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Fire Haired14
30-03-16, 23:34
I'm opening this thread for postings of admixture proportions from a PCA. I already have a thread for posting admixture proportions from D-stats, here (http://www.eupedia.com/forum/threads/32091-Modelling-Admixture-with-D-stats).

Fire Haired14
30-03-16, 23:39
David Wesolski at Eurogenes, has created a global PCA with 50 dimensions. Normal PCAs only have 2 dimensions. His PCA has so many dimensions it is impossible for our eyes to comprehend it. He posted the locations of all the global samples in all 50 dimensions, to use to produce admixture results.

I've been playing around with Europe, and the results are 100% consistent with everything we've seen before.

Here are some results.


Population
Yamnaya_Samara
Loschbour
Sweden_MN
D statistic


Czech
51
4
45
0.0097


Belarusian
55
13
32
0.0172


Lithuanian
56
21
23
0.0177


Norwegian
49
7
44
0.0082


Andronovo
73
3
24
0.0105






Population
Cypriot
Hungary_CA
Mozabite
Yamnaya_Samara
D statistic


Italian_Bergamo
10
66
0
24
0.0148


Italian_EastSicilian
48
37
2
13
0.0096


Italian_Tuscan
30
48
0
22
0.0109


Italian_WestSicilian
46
37
2
15
0.0098






Population
Cypriot
Iberia_Chalcolithic
Mozabite
Yamnaya_Samara
D statistic


Spanish_Andalucia
22
51
3
24
0.0081


Spanish_Aragon
13
60
1
26
0.0079


Spanish_Baleares
20
50
1
29
0.0094


Spanish_Cantabria
12
58
1
29
0.0079


Spanish_Castilla_la_Mancha
20
55
0
25
0.009


Spanish_Castilla_y_Leon
15
51
7
27
0.0091


Spanish_Cataluna
15
52
3
30
0.0103


Spanish_Extremadura
18
48
6
28
0.0102


Spanish_Galicia
18
49
5
28
0.0081


Spanish_Murcia
19
52
3
26
0.0078


Spanish_Pais_Vasco
0
70
0
30
0.0117


Spanish_Valencia
17
55
1
27
0.0086

ElHorsto
31-03-16, 00:13
Spanish_Pais_Vasco
0
70
0
30
0.0117




Yamnaya is unusually high for Basques. Probably because there is much Loschbour in Yamna?

Angela
31-03-16, 00:34
It's also too high for Spaniards, and for the same reason.

Also, this doesn't tell us anything about the gene flows that formed the Spanish and the Italians; there was no migration of "Cypriots" into those countries at the kind of levels which would be required to get these kinds of admixture results.

I'm not even sure that it's accurate for northern Europeans. The Yamnaya percentage might be inflated by high WHG/EHG genes that were absorbed as the actual Yamnaya type people moved across Europe.

ElHorsto
31-03-16, 00:45
I'm not even sure that it's accurate for northern Europeans. The Yamnaya percentage might be inflated by high WHG/EHG genes that were absorbed as the actual Yamnaya type people moved across Europe.

Yes, except that WHG in Basques as in Sardinians came mostly with EEF farmers, not Yamnaya people.

Pax Augusta
31-03-16, 01:40
It's also too high for Spaniards, and for the same reason.

Also, this doesn't tell us anything about the gene flows that formed the Spanish and the Italians; there was no migration of "Cypriots" into those countries at the kind of levels which would be required to get these kinds of admixture results.

I'm not even sure that it's accurate for northern Europeans. The Yamnaya percentage might be inflated by high WHG/EHG genes that were absorbed as the actual Yamnaya type people moved across Europe.

Yamnaya admixture wasn't already studied in a peer review paper as Haak (2015)?

http://4.bp.blogspot.com/-NoGN9ni1kms/VOSGkPjblNI/AAAAAAAACBo/ROwmMxVJFpI/s1600/Untitled3.png


David Wesolski at Eurogenes, has created a global PCA with 50 dimensions. Normal PCAs only have 2 dimensions. His PCA has so many dimensions it is impossible for our eyes to comprehend it. He posted the locations of all the global samples in all 50 dimensions, to use to produce admixture results.

I've been playing around with Europe, and the results are 100% consistent with everything we've seen before.

Here are some results.


Population
Yamnaya_Samara
Loschbour
Sweden_MN
D statistic


Czech
51
4
45
0.0097


Belarusian
55
13
32
0.0172


Lithuanian
56
21
23
0.0177


Norwegian
49
7
44
0.0082


Andronovo
73
3
24
0.0105




(...)

