exaggerates WHG?

Davidski said...

Colin,

Not only are MA-1 and the Western Hunter-Gatherers derived from the same clade, but there was contact between the former and the ancestors of the latter, as shown by the Motala12 genome.

We also have the AG-2 genome, which appears more European than MA-1. This might be due to contamination or other factors, but I doubt it.

So there's no reason why there couldn't have been a very smooth WHG/ANE cline across Northern Eurasia during the Mesolithic, all the way from Iberia to Siberia.

In fact, I don't see any reason why MA-1's relatives, or even ancestors, to the west couldn't have been the progenitors of the Western Hunter-Gatherers after the Ice Age.

barakobama said...

Shaikorth,

I don't see an obvious African shift in PCAs of European farmers, some interpret them as showing some African ancestry some do not. The only Europeans in PCAs that include Africans in Laz are Basque and Sardinians who are probably the two most Stuttgart/Otzi like modern Europeans.

Sardinians are not a clad with Otzi and Stuttgart, they have more WHG and their Y DNA shows post Neolithic(probably mainly Italian) admixture. Don't Sicilians and some southern Italians have small amounts of sub Saharan ancestry? If so why couldn't Sardinians sub Saharan ancestry be from the same post Neolithic admixture events?

There are no mtDNA L(M-, N-) samples from Neolithic Europe outside of Iberia. Is there evidence of Sub Saharan ancestry throughout Europe? Since EEF is majority in most of Europe that is expected. Why would a very small amount of ancient Sub Saharan ancestry and a very high amount of WHG-like near eastern ancestry be interpreted as ~44% basal Eurasian ancestry?

There are many Y DNA and mtDNA(N1, R2'JT, X) haplogroups that could be from basal Eurasians, but not from Sub Saharan Africans expect maybe Y DNA E.

I don't think African ancestry in early European farmers is impossible i am just thinking critically about what you say.

Davidski's new PCA's and admixtures are very constant with what is in this preprint. The closeness of MA-1 and La Brana-1 is not an error, it means something. The only thing i am certain about MA-1 is that he is 100% west Eurasian.

Table S14.1 shows WHG is not significantly closer to Stuttgart than to MA1. It would be interesting to see how close modern near easterns are, i remember reading a quote that said they are closer to Loschbour but i can't find it.

I bet if all the basal Eurasian and sub Saharan ancestry of Bedouin was erased they would be very close to Loschbour, much closer than MA1 is. I think the reason west Asian components(who are a mixture of near eastern and ANE) are closer to north European components(mainly WHG) than south-west Asian and Mediterranean is because ANE is pure west Eurasian and reduces the amount of basal Eurasian. That explanation though would not make sense if Bedouins are more related to Loschbour than MA1 is.

I have read many times that people at the Mal'ta site had a similar culture to Gravettian Europeans. If true there had to of been similar cultures in the near east.

Davidski said...

Yeah, my PCA of MA-1 and La Brana are better than the ones in this preprint. I think it's because they keep projecting them onto their plots, which makes it look as if the ancient samples are within range of modern variation, when they're obviously not.

Shaikorth said...

Colin, the situation with Icelandic population could and probably is just their fitting algorithm mixing similar WHG and ANE. If you look at the Icelandic ANE, it's lower than in Norway and even more so compared to Scotland. The sum of mean WHG and ANE in the Icelandic sample is equal to Scotland's.

BarakObama, the Stuttgart in the PCA is indeed a projection which does cause issues. I think there's an African shift in "Basal Eurasian" and thus Stuttgart because it seems to be very similar to Sardinians (who show the shift), just with more Basal Eurasian and less WHG that certainly does not cause African shifts.

Whether I'm right will be seen when Stuttgart genome is released and compared more thoroughly to Sardinians and Africans than the Lazaridis study did.

Matt said...

Barak - Why would basal Eurasian not have it's own drift? I could not find anywhere in the preprint that says basal Eurasians had no drift.

It's not really stated as such like that in a quote, however if you look at the models -

http://imgur.com/fPXIFDZ

http://imgur.com/XYzFEo9

You add up the sum of the lines between two clades / nodes to get the distance between them (this doesn't scale to the distance between the nodes on the paper).
When you do this, Basal Eurasian works out to have a fairly low distance from all nodes and fairly low drift (e.g. Western Eurasian -> ENA (Eastern Non-African) is 41+24+34 = 99, while Basal Eurasian -> ENA is 88, and Western Eurasian -> R (African) is 237, while Basal Eurasian -> R is 200).

Bear in mind though, with Basal Eurasian, it really only exists to "make" Stuttgart and then the Europeans who are modelled as a mix of Stuttgart-like people with ANE and WHG.

So its levels of drift are only really what are necessary to make Stuttgart's and Europeans'.
And I think (I realised after my earlier response to you) because they are looking for the most efficient model, it makes sense for them to put what they can of Stuttgart's drift in Stuttgart's slight majority of WHG-like ancestry (node Y, around 60% ), rather than the slight minority Basal Eurasian (around 40%). E.g. 60% of 80 and 40% of 120 would both be the same number (48), so if you want to keep the numbers low....

