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Monday, November 28, 2016

Fund-raising offer: Basal-rich K7 and/or Global 10 genetic map


I'm now taking donations for 2017. Anyone who donates $12 USD or $16 AUD, or more, will get the Basal-rich K7 ancestry proportions. Of course, you'll need to send me your genotype data for that to happen (Ancestry.com, FTDNA or 23andMe).

The Basal-rich K7

Please send your non-tax deductible donations via PayPal to eurogenesblog at gmail dot com. E-mail your genotype data to the same address. Please don't assume that I already have your data. I'll try and get back to everyone within a day and will put things on hold if that becomes an unrealistic target.

Using your Basal-rich K7 ancestry proportions, I'll show you where you cluster in the new and improved Fateful Triangle. Many people will probably land somewhere along the cline made up of Late Neolithic/Early Bronze Age Europeans and Middle/Late Bronze Age steppe herders and warriors. This, to me, looks like a cline produced by the expansion of early Indo-Europeans into Western and Central Europe.


For an extra donation of $16 USD or $21 AUD, those of you feeling more adventurous will also receive the Global 10 genetic map, and, more importantly, coordinates for ten dimensions.

A fresh look at global genetic diversity

The Basal-rich K7 is the best ancient ancestry test that I've been able to come up with. It correlates strongly with latest research reported in scientific literature. And, in fact, in some instances it probably trumps latest scientific literature.

For instance, Broushaki et al. 2016 characterized Early Neolithic farmers from the Zagros Mountains, Iran, as 62% Basal Eurasian and 38% Ancient North Eurasian-related (Figure S52). This, considering formal statistics like the D-stat below, with AfontovaGora3 (AG3) as the ANE proxy, is unlikely to be correct, despite the fact that AG3 is a relatively low quality sample.

D(Yoruba,Iran_Neolithic)(Villabruna,AfontovaGora3) 0.0223 Z 2.812

On the other hand, the Basal-rich K7 models the early Zagros farmers as 39.05% Ancient North Eurasian and 56.67% Basal-rich (which is probably a composite of Basal Eurasian and something Villabruna-related). To me this appears to be the more sensible solution.

Moreover, Lazaridis et al. 2016 characterized South Caspian forager Iran_HotuIIIb as more Basal Eurasian than the early Zagros farmers (Supplementary Information 4). The Basal-rich K7, on the other hand, shows the opposite. The D-stat below suggests that the Basal-rich K7 is closer to the truth.

D(Chimp,Ust_Ishim)(Iran_Neolithic,Iran_Hotu) 0.0156 Z 1.337

There are other such examples, and I might post them in the comments. In any case, the point I'm making is that the Basal-rich K7 is a solid piece of work and it's likely to remain relevant for a long time. Indeed, I'll be updating the Basal-rich K7 spreadsheet regularly as new ancient samples roll in, which means that you'll be able to model yourself as newly sampled ancient populations using the Basal-rich K7 ancestry proportions (for instance, see here).

The only problem with this test is that it's optimized for Eurasians. As a result, it might be sensible for anyone with significant (>5%) Sub-Saharan ancestry to skip the Basal-rich K7 and just ask for the Global 10 genetic map and coordinates.


You can use the Global 10 coordinates to model your ancient and recent fine-scale ancestry, just as you would using mixture proportions. In fact, I'd say the Global 10 coordinates are more useful in this respect than any mixture test, including the Basal-rich K7.

Thanks in advance for your support. Keep in mind that the more cash I raise the busier things will be on this blog in 2017, which, by all accounts, is shaping up to be the year for ancient DNA.

79 comments:

khana said...

Awesome! Have been waiting a while for this calculator.

Kurd Dgk said...

Good work David! They look like some very informative tests , which will lend an informative new perspective not offered by the existing calculators at Gedmatch. You have my thumbs up.....

khana said...

@Kurd Dgk

He is running some samples for me. I'll post them on AG so we can all have a good look!

Kurd Dgk said...

Sounds good Khana....I'll also be sending him one of my Kurd samples.

Eren said...

@Davidski:
Do I understand this correctly: Basal-rich K7 + Global 10 = $28 USD? Or $16 USD for both?

