New additions to the Eastern Non-African family tree

It looks like we finally have some Jomon ancient genomes from Japan. We have five ~3,000 year old samples from around Fukushima who've been genotyped for their autosomal DNA and they're quite intriguing to say the least.

They seem to look like proto-East Asians of some sort. Genetically distinct enough to be separate from Eastern Non-Africans like Papuans but clearly not exactly like East Asians such as the Han Chinese.

However, I think I should give some people a low-down on the Jomon before I go any further. Japan used to be entirely inhabited by Hunter-Gatherers between ~10,000 BCE to roughly ~300 BCE (Jomon period). They were quite an intriguing Hunter-Gatherer culture as they produced a certain degree of sedentism thanks to the rich resources around them allowing for such a life-style.

Another interesting fact about them that's long had people's curiosities piqued is that they didn't seem traditionally East Asian in terms of phenotypic traits like facial morphology, hair & eye type, teeth shape and so on. They, at best, looked like the traditional East Asian looks still in their "proto-stage" of development:

Jomon man reconstruction

They were seemingly quite hairy, lacked epicanthic folds as well as the more thick straight hair you often see among East Asians while having perhaps more wide facial features as well as fuller-lips (see here, for example). They did, however, seem to be de-pigmented in a manner similar to modern East Asians so they weren't dark-skinned like the Villabruna-cluster Hunter-Gatherers of Europe.

However, much like in Europe, Japan was eventually settled by farmers from the outside. In the case of Europe the farmers came from West Asia (specifically Anatolia) but the farmers came from mainland East Asia in Japan's case. They were people carrying the rice-farmer cultural package which formed in China and they seemingly migrated to Japan from mainland East Asia. Their advent brought about the Yayoi period of Japanese history.

Above is a reconstruction of what some Yayoi period farmers looked like. They looked much more traditionally East Asian than the Jomon period Hunter-Gatherers (epicanthic folds, thicker straight hair etc.). It was these people who seemingly brought alleles in genes like EDAR which are responsible for certain East Asian phenotypic traits, traits that were seemingly missing in pre-agricultural Japan. (see here)

Anyway, due to the interesting phenotypic differences at play, some people have wondered if the Jomon Hunter-Gatherers would turn out notably distinct, from a genomic standpoint, from other East Asians and that does indeed seem to be the case based on these samples:

When more "regional PCAs" (principal component analyses) based on autosomal SNPs are produced; they definitely seem notably distinct from virtually all modern East Asians and Southeast Asians with the modern Mainland Japanese, Ainus and Ryukyuans coming off as intermediates of sorts between them and other East Asians like the Han Chinese which clearly implies that they're some sort of mixture between Sanganji Jomon-related people and Han Chinese-related people. [note]

And if you're wondering who the Ainu and Ryukyuan are... The former are considered the indigenous people of Japan (Hokkaido and Northeastern Honshu) and latter are considered the indigenous people of the Ryukyu islands. Both groups seem to have more ancestry from Jomon Period Hunter-Gatherers than Yamato Japanese do. 

At any rate, when thrown into a global PCA- :

- these Jomon samples don't seem too distinct from East Asians like the Han Chinese. But it does say something that virtually all modern East Asians in that global PCA cluster rather tightly together whilst the Sanganji Jomon break off on their own. So they're notably distinct from modern East Asians but still clearly closer to them than to other groups. 

It's intriguing how they pull downward along the Y-axis and a bit more toward West Eurasians than groups like the Han Chinese do (if you're having trouble with the population acronyms click here). This is something Melanesians and Papuans also do in comparison to East Asians like the Han Chinese:

Though those groups also show a strange pull towards African populations (how they pull downward on the above Y-axis) even though they're, in terms of genetic drift (i.e. as noticeable via Fst values) and divergence datings (likely slightly exaggerated by their Denisovan admixture), more distant from African populations with little to no Eurasian ancestry than East Asians are. (see here) 

At any rate, these Jomon samples seem "East Asian" but not "East Asian" if that makes any sense. They're essentially distinct enough Eastern Non-Africans to be split from Papuans yet they're not exactly like East Asians such as the Han Chinese, though they definitely share a lot of genetic drift with modern East & Southeast Asians in general and are closer to them than they are to populations like Papuans and Melanesians:

This is quite intriguing as it implies much of what makes "East Asians" genetically East Asians (as in differentiated from other Eastern Non-Africans) formed well before the phenotypic traits we traditionally associate with them developed. 