So Basal Eurasian only gets drift that they *can't* model as descending from a descendent of WHG (I think), and Stuttgart gets modelled as a mix of a "most West Eurasian" / "ultra West Eurasian) clade Y (essentially all the distinctive drift WHG has plus some more) and a low drift Basal Eurasian clade.

And in reality, the drift lengths might be more even (so WHG and BE have more similar levels of drift overall) or BE might have more drift, but it is less efficient to model them that way for now, and unless and until samples are taken which show this has to be the case.

About Time said...

@Colin, wrt Iceland, my first thought is the Irish. Although I'm not convinced that Ireland has been more geographically isolated from Sourhern Britain and the Continent than, say, the Hebrides or Highland Scotland. Wales might have its own pocket of semi archaic (prob more French like) population structure within Britain.

Another factor could be any difference the Scandinavians who went to Iceland and their modern counterparts ore mixed or effected by intra FennoScandian migration). Vikings went east and bought back brides.

There's also the issue of whatever "skraelings" the early Icelanders might have brought in during early settlement.

barakobama said...

Isn't Western Eurasian -> R (African) 41+24+25+171=261?

James said...

Hunter gatherers are _not_ 100 % west Eurasian. When the authors say that MA1 is "unadmixed" they just mean it doesn't have direct admixture from modern-like populations, but it _does_ share ancient ancestry with them which is "eastern non-African" and _not_ west Eurasian.

The ancient samples appear to be mostly West Eurasian in their ancestry, although the hunter gatherers are also inferred to have greater or lesser extents of an eastern non-African (ENA) component lacking in Stuttgart. . . . We note that the ancestry proportions in ancient samples like MA1 are more likely explained by shared ancestry than admixture. This is more likely to explain the nearly three-way distribution of South Asian, West Eurasian and Native American (plus Northeast Siberian) ancestry proportions in MA1, than three-way admixture of established populations.

EEFs don't have any of that eastern ancestry, nor any (detectable) SSA. They're the closest of the ancient samples to being 100 % west Eurasian.

Davidski said...

James,

You're taking those quotes out of context. They refer specifically to the ADMIXTURE results, and not to MA-1's ancestry. That's why the authors make it very clear that this "eastern non-African (ENA) component" is not admixture, but shared ancestry.

Modern Europeans also carry this shared ancestry, but it often doesn't show up in ADMIXTURE analyses because of recent genetic drift and Neolithic admixture from the Near East.

So again, MA-1 is not part East Asian, but rather modern Europeans are part Neolithic Near Eastern farmer.

If modern Europeans weren't so admixed, they'd be much more similar to Loschbour and MA-1.

mikej2 said...

Davidski, you are right about the Near Eastern later admix among Western (and of course southern) Europeans. It can be easily seen also in intra-European PCA-analyses where Lithuanians reveal no Asian admix and minimal Near Eastern admix, and then adding Near Easteners to see the difference. But this fact is difficult to sell because the racial western ideology strongly supported by people from the Western Hemisphere see things differently. People miss the point, the difference between history and racial aspects.

Ryan said...

Davidski - you quoted this earlier:

" If MA1 had more basal East Asian admixture than Loschbour, these statistics should be negative. It is possible that both Loschbour and MA1 experienced eastern non-African gene flow, but it is not parsimonious (under the model of eastern non-African gene flow) that two samples from widely separated geographical locations (Western Europe and Siberia) and times (8-24 thousand years ago) would experience such gene flow in amounts that precisely cancel themselves out to produce perfectly symmetric statistics of the given form. "

Are the authors forgetting that La Brana's Y-DNA shows an ENA affinity?

Would this "basal Eurasian" group explain why there were some signals of SE Asian / Melanesian admixture in your earlier work? IE the SE Asian component of La Brana isn't really Melanesians, but just shows up as such because both Melanesians and this "basal European" would group together not because they're closely related, but because they both aren't on the main Eurasian branch.

Shaikorth said...

Don't forget that it could also be only noise. IIRC Davidski's IBS sharing showed Siberians as the closest East Eurasian group to La Braña, closer than SE-Asians and Amerindians in fact, and Oceanians as the most distant.

Ryan said...

Yah, definitely could just be noise. I'm just wondering if this data makes that more or less likely, and if the previous work tells us anything about who these "basal Eurasians" were, if they existed at all.

C-V20 shouldn't be noise (though it could be an outlier due to sample size), so there may be some sort of deep connection at work here too.

Matt said...

Barak - Isn't Western Eurasian -> R (African) 41+24+25+171=261?

Yep, well spotted, I skipped X->W when adding.

Shaikorth said...

C-V20 is, according to the current C tree, most closely related to C-M8 found in Japan. This probably supports a Siberian affinity more than Oceanian affinity, but who knows.

