Modelling Admixture with PCA

clearly this makes sense.........just looking at Bergamo and Tuscan you can see the North-Caucasus association with Bergamo and the cypriot association with the Tuscans

good job

And the Mozabite with Bergamo, just lol. I still think that all these results change too much to be plausible. Not to mention that always the same samples have been tested and I think it's unuseful if you don't use exactly the same reference populations. There is no historical association between Tuscans and Cypriots.
 
@Fire Haired.

I found these in the Eurogenes comments. Fire Haired, have you made ​​them?

ANE K8.
Tuscan: 29.75% MN10, 36.45% German Bell Beaker, 33.8% Cypriot: 0.006936
D-stats.
Tuscan: 32.25% MN10, 32.25% German Bell Beaker, 35.5% Near East(26.6% Turksih, 8.9% Georgian): 0.003571
Eurogenes K15
Tuscan: 28.95% Otzi, 36.45% Irish, 34.6% Near East (20.45% Leban_Christain, 6.15% Georgian, 4.15% Samartian, 3.85% Palestinian): 0.008142

ANE K8
West Sicilian: 16% MN10, 22% German Bell Beaker, 58% Cypriot, 4% Mozabite: 0.001823
D-stats.
West Sicilian: 14.1% MN10, 20.85% German Bell Beaker, 60.6% Near East(44.55% Cypriot, 16.05% Turkish), 4.45% Mozabite: 0.00211
Eurogenes K15
South_Italian: 20.9% Otzi, 16.35% Irish, 61.05% Near East(29.75% Cypriot, 22.75% Leban_Druze, 8.55% Georgian): 0.00376

ANE K8
Central_Greek: 27.5% MN5, 29.75% BeloRussian, 42.5% Near East(21.4% Georgian_Laz, 21.1% Cypriot): 0.002436
D-stats.
Greek1: 23.8% MN5, 37.85% BeloRussian, 38.35% Near East(16.3% Cypriot, 13% Turkish, 9.05% Georgian): 0.00164

ANE K8
Spain_Aragon: 54.85% MN30, 31.1% German Bell Beaker, 13.55% Near East(5.3% Cypriot, 8.25% Turkish), 0.5% Mozabite: 0.008961
D stats
Spain_Aragon: 36.6% MN20, 38.2% German Bell Beaker, 23.5% Turkish, 1.7% Mozabite: 0.004955
Eurogenes K15
Spain_Aragon: 37.35% Spain_MN, 47.2% Irish, 15.28% Near East(9.15% Leban_Druze, 6.3% Palestinian): 0.018645
 
I 'm not so astonished by the respectable supposed weight of "Yamnaya" or "steppic" among Basques (and Iberians at a lower level). Looking at diverse studies admixtures and PCA's and Y-haplos, I see some imput come from North in Iberia, even if some proximity can be explained by the partly remaining WHG imput, not so completely different from a element (HG) among "steppic" people. But I admit I don't manage too well all these D-stats and Co...

You are right, "steppic" or "Yamnaya" (=Bell-Beaker?) is not absent in Basques. But it is still lower than elsewhere. Sardinians are the ones who don't have any significant "steppe".
And yes steppe people where partly WHG (being part of EHG) for sure.
 
And the Mozabite with Bergamo, just lol. I still think that all these results change too much to be plausible. Not to mention that always the same samples have been tested and I think it's unuseful if you don't use exactly the same reference populations.

The results change, because there's 50 differnt variables. You can't expect every little decimal to be exactly correct. Yes, there's incorrect 1% Mozabite score, but that doesn't disqualify all the results. Trust me, these results are 90% correct. You'll see them in studies in the next few years, once we get ancient DNA from Spain and Italy.

There is no historical association between Tuscans and Cypriots.

Put yourself in the perspective of someone in 500 BC. There's no historical association between Romans and Sycthians. Yet, it's clear Romans have ancestry from Sycthian-like people.

99.99999% of human history was in pre-history. Writing has existed for a short period and till recently had limited ability to tell us about genetics/history of people movements. Written history in Italy starts shortly before 0 AD. Still, written documents from Italy from before 0 AD don't tell us a lot about the people who lived there. Before that Italy is in pre-history. There were certainly people from West Asia who migrated into Italy, between 2000 BC and 0 AD.
 
Yes, except that WHG in Basques as in Sardinians came mostly with EEF farmers, not Yamnaya people.