This is of course possible because phenotypic traits like hair-type, facial morphology as well as skin, eye and hair pigmentation (major traits that tend to distinguish modern Humans from each other) seem to be, collectively, controlled by a few hundred SNPs among the 10 million SNPs found in our genomes. It doesn't take radical genetic shifts to create notable phenotypic differences between modern Humans. I.e. less than 10 SNPs are responsible for most of the skin pigmentation difference between Norwegians and Yorubans.

References:

1. A partial nuclear genome of the Jomons who lived 3000 years ago in Fukushima, Japan, Kanzawa-Kiriyama et al. 

Notes:

1. Should be interesting when some third-parties get their hands on these genomes. I'll be interested to see qpAdm and ADMIXTURE results using these samples so we can see exactly how much ancestry the average Japanese person owes to Jomon-type people. The PCA implies it's rather significant but the allele sharing and tree-mix imply somewhat otherwise... Modern Japanese people also have a whole lot of Y-DNA D which really peaks in Ainus and has, as a result, long been thought to trace back to Jomon Hunter-Gatherers, for example.

2. I also wonder if these samples show any Ancient North Eurasian-related ancestry (also see here). Though the study did include MA-1/Mal'ta boy and they make no mention of such admixture.

How things are looking so far

As David's recently pointed out, it does seem as though the old fateful triangle still remains:

Most West Eurasian populations still look like they're mostly, on a basal level, divvied up between a Basal Eurasian rich component (rather similar to the old "ENF" cluster), Ancient North Eurasian-related ancestry and Western European Hunter-Gatherer/Villabruna-cluster-related ancestry.

It seems that, in this set-up, the main distinction between groups such as Neolithic Iranians (alongside Caucasus Hunter-Gatherers) & Neolithic Levantines is that one is "Basal-rich + ANE"  and the other is "Basal-rich + Villabruna":

The first PCA where the triangle is clearly visible is directly based on David's new Basal-rich K=7 ADMIXTURE run but it's data is still in line with what we see in a PCA directly based on autosomal SNPs like the one below:

Here, you can see relatively the same population structure. The more north a population pulls correlates with how much ANE-related ancestry they have, the more east a population pulls correlates with how much "Basal-rich" type ancestry they have and, finally, the more west a population pulls correlates with how much Villabruna-related ancestry they have.

So it seems David's indeed come up with a decent model here. What we really need now is to figure out exactly what "Basal Eurasian" is and to understand some of the earlier pre-history of West Asia to a point where we can grasp how the substantial Ancient North Eurasian-related and Villabruna-related ancestry, found in its Neolithic and Epipaleolithic inhabitants, got there. [note]


References:

1. The genetic structure of the world's first farmers, Lazaridis et al. 2016

2. The Demographic Development of the First Farmers in Anatolia, Kılınç et al.

Notes:

1. The "Basal-rich" cluster itself is likely to be a mixture between something related to European Hunter-Gatherers like those of the "Villabruna/WHG" cluster and Basal Eurasian ancestry. Even the new Lazaridis pre-print implies as much via this figure when demonstrating what makes up the Natufian samples.

Some new Neolithic Anatolians

Well, thanks to a new study, we now have some new Neolithic Anatolian samples. This time they're from South-Central Anatolia and date to between 8300 and 5800 BCE.