If Ust-Ishim is C or even C1 things get interesting.

Ryan said...

I definitely agree that C-V20 must have passed through Siberia at the least. If C-M8 reached Japan by travelling up the coast from SE Asia that doesn't entirely exclude a very deep Oceanian affinity though (I'm not saying it's likely either).

Davidski said...

La Brana does show a little bit of affinity to Oceania in the new ADMIXTURE analysis, especially at K=8.

barakobama said...

If anyone is interested i made my own thread about the revised Laz.

http://www.theapricity.com/forum/showthread.php?121668-Revised-Lazaridis&p=2553616#post2553616

Most of what i think about it is in the thread, so please take pieces and critic it.

One of my strongest believes is that Loschbour was not a pure La Brana-1 like west European hunter gatherer, he also had many of the same central European hunter gatherer ancestors as Motala12.

Equally important i believe that basal Eurasian ancestry in near easterns is the main reason why MA1 seems to be a brotherclade of Mesolithic Europeans. MA1 was not a basal west Eurasian, his clade had already diverged from the European-west Asian clade by 24,000 years ago. It is very interesting that the most popular Y DNA haplogroup of west asia(J) is a brotherclade to the main Mesolithic European Y DNA haplogroup(I).

Colin Welling said...

Not only are MA-1 and the Western Hunter-Gatherers derived from the same clade

Doesn't matter. ANE and WHG aren't close to each other relative to EEF. It means that they have drifted apart from one another so that the resulting group WHG is something closer to EEF than ANE.

In fact, I don't see any reason why MA-1's relatives, or even ancestors, to the west couldn't have been the progenitors of the Western Hunter-Gatherers after the Ice Age.

The researchers don't have WHG descending from ANE. Furthermore the two lineages separated before the ice age.

So there's no reason why there couldn't have been a very smooth WHG/ANE cline across Northern Eurasia during the Mesolithic, all the way from Iberia to Siberia.

Ummmm, I guess that's possible.

Colin Welling said...

Colin, the situation with Icelandic population could and probably is just their fitting algorithm mixing similar WHG and ANE.

Another options is that the WHG/ANE for the Scottish is a poor fit.

Out of the Europeans populations which fit a 3 way admixture, page 118 says the Scottish have the 2nd most ANE and the 3rd least EEF. Page 119, which only estimates EEF, says the Scottish have the 2nd least EEF, implying that the Scottish have even more (WHG + ANE) than the Lithuanians.

So there it is. The Scottish either have a LOT of ANE or maybe some of their ANE should be WHG.

As unusual as it is, I could imagine Scotland being populated by early Scandinavians high in ANE and preserving those high levels more so than Norway, creating an island of high ANE in Western Europe. Still, I think its more likely that Scottish WHG is being under estimated. I wish they included the Irish.

Colin Welling said...

does anybody else find it strange that the EEF model fits most of Europe so well? I would have expected quite a bit of divesity in farmers when considering their non WHG DNA.

I expected some large gap between the farmers of Britain and the farmers of Ukraine. Though, I do recall the most recent paper saying the north Spanish farmers were different from the Mediterranean farmers...

Davidski said...

They only tested four Scots, and all four were from Argyll in the west of Scotland, where Scandinavian influence is relatively low. Indeed, three of these individuals fell into the Irish + West British cluster in my ChromoPainter/fineSTRUCTURE analysis, which appeared to be the least Scandinavian of the British-centered clusters.

http://eurogenes.blogspot.com.au/2012/01/eurogenes-north-euro-clusters-phase-2.html

A larger and more representative Scottish sample set would probably be indistinguishable from the English and Orcadians in terms of EEF/WHG/ANE ratios.

Davidski said...

By the way, there's no evidence for any "gap" between the early farmers in western and eastern Europe. Both were a lot like present-day Sardinians and the ANE-poor subset of Bedouins (termed BedouinB in the Lazaridis et al. paper). In other words, they were very West Mediterranean-like in terms of modern genetic diversity, because they lacked ANE, which is now all over the Near East, and especially pronounced in the Northeast Caucasus.

Collin, you seem to be clutching at straws, and the same time ignoring some of the really obvious things that are now very difficult to argue against.

Colin Welling said...

"Collin, you seem to be clutching at straws, and the same time ignoring some of the really obvious things that are now very difficult to argue against."

What are you talking about?

You're reading way too much intent.

About Time said...

@Colin, uniformity of EEF could be due to endogamy of farmer "core" that moved around from place to place when local populations became less friendly/cooperative or soil depletion). Esp if farmers had trade networks, they'd just shift to a more favorable node in the network when times got tougher.

Endogamous EEF core moves on but leaves behind mixed marginal populations that blend back into hunter or more likely pastoralists / subsistence farmer settlements. Effect over many repeats of this process is that basically similar EEF seeps into many local pops.

EEF core might or might not survive as independent pop that seems related to many surrounding local pops. EEF might seem "mixed" but is actually at the root of part of local ancestry from the old intermarriages.

barakobama said...