Helgenes50 said...

Thanks David

Davidski said...

@Eren

Basal-rich K7 + Global 10 are $28 USD.

But you can just ask for the Global 10 if you like.

...

First results will be mailed out in a couple of hours.

David Rabaez said...

Hi Davidski, I am R1b> U152> L2. The information provided by 'Basal-rich K7' ancestry proportions + 'Global 10 genetic map' could be useful for me. Would it be useful for the community? What data would you need? Chrom_Autoso, Autosomal_o37_Results, or XChromosome_o37_Results?

What would be the approximate date the information would receive? Would it come with some description text for beginners?

Regards

Thanks

Davidski said...

These tests are for fairly advanced users, and probably for those who are familiar with the topics covered on this blog.

I won't be able to spend much time discussing the results with people over e-mail. But all of the information is on this blog, and there are lots of people active in the comments here who can analyze and comment on the K7 and Global 10 output.

I think Autosomal_o37_Results should be fine. Any genotype file with data from the 22 autosomal chromosomes will work.

Onur said...

@Davidski

What should we do if PayPal does not give service to our country?

Davidski said...

I don't know. I'll look into it.

Samuel Andrews said...

@David,

How many SNPs are you using for each product(Basal-rich K7, Global10) according to testing companies.

Number of SNPs for 23andme:
Number of SNPs for FTDNA:
Number SNPs for AncestryDNA:

Davidski said...

Well over 200K for each type of file, so the exact counts make no difference. That's plenty enough for accurate results.

Simon_W said...

Nice offer, but I'm not liquid right now. I'll come back to this in about a week.

FeyliDNAprojectadministrator said...

Hello!

Will we see a test with an accurate ASI/ENA ancestry?

Davidski said...

@Simon

Yeah, no hurry, this will be up over the whole Xmas/New Year season.

@FeyliDNA

I'm pretty sure this is accurate for ASI/ENA.

Although please keep in mind that at some point I will create a single ASI component for the K7 when the relevant ancient genomes from South Asia come in.

But the Globe 10 will always be current, because all I have to do is stick new ancient samples in the sheet so that they can be used as references.

Simon_W said...

Great, thanks.

Samuel Andrews said...

I know this isn't the threat for discussion but I have to say I'm impressed especially by the Global10 PCA. If you only want to buy one test you should buy Global10.

It's gives what look like accurate precise percentages. It's surprisingly able to pick up my very slight non-European ancestry; 3% Native American and 1-2% West African.

@D=0.005708
"English_Kent" 69.1
"Spanish_Castilla_y_Leon" 26.9
"Clovis:Anzick" 2.95
"Yoruba" 1.05
"Norwegian" 0
"German" 0

Davidski said...

I don't think most people who have been looking for a test like this have any clue how valuable it is.

Sadly, they'll keep playing around with all of the other crap out there and never have a clue.

Helgenes50 said...

Global 10 and nMonte2 results
By using only the populations before the bronze age.


English_Cornwall

"Yamnaya_Samara:I0429" 34.4
"LBK_EN:I0054" 24.95
"Baalberge_MN:I0559" 10.3
"Hungary_HG:I1507" 9.95
"LBK_EN:I0056" 8.15
"Motala_HG:I0015" 5
"Yamnaya_Samara:I0444" 4.75
"Iberia_Chalcolithic:I1303" 2.5

French_South

"Yamnaya_Samara:I0444" 26.9
"Barcin_Neolithic:I1096" 16.35
"Baalberge_MN:I0560" 15.05
"Iberia_Chalcolithic:I1284" 14.2
"LBK_EN:I0054" 7.65
"Baalberge_MN:I0559" 7.4
"Motala_HG:I0014" 6.55
"Iberia_MN:I0405" 3.35
"Loschbour:Loschbour" 2.55

Normand ( Helgenes)

"Iberia_Chalcolithic:I1284" 17.45
"Yamnaya_Samara:I0441" 17.45
"Salzmuende_MN:I0551" 14.25
"Loschbour:Loschbour" 13.5
"LBK_EN:I0048" 10.85
"Iberia_Chalcolithic:I1303" 10.45
"Afanasievo:RISE507" 7.7
"Satsurblia:SATP" 6.15
"Yamnaya_Samara:I0429" 2.2

Helgenes50 said...