This work is showing EEF type "WHG" as "real" WHG and Cypriot is eating up some EEF too. The EEF percentages are too low and the Yamna genes are too high in some populations.


I haven't seen any perfect calculator out so far. Be it Eurogenes, Gedrosia or puntDNAL. Partyl because of personal reasons of the creators and partly because it is hard to find a perfect working solution.
Bell_Beaker is not steppic. Bell Beaker is an Late_Neolithic/Bronze Age phenomenon of Central Europe.
 
@Fire Haired.

I found these in the Eurogenes comments. Fire Haired, have you made ​​them?
..........

Yes. Thanks for posting that. It shows the consistency between several differnt methods.

Basques are definitely no 70% Yamna related. In any of the studies they had the least of it. There is WHG like ancestry getting eaten up as "Yamna".

Basque scored 30% Yamnaya.
 
And the Mozabite with Bergamo, just lol. I still think that all these results change too much to be plausible. Not to mention that always the same samples have been tested and I think it's unuseful if you don't use exactly the same reference populations. There is no historical association between Tuscans and Cypriots.

I think Moesan put it very well.

On one thread we've seen percentages that are all over the place depending on which tool is used. In fact, even using one tool gives different numbers depending on the populations that are fed into the algorithm. Is that supposed to inspire confidence? Not to mention that since people started playing with these programs, we've been treated, at every step of the way, with the confident claim that this is the method, and these are the percentages. Meanwhile, people who don't know the difference between dstats and fstats are convinced dstats are the answer, even in light of the fact that Patterson has said that there are also issues with them. Plus, despite the protestations, results from runs using modern populations in combination with ancient genomes shouldn't, in my opinion, be taken as gospel, just as results adding in Malta should be treated with caution, because it's too old.

It amazes me that there's so little self awareness out there, seemingly no memory about how often their percentages have been so wrong.

To be honest, it's totally turned me off. When the Reich Lab or equivalent comes out with results based on more ancient genomes, I'll take an interest again. Until then, I'm going with the analysis in Haak et al. With every reading of the supplement I'm more impressed with it.

@Alan,
I have to say that when I was following his work more closely, I was impressed that Kurd is at least totally transparent, and acknowledges the issues with all of the methods.
 
@Angela,

The percentages aren't changing very much. The consistency between differnt methods is incredible. I've been getting the same results for over a year now. Trust me, when we get more aDNA, it'll be confirmed. I've explained to you why modern populations(Cypriot) can be used alongside ancient ones and why percentages change a little bit.

Yes, according to Haak a bit less than Tuscans.

According to Haak and the results I've been posting.
 
Bell_Beaker is not steppic. Bell Beaker is an Late_Neolithic/Bronze Age phenomenon of Central Europe.

Yet Bell Beaker is significantly steppic, but of course less than Corded Ware and especially Yamnaya. I believe the steppic element in Basques came from Bell Beakers, although the amount is small.
 
Yet Bell Beaker is significantly steppic, but of course less than Corded Ware and especially Yamnaya. I believe the steppic element in Basques came from Bell Beakers, although the amount is small.

30% is pretty big, considering Yamnaya lived about 5,000 miles away from the Basque country.
 
@Fire-Haired,

You can't constantly change the points in dispute. That isn't how a logical discussion should be conducted. You're jumping from total genome similarity to statements about when that genetic similarity was "baked in". Plus, you're attributing positions to me that I don't hold.

Am I saying that I think there was no genetic input at all into Italy from 2,000 BC to 0AD? That was a rhetorical question. No, I'm not. I know there was such input from the archaeology and history that you so cavalierly dismiss, both from the north with the Gauls and from the southeast with Greeks, if nothing else, both of which movements took place in the first millennium BC. In both of those cases though how do you know the magnitude of the change, or even if there was much of a change in the genetic signature at all, particularly in the south, when we don't have a single ancient Italian genome from south of the most northern region of Italy. How do you know that the people who were in southern Italy in 2000 BC weren't almost identical to the Greeks who later colonized it? How do you know how much "Cypriot like" genetic material they already carried before 2000 BC ?The answer is that you don't, so your claim that whatever percentage of "Cypriot like" genes the Sicilians possess is definitely from after 2000 BC is baseless.