This is somewhat on subject, it's about the origin of modern European pigmentation.

Since Basque have a very small amount of ANE ancestry, have much more WHG than other Iberians(probably 40% or more in total) and most of it is indigenous(La Brana-1 like), and the majority of their ancestry is probably from Stuttgart/Otzi/Cardiel like farmers shouldn't we see a dark skin-black hair-blue eye coloration(Mesolithic) and brown eye-black hair-light skin correlation(Neolithic)?

I have seen very few Iberians, but i took my own hair-skin color survey of Basque based on what's on this link. I was hoping to find La Brana-1/Loschbour like pigmented people.

http://www.theapricity.com/forum/showthread.php?106927-Guide-to-Spanish-phenotypes-(by-regions)

I saw(recorded) a pretty clear correlation with light hair and light skin. Nearlly every single person had dark brown-black hair but the lighter haired ones had overall lighter skin. Their skin color is deifntley darker than European Americans. Many have oliveish skin. Most had pale skin with blackish hair.

Where are the blue eyed-dark skinned people La Brana-1/Loschbour looking people? Where did the olive skin come from, the farmers, hunters, or both? Where did the light skin come from? Is the light hair-light skin correlation from admixture with people who came after the Neolithic, is it from the Neolithic farmers the Mesolithic hunter gatherers?

This German study shows that at least in Germany the lighter the hair the better chance of light eyes.

http://www.haar-und-psychologie.de/haarfarben/hair-colors-eye-colors-germany.html

This is totally inconstant with La Brana-1, Loschbour, and Motala12 who all had black or dark brown hair and light eyes.

In my opinion there are three simple possibilities to explain modern European pigmentation.

1.A decent amount of olive skin and vast majority dark hair in southern Europe is continuum with both European hunter gatherers and near eastern farmers. The lighter skin and mainly brown eyes is from the farmers. Lighter hair-eyes and somewhat light skin in northern Europe is not because of more Mesolithic ancestry but just because their ancestors evolved those traits recently during and after the Neolithic.

2.Light hair-eyes-skin(which are obviously connected somehow) all have mainly a Mesolithic origin and may or may not have gone up and down in frequencies overtime.

3.Light skin-hair came originally from near eastern farmers, went through powerful selection and became attached to European hunter gatherer light eyes.

I have not studied this that much, so i am very undecided. I am leaning a little more towards the view that overall light pigmentation in Europe has common origins and the origins are Mesolithic. Ancient DNA has already nearly proven that hypothesis incorrect though, but i expect ancient DNA evidence to eventualley pop up.

barakobama said...

I googled Sardinians to see if i could find dark skinned-black haired-blue eyed indviduals because they are nearly no differnt from Neolithic central-west-north-other regions(?) European farmers genetically. If through evolution after the Mesolithic light hair-eyes-skin in northern Europeans ancestors became popular and connected, it did not occur in nearly all Sardinians ancestors.

Here are all of the likely Sardinian light eyed people i could find. Like with Basque it seems the light eyed people are lighter and haired and skinned on average. The only none brown or black haired person, had red hair and brown eyes but the light eyed ones hair was usually a tad lighter. It's hard to make conclusions yet but i it seems likely that the light eye-skin correlation is from Mesolithic Europeans, for Sardinians the argument of recent admixture with other Europeans to explain the light eye-skin correlation is not very valid.

http://gallery.photo.net/photo/4216530-lg.jpg

http://1.bp.blogspot.com/-rUWEGXh3Hhs/UFkDWR8tPOI/AAAAAAAABdA/tYP8HVotCxM/s1600/sardinians+sardinian+people+++sardinia+(5).jpg

Ginger Sardinian? Maybe it came to Europe from the near east with farming, since red hair also exists in Samartians(south-west asia) who have no WHG ancestry,

http://www.lorenzobellu.com/sito/gallerie/eventi/2010%20-%20Sassari,%20Cavalcata%20Sarda/slides/_PLB5157.jpg

http://upload.wikimedia.org/wikipedia/commons/7/71/Folk_Costume_of_Sardinia_in_Oliena_2.jpg

http://sphotos-g.ak.fbcdn.net/hphotos-ak-ash4/307977_124226131016852_1906347239_n.jpg

http://1.bp.blogspot.com/-ufHqFXaU9zw/Ub0x7exaUNI/AAAAAAAADZc/hsy_X602vmQ/s1600/sardinians+sardinian+people.jpg

http://2.bp.blogspot.com/-MdTlLnNXDJ8/UFxWbDHWzLI/AAAAAAAABz0/3zZsDYbI2ww/s640/sardinians+sardinian+people.jpg

http://3.bp.blogspot.com/-mjMcpbi6OpM/UhAwKl_-BaI/AAAAAAAAEAI/aPkc94k8iNM/s1600/sardinians+sardinian+people+girls.jpg