@ David,
I don't think most people who have been looking for a test like this have any clue how valuable it is.

Sadly, they'll keep playing around with all of the other crap out there and never have a clue.


Yes, it's very sad, your K7 and Global 10 are very great.
That already was the case for K8, with results pretty similar.

Gui S said...

I think you already have my data (FR7). Either way, I sent my little contribution!
Cheers!

Balaji said...

How do we contact you by email?

khana said...

@Davidski: I've been encouraging people to at least opt for the Global 10. Hopefully, you've got some requests in! I've been adding everyone that posts their coordinates to a plot.ly plot. Should be interesting. Question, in your opinion is it more accurate to plot the Global 10 with 2PC or 3PC? I've done both, but for now I'm plotting with 2PC to match up with your plot. The 3D-PCA seems to better reflect the Basal-rich K7 oracles. BTW, we've attempted to make some admix-4 Oracle files from the Basal-rich test by only using the averages and separating the moderns and ancients into respective files.

Any word on my Global 10 modeling?


@Helengenes50: Have you posted the nMonte files on AG? I'm curious to give it a try. Have you made an nMonte file for the moderns as well?

Davidski said...

@Gui

I'll get back to you this weekend.

@Balaji

The e-mail is listed in the post above.

@Khana

I'd go with 3D PCA. More data that way, so more accuracy.

I've seen your work at AG. Not sure if I'll be able to give you more insights than you can get yourself, but considering your Y-HG, I'll try some formal stats models once I manage this first wave of requests.

khana said...

@Davidski

Thanks! No rush. I'm a patient man.

Folks are asking what the average turnaround time is to expect results back from you. I told them to assume 2 days, is that a fair estimate?

Davidski said...

Yep, it's two days now.

David Rabaez said...

@Davidski Donation made :)

All for science!!!

Thanks

Regards

Вячеслав Слава said...

And this calculator will be in free form in Gedmatсh?

Davidski said...

This analysis won't be at GEDmatch.

CleverPrimate said...

I'm on board and looking forward to the results.

Davidski said...

Needless to say, if anyone gets results that are a bit strange for one reason or another, then get back to me ASAP and I'll try to find the problem. Mistakes can and do happen.

Sam Hilsen said...

I'm not seeing the donate button - how do I donate?

Davidski said...

Via...

eurogenesblog at gmail dot com

Sam Hilsen said...

Done :)

Unknown said...

Hello could you test some saudi samples(especially basal eurasian rich ones) and put them on a PCA? Some saudis are supposed to be 89% basal eurasian so they seem to be the best proxy for BE.

Davidski said...

I've added a few Saudi samples to the K7 spreadsheet. They're representative of around 20 Saudi individuals that I have.

https://docs.google.com/spreadsheets/d/1tFAa7oxWpcNN-OdMMjBdb4NeWKG7EkpKMzZJVW2_MME/edit?usp=sharing

Since they only have around 69% of Basal-rich admixture, then based on my current estimates it's unlikely that they have more than 35% Basal Eurasian ancestry.

Onur said...

I have written a guide for people who participated in one or both of Davidski's Basal-rich K7 and Global 10 tests on how to run their test results with nMonte and 4mix_multi.

https://drive.google.com/file/d/0B9n4j3PQ81RcRlFWTWczNDR5Q0ZrSWVNT0tDYlNoV01TTnVB/view?usp=sharing

Also on Anthrogenica:

http://www.anthrogenica.com/showthread.php?9291-An-nMonte-and-4mix-Guide-for-the-Participants-of-the-Basal-rich-K7-and-or-Global-10-T

Unknown said...

What does basal-rich mean exactly, because I remember seeing some saudi admixture charts previously and some of them had like an almost zero WHG and ANE with over nearly 90% ENF and some SSA admixture then what is contained in ENF? Is it basal+some still uncategorized OOA isolate admixture because it can't be just UHG-WHG since some saudis have zero or almost zero of UHG-WHG. Have you added early Zagros farmer samples? I see some ancient Iran samples but not sure if any of them are from the earliest Zagros farmers, who may have had more basal than Jordanian EBA. Wouldn't it be a problem to add modern Qatari samples too.

