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Fire Haired14
11-05-14, 12:18
http://info-bg.narod.ru/heritage_files/konqri.jpghttp://info-bg.narod.ru/heritage_files/kochiash.jpghttp://info-bg.narod.ru/heritage_files/vino.jpg
I got the picture above from this site (http://info-bg.narod.ru/heritage1.htm), which claims it is from the Thracian tomb of Kazanlak, 'near the town of Kazanlak (http://en.wikipedia.org/wiki/Kazanlak)in central Bulgaria (http://en.wikipedia.org/wiki/Bulgaria)" and is from 500BC.

Ancient individuals









Number of SNPs Final merger




Sample
Region
Age(years)
Group*

HGDP

CG

100G/Sardinia


Iceman/Otzi
Asutria/Italy
5,300

F

162,537

3,730,194

7,974,125















Ajv70
Gotland, Sweden
5,300-4,400
HG

12,931

387,642

730,201















Gok4
Sweden
4,921+ or - 50
F

7,250

220,491

434,348















La Brana-1
Spain
6,980+ or - 50
HG

3,996

120,938

225,271















P192-1
Bulgaria
2,800-2,500
F

1,270

40,022

75,510















K8
Bulgaria
2,450-2,400
F

1,046

32,767

59,128



This study was primarily focuses on Otzi's genetic affinities. Because they were repeating alot of old news I tried to focus on the two new Iron age Thracian samples, or anything else I saw as new and important. I did not write about Underhill 2014's PCA because it's screwed up. The abbreviations for HGDP populations in this study may get confusing, here (https://www.sanger.ac.uk/resources/downloads/human/hapmap3.html) is a good source to learn what the abbreviations stand for.


Conclusions.

My conclusions after studying Underhill 2014 for hours and hours and hours:

The two Iron age Thracians were apart of two separate social classes which can explain why they are so differnt genetically. K8 was buried in a Tumulus in southeastern Bulgaria with rich grave goods, was likely an upper class person. He is surprisingly most related to northern Europeans, but at the southern end of northern European genetics, so probably similar WHG+ANE percentage as French and Basque. K8's extra WHG-ANE ancestry may be descended of proto-Thracians who at some point came down to Bulgaria from eastern Europe(WHG-ANE are highest in eastern Europe today).

The dark eyes(90% or more) of likely proto-Indo European speaking bronze age Yamna and Catacomb cultures (http://www.theapricity.com/forum/showthread.php?118795-List-of-65-ancient-Pontaic-steppe-individuals-and-DNA-results), probably means they did not have alot of WHG-ANE ancestry, because 3/3 Mesolithic Europeans tested so far are light eyed (https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=0CCsQFjAA&url=http%3A%2F%2Fwww.eupedia.com%2Fforum%2Fthreads %2F29789-Revised-Laz-Ancient-genomes-suggest-three-ancestral-populations-for-Europeans&ei=nEVvU9isEoSoyASmg4CoBQ&usg=AFQjCNHIw3jMHNFjJin0Ba8GL14cW2df1g&bvm=bv.66330100,d.aWw). They did though have a very high amount of typical Mesolithic European mtDNA haplogroups U5, U4, and U2e. Also, I might be wrong making assumptions about the ancestry of people who lived around 5,000 years ago based on eye color. Ancient DNA has shown early Indo Iranians were primarily light eyed and so proto-Indo European speaking people probably had many differnt ancestral backgrounds. If proto-Thracians are not the source of K8's extra WHG-ANE ancestry, then that opens the door for alot of possibilities including admixture with another Iron age people like Sycthians.

The other Iron age Thracian individual, P192.1, was buried in a pit sanctuary near Svilengrad, Bulgaria and was likely a commoner. In D-statistics he is clearly shown to be closely related to Sardinians, like early European farmers. In the admixture though P192.1 is most similar to Tuscans and Gok4. I think that P192.1 had some post-Neolithic southwest Asian ancestry like it seems modern Italians and Balkaners do, and in the D-statistics P192.1 seems to have some type of connection to Tuscans.

I am very very very very surprised by how Sardinian/EEF-like P192.1 is, since he lived in Bulgaria just 2,500-2,800 years ago. I am disappointed that Underhill 2014 was not able to test modern Bulgarians who may be his closest modern relatives. There are very limited sources in Underhill 2014 to make detailed conclusions on the origins of these two Iron age Thracians.



Admixture

Click here (http://file:///C:/Users/A%20Desktop/Downloads/Figure_S1.pdf) to view the admixture, it goes from K2-K8. It included all of the ancient samples listed above and 11 modern populations in HGDP: Five Europeans(Russian, Basque, Italian, Tuscan, Orcadian), two south-west Asian(Druze, Palestine), one north African(Mozabite), and one Caucasus(Adygei).


Here are descriptions of all the K's.

I didn't mention this in the descriptions: Mozabite score ~100% in their own component from K2-K8, and it's colored red from K2-K8. Of the other populations and ancient individuals, Palestine, and then P192.1 score the highest in it. Membership in the Mozabite component significantly drops from K2-K3. It is non-existent in every population-ancient individual from K4-6, except for most Palestine individuals, P192.1, one Druze, and possibly one or a few Italian individuals from K4-K5.