The source? A link?

Angela
31-03-16, 03:16
Yamnaya admixture wasn't already studied in a peer review paper as Haak (2015)?

http://4.bp.blogspot.com/-NoGN9ni1kms/VOSGkPjblNI/AAAAAAAACBo/ROwmMxVJFpI/s1600/Untitled3.png





Indeed, and by a more sophisticated method than a simple Admixture run.

Fire Haired14
31-03-16, 05:13
Yamnaya admixture wasn't already studied in a peer review paper as Haak (2015)?

The source? A link?

These results were created by amateurs, using the same tools academics use.


It's also too high for Spaniards, and for the same reason.

Also, this doesn't tell us anything about the gene flows that formed the Spanish and the Italians; there was no migration of "Cypriots" into those countries at the kind of levels which would be required to get these kinds of admixture results.

I'm not even sure that it's accurate for northern Europeans. The Yamnaya percentage might be inflated by high WHG/EHG genes that were absorbed as the actual Yamnaya type people moved across Europe.

Yamnaya has hardly any or no WHG. WHG and EHG behave in significantly differnt ways in PCA and D-stats. Trust me, Iberia Middle Neolithic/Copper age, provides all the WHG Iberians need. Actually it gives too much, which is why they need Cypriot admixture. Cypriot are a proxy for unsampled Near Eastern ancestors of mostly Southern Europe, but also Central Europe. When you see the basically the same results from two completely differnt methods(PCA and D-stats), you got to admit, there's something legitimate about the results.

In 500 BC, if they discovered DNA, someone would have figured out Europeans are mostly Sycthian+Sardinian. It wouldn't mean, Europeans literally had Sycthian and Sardinian ancestry, but that they have ancestors who were similar to Sycthians and Sardinians. We're in a similar situation in 2000 AD, with Cypriots and Southern Europe.


Indeed, and by a more sophisticated method than a simple Admixture run.

They used the exact same method as D-stat admixture. They tested the relatedness of test populations to outgroups, then modeled modern test populations as a mixture of ancient ones. I think they used F-stats instead D-stats(don't know the difference between the two), but it's the same idea.

Haak 2015.

We estimate mixture proportions using a method thatgives unbiased estimates even without an accurate model for the relationships between the
test populations and the outgroup populations (SI9).

Fire Haired14
31-03-16, 05:30
@Everyone,

There's no doubt Steppe admixture is significant for Spain and Italy. 20-30% from the Pontic-Caspein Steppe, not Ukraine where they had EEF admixture, is reasonable. When you model Spain and Italy, as Steppe+WHG+EEF, you still get 20-30% Steppe, but a bad fit(because they need Cypriot or something similar).

Sile
31-03-16, 06:58
@Everyone,

There's no doubt Steppe admixture is significant for Spain and Italy. 20-30% from the Pontic-Caspein Steppe, not Ukraine where they had EEF admixture, is reasonable. When you model Spain and Italy, as Steppe+WHG+EEF, you still get 20-30% Steppe, but a bad fit(because they need Cypriot or something similar).

I have my doubts

Fire Haired14
31-03-16, 12:30
Here are better results. I used the nMonte system instead of 4mix. nMonte, breaks down percentages to decimals.




Anatolia_Neolithic
Yamnaya_Samara
Loschbour
Cypriot
@ D
Cycles


Italian_Tuscan
42.6
25.5
6.4
25.5
0.007143
100


Scottish_Argyll
28.85
39.6
21.75
9.8
0.009478
100






Iberia
Iberia_Chalcolithic
Bell_Beaker_Germany
Cypriot
@ D


Spanish_Aragon
39.6
45.9
14.9
0.006734


Basque_Spanish
61.8
38.2
0
0.018822






Italy
Iceman_MN
Bell_Beaker_Germany
Cypriot
@ D


Italian_Bergamo
29.45
48.6
21.95
0.008345


Italian_Tuscan
16
42.25
41.75
0.007458


Italian_WestSicilian
12.7
29.75
57.55
0.010929





Anatolia_Neolithic
Yamnaya_Samara
Loschbour
@ D
Cycles


Scottish_Argyll
36.1
44.25
19.65
0.009592
100


Italian_Tuscan
61.45
37.55
1
0.008183
100


Hungary_BA
41.4
32.9
25.7
0.013439
100

Angela
31-03-16, 15:38
I don't doubt that there is steppe admixture in southern Europe. Just results from yDna indicate that this is the case, and, as has been pointed out, it was found through the extensive modeling presented in Haak et al.