Unknown said...

By the way, I've some additional questions. Do we know if ENAs like mongoloids and australoids had multiple ancestral groups like europeans(WHG, CHG, EEF etc) or they evolved from a single population and just drifted apart without extensive mixing with other unrelated populations. SE asians have ASI admixture that differentiates them but their mongoloid component seems to be also genetically distinct from the main component in Japanese, Koreans and Han chinese. Studies about the ancestry of prehistoric ENAs and sub-saharans seem to be very lacking compared to europeans and middle easterners. I couldn't really find anything. Speaking of which, amerindians and Uighurs are mostly east asian+ANE yet they look nothing alike. I know Uighurs have additionaly some WHG but such a difference in appearence can't be explained just by that. Is it because of them containing different types of east asian or is it the genetic drift? Same with amerindians, they are poorly modeled by a mix of modern east asians and ANE so do they contain some ancestral east asian population that is poorly represented in modern east asians? The same problem is with africans we know negroids and capoids are distinct and so are the west africans and east africans but do we know why are they different(aside from the obvious basal admixture in horners and some east africans) and what ancestral populations these africans contain? Same with Papuans, Onge, and Australian Aborigenes who are related yet all look very different and we know there were multiple waves of australoids, yet they don't seem to have any concrete categorizations like CHG, ANE etc.

Davidski said...

You have to be careful when comparing different tests. Sometimes the cluster names are similar or the same but you'll be looking at very different phenomenon.

In this K7, the Basal-rich cluster is essentially Villabruna-like UHG mixed up with something Near Eastern, or maybe even African, that is more basal and, I suppose, closer to the Out of Africa bottleneck. Here's a PCA showing how the seven components relate to each other in the main two dimensions.

https://4.bp.blogspot.com/-RfmYb9e6riM/WE_m0x07WiI/AAAAAAAAFHg/ik-D0M6BO4EQOsueYkRfdYtXS2c3kkILwCLcB/s1600/K7_PCA.png

I think the Basal-rich cluster will end up approximating closely a real ancient population from the Near East. On the other hand, I have some doubts whether anyone will actually find a pure Basal Eurasian sample. The reason I say that is because the Epipaleolithic Natufians from Israel already have some UHG and they're nowhere near pure Basal.

The ancient Iranian samples in the spreadsheet include the earliest Neolithic farmers. They're not very Basal either. They appear have some minor Central Asian and/or ANE-related ancestry that makes them look much more Basal than they are in some tests.

I do have some Qatari samples, but not sure where at the moment. From memory they show a lot of variation and admixtures from various places.

I've blogged quite a bit about East Asians. You can find those posts using the search box. But most of that stuff is speculation, because we're still waiting for some decent genomes from Eastern Asia.

Unknown said...

So I get that nobody categorized ancestral ENAs and Africans yet because there is not enough data? With africans I guess it's because DNA didn't survive in the hot climate of Africa but yet again ME is even hotter but they found quite a lot of prehistoric DNA there. However Asia should have a lot humid places where DNA can survive for a long time so this is strange. Do you have any Emirati samples? I couldn't find any studies about UAE either. Have you checked a few available prehistoric african samples like Jebel Moya and KNM-LH1, not sure if I remember it right but Kumptepe6 and GD13A may have been african too.

Davidski said...

There's only one ancient African genome available at the moment: Mota.

He comes out mostly Sub-Saharan/Basal-rich in the K7, roughly 70/30.

Unknown said...