The Mozabite component is most likely a mixture of African and middle eastern(mixture of west Eurasian and basal Eurasian) alleles, so the more African ancestry any of the populations have the higher they will score in the Mozabite component, southwest Asian-specific ancestry may also add on to the Mozabite component. Therefore Iron age Thracian P192.1 probably had some African ancestry, probably via his modern southwest Asian-like ancestry. The other Iron age Thracian K8, though probably has 0% or close to 0% African ancestry.

K2-K5: From K2-K4 there is a blue Caucasus-European component, that is a mix of middle eastern and north Eurasian hunter gatherer(ANE and WHG) alleles. It is ~100% in Basque, Orcadian, Russian, European hunter gatherers La Brana-1 and Ajv70(score a little line of Palestin epurple in K4), and Iron age Thracian K8. Adygei, Tuscan, Sardinian, Italian, Iron age Thracian P192.1, and early European farmers Otzi and Gok4 though also score in the southwest Asian components(centered in Druze and Palestine). Which means south Europeans, Adygei, early European farmers Gok4 and Otzi, and Iron age Thracian P192.1 have more middle eastern ancestry.

It is important to note, that at K4 Tuscan and P192.1 score higher in the southwest Asian components than any of the ancient individuals and modern European populations, meaning they probably have more middle eastern ancestry. Also, At K4 the Palestine purple-Druze green ratio in P192.1, Tuscan, and Italian is more purple than it is for Sardinian, Italian, and early European farmers Otzi and Gok4, meaning P192.1 and Tuscan may have a type of middle eastern ancestry they lacked.

K5: Mozabite red. Palestine purple, Druze green, Sardinian orange, and Russian blue The orange component that is ~100% in Sardinians absorbs most of the samples EEF ancestry. Basque score about 50-70%, Tuscan and Italian score about 50%, French score about 40%, Orcadian score about 15-20%, Russian scores a little line, Adygei don't score anything(evidence it's a middle eastern-WHG component descended of early European farmers), Palestine and Druze though score what seems to be around 1-5%(Druze more than Palestine), Ajv70 scores ~15-20%, La Brana-1 scores ~25-35%, Gok4 scores ~60-70%, Otzi scores ~90%, P192.1 scores ~25-35%, and K8 scores ~30%.

Of the ancient and modern Europeans, only Tuscan, Italian, French(very insignificant, and only in a few individuals) Gok4(only green), ajv70(very insignificant, and only green), Otzi(only green, very insignificant), and P192.1 score in the southwest Asian Purple(Palestine) and green(Druze) components. Iron age Thracian P192.1's results are very similar to Tuscan(besides scoring in the Mozabite red component), as it is in latter K's and suggests he is very similar to modern Italians and Balkaners. K8 though fits best with French, in K5.

Sardinian score about 100% in the orange component. Basque score about 50-70%, Tuscan and Italian score about 50%, French score about 40%, Orcadian score about 15-20%, Russian scores a little line, and Adygei don't score anything(evidence it's a middle eastern-WHG component descended of early European farmers). The only Europeans to score in the Druze-Palestine components are Tuscan and Italian, they score mostly in the green component and Tuscan more than Italian.

European hunter gatherers Ajv70(~20%) and LA Brana-1(~30%) score significant amounts in the Sardinian orange component, probably because it has north and western European hunter gatherer alleles, and because the components in this admixture were created using modern populations while the ancient samples were forced into it.

Tuscan, Italian, P192.1, and Gok4 score in the Druze(green) and Palestine(purple components, Gok4 only scores in the green), unlike any modern Europeans and Iberian Mesolithic hunter gatherer La Brana-1, which suggests they have non early European farmer southwest Asian ancestry. There is also a little line of green for hunter gatherer Ajv70 which may be because he has some Gok4-like ancestry.

K6: Mozabite red, Palestine purple, Druze green, Sardinian orange, Basque yellow, and Russian blue. It tells the same story as K5, just now European-farmer orange is split between Sardinian orange and Basque yellow. non Basque and Sardinian Europeans, score a mix in the two European-farmer components. Tuscan and Italian score more in the Sardinian component, French score much more in the Basque component, Orcadian and Russian score almost entirely in the Basque component, Russian though scores a very very very skinny line in. Of the former orangein K5, Druze and Palestine score more in Sardinian orange, probably because Basque have more WHG ancestry than Sardinians. Adygi results are nearlly identical as in K5 and suggest 0% or close to 0% European ancestry.

Otzi(~95%) and Gok4(~60-70%) score very high in the Basque yellow and Sardinian orange components. Both score much more in the Sardinian orange than Basque yellow, but Gok4's ratio is a little higher in the Basque yellow than Otzi's. Gok4 like in K5, scores a little in the Druze green and more in north Eurasian hunter gatherer(WHG+ANE) blue than Otzi. La Brana-1(~25%) and Ajv70(~10-15%) surprisingly score in the Basque yellow and Sardinian orange components. Both score much much more in the Basque component than the Sardinian component.