What I'm questioning is the amount, which seems about right for certain groups and pretty off for others (I highly doubt that the Basques are 70% Yamnaya related). I'm also questioning modeling groups using a mixture of ancient and modern genomes. In this particular case, Cypriots have their own particular population history and admixture. Throwing them into the mix may be altering the other percentages in ways we can't really predict.

Why not just wait for aDna? It won't be long.

Oh, and last I heard there are problems with the use and interpretation of Dstats, and we have that from the people who know the most about them, like Patterson. All these methods have their limitations. We have to try to take into account the results from all of the tools at our disposal, not constantly proclaim that this is the definitive tool and these are the only correct conclusions.

Fire Haired14
31-03-16, 18:50
I don't doubt that there is steppe admixture in southern Europe. Just results from yDna indicate that this is the case, and, as has been pointed out, it was found through the extensive modeling presented in Haak et al.

What I'm questioning is the amount, which seems about right for certain groups and pretty off for others (I highly doubt that the Basques are 70% Yamnaya related). I'm also questioning modeling groups using a mixture of ancient and modern genomes.

Basque came out 30% Yamnaya. BTW, what makes Basque unique in these tests(D-stats, ADMIXTURE, PCA) is they lack the Near Eastern-signal other Iberians and French have. They have as much Steppe admixture.




In this particular case, Cypriots have their own particular population history and admixture. Throwing them into the mix may be altering the other percentages in ways we can't really predict.

In D-stats, Cypriots unique history isn't expressed. This is because there are no Near Eastern-outgroups. Cypriots relationship to non-West Eurasian outgroups, European HGs, and CHG, is basically the same as Anatolia_Neolithic. The only difference is Cypriot isn't as close to EEF outgroups as Anatolia_Neolithic is. So, Cypriot is like EEF but not EEF.

Using simple math, you can suck out a zombie ancestor out of test populations. So, for Georgians and Mozabite I did this. Georgian's non-CHG side in D-stats, behaves similar to Cypriot. Mozabite's non-African side, behaves similar to Cypriot. So, Cypriot in D-stats with the outgroups used, is like a pure Near Eastern. They're not EEF or CHG, and they don't appear to have exotic admixture(African, East Asian, South Asian, Steppe). That's why I use them as a Near Eastern ancestor proxy for South Europe.

In other methods, Lebanese or Turkish work better than Cypriot for South Europe. In D-stats however Cypriots work better.


Why not just wait for aDna? It won't be long.

Oh, and last I heard there are problems with the use and interpretation of Dstats, and we have that from the people who know the most about them, like Patterson. All these methods have their limitations. We have to try to take into account the results from all of the tools at our disposal, not constantly proclaim that this is the definitive tool and these are the only correct conclusions.

I'm impatient. It's been a year since any big ancient DNA paper was published. I've used D-stats, PCA, and ADMIXTURE(not just ANE K8, but also old ones based on moderns), and have gotten the same results.

Sile
31-03-16, 19:25
Basque came out 30% Yamnaya. BTW, what makes Basque unique in these tests(D-stats, ADMIXTURE, PCA) is they lack the Near Eastern-signal other Iberians and French have. They have as much Steppe admixture.





In D-stats, Cypriots unique history isn't expressed. This is because there are no Near Eastern-outgroups. Cypriots relationship to non-West Eurasian outgroups, European HGs, and CHG, is basically the same as Anatolia_Neolithic. The only difference is Cypriot isn't as close to EEF outgroups as Anatolia_Neolithic is. So, Cypriot is like EEF but not EEF.

Using simple math, you can suck out a zombie ancestor out of test populations. So, for Georgians and Mozabite I did this. Georgian's non-CHG side in D-stats, behaves similar to Cypriot. Mozabite's non-African side, behaves similar to Cypriot. So, Cypriot in D-stats with the outgroups used, is like a pure Near Eastern. They're not EEF or CHG, and they don't appear to have exotic admixture(African, East Asian, South Asian, Steppe). That's why I use them as a Near Eastern ancestor proxy for South Europe.

In other methods, Lebanese or Turkish work better than Cypriot for South Europe. In D-stats however Cypriots work better.