Mota's DNA unfortunately isn't very iterersting as that guy was just a proto-horner but paleolithic africans had very different looking skulls than than later semi-modern negroid types thus there probaby was a population shift in Africa.
Do you know if there are any prehistoric asian genotypes available other than Tianyuan's whose primary genetic component according to Geniteker's blog was australoid but starting to evolve towards amerindians and mongoloids. We need something more recent than Tianyuan butnot too young.
https://genetiker.wordpress.com/2013/12/02/more-analyses-of-the-tianyuan-genome/comment-page-1/

https://genetiker.wordpress.com/2015/06/24/analyses-of-the-oase-1-genome/

Speaking of australoid, ANE according to admixture programs is something like a blue north european(but a north european divergent from WHG as they show 0% WHG)+ green Karitiana like Amerindian+ Purple ASI/South Asian and he is even showing small red and orange negroid and capoid components. You can see his proportions here http://img.4plebs.org/boards/pol/image/1457/11/1457117821718.png
We poles have around 20% ANE so do you know if we're showing any australoid admixture because I know north caucasians who've even higher ANE do show some and a majority of Europeans show the amerindian component which must be from ANE. http://img.4plebs.org/boards/pol/image/1398/88/1398888033132.png

Unknown said...

Your Iranian Hotu sample has strangely small basal admixture, it's supposed to be the most basal-rich sample yet with over 60% basal.
https://abload.de/img/hotu13up0.png

Davidski said...

The paper discusses why Iran Hotu might not be more Basal than the Iranian Neolithic farmers. Have a look at the supplementary info.

And this is what I say in the post above...

Moreover, Lazaridis et al. 2016 characterized South Caspian forager Iran_HotuIIIb as more Basal Eurasian than the early Zagros farmers (Supplementary Information 4). The Basal-rich K7, on the other hand, shows the opposite. The D-stat below suggests that the Basal-rich K7 is closer to the truth.

D(Chimp,Ust_Ishim)(Iran_Neolithic,Iran_Hotu) 0.0156 Z 1.337

Unknown said...

Hello again, could you add amerindians to this PCA https://4.bp.blogspot.com/-RfmYb9e6riM/WE_m0x07WiI/AAAAAAAAFHg/ik-D0M6BO4EQOsueYkRfdYtXS2c3kkILwCLcB/s1600/K7_PCA.png
ANE, Villabruna cluster and basal-rich are suprasingly close to each other. Does this mean a pure WHG without ENA could have been closer to a pure basal eurasian than to ENAs like mongoloids and autraloids?
By they way, was CHG just basal eurasian+ANE and isolation or did it also have WHG-UHG admixture? Did you ever run admixture tests on CHGs like Sintasha and Satsurblia?

Unknown said...

Also what populations exactly are the southeast asians on your PCA, why are they so close to oceanians yet so far away from east asians? That suggests they're heavily admixed.

Davidski said...

I can't add Amerindians to that PCA because there's no Amerindian cluster in the K7 test. Amerindians are a mixture of East Eurasians, Ancient North Eurasians and Southeast Asians.

You can see the populations that make up the Global 10 PCA by plotting this sheet with any graph plotting software, like Past3 or Excel.

https://drive.google.com/file/d/0B9o3EYTdM8lQd1hLRFl4OUdiME0/view?usp=sharing

Unknown said...

Do you have some other test where amerindians can be added? They are a mix but a special one since they developed unique racial features distinct from asians and other ANE admixed populations due to isolation in America. Moreover could you add papuan, australian aborigene, paniya or ust ushim cluster to http://eurogenes.blogspot.com/2016/11/fund-raising-offer-basal-rich-k7-andor.html because oceanian doesn't seem to fully model ASI/australoid admixture as boloch should have at least 20%.
Srubnaya and Kotias samples have WHG admixture according to your diagram but did CHG had it from the beginning like EEF during its differentiation or acquired it later in Europe?

Davidski said...

You can see where Amerindians cluster on the Global 10 plot. They look like a mix of East Eurasians and Ancient North Eurasians. That's just what they are.

ASI in the K7 test is a composite of East Eurasian, Oceanian, Southeast Asian and probably minor Ancient North Eurasian. That's how Mesolithic South Asians will probably come out in the K7. No point adding any other eastern clusters for now.

Balochs don't have 20% ASI. They have 10-15%, which is what the K7 shows.

Unknown said...

I found here http://www.eupedia.com/forum/archive/index.php/t-32990.html that MA1 was: Siberian:1.6%, Oceanian: 3.3%, WHG:16.3%, Sub-Saharan:0.5%, Hindu-Kush:24.4%, Steepe:33.8%, Amerindian: 20.1%

Davidski said...