http://upload.wikimedia.org/wikipedia/commons/7/71/Folk_Costume_of_Sardinia_in_Oliena_2.jpg

http://2.bp.blogspot.com/-tkubYeEMQpo/UFkDeQw0BRI/AAAAAAAABdY/UrvKDxhXn-s/s1600/sardinians+sardinian+people+++sardinia.jpg

http://2.bp.blogspot.com/-uUSInqYbbRA/UCqTglcG9VI/AAAAAAAABDo/PAS6H0xzJl8/s1600/sardinians+sardinian+people+%252816%2529.jpg

http://3.bp.blogspot.com/-ewbS8ckakVE/UxUPWEaFv8I/AAAAAAAAFDQ/M2XZXK3wzM0/s1600/sardinians+sardinian+people+%25288%2529.jpg

Davidski said...

The fact that the Neolithic farmer-like Sardinians are amongst the most brunet of Europeans is a strong argument that the light pigmentation of North-Central-East Europeans can't simply be ascribed to a Neolithic diet.

But the thing is that North-Central-East Europeans don't live on Sardinia, where I'm sure it's a lot more sunny than north of the Pyrenees, Alps and Carpathians.

In other words, maybe what you need is a Neolithic diet, cloudy climate, and the right blend of Neolithic farmer and European hunter-gatherer DNA to lighten up significantly in a just a few thousand years.

spagetiMeatball said...

The mal'ta boy was very dark right?

Davidski said...

Probably...

"MA-1 individual was predicted as having relatively dark pigmentation for hair, skin and eyes. However, we note that this analysis is based on only 17 SNPs at low depth-of-coverage, and even with the full set of SNPs the method has limited prediction accuracy."

But apparently he had freckles.

barakobama said...

"In other words, maybe what you need is a Neolithic diet, cloudy climate, and the right blend of Neolithic farmer and European hunter-gatherer DNA to lighten up significantly in a just a few thousand years."

Were Sardinian-like late Neolithic northern European farmers lighter pigmented than their early Neolithic ancestors who lived a couple thousand years before? If not, a high amount of common ancestry between all modern northern Europeans which modern southern Europeans share less of makes more sense. The same basic pigmentation change probably didn't occur multiple times in the same time period.

nanuk said...

It's funny to see everyday all these incompetents obsessed in we sardinians, arguing idiotic theories about us, on the basis of unscientific studies realised on samples of 10-20 volunteer persons.
May be they think to be true genetists, while we are a sort of guinea pigs in a lab.

About Time said...

Shrug. Similar might be true for Corsicans or Balearics or Icelanders or Manx or Aran Islanders for that matter. Islands can preserve aspects of genetic diversity that are harder to see elsewhere (still there, but more swamped out among many other aggregating favors).

It's just endogamy by geography instead of by mating choice. Different cause, same effect.

Davidski said...

Uh oh, we have an intellectual giant amongst us, from Sardinia no less, and his name's Nanuk.

barakobama said...

"It's funny to see everyday all these incompetents obsessed in we sardinians, arguing idiotic theories about us, on the basis of unscientific studies realised on samples of 10-20 volunteer persons.
May be they think to be true genetists, while we are a sort of guinea pigs in a lab."

Many studies have found Sardinians are the closest modern relatives to early European farmers.

For example here are two ancient DNA studies which proved it.

http://www.ancestraljourneys.org/bibliography.shtml#Keller2012

http://www.ancestraljourneys.org/bibliography.shtml#Lazaridis2013

I don't really see a reason to argue about this because it's plain fact. Sardinians are a relic of Neolithic Europe(we should put y'all in a museum), that's why people are so interested in your guys DNA.

Nanuk, I hope you keep posting because i am interested in how Neolithic European farmer's brains functioned. When you see wheat do you instinctfully farm it?

barakobama said...

Fossil from Neolithic Europe(Nanuk). Are light hair-eyes-skin connected in Sardinians. It's very frustrating trying to figure this stuff out, and learning whether that is true or not for Sardinians is key.

Grey said...

"Yes, I think the more recent SSA admix among the Bedouin is likely to show up, while the more ancient stuff often won't."

Is it possible that people are using post Bantu expansion SSA to compare with instead of whatever kind of SSA was in East Africa before the Bantu expansion?

#

@About Time

"Maybe WHG-SHG were trampsing around in the Sahara or Mediterranean in general."

I was imagining the WHG/SHG may have originally covered the area between the edge of the mammoth steppe, near east and north Africa.

#

@Colin Welling

"Does anybody have any ideas on why the island Iceland has more WHG than Norway and Scotland, two progenitors of the country?"

If WHG were better adapted for Icelandic conditions might there have been selection in place?

A population that was 50% A and 50% B move to two new environments one of which is more suited to A and the other to B couldn't they become 60% A, 40% B and 40% A and 60% B over time?

#

"does anybody else find it strange that the EEF model fits most of Europe so well"

Same idea again. If 50% of group A's genes are better than group B's and vice versa might not different levels of initial admixture end up with the same final percentages over time?