I'm impatient. It's been a year since any big ancient DNA paper was published. I've used D-stats, PCA, and ADMIXTURE(not just ANE K8, but also old ones based on moderns), and have gotten the same results.

was'nt there a recent paper indicating the Balkan E haplogroup origins as Cyprus and they had a lot of EEF ................IIRC , these 2 major E Haplogroups came into cyprus vis the northern levant

Pax Augusta
31-03-16, 22:03
Here are better results. I used the nMonte system instead of 4mix. nMonte, breaks down percentages to decimals.

To be honest all these results seem to change too much.

MOESAN
31-03-16, 22:47
I don't doubt that there is steppe admixture in southern Europe. Just results from yDna indicate that this is the case, and, as has been pointed out, it was found through the extensive modeling presented in Haak et al.

What I'm questioning is the amount, which seems about right for certain groups and pretty off for others (I highly doubt that the Basques are 70% Yamnaya related). I'm also questioning modeling groups using a mixture of ancient and modern genomes. In this particular case, Cypriots have their own particular population history and admixture. Throwing them into the mix may be altering the other percentages in ways we can't really predict.

Why not just wait for aDna? It won't be long.

Oh, and last I heard there are problems with the use and interpretation of Dstats, and we have that from the people who know the most about them, like Patterson. All these methods have their limitations. We have to try to take into account the results from all of the tools at our disposal, not constantly proclaim that this is the definitive tool and these are the only correct conclusions.


I agree. All these methods give us, internally, some respective weights of "componants" between populations, not absolute %s, these last ones varying in every run.. And as you I dont like too much thses groupings of different ages reference populations. The results, taken with caution, can tell something about global ancient affinities but very little about History of populations moves (who. when?).

MOESAN
31-03-16, 22:55
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...

Fire Haired14
01-04-16, 08:34
I agree. All these methods give us, internally, some respective weights of "componants" between populations, not absolute %s, these last ones varying in every run.. And as you I dont like too much thses groupings of different ages reference populations.

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.


The results, taken with caution, can tell something about global ancient affinities but very little about History of populations moves (who. when?).

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.

Fire Haired14
01-04-16, 08:46
Look at these results. This is a totally unbiased approach, to find what changed in Spain, Italy, Greece, Norway, and Turkey after 3000 BC. I used people who lived in their regions in 3000 BC, other Europeans from 3000 BC(Yamnaya), and all modern non-Europeans as possible ancestors. For Italy and Spain, I only used moderns from the same regions as the 3000 BC genomes are from.




Iceman_MN
Yamnaya_Samara
Adygei
Cypriot
Mozabite
BedouinB
Druze
@ D


Bergamo
60.85
27.4
5.45
4
2.3
0
0
0.011837


Tuscan
42.9
25.7
0
30.3
0.3
0.15
0.65
0.009941



Norway.



Sweden_MN
Yamnaya_Samara
Chechen
Mozabite
BedouinB
@ D


Norway
47.1
52.15
0.3
0.25
0.2
0.011449



Spain.



Iberia_Chalcolithic
Yamnaya_Samara
Adygei
Cypriot
Mozabite
Chechen
Druze
@ D


Cantabria
59.05
28.1
2.55
8.25
1.25
0.15
0.65
0.007823



Greece.



Anatolia_Neolithic
Yamnaya_Samara
Adygei
Cypriot
Druze
Abkhasian
Armenian
Druze
Georgian
Kotias
Lebanese
Palestinian



Greek
52.7
36.35
2.75
7.65
0.55
0
0
0.55
0
0
0
0
0.007823


Turkish
25.2
0
0
0
0
13.25
4.5
8.3
27.1
16.85
1.15
3.65
0.01017

Sile
01-04-16, 09:54
Look at these results. This is a totally unbiased approach, to find what changed in Spain, Italy, Greece, Norway, and Turkey after 3000 BC. I used people who lived in their regions in 3000 BC, other Europeans from 3000 BC(Yamnaya), and all modern non-Europeans as possible ancestors. For Italy and Spain, I only used moderns from the same regions as the 3000 BC genomes are from.




Iceman_MN
Yamnaya_Samara
Adygei
Cypriot
Mozabite
BedouinB
Druze
@ D


Bergamo
60.85
27.4
5.45
4
2.3
0
0
0.011837


Tuscan
42.9
25.7
0
30.3
0.3
0.15
0.65
0.009941



Norway.



Sweden_MN
Yamnaya_Samara
Chechen
Mozabite
BedouinB
@ D


Norway
47.1
52.15
0.3
0.25
0.2
0.011449



Spain.