Those test results are nonsense.

MA1 is just ANE, and Amerindians are part ANE.

Davidski said...

Alternative e-mail for raw data...

dpwes at hotmail dot com

jv said...

So I need an Autosomal DNA test so I can find this out, I guess! I've seriously have been identifying with my ancient maternal line from the Pontic-Caspian Steppe( to a fault says my husband!) I'm afraid my paternal line will give me a big old dose Neolithic LBK genes as my paternal Grandma was mtDNA K2a. My mtDNA is H6a1a2b1. But of course, there are lots of other ancestors to mix it all up. That's why I love mtDNA. It's so pure! jv

Unknown said...

ANE seems to be a hybrid component like ASI and EEF and CHG. It looks like a hybrid of proto-whg, proto-amur river(gene flow could have been in both directions) and something south asian/australoid/ASE related.
Studies show this http://www.nature.com/articles/ncomms9912
http://s1.zetaboards.com/anthroscape/topic/5955645/1/

Davidski said...

ANE can't be a mixture of EEF and CHG, obviously because it doesn't have any Basal Eurasian.

Unknown said...

I'm not saying it's a mixture of EEF and CHG but it seems to be a mixture of a west eurasian of some kind most likely related but older than WHG, amur-river like proto-amerindian mongoloid and some kind of australoid, related to australoid admixture in modern south asians. Just like EEF is ENF+WHG and CHG seems to be ENF+ANE+small amount of WHG. MA1 also seems to have very small capoid admixture according to these admixture diagrams on zetaboards.

Davidski said...

That discussion about MA1 on Anthroscape is garbage. I'm not sure why you think that forum is a useful source for anything?

Unknown said...

They didn't make thi image with admixture ratios http://2.bp.blogspot.com/-YECMQQMgnlk/VFw0eBTGjRI/AAAAAAAAJ14/itneofdPteI/s1600/F1.large.jpg
It's from some study and that smaller picture is from K9.

Unknown said...

By the way it seems basal eurasian/farmer admixture diluted americoid/Amur/Siberid admixture in Europeans since the majority of Mesolithic HGs had at around 10% siberian(except maybe Bichon and K01?) and ANE had both siberian and amerindian admixture though Europeans still show it now.
http://s1.zetaboards.com/anthroscape/topic/5331473/1/

Davidski said...

But they're reading it incorrectly because they don't know how to read or use these types of algorithms.

Admixture is not a formal mixtures test, so in most analyses it shows affinity not ancestry proportions.

Based on formal models it's clear that those clusters have MA1-related admixture. In other words, Caucasians and Indians have ANE, rather than ANE being part Cauacsus or Indian.

Davidski said...

You're not very good at this. You need to educate yourself in formal statistics. Come back when you've done that.

Unknown said...

No shit,I never said ANE is native to Caucasus or India. It seems to be native to areas around Siberia, nonetheless it spread around in admixed populations and according to Lazaridis there could have been a gene flow from ANE-like populations(or even from pure amur like populations) to WHGs that's why they show admixtures of siberian and amerindian types of east eurasians.

Davidski said...

You're all over the place at the moment. Seriously, read the sections on formal stats in a few of the recent ancient DNA papers and then get back into the debate. This is something that anyone interested in this sort of stuff has to do, instead of reading the discussions at Anthroscape.

Unknown said...

I already did that's why I'm discussing now.

Davidski said...

Then why did you use an Admixture bar graph to claim that MA1 was mixed?

Unknown said...

Well there are two options it was mixed or it was ancestral to these groups but from what we know it seems to be both mixed and ancestral to these groups and many other. Gene flow has been in both directions in this case. All points to ANE being a mix of proto-west eurasian, proto-siberian/amerindian like east eurasian and australoid, We know pure australoids don't have any ANE so it couldn't be ancestral to them.

Onur Dinçer said...

@Unknown

All points to ANE being a mix of proto-west eurasian, proto-siberian/amerindian like east eurasian and australoid, We know pure australoids don't have any ANE so it couldn't be ancestral to them.