Seems the Boncuklu samples (~8300-7500 BCE) are nearly identical to the Barcın (Northwestern) Neolithic Anatolians in terms of WHG/Villabruna-related ancestry and "ENF-like/Basal-rich"-related ancestry whilst the Tepcek samples (~7500-5800 BCE) are less Villabruna-shifted and thus pull a bit more toward Neolithic Levantines and Natufians. You can see this in David's PCA (Principal Component Analysis based on autosomal SNPs) below:

The more left a population pulls; the greater the affinity for Villabruna-type Hunter-Gatherers whilst the more right the pull indicates how ENF-like/Basal-rich they are. Finally, the more north a population pulls indicates how "ANE" shifted they are. Neolithic Anatolians, Neolithic Levantines and Natufians pull the absolute least toward the north as they seem to lack ANE-related admixture.

References

1. The Demographic Development of the First Farmers in Anatolia, Kılınç et al.

Notes:

1. The mtDNA diversity among these samples is rather interesting to me as someone from the Horn of Africa, to be honest. N1a1a1, N1b, K1a, K1a12a, U3: these are quite close to or directly overlap with the mtDNA Haplogroups you can find among Somalis and other Horn African populations. 

East Asians are part Ancient North Eurasian?

This was one helluva bomb the new Lazaridis et al. paper managed to drop at the end of their supplemental where they claimed East Asians are a mixture between MA-1-related peoples and a truly "Eastern Non-African" population:

To be fair, the ANE-related admixture doesn't seem substantial (10-15% ANE + 85-90% ENA/South Eurasian-like) when dealing with East Asians like the Japanese and Han Chinese who still seem mostly Eastern Non-African derived:

Once again we have formal stat based methods like qpAdm picking up on gene-flow which wasn't really caught by ADMIXTURE, to my knowledge. 

Now, it is intriguing to point out that, at least at the higher Ks of some runs, the Japanese & Han did show some Nganasan-like ancestry:

However, the Nganasan-like admixture seems minuscule in the Japanese, Korean and Northern Han Chinese samples and doesn't even show up in the non "Northern" Han Chinese sample-set. Nganasans are a Siberian population whom you'd expect to show some notable ANE-related ancestry but the amounts of ancestry the Japanese, Korean and Northern Han samples are showing from a population like them aren't enough to explain the levels of ANE-related ancestry we see with this study's qpAdm models.

So, ADMIXTURE, in this case, really didn't pick up on something qpAdm did, as far as I can see. David Wesolowski's own K=8 at most had the Japanese at about ~1-3% Ancient North Eurasian and those are negligible/noise levels.

ADMIXTURE might've mildly caught wind of this ANE-related admixture but it's results are definitely not consistent with what these new qpAdm runs are implying.

But I suppose the argument one can make is that how East Asian populations usually form their own cluster at the very early Ks is the problem with ADMIXTURE. It's being heavily skewed by how drifted East Asians are from West Eurasians.

That same substantive genetic drift helps form the genetic structure in the above PCA. The Y-axis marks the divide between African populations (with very little to no Eurasian admixture) and Out-of-Africa populations whilst the X-axis marks the divide between Eastern Non-Africans and West Eurasians (East Asians pulling farther away from West Eurasians than Papuans do in this case).

So, it is possible, I suppose, that all prior ADMIXTURE analyses were being fooled by this substantive and perhaps somewhat recently cemented drift (last 10,000-20,000 or so years?) which analyses like qpAdm are more resistant to. But, what's even more intriguing is that tree-mixes from David Wesolowski support this new paper's claims & data:

Nevertheless, I'm remaining somewhat skeptical about this until we have ancient DNA from around East Asia that might refute or reaffirm these new findings. We might discover something more interesting than these populations simply being part ANE-related. 

What I find especially odd is that even Southeast Asians show such admixture at levels comparable to those of the Japanese, Han and Koreans whom they're somewhat distinct from in terms of their genetic history. ~14% for the Thai and ~12% for Cambodians? Why is everyone so uniformly Ancient North Eurasian here (between 10-15%)? This somewhat brings the whole Mota debacle to mind, actually. [note]

Everyone (other than Siberians, Mongolians & Central Asians whom we've known for a while now have some Ancient North Eurasian-related ancestry) is turning up as 10-15% "ANE" and that's honestly a bit suspicious and is why I'm skeptical about this new data.