Iberia_Chalcolithic
Yamnaya_Samara
Adygei
Cypriot
Mozabite
Chechen
Druze
@ D


Cantabria
59.05
28.1
2.55
8.25
1.25
0.15
0.65
0.007823



Greece.



Anatolia_Neolithic
Yamnaya_Samara
Adygei
Cypriot
Druze
Abkhasian
Armenian
Druze
Georgian
Kotias
Lebanese
Palestinian



Greek
52.7
36.35
2.75
7.65
0.55
0
0
0.55
0
0
0
0
0.007823


Turkish
25.2
0
0
0
0
13.25
4.5
8.3
27.1
16.85
1.15
3.65
0.01017





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

Pax Augusta
01-04-16, 13:30
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.

Pax Augusta
01-04-16, 13:46
@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

ElHorsto
01-04-16, 14:31
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.

Fire Haired14
01-04-16, 15:27
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.

Alan
01-04-16, 15:28
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 Haired14
01-04-16, 15:35
@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.

Pax Augusta
01-04-16, 15:48
Bell_Beaker is not steppic. Bell Beaker is an Late_Neolithic/Bronze Age phenomenon of Central Europe.

Bell_Beaker is not fully steppic but they do have some relation.



Basque scored 30% Yamnaya.

Yes, according to Haak a bit less than Tuscans.

Angela
01-04-16, 15:59
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.

Fire Haired14
01-04-16, 16:23
@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.

ElHorsto
01-04-16, 16:59
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.

Fire Haired14
01-04-16, 17:14
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.

ElHorsto
01-04-16, 17:19
30% is pretty big, considering Yamnaya lived about 5,000 miles away from the Basque country.

Either that, or the 30% are not real.

Angela
01-04-16, 18:11
@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.

Sile
01-04-16, 18:47
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?:laughing:

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

Fire Haired14
01-04-16, 20:17
@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.

ThirdTerm
01-04-16, 23:26
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.

MOESAN
02-04-16, 18:05
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?).

MOESAN
02-04-16, 18:30
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)

Rethel
03-04-16, 00:46
What is it PCA?

Fire Haired14
03-04-16, 03:22
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.

ElHorsto
03-04-16, 12:29
What is it PCA?

PCA=Principal Component Analysis (https://en.wikipedia.org/wiki/Principal_component_analysis)

"The principal components are orthogonal because they are the eigenvectors (https://en.wikipedia.org/wiki/Eigenvector) of the covariance matrix (https://en.wikipedia.org/wiki/Covariance_matrix), which is symmetric (https://en.wikipedia.org/wiki/Symmetric_matrix#Real_symmetric_matrices)."

Angela
03-04-16, 18:33
Fire-Haired: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.

We should strive to be less scientific? Really?

If you want to engage in these kinds of discussions with people, you have to stop claiming people are saying things they didn't say, stop drawing illogical conclusions from facts that are not even in evidence, and stop jumbling a bunch of half-truths together and claiming it is the answer.

Where did I ever say that steppe ancestry isn't significant in southern Europeans?

How on earth can you know that a mystery, unknown population is the source of any particular component in Italians (or anyone else for that matter) when you haven't yet tested any of the known groups like the Etruscans, or the immigrants who might have arrived from Crete in the Bronze Age, or the Greeks of the first millennium, who might, for all you know, have been very Cypriot like before the arrival of the Goths or the Slavic migrations in the Balkans. Or, going back before 3000 BC, when you haven't yet tested anyone who might have been part of a second wave of the Neolithic for that matter, or when we don't know whether copper workers who fled the collapse of the Balkan complex migrated to Italy. For someone who knows anything about the pre-history of Europe those are KNOWN populations, not mystery populations, whatever that even means.

Also, for your information, Northern Italians and Tuscans can indeed be modeled as 40=50% and more Gaulish. So you're wrong about that as well.


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.

Do you even bother to really read people's posts? To repeat what I said above, how can you know the timing of the incursion of these components in Italians, as just one example, based on Oetzi, for goodness sakes? You don't have a clue as to the genetic signature of any ancient Italians other than Oetzi and a few Remedello genomes from far northern Italy. Depending on which group was present at which time in which place with a particular genetic signature, all the succeeding percentages change in terms of timing. Even for Northern Italians, while one could perhaps speculate that the group that admixed with the steppe groups was Remedello like, how do we know that the populations closer to Rome and southern Tuscany were the same, much less the far south? They might have been, perhaps it's even probable that they were the same, but that isn't the point. The point is that you can't know, and yet you pretend that you do. How do you know there wasn't a change around the time of the Copper Age, instead of after the Bronze Age as you claim? If you were more informed, and a bit older maybe you'd understand that this isn't how scientists work and think, or historians, or any well educated and well-informed people for that matter. I'm telling you this for your own good; this is not going to fly when you're in real life, professional situations.