You also fail to grasp that not everyone is obsessed with parsing out how much "additional West Asian" x or y population have or don't have. It's the migrations of various actual pre-historical and historical groups that interests me. Yes, I want to know the impact on our genome of the Anatolian farmers, and the Yamnaya people, but I also want the questions about the Etruccans answered, and maybe the impact of the Greeks and what were they like, anyway, and maybe the people of Crete before them, and the Sea Peoples, and Gauls, and the Lombards, and the Moors in the south etc. I also want to know whether some of the Indo-European speakers who came into Italy from the south might have had a different signature from the ones who went through central Europe, perhaps because they traveled south through the Caucasus and then west. You may not have heard of Drews, but some of us have, and we'd like to know if he was right.

Your "analysis" doesn't answer any of those questions.

Take Spain as an example if you're more familiar with their history. I think the original figure you gave for Andalusia using the PCA based method is 22% Cypriot (I don't think you published the dstat figure for them). You think that Cypriots came to Spain in such numbers that the people of southern Spain owe 22% of their ancestry to them? That was a rhetorical question. They didn't. One big change that did happen is that southern Spain was part of a Muslim Empire for 800 years in some places. The North Africans are basically still considered an EEF/WHG population with a big dose of SSA aren't they? (and we don't know how much SSA they had then) What we need is a "Moorish genome" and a "Spanish genome" from that period to figure out what the percentages are for the two groups, and how much admixture might have affected the modern population. It would be nice to know the changes from the Bronze Age to the Iron Age too. What about the Phoenicians and Carthaginians? I always thought the impact might be rather minimal, but it would be nice to know. What about the Iberian speakers versus the descendants of mixed Celt/Iberians? Perhaps the Iberian speakers were always higher in certain components. This is what archaeologists, historians and the general public want to know. Even then we may not be able to totally nail it down, but at least we'll be in a better position to understand the changes in Europe than with this constant estimating by playing with programs and numbers.

Plus, this is a discussion about whether we should be accepting the latest round of percentages about this overall genome similarity at face value. Just a little while ago, didn't someone want us to believe that the Pathans were 2/3 Eastern European? Even if we use Cypriots as one of the included populations for Europeans, you think it's a trivial matter that the percentage for them goes from 29% to 42% in certain populations depending on which MN group you use? I'm also not sure about using Mozabites as a population, for what it's worth.

I'm sorry, but people should never lose their critical faculties when dealing with abstract theories, not even their own. In fact, if someone is being honest, the best way to figure out the most probable scenarios is to do an exercise where you take an attacking position to find out all the weaknesses present in your theory. Internet people in general, in addition to whatever agenda they may or may not have don't seem to do that enough.
 
And the Mozabite with Bergamo, just lol. I still think that all these results change too much to be plausible. Not to mention that always the same samples have been tested and I think it's unuseful if you don't use exactly the same reference populations. There is no historical association between Tuscans and Cypriots.

It's a fact in all admixture tests , that up to 4% is known as noise ...............erred percentage .............where have you been?:LOL:

Only one to my knowledge has declared that they have eliminated noise, that is test MDLP 23k
 
@Fire-Haired,

Am I saying that I think there was no genetic input at all into Italy from 2,000 BC to 0AD? That was a rhetorical question. No, I'm not. I know there was such input from the archaeology and history that you so cavalierly dismiss, both from the north with the Gauls and from the southeast with Greeks, if nothing else, both of which movements took place in the first millennium BC. In both of those cases though how do you know the magnitude of the change, or even if there was much of a change in the genetic signature at all

You're being too scientific. The sources of differnt types of ancestry in modern Italians doesn't have to trace back to historically known migrations to Italy. I'm not referring to Gauls or Greeks of history, I'm referring to unknown Pre-Historic people who arrived before there was any writing in Italy, and are hard to track in archaeology. If people like modern Greeks are the source of a Near Eastern shift in Italy, then most Italians would have to be like 80% Greek. If people in former Gaulish territory are the source of the Steppe ancestry, Central/North Italians would have to be 40-50% Gaulish. The Steppe ancestry especially isn't just a minor topping, it's very significant.

,
particularly in the south, when we don't have a single ancient Italian genome from south of the most northern region of Italy. How do you know that the people who were in southern Italy in 2000 BC weren't almost identical to the Greeks who later colonized it? How do you know how much "Cypriot like" genetic material they already carried before 2000 BC ?The answer is that you don't, so your claim that whatever percentage of "Cypriot like" genes the Sicilians possess is definitely from after 2000 BC is baseless.

You're right. That's why in the last test results I posted, I only tested Bergamo and Tuscan.