(I don't know if that makes sense, just wondering aloud.)

About Time said...

@Grey, my idea is that WHG were more sea-littoral (coast) adapted, and ANE were more continental adapted. Culturally and (esp in early technology phases) maybe physically.

So far ANE shows up in interior continental spots mostly. Even Sweden counts as far as weather goes (Siberian winter with cold/dry air and lots of snow).

WHG is Spain, France (I can almost smell the wine), but attenuated in Sweden.

Notice Siberian winter does not effect Britain/Ireland, which have a much milder maritime climate despite latitude. Sweden/Germany/Poland get covered in snow in a way Ireland does not.

Question is, how old is ANE in Scotland/England?

Environmental natural selection in Viking age Icelanders should not have any effect on WHG levels, which would be chopped up in fine pieces after all that time. Maybe individual genes, but not WHG ancestry overall (far too old if it was in Europe thousands of years).

Natural selection should only have an effect of raising general admixture % for very recent admixture events, such that linkage would pass down big segments that happened to carry beneficial genes. Maybe this mattered for Ust Ishim etc.

barakobama said...

I have some more thoughts on the origins of modern European pigmentation.

Many genes have SNPs that are suppose to help cause light skin in Europeans. La Brana-1 and Loschbour had no notable ones(missing multiple which are fixated in modern Europeans), except for rs12203592 T/T(Loschbour) T/C(La brana-1. Motala12 though notably had the C11 haplotype, rs28777 A/A(in gene SLC45A2), and rs12203592 T/T(in gene IF4R). Motala12 was not tested for SNP rs16891982(in gene SLC45A2) though, if he had it that would maybe mean skin color varied in Mesolithic Europeans. It is definitely a valid argument that Motala12 had light skin.

The source of European light skin is not even close to being discovered, but it's still pretty reasonable to say Mesolithic Europeans had dark skin. It's hard to believe that randomly all of these mutations scientists say help lighten European light skin and are very popular in modern Europeans are absent in Mesolithic ones. Why would Europeans need these mutations, if they already got light skin from their Mesolithic European ancestors?

It is possible though that Mesolithic Europeans had relatively light skin, and their near eastern admixed descendants got new light skin mutations, and when combined created modern European-like light skin.

rs16891982 G/G, is more popular in Europe than the near east and more popular in northern Europe than in southern Europe.

http://www.web.proxygogo.info/b.php?u=NzXXRW%2BmkIUxoB9pbjufPLEC%2BKI0tNmIwajvCxvmwBvLDYVWdX7%2F8xPAB6%2BGTTSnFD9zZcKvpQDtFze1dZp3XH6y304B4x0ViGGgbILXWFSzT0CXBw%3D%3D&b=29

It's distribution probably effects hair more than skin color. Because SNPedia references a source which states that if a European doesn't have it they are 7x more likely to have black hair. Sardinians have the lowest amount of this mutation and are the darkest haired people in Europe.

Loschbour and La Brana-1 did not have this mutation and based on other SNPs associated with hair color, all three(incl. Motala12) most definitely had dark hair. Mesolithic Europeans were probably entirely or primarily dark haired.

I don't even need to talk about the three Mesolithic individuals eye color, there is no doubt all had blue eyes.

Hypothesis on origin of modern European pigmentation.

Many of the mutations associated with European light skin are mainly descended of their farmer ancestors and they were selected and became dominate after the farmers mixed with hunter gatherers.

I think light(incl. red) hair first became popular in a population during or after the Mesolithic which was mainly descended of hunter gatherers(WHG and ANE). This population, also selected Mesolithic-descended light eyes which became popular for the first time since the Mesolithic. The light hair-eye combo, maybe some new light skin mutations, and farmer light skin mutations could have made their skin lighter than their farmer ancestors.

This(These) very light pigmented population(s), are the main ancestors of modern north Europeans and bronze age Indo Iranians and Tocherians. They rapidly spread their genes after the Neolithic.

The reason today Mesolithic ancestry correlates with light pigmentation is because north Europeans with lower amounts have admixed with darker pigmented south Europeans who also raise their EEF ancestry. Basque and Sardinians have much higher amounts of Mesolithic ancestry than other southern Europeans(primarily native, not recent north European admixture) but Basque are just as dark as Spanish and Sardinians are darker than Italians.

A European-record low amount of light eyes in Sardinians and a possibly connection with light hair-eyes-skin are inconstant with ancient DNA and my hypothesis, so i could be totally wrong. Also, the same light skin mutations in Europe had to of been selected separately many times, which is hard to believe. Possibly Motala12, Loschbour, and La Brana-1 are not good representations of Mesolithic Europeans pigmentation wise.

Grey said...

@About Time
"my idea is that WHG were more sea-littoral (coast) adapted, and ANE were more continental adapted. Culturally and (esp in early technology phases) maybe physically."