You are still talking based on the ADMIXTURE results. Formal statistics show that BOTH WHG and ANE (also SHG and EHG) have some connection with East Asians and Amerindians, and not with Australoids, but the direction(s) and timeline of the gene flow are still hotly debated, we need ancient East Asian genomes to have a better grasp of them.

Unknown said...

ANE can still be related to australoids too because some prehistoric mongoloid strains were inbetween mongoloids and australoids like Minatogawa Man.

Onur Dinçer said...

Well, by Australoid I meant Aboriginal Australians, Papuans and Melanesians.

Unknown said...

ASI is racially mixed but predominantly australoid component. In K7 ASI is 22% Papuan, 19% Nganasan, 23% Atayal, and 36% Onge
ASI os genetically very similar to Ust-Ishim, 83% ASI Paniyas cluster near him. Siberian admixture in ASI probably makes south asians so much related to ANE because they already had it and received even more from Yamnaya/Aryans.
Amerindians have significant north european and south asian(australoid as ''pure'' amerindians don't have basal eurasian) genetic components. They most likely got them from ANEs who also had them.
https://genetiker.wordpress.com/2015/03/22/k12b-analysis-of-prehistoric-and-modern-genomes/

Onur Dinçer said...

@Unknown

As long as you stick to the ADMIXTURE results and ignore the formal tests, we will not agree with you.

Unknown said...

Do what you want but admixture results agree with each other and formal distance results can be confounded by multidirectional geneflows+things like drift, meiotic drive, isolation, mutations and natural/sexual selections so some alleles can be lost, gained or mutated even in very similarly admixed populations and change distance due to different allele frequencies.

Davidski said...

You've got things backwards, as usual.

D-stats and f4-stats are based on allele correlations deep in the phylogeny, so they're less likely to be skewed by recent drift, unlike Admixture, which mostly relies on recent drift in tests above a couple of clusters or K.

Unknown said...

By recent, you mean how recent? Drift is a random change in allele frequency unrelated to gene flows, natural selection and mutations. If amerindians received north european(WHG-like) and south asian(australoid-like) components through drift it still means there were WHG/australoid and/or australoid/WHG/ANE admixed individuals among them from the beginning, they just later spread more of their alleles among populations due to some random events. However Anzick and Kennewick show the same components so this isn't a recent drift.
D and F4 stats aren't be all end all and ignoring all admixture component resuls is foolish.
Some admixtures skew results of other admixtures in D-stats.

Davidski said...

I ignore all Admixture results when I'm looking at ancient ancestry, and only use Admixture to reproduce patterns that I see with formal stats and models, by calibrating my Admixture tests to avoid recent drift, like Jewish-specific, Balto-Slavic-specific, Kalash-specific, etc. drift.

This is the smart thing to do. Not foolish.

Unknown said...

Well in my opinion it would be more useful if you used admixture results more. Since all of them can be skewed by many factors so PCA plots and formal stats alone don't tell the whole picture. Genetic drifts is revelant the most in small inbred populations because in such populaions alleles can reach fixation pretty fast. Of course you can have two small populations with identical genotype/admixture components and if you separate them for thousands of years in different evironments and prevent them from mixing with other populations then they will become somewhat different due to evolutionary mechanism however admixture software should still show that they have the same amcestral components.
So the best option is to make admixture graphs, pcas and stats, all with a few types of software and compare results.
Admixture results are very useful because thanks to them you can to an extent see historical ancestry of pupulations and in case of paleolithic populations(often even more ''mixed'' than modern ones according to the admixture, probably due to being less differentiated and ancestral, though some were already truly mixed even back then) you can extrapolate evolutionary process of races, populations and traits.

Unknown said...

By the way, do we finally know what Unknown Hunter Hathere(UHG) is?
I read that basal eurasian mixed with UHG to create the original proto-semitic population ENF that later mixed with WHG and ANE to create respectively EEF and CHG after long periods of isolations. However ENF and EEF were both largely replaced by CHG in the Middle East and today ENF peaks only among bedouins, some saudis and iraqis but is mostly mixed. Had full UHG genome been ever found and how far away was it from WHG? Was it just WHG without amerindian like east asian admixture, can someone tell me?