References:

1. The genetic structure of the world's first farmers, Lazaridis et al.

2.  Ancient human genomes suggest three ancestral populations for present-day Europeans, Lazaridis et al. 

Notes:

1. I think this is honestly a quirk of the qpAdm model they used. Basically modeling these populations as "Onge + ANE"; it could be that all we're seeing is that these populations have an understandable shift away from Onge-like Eastern Non-Africans that may not necessarily be characterized by Ancient North Eurasian-related admixture. However, it does say something that the same pattern presented itself (when dealing with the Han) via tree-mixes. At any rate, we should wait on some East Asian ancient DNA.

Natufians were dark-skinned?

The creator of the PuntDNAL ancestry project (Abdullahi Warsame) managed to convert one of the Natufian samples' raw data (I1072) into a .txt file [note] and it seems, as per his findings, that the sample is GG for the SLC24A5 gene's rs1426654 SNP.

I've somewhat gone over this before but that would mean he lacks the derived A allele for the SNP which is important in modern West Eurasians' de-pigmentation. It's responsible for 1/3 of the skin pigmentation difference between Europeans and mostly non-Eurasian admixed African populations.

Lacking it as well the derived alleles for SLC45A2's rs1891982 SNP is why the reconstruction of La Braña-1 above has him being rather pigmented/dark-skinned. Western European Hunter-Gatherers like him had the alleles required for light-eyes but not for light-skin:

Neolithic farmers from Western Anatolia are responsible for bringing the derived alleles required from SLC24A5 and Eastern European Hunter-Gatherers seemingly carried the derived alleles required from SLC45A2 (the farmers carried this particular derived allele at very low frequencies). So, Bronze Age pastoralists from the steppe and Neolithic Farmers from West Asia ultimately brought de-pigmentation/light-skin to much of Peninsular Europe.

Anyway, if this Natufian is really GG for that SNP (he's most likely ancestral for SLC45A2's rs1891982 SNP as well), and none of this is caused by DNA damage and is quite legit, then it seems like this particular Natufian was an individual lacking in modern West Eurasians' de-pigmentation. No idea if the other samples are the same but they might be and it'd be pretty intriguing if they are.

General spread of the Natufian culture

What's even more interesting is that the Neolithic Levantines whose data I've managed to sift through (4 samples) are AA for SLC24A5's rs1426654 SNP, making them more similar to Western Neolithic Anatolians and Early European Farmers in this respect.

If this Natufian's result is truly legitimate and the other samples and numerous future Natufian samples prove to be just like him in this respect; it seems like something from outside the Levant brought the derived allele to the region as Caucasus Hunter-Gatherers carried it, Neolithic Iranians seemingly carried it and Western Neolithic Anatolians did as well. For Neolithic and not Epipaleolithic Levantines to carry it could mean an outside population brought it in perhaps from somewhere more north or east. But we'll see what future data on Natufians reveals.

Reference List: 

1. The genetic structure of the world's first farmers, Lazaridis et al. 2016

2. The genetic history of Ice Age Europe, Fu et al.

3. Eight thousand years of natural selection in Europe, Mathieson et al.

Update:

I originally made a mistake in not noting that the early farmers (Neolithic Anatolians and Early European Farmers) did seemingly carry the derived allele in SLC45A2's rs1891982 SNP. They did seem to carry the derived (C) allele for this gene but at what look to be somewhat low frequencies (see here). I used to be under the incorrect impression that they didn't carry it. Apologies...