That fits my mental model better than south and north now you mention it.

#

"Environmental natural selection in Viking age Icelanders should not have any effect on WHG levels, which would be chopped up in fine pieces after all that time ...
Natural selection should only have an effect of raising general admixture % for very recent admixture events"

Yeah but that's the thing. Although WHG and ANE may be ancient their admixture in Iceland is recent: broadly ANE males from Scandinavia and WHG females from Ireland.

About Time said...

@Grey, hmm well so you are saying medieval Irish were more WHG, and medieval Vikings were more ANE?

Well good point is that Viking pops weren't necessarily the same as general pops of modern Scandinavia. They might have had fighters from more remote pockets of Scandinavia (higher ANE? Maybe, why not) plus random mixture from their domains all around Baltic and North Sea coasts (not just Scandinavia proper).

Didn't that medieval Dane come out as Finnish like in a PCA plot?

It would be good to get a nice Irish sample. Also modern Gotland. Also Pomeranians (arguably partly descended from Goths/Baltic Old Prussians/early wave Slavs/Nordic Bronze Age), Denmark, Frisia, North Germany.

Grey said...

@Barak

There are two forms of melanin: eumelanin and pheomelanin. Pale skin, green eyes and red hair is the natural result if you reduce eumelanin while keeping pheomelanin the same.

http://realhistoryww.com/world_history/ancient/Misc/Common/India/Indian_Albinos/The_Bhatti.jpg

(Similarly blonde hair and blue eyes occur if you reduce *both* eumelanin *and* pheomelanin.)


It seems plausible to me (to the point it ought to be the default assumption) that in sunny climates this phenotype would be strongly selected against but in cloudier climates maybe not.

(And during the LGM "cloudier" climates may have extended much further south e.g. perhaps as far south as North Africa and Iran.)

So I think that phenotype is likely to have been very common across a very large swatch of western Eurasia, starting somewhere NW of India.

(nb If it was positively selected for specifically in colder / cloudier latitudes then after the LGM the dividing line between sunny and cloudy may have moved north so a region like North Africa may have switched from positive to negative selection.)

The problem with this theory is the only way to test it is to find someone who has one of the variants of the MC1R red-hair phenotype who *doesn't* have the SLC genes but as SLC genes are fixed then individuals like that are likely to be very rare.

Another possibility may be testing the DNA of European royalty who were known to be red-haired from their portraits or written descriptions. That only pushes the dates back a few centuries though.

http://static.bbc.co.uk/history/img/ic/640/images/resources/people/elizabeth_i.jpg

#

"Why would Europeans need these mutations, if they already got light skin from their Mesolithic European ancestors?"

1) tanning

If people with the pale skin / red hair phenotype existed as far south as the line North Africa - Levant - Iran during the LGM then as the climate got hotter / sunnier after the LGM then selection pressure for very pale skin may have gone into reverse.


2) something else

One candidate for that something else is iodine in breast milk which is an effect of one of the SLC genes - and iodine is necessary in brain development so very important indeed.

Grey said...

@About Time

"hmm well so you are saying medieval Irish were more WHG, and medieval Vikings were more ANE?"

Actually I was just about to correct that bit of my post when I saw your comment. I haven't actually thought about which is which or even if they were distinct in the first place.

My original point was purely wondering aloud about what might have happened if they were distinct WHG and ANE when they mixed. They may not have been at all.

About Time said...

@Grey, there is also neuromelanin. No idea if the genes for neuromelanin production/regulation interact with the molecular pathways involved in skin/hair/eye pigment.

There is a dark part of the brain (substantia nigra) involved in behavior and motor function. It's related to cells involved in dopamine (important neurotransmitter) regulation.

Whole other can of worms though and idk much about this. But if you think human evolution was largely cognitive and thus neurophysiological (I do, strongly), this matters.

If neuromelanin has any link to pigmentation on cells in other parts of the ectodermis. In embryonic development, hair/skin cells are connected to the brain and retinal cells (same germ layer).

So maybe skin depigmentation started out as partly a "side effect" of natural selection on the brain. That's kind if my intuitive guess, since the other factors we talk about seem sort of underwhelming for genes hat reached near fixation in places.

Grey said...

@About Time

"So maybe skin depigmentation started out as partly a "side effect" of natural selection on the brain."

Interesting thought.

"since the other factors we talk about seem sort of underwhelming for genes hat reached near fixation in places."

I dunno. I'd agree if it was dark-skinned people developing a tanning version of light skin out of the blue but if they were *already* very light skinned as an adaptation to a cloudy environment and then warming after the LGM led their environment to get a lot sunnier then a tanning adaptation suddenly has a purpose.

However that only applies to people in the south though. It doesn't apply to those genes coming to fixation in regions in the north where it stayed cloudy.

However the iodine angle - if correct - would be a very big deal.

SLC5A5

http://en.wikipedia.org/wiki/Sodium-iodide_symporter

"NIS expression in the mammary glands is quite a relevant fact since the regulation of iodide absorption and its presence in the breast milk is the main source of iodine for a newborn."

