The Basal-rich K7

Update 25/01/2018: The Basal-rich K7 is now available to personal genomics customers for $6 USD a pop (see here).

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I've got a new test. Currently I'm only using it to explore ancient genomes, but at some point I'll make another version available to personal genomics customers, one way or another. However, that might take a little bit of work and time to mitigate the effects of the calculator effect and so on.

Below is a spreadsheet featuring a wide range of ancient and present-day samples from recent papers. A table with the Fst genetic distances between the seven ancestral populations is available here.

Please note that the Basal-rich component is unlikely to be a perfect representation of the hypothetical Basal Eurasian population. At the same time, it's likely that the two hunter-gatherer components, Ancient North Eurasian (or AG3-related) and Villabruna-related, contain some Basal Eurasian admixture.

Here's a Principal Component Analysis (PCA) of the West Eurasian populations based on their K7 ancestry proportions. It captures all of the main features of West Eurasian genetic diversity, including the two parallel clines made up of Europeans and Near Easterners, and the intermediate position of South Central Asians between the ancient samples from Neolithic Iran and Bronze Age Europe.

An extra large version of the same PCA, with the samples labeled individually, can be downloaded here.

Also, using the K7 ancestry proportions, I modeled the ancient ancestry of a few present-day populations from the Near east, Northern Europe and South Central Asia with the nMonte R script. Bronze Age steppe admixture in groups from the latter two regions is usually inferred at 40-50% with tools based on formal stats, such as qpAdm and TreeMix, so I wanted to check if I could reproduce such results.

Iranian_Mazandarani
Iran_Chalcolithic 42.05
Iran_IA:F38 31.35
Iran_Neolithic 14.95
Andronovo_Kytmanovo 7.6
Yamnaya-Catacomb_Ulan 1.95
Han 1.35
Andamanese_Onge 0.75
Papuan 0

distance%=0.285 / distance=0.00285

Iranian_Zoroastrian
Iran_Chalcolithic 40.95
Iran_IA:F38 38.25
Yamnaya-Catacomb_Ulan 11.25
Iran_Neolithic 6.45
Andronovo_Kytmanovo 2.8
Andamanese_Onge 0.15
Han 0.15
Papuan 0

distance%=0.2979 / distance=0.002979

Kurdish
Iran_IA:F38 96.3
Andronovo_Kytmanovo 2.35
Han 0.6
Andamanese_Onge 0.55
Papuan 0.2
Iran_Chalcolithic 0
Iran_Neolithic 0
Yamnaya-Catacomb_Ulan 0

distance%=1.3845 / distance=0.013845

Latvian
Yamnaya_Peshany 44
Loschbour 30.65
Sweden_MN:Gokhem4 25.35
Barcin_Neolithic 0
Ulchi 0

distance%=1.2569 / distance=0.012569

Polish
Sweden_MN:Gokhem4 39.4
Yamnaya_Peshany 39
Loschbour 21.6
Barcin_Neolithic 0
Ulchi 0

distance%=0.5208 / distance=0.005208

Swedish
Sweden_MN:Gokhem4 42.15
Yamnaya_Peshany 36.55
Loschbour 21.3
Barcin_Neolithic 0
Ulchi 0

distance%=0.939 / distance=0.00939

Kalash
Iran_Neolithic 54.05
Yamnaya-Catacomb_Ulan 25.5
Andronovo_Kytmanovo 9.35
Han 7.6
Andamanese_Onge 1.95
Papuan 1.55

distance%=0.4592 / distance=0.004592

Pashtun_Afghanistan
Iran_Neolithic 54.8
Andronovo_Kytmanovo 31
Han 7.5
Yamnaya-Catacomb_Ulan 3.5
Andamanese_Onge 1.75
Papuan 1.45

distance%=0.4921 / distance=0.004921

Pathan
Iran_Neolithic 55.25
Yamnaya-Catacomb_Ulan 19.1
Andronovo_Kytmanovo 12.3
Han 8.45
Andamanese_Onge 3.4
Papuan 1.5

distance%=0.4848 / distance=0.004848

Tajik_Pomiri
Iran_Neolithic 41.7
Andronovo_Kytmanovo 30.65
Yamnaya-Catacomb_Ulan 19.15
Han 6.95
Andamanese_Onge 1.05
Papuan 0.5

distance%=0.5318 / distance=0.005318

Admittedly, these estimates look very conservative, but certainly not out of the ballpark. I suspect that I'll be able to improve the models and statistical fits as new Bronze Age steppe samples become available. Indeed, I'll be updating the spreadsheet above regularly.