You also fail to grasp that not everyone is obsessed with parsing out how much "additional West Asian" x or y population have or don't have. It's the migrations of various actual pre-historical and historical groups that interests me. Yes, I want to know the impact on our genome of the Anatolian farmers, and the Yamnaya people, but I also want the questions about the Etruccans answered, and maybe the impact of the Greeks and what were they like, anyway, and maybe the people of Crete before them, and the Sea Peoples, and Gauls, and the Lombards, and the Moors in the south etc.

Those are the finer details. With the methods I'm using, all you can do is know the large genetic groupings new people who arrived after 3000 BC were apart of. It's impossible to figure out ethnic or regional origins.

I also want to know whether some of the Indo-European speakers who came into Italy from the south might have had a different signature from the ones who went through central Europe, perhaps because they traveled south through the Caucasus and then west. You may not have heard of Drews, but some of us have, and we'd like to know if he was right.

Who's that?

Your "analysis" doesn't answer any of those questions.

Take Spain as an example if you're more familiar with their history. I think the original figure you gave for Andalusia using the PCA based method is 22% Cypriot (I don't think you published the dstat figure for them). You think that Cypriots came to Spain in such numbers that the people of southern Spain owe 22% of their ancestry to them? That was a rhetorical question. They didn't. One big change that did happen is that southern Spain was part of a Muslim Empire for 800 years in some places.

Do we know anything about the history of people in Spain before 0 AD Some, but probably not a lot. Why is it easier to believe Spanish are 25-30% from Yamnaya-like, than they are 10-25% Cypriot-like? Both could have arrived in large numbers but were left unrecorded in history.

The North Africans are basically still considered an EEF/WHG population with a big dose of SSA aren't they?

Yes. According to D-stats, they're probably about 20% SSA.

Plus, this is a discussion about whether we should be accepting the latest round of percentages about this overall genome similarity at face value. Just a little while ago, didn't someone want us to believe that the Pathans were 2/3 Eastern European? Even if we use Cypriots as one of the included populations for Europeans, you think it's a trivial matter that the percentage for them goes from 29% to 42% in certain populations depending on which MN group you use? I'm also not sure about using Mozabites as a population, for what it's worth.

I dis agreed with those numbers. Using D-stats, I've sucked out the non-Dravidian like part of Pathans, and it looks like a mixture of Andronovo and CHG. SC Asians have lots of EHG and CHG. There's no doubt about it. It isn't MA1, it clearly has WHG inside of it, and EHG is our best representative. I'm not confident about anything, because it assumes they're part Dravidian-like. Results I've seen, does suggest there's lots of Andronovo(Not like any modern Europeans. Andronovo is 80% Yamnaya, no one is close to that today). Either that, or they're largely of EHG/ANE origin. Which is equally possible in my mind considering Y DNA R2 and most mtDNA U2 clades are exclusive to SC Asia. I doubt Andronovo ever went to SC Asia, because their form of Z93 is mostly found in Central/North Asia.

I'm sorry, but people should never lose their critical faculties when dealing with abstract theories, not even their own. In fact, if someone is being honest, the best way to figure out the most probable scenarios is to do an exercise where you take an attacking position to find out all the weaknesses present in your theory. Internet people in general, in addition to whatever agenda they may or may not have don't seem to do that enough.

I am too confident sometimes. I do take the attacking position too. The stats I post here, are the what I do after going on attack mode. I test every possibility. I just posted a stat, modelling Italians as Otzi+Yamnaya+all modern non-Europeans. It's an unbias test to see what differnt about modern Italians and Otzi.
 
Caucasus hunter-gatherers (CHG) also spread into South Asia and Central Asia and some populations in these regions have the CHG ancestry. The Yamnaya culture originated in the Pontic steppe spread westwards into Europe and east into Central Asia (Jones et al. 2015). For example, the Uyghurs in wetern China are culturally and genetically linked to the Yamnaya culture and haplogroups R1a and P*(xR1a), which are associated with the CHG ancestry, are also found in Mongolia at moderate frequencies. Moreover, less than few percents of the Korean population belongs to these haplogroups and I wonder if ancient Korean kingdoms were founded by the Caucasus steppe herders.