Somali qpAdm models using new ancient genomes

So, I asked David over at Eurogenes to run Somalis as a mixture between South Sudanese people and Natufians in order to see how well the model would fit using a formal statistical method like qpAdm and he got some pretty surprising results overall:


Natufian + Sudanese (south):

Sudanese: 54%
Natufian: 46%

Neolithic Levant + Sudanese (south):

Sudanese: 54%
Neolithic Levant: 46%

Neolithic Levant + Chalcolithic Iran + Sudanese (south):

Sudanese: 55%
Neolithic Levant:  34%
Chalcolithic Iran: 11%


Now, what's going to surprise you is that the third model is the one that fits the best, and by a long shot when compared to the first model. Natufian + Sudanese (south) fits the worst (chisq: 26.256, tail prob: 0.09%, std. errors: 0.009), Neolithic Levant + Sudanese (south) fits much better (chisq: 7.593, tail prob: 47%, std. errors: 0.006) and Neolithic Levant + Chalcolithic Iran + Sudanese (south) fits even better (chisq: 4.975, tail prob: 66%, std. errors: 0.057).

The last one almost fits as well as a Corded Ware sample being modeled as ~70% Yamnaya & ~30% Esperstedt Middle-Neolithic (chisq: 2.621, std. errors: 0.060) which roughly fits with the data from peer-reviewed studies like Haak et al. 2015:

This oddly reminds me of some models the new Lazaridis et al. pre-print shared where they were asserting that Somalis were a mixture between Mota & population along the Iran_ChL→Levant_BA cline:

I didn't make much of the above at the time. For one, Mota is a poorer fit for Somalis' African ancestry than the South Sudanese (due to various reasons alluded to here), and it made little sense that Somalis' West Eurasian ancestry corresponded better with Bronze Age Levantines and Copper Age Iranians than Neolithic Levantines, for example. At least in my humble opinion.

I figured Lazaridis & company just didn't try a different model that would probably fit better but it's now odd that this fits a bit well with what the above qpAdm models imply which is that "Neolithic Levantine + Chalcolithic Iranian + Sudanese (south)" fits much better than "Natufian + Sudanese (south)" and somewhat better than "Neolithic Levant + Sudanese (south)".

Future analyses and data will be needed but I should point out that some current ADMIXTURE runs don't seem entirely supportive of such a model but ADMIXTURE is not necessarily as precise as qpAdm can be.

For one, qpAdm is preferable because it outright allows you to take a Natufian and then a Neolithic Levantine and see which one you have a greater affinity for (mixture wise) but ADMIXTURE is a lot more messy in that it allows all of these clusters to form among various modern & pre-historic populations and could thus be more prone to producing perhaps more clunky results. Formal statistical methods like qpAdm also seem to be "drift resistant" / resistant to being skewed by recent genetic drift and can thus notice deeper ancestry better than ADMIXTURE to a certain degree.

But we should see what some other analyses say like d-stats and tree-mix. I'm skeptical about the third model in particular (for the time being), despite how well it fits.

Reference List:

1. The genetic structure of the world's first farmers, Lazaridis et al. 2016

Notes: 

1. Link to the full qpAdm results.

David's Treemix results for Natufians & Neolithic Levantines

I hesitated to make this post as David made it himself adequately enough and you can check his post out for all the tree-mixes but it is worth-noting that even tree-mixes show that Natufians and even Neolithic Levantines have some African ancestry:

This is a strange puzzle, quite frankly. Especially given the Lazaridis et al. 2016 Pre-Print's claim below:

"However, no affinity of Natufians to sub-Saharan Africans is evident in our genome-wide analysis, as present-day sub-Saharan Africans do not share more alleles with Natufians than with other ancient Eurasians (Extended Data Table 1). (We could not test for a link to present-day North Africans, who owe most of their ancestry to back-migration from Eurasia)."