Who's that?

http://rbedrosian.com/Ref/Drews/Drews_1988_Coming_of_Greeks.pdf



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.

Is that a serious question? We've known for more than a hundred years through archaeology and linguistic studies of the movement of this group of people across Europe.


I am too confident sometimes

Indeed. Maybe if you go back over the last year or two and see how confident and dogmatic you were about numerous issues, only to be proven wrong, it would give you pause.

Fire Haired14
03-04-16, 21:04
@Angela,

Like I said in my last post, I only modeled Bergamo and Tuscany as Otzi+Other. I didn't make the assumption everyone in Italy in 3000 BC was like Otzi. Because we don't have any non far Northern 2000-3000 BC genomes from Italy, doesn't mean I can't start making theories about Italian origins.

A Near Eastern-like people could have lived in other parts of Italy and could have been the Etruscans or Cretans or Greeks or someother historical people. All I'm doing, is finding what's differnt between modern North Italians and Otzi. I'm not concerned with arguing about the exact geographic location and time period of the signals come from. The Cypriot one could be from Southern Italy or Greece or Crete, I don't care. All I care about is that it is there. I take little looks at geography and make simple conclusions, so that's why I claim sometime after 2000 BC people from the Near East migrated into Italy. I might be wrong, but that isn't the focus of my statements. The focus is that there is a Near Eastern signal, where/when it came from is secondary.

So, don't get hooked on my theories on where the differnt types of ancestry in Europeans came from. That information will be made clear after lots of ancient DNA testing. Just like, 2 years ago, we knew the MA1-like ancestry arrived from the Steppe sometime after 3000 BC, but didn't know about the details.

"Also, for your information, Northern Italians and Tuscans can indeed be modeled as 40=50% and more Gaulish. So you're wrong about that as well."

I know they can(if we assume Gauls were like French). Although, IMO it's unlikely though that an immigrant population could contribute so much blood. We'll have to wait for aDNA.

Sile
04-04-16, 07:57
@Angela,

Like I said in my last post, I only modeled Bergamo and Tuscany as Otzi+Other. I didn't make the assumption everyone in Italy in 3000 BC was like Otzi. Because we don't have any non far Northern 2000-3000 BC genomes from Italy, doesn't mean I can't start making theories about Italian origins.


.

what about the 3 x remendello haplogroup I from the period you noted above.

They are in Eastern Lombardy Northern italy

Alan
04-04-16, 14:48
@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.

I know and that is the major difference. He is fully aware of the mistakes that can happen and also always tells people to be cautios. And if some of his work has errors in it he mentiones them and tells the people to not concentrate so much at it since the purpose is something different.

Alan
04-04-16, 14:59
The North Africans are basically still considered an EEF/WHG population with a big dose of SSA aren't they?
The "WHG" in North Africans is solely attributed to their EEF ancestry the reason why the WHG was so high in "older" calculators was that back than we didn't had Anatolian_Farmer samples and some bloggers created their own "ENF" component.

Northwest Africans are basically EEF with 1/5 SSA.

Tomenable
05-04-16, 17:30
Alan,

Neolithic Western Anatolian Farmers were not "pure Middle Easterners". They already did have a dozen or so percent Western European WHG admixture. Apparently WHG from Europe migrated into Western Anatolia where they admixed with EEF, forming Western Anatolian Farmers. Typically WHG Y-DNA haplogroups - such as I2c and C1a2 - were also present among Western Anatolian Farmers.

Tomenable
05-04-16, 17:32
some bloggers created their own "ENF" component.

Anatolian_Farmer is not a "pure component". It was a racially mixed group with partially WHG ancestry.

WHG ancestry came from Western Europe to Anatolia. We are yet to find "pure Middle Eastern Farmer".


the reason why the WHG was so high in "older" calculators

WHG is not "too high" anywhere. WHG ancestry was present in Anatolia because WHGs migrated there.

Not sure why do you think that it was "fake" WHG considering that I2 and C1 haplogroups were there too.