Iodine is critical for brain development and IQ and the brain reaches 90% of adult size by age three so the first years are the most critical.

So if farmers brought this along with them at the same time as the de-pigmentation genes then there is a very strong reason for the *package* to have been strongly selected for.

barakobama said...

Grey,

"It seems plausible to me (to the point it ought to be the default assumption) that in sunny climates this phenotype would be strongly selected against but in cloudier climates maybe not.

(And during the LGM "cloudier" climates may have extended much further south e.g. perhaps as far south as North Africa and Iran.)

So I think that phenotype is likely to have been very common across a very large swatch of western Eurasia, starting somewhere NW of India."

That is very unlikely. Do you really think south Asians and middle easterns during the LGM were largely red haired and green eyed?

Majority light eyes is a European phenomenon. Upper Palaeolithic Europeans were probably the first people to be mainly light eyed, and it should be no surprise that today light eye's distribution correlate very closely with WHG ancestry.

You need to consider the likely genetic makeup of people in India, west Asia, etc. during the LGM before you start saying they were pale like northern Europeans and somehow changed back to ancestral pigmentation after the LGM.

"The problem with this theory is the only way to test it is to find someone who has one of the variants of the MC1R red-hair phenotype who *doesn't* have the SLC genes but as SLC genes are fixed then individuals like that are likely to be very rare.

Another possibility may be testing the DNA of European royalty who were known to be red-haired from their portraits or written descriptions. That only pushes the dates back a few centuries though.

http://static.bbc.co.uk/history/img/ic/640/images/resources/people/elizabeth_i.jpg
"

I doubt a high amount of European royalty at any point in the past was largely red haired. Their genetic makeup and pigmentation of royalty would be no differnt from the people they ruled.

I am starting to think more and more that Mesolithic Europeans had light skin. Mesolithic ancestry is much higher in Europe than WHG percentages given by Laz. WHG+ANE ancestry is 40-50%(up to 55% in Basque) in most of southern Europe, 50-60% in north-western Europe, 60-67% in the Norse and east Europe(Balkans-), and a shocking ~70% in the Baltic.

Whatever causes uniform light skin in Europe, is from European-specific ancestors(aka WHG), and WHG ancestry correlates very closely to light skin in Europe.

The only inconsistency with the hypothesis that light skin in Europe is descended of WHG, is that known light skin mutations for some reason were fixated in European's ancestors and most of it came from their near eastern ancestors.


About Time said...

Not this again. Dipping in anyway:

Not clear to me that the palest skin goes with blond/blue and was effect of same natural/sexual selection.

Most Scandinavian/German/Slavic blonds with light hair/eyes can tan really well.

The nontanners are the Irish and some Brits (not including the Scandi looking English type though). Irish are not especially blond, with very few platinum blond types. They are the palest people, maybe the palest in the world.

Gingers have it the worst, some can only freckle. But that complexion might or might not have same evolutionary origin as "Irish" no taming brunettes or even raven haired types (mixed?).

Light skin that doesn't tan has a clear functional relationship to sunlight. I still stick to the Vitamin E theory.

But---any natural function of blond hair is utterly unknown to me. It's very sociologically important as mark of "group ness" for some people. Again in more urban (post-agricultural) contexts could have been important. (Hunter bands know each other personally and do not require psysiological marks of "group ness").

Eyes idk. People once argued that blue eyes see differently than dark eyes. Idk.

There is also the issue of neuromelanin, which maybe (maybe -zero evidence as far as I know) relate to eye color. Eyes are developmentally related (in process of embryonic cell division into germ layers) to neural cells.

So maybe eye color is an effect of natural selection on something else (behavior/cognition).

Worth pointing out: Pagan Cen Europe and Scanndo was mostly farmers/agricultural in Proto Germanic period. Unlike Pagan Celts (Irish / Britons) who kept traces of strong pastoral lifestyle - shown in calendar holidays like Beltane which matters for cows but not for wheat (find me some fields of wheat in Ireland - not so common). English criticized the "Scythian like" Irish/Scotti (Erse) for their barbaric and un-English seasonal transhumance even in the Middle Ages.

About Time said...

Cite for English criticisms of late Celtic/Irish transhumance: http://en.wikipedia.org/wiki/Scythians#cite_ref-59

As proofs for this origin Spenser cites the alleged Irish customs of blood-drinking, nomadic lifestyle, the wearing of mantles and certain haircuts and

Cryes allsoe vsed amongeste the Irishe which savor greatlye of the Scythyan Barbarisme.


... but also that:

For where yee say that the Irish have allwayes benn without letters, yee are therein much deceaved, for yt is certen, that Ireland hath had the use of letters very auncientlie, and longe before England.

The full text (kind of interesting and entertaining insight into the English view of the Irish) is at http://www.ucc.ie/celt/published/E500000-001/index.html