In fact, as David's found, formal stats don't imply that Natufians have African admixture the way these tree-mixes, ADMIXTURE & PCAs do:

Chimp Biaka Anatolia_Neolithic Israel_Natufian -0.000422 -1.539 414749

Chimp Biaka Iran_Hotu Israel_Natufian 0.000981 1.199 70803

Chimp Biaka Iran_Neolithic Israel_Natufian -0.000223 -0.566 367632

Chimp Mbuti.DG Anatolia_Neolithic Israel_Natufian -0.000312 -1.113 481333

Chimp Mbuti.DG Iran_Hotu Israel_Natufian 0.000703 0.906 81688

Chimp Mbuti.DG Iran_Neolithic Israel_Natufian -0.000043 -0.104 425175

Chimp Mota Anatolia_Neolithic Israel_Natufian -0.000734 -1.933 481191

Chimp Mota Iran_Hotu Israel_Natufian 0.000686 0.644 81676

Chimp Mota Iran_Neolithic Israel_Natufian -0.000388 -0.768 425056

Chimp Yoruba Anatolia_Neolithic Israel_Natufian -0.000407 -1.407 414749

Chimp Yoruba Iran_Hotu Israel_Natufian 0.000552 0.654 70803

Chimp Yoruba Iran_Neolithic Israel_Natufian 0.000026 0.063 367632

The above shows that they don't have any "shift" toward Africans away from other pre-historic Eurasians and thus don't share any alleles with Africans that Neolithic Iranians (who don't seem to show such admixture in tree-mixes and such) or Neolithic Anatolians do not which is in line with what the Lazaridis Pre-Print was asserting.

It's quite strange because essentially all analyses other than D/f4 stats show that the Natufians in particular supposedly have African admixture. It's also interesting how the tree-mixes David's released show two migration edges (arrows) going toward the Neolithic Levantines and Natufians:

One tends to look more overtly African and comes in from either Mota's branch or, as it is above, from in-between Biakas and Yorubas whilst the other tends to sit between Mota and all the Eurasians present in the tree. David suggests that the latter is a sign of "Basal Eurasian", and it is interestingly the migration edge that tends to go directly into the Natufians themselves. The other seems more overtly African and tends to go to the root of both Natufians and Neolithic Levantines while being less significant.

We've had Natufian~Neolithic Levantine-like samples show African affinities via tree-mixes in the past such as Stuttgart (an Early European Farmer):

And interestingly; Stuttgart's African admixture in that tree-mix above (also made by David) looks Hadza-like which is interesting because of the similarity between Hadzas and Mota (see here). But, there aren't two migration edges or two distinct elements like the African samples present going into Stuttgart. 

Perhaps it's a quirk of  Stuttgart's heightened WHG-related admixture in comparison to Neolithic Levantines and Natufians or perhaps the latter two groups of samples actually do have some African admixture alongside their Basal Eurasian ancestry and the formal stats and such are wrong? Or all of this, in all the tree-mixes, including the new ones; are caused by Basal Eurasian and we shouldn't make too much of this? 

Though, it's worth noting that Stuttgart's PCA position does not imply a pull toward African populations when compared to various West Eurasians and North Africans. There is a slight pull in the case of Neolithic Levantines and a more overt one in the case of Natufians, however (see here). And, whilst I haven't seen the ADMIXTURE results of a Neolithic Levantine sample, unlike that one Natufian from earlier, Stuttgart clearly shows no African admixture via ADMIXTURE runs.

Puzzle indeed.

Reference List:

1. The genetic structure of the world's first farmers, Lazaridis et al. 2016 pre-print 

Notes:

1. I said Stuttgart/Early European Farmers have Natufian-like ancestry because that's what this new Pre-print actually implies with it's ADMIXTURE run. The Neolithic Anatolian Farmers and Neolithic/Early European Farmers look like they're a mixture between the blue cluster which dominates Neolithic Levantines and Natufians (Epipaleolithic Levantines) and the red cluster which dominates "WHGs". The farmers who hit up Europe clearly seem more related to those in the Levant than those in Iran if that ADMIXTURE and mostly Pan-West Eurasia PCA are any indication.

2. Stuttgart's Gedmatch kit number: F999916

3. At this point; ADMIXTURE & PCAs imply African admixture in these Natufian samples but the formal stats just aren't picking up on this which is odd. The formal stats impart that Africans don't share more alleles with Natufians when compared to other pre-historic Eurasians as this new Pre-Print asserts at one point.