In modern populations, the impact of CHG also stretches beyond Europe to the east. Central and South Asian populations received genetic influx from CHG (or a population close to them), as shown by a prominent CHG component in ADMIXTURE (Supplementary Fig. 5; Supplementary Note 9) and admixture f3-statistics, which show many samples as a mix of CHG and another South Asian population (Fig. 4b; Supplementary Table 9). It has been proposed that modern Indians are a mixture of two ancestral components, an Ancestral North Indian component related to modern West Eurasians and an Ancestral South Indian component related more distantly to the Onge25; here Kotias proves the majority best surrogate for the former28, 29 (Supplementary Table 10). It is estimated that this admixture in the ancestors of Indian populations occurred relatively recently, 1,900–4,200 years BP, and is possibly linked with migrations introducing Indo-European languages and Vedic religion to the region28.

We investigated the temporal stratigraphy of CHG influence by comparing these data to previously published ancient genomes. We find that CHG, or a population close to them, contributed to the genetic makeup of individuals from the Yamnaya culture, which have been implicated as vectors for the profound influx of Pontic steppe ancestry that spread westwards into Europe and east into central Asia with metallurgy, horseriding and probably Indo-European languages in the third millenium BC5, 7. CHG ancestry in these groups is supported by ADMIXTURE analysis (Fig. 1b) and admixture f3-statistics14, 25 (Fig. 5), which best describe the Yamnaya as a mix of CHG and Eastern European hunter-gatherers. The Yamnaya were semi-nomadic pastoralists, mainly dependent on stock-keeping but with some evidence for agriculture, including incorporation of a plow into one burial26.
 
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The reason the scores change is the differnt ancestors are made up of the same older components. Cypriot and EEF are made up of a lot of the same stuff. Cypriot can swallow some EEF and vice versa. I explained to Anegla why in D-stats(not PCA), Cypriot is a good Near Eastern proxy. Their unique recent history has no affect.



You've got to understand the genetic diversity in West Eurasia 10,000 years ago was much greater than it is today. Modern day Europeans are all a fusion of the same Holocene era populations. We can differentiate differnt ethnic ancestries in Europe today, but no population in Europe has accumulated 1,000s of years of unique evolution, like Holocene era West Eurasians had.

In these tests, the main sources of diversity in Europe, are differnt ratios of ancestry from the same Holocene era populations. Local ethnic and region ancestry has hardly any affect. There's really no difference between English and Czech or Tuscan and Spanish, even though they have no ethnic or regional connections. We can't identify the exact ethnic or regional origin, of the people who migrated into Spain and Italy after 3000 BC. However, with genomes from Spain and Italy dating 3000 BC, we can get a good idea what large genetic groupings the people migrated into both places after 3000 BC were apart of. We can't get ethnic/regional/cultural/etc information, because it makes a small affect on DNA.


I understand your point as a whole:
Some details: English and Spanish and Czech people ARE NOT THE SAME; they are just close compared to some of their "parents" before "wedding" in Europe (or elsewhere).
Even the old populations taken as references are not always PURE populations if ever; I don't know how scentists isolated Yamanya DNA imput; surely Yamnaya people were not born from a moon population without contacts with other ancestors of ours. But I 've some confidence in these scientists (obliged!) The distances calculations you produced, you and others, with diverse (unrelatied in time) populations HAVE ALL OF THEM SOME SIGNIFICATION; the question is the degree of accuracy of our interpretations of this signification.
ex: CHG: can we date seriously the introgression(S) of CHG into India and into the Steppes, with these calculations? concerning History, source and target this has some weight.
Keep quiet: I read often if not always what you and others post (lack of time), but I avow I'm going very more slowly to jump to conclusions. No offense, you know I have nothing against anybody (why would I have?).
 
This work is showing EEF type "WHG" as "real" WHG and Cypriot is eating up some EEF too. The EEF percentages are too low and the Yamna genes are too high in some populations.


I haven't seen any perfect calculator out so far. Be it Eurogenes, Gedrosia or puntDNAL. Partyl because of personal reasons of the creators and partly because it is hard to find a perfect working solution.
Bell_Beaker is not steppic. Bell Beaker is an Late_Neolithic/Bronze Age phenomenon of Central Europe.


BBs are still a kind of mystery to me, and I manipulate the concept with caution because I believe there has been BBs and BBs. BBs were not an Iberia "product" only and I think their starting point was in East, not in West, whatever the road they took. And let's keep in mind the steppic introgressions are older than EBA in Central East Europe, if we rely on archeology. Some mixture was already present too in early period of Cucuteni-Tripolje if I rely on someones (Wikipedia? Forgotten)
 
What is it PCA?

It looks at variables(for example, DNA markers) in populations and then plots those populations on a graph based on those variables. So, the more related a population is the closer they will plot with each other on a PCA.
 

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