Layers of Ancient North Eurasian-related ancestry in East Asia

Back in May I hypothesized that present-day East Asians were prehistoric hybrids of partly Ancient North Eurasian (ANE) origin. I got the idea from a series of TreeMix runs (see here).

This was essentially confirmed recently in the Lazaridis et al. 2016 preprint. Refer to page 147 in the paper's supplementary information PDF here.

However, based on more recent TreeMix runs featuring data from Lazaridis et al., I'd say the situation is more complex than just some minor ANE-related admixture in East Asians. I suspect now that all East Asians, including even the Onge, an ancient isolate population from the Andaman Islands, harbor significant ANE-related ancestry that may have arrived in East Asia in separate waves.

Here's what I'm talking about. Note that all of the samples on the East Asian node - Upper Paleolithic west Siberian forager Ust-Ishim, Han Chinese and Onge - are influenced by a massive migration edge from the base of the AG3-MA1 or ANE branch. However, as per the second graph, only the ancestors of more northerly East Asians, like those of the Han, appear to have been recipients of the latest ANE-related admixture into East Asia.

Indeed, when I add the Natufians from the Epipaleolithic Levant to the analysis, Ust-Ishim and the East Asians join AG3-MA1 on the same branch, but now receive a 36% migration edge from a point basal to all Eurasians. This is not admixture from the hypothesized Basal Eurasian clade, but probably from another basal clade, specific to East Asians, which I'd say occasionally shows up as pseudo Sub-Saharan admixture in East Asians.

But obviously, we'll need a solid selection of ancient genomes from across space and time in East Asia to confirm these results. Rumor has it that they're on their way.

See also...

East and West Eurasians seperated at least 45,000 years ago, but...

Modeling Steppe_EMBA

Lazaridis et al. showed that their Steppe_EMBA grouping, which included Afanasievo, Poltavka and Yamnaya, as well as two Potapovka samples, one Russia_EBA sample and one Srubnaya_outlier sample, were best modeled in the following two ways using qpAdm:

Steppe_EMBA
Eatern Hunter-Gatherer (EHG) 0.568
Iran Chalcolithic (Iran_ChL) 0.432

Steppe_EMBA
Caucasus Hunter-Gatherer (CHG) 0.181
Eastern Hunter-Gatherer (EHG) 0.527
Iran Chalcolithic (Iran_ChL) 0.292

I'm not a huge fan of either of these models, but especially the first one, even though I understand that they're both statistically very sound. For one, the uniparental markers don't match, and two, TreeMix seems to disagree (see here).

So let's try something a little different and see what happens when I model Steppe_EMBA as EHG, CHG, and Anatolia Chalcolithic.

Outgroups
Anatolia_Neolithic
Andamanese_Onge
Chukchi
Han
Israel_Natufian
Karitiana
Kostenki14
Levant_Neolithic
MA1
Mbuti.DG
Papuan
WHG

Steppe_EMBA
Anatolia Chalcolithic (Anatolia_ChL) 0.128
Caucasus Hunter-Gatherer (CHG) 0.375
Eastern Hunter-Gatherer (EHG) 0.497

As far as I can tell, it's a very decent fit, especially considering that I'm using 12 outgroups and three reference populations. To me, at least, the standard errors look surprisingly low for such a complex model: 0.033, 0.046 and 0.020, respectively.

Now, I'm not arguing here that Chalcolithic Anatolia is the answer. What I'm saying is that multiple lines of evidence do not support Chalcolithic Iran as a real source of admixture for Steppe_EMBA, and I'm offering what I see as a plausible alternative among the currently available samples.

I know that this is a work in progress for the Broad MIT/Harvard team, and we'll have to wait for more ancient samples and another paper or two before a consensus is reached on the topic.

But here's my prediction: Steppe_EMBA only has 10-15% admixture from the post-Mesolithic Near East not including the North Caucasus, and basically all of this comes via female mediated gene flow from farming communities in the Caucasus and perhaps present-day Ukraine.

See also...

Another look at the genetic structure of Yamnaya