Ajv70 seems to score a skinny line in purple at K6. P192.1 at K6 like in all of the lower K's scores a skinny line in the red Mozabite component, he also scores in the green and purple components and more than Tuscans do, but still a similar amount. K8, though only scores in the orange and yellow components, and in ratio, yellow is a bit higher than orange. P192.1's orange-yellow ratio is about even.

K7: Mozabite red, Palestine brown, Palestine purple, Druze green, Sardinian orange, Basque yellow, and Russian blue. There is nothing differnt from K7 except now there are two Palestine components. None Palestinens only score in the brown one, except P192.1 who scores in both. K8 and Ajv70 score in the brown Palestine component, and K7 is the first K he scores in a Palestine-Druze component.

K8: Mozabite red, Palestine brown, Palestine purple, Druze pink, Druze green, Sardinian orange, Basque yellow, Russian blue. Noth new except: All of Adegyi's percentage in the southwest asian components is absorbed by the new Druze pink component. The new Druze pink takes the place of the Palestine bron of K7, except all of the ancient farmers and Ajv70 still score in the brown Palestine component.

Like in all of the other K's P192.1 has very similar results to Tuscan, except Tuscan does not score any green or brown like P192.1 does.


D-statistics, F3-statistics, and Derived allele sharing


Charts((Figure 2A (http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004353#pgen-1004353-g002), Figure S3 (http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004353#pgen.1004353.s003)) presenting Otzi's derived allele sharing ratio with modern populations.


It is very hard to find an explanation for why TSI(Tuscany, Italy Hapmap) shares only slightly more derived alleles with Otzi than CEU(northwest European Americans, Hapmap) does. Mexican sample's European ancestry segments share significantly more derived alleles with Otzi than TSI and CEU, but Underhill 2014 said they did not find a difference in derived allele sharing with Otzi in modern Iberians, TSI, and CEU. There is probably some type of complicated explanation for this. Underhill 2014 suggested that north African and east Asian alleles spread across Europe after Otzi's time, and such alleles were used to compare Otzi with CEU, TSI, and Iberians but were not used to compare Otzi to Mexiacan's European ancestry segments because they are seen as non-European. I haven't seen any evidence of north African or east Asian ancestry throughout most of Europe, especially in northwest Europe, so i think there is another explanation.

D-statistics with Otzi and modern populations (Figure S4 (http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004353#pgen.1004353.s004)). D-statistics of ancient European individuals and modern European populations Figure S5. (http://www.plosgenetics.org/article/fetchSingleRepresentation.action?uri=info:doi/10.1371/journal.pgen.1004353.s005)

Gok4 acts like Otzi does in the D-statistics, just with extra WHG. P192.1 acts very similarly to Gok4(Including a strange connection to Sardinia), but has sometype of special connection to TSI(Tuscan) and northwest European GBR. His connection to TSI may be recent southwest Asian ancestry. I am most surprised by how similarly the farmers are related to northwest European CEU and GBR as they are to southern European TSI and IBS. This probably means EEF/WHG/ANE proportions can't explain everything, there have to be other variables that can explain the complex relationships Gok4, Otzi, and P192.1 have with modern Europeans. All of the farmers not counting K8, have a strange push towards Sardinians even though Iberians should be very similar to Sardinians.

K8 is totally differnt than P192.1, and like in the admixture shows more northern European-like ancestry. K8 does not show anymore connection to Sardinia than he does to IBS, and is closest to northern Europeans: CEU, GBR, and FIN. OF southern Europeans K8 is most distant from TSI, unlike P192.1 who has sometype of connection to TSI, but like P192.1 K8 shows a connection to GBR. K8 is certainly not as northern as CEU, GBR, or FIN, and based on his admixture results i think he was about as northern as French.

TreeMix analyis of Otzi and modern populations Figure 3. (http://www.plosgenetics.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pgen.1004353.g003&representation=PNG_M) TreeMix analyis of all the ancient European individuals in this study and modern populations (Figure S8 (http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004353#pgen.1004353.s008)). F3 statistics with modern populations Table S4. (http://www.plosgenetics.org/article/fetchSingleRepresentation.action?uri=info:doi/10.1371/journal.pgen.1004353.s014) and F3 statistics with modern and ancient samples Table S5. (http://www.plosgenetics.org/article/fetchSingleRepresentation.action?uri=info:doi/10.1371/journal.pgen.1004353.s015)

The TreeMix analysis results for all of the ancient Europeans, modern European, African(LWK, YRI), and east Asian(JPT, CHB, CHS) samples, show expected results. The only new knowledge is of the iron age Thracians K8 and P192.1. P192.1 fits as a clade with Sardinians with a bootstrap support of 56%, while Gok4 had a bootstrap support of 83%, and Otzi had an even higher bottstrap support of >96%. Tuscans fit as a clade with Sardinians when La Brana-1 is the ancient sample, so i don't think P192.1 being a clade with Sardinians means much. K8 also shows his north European affinities in the TreeMix analysis, where he does not fit in the south European clade(TSI, Sardinian, IBS).

P192.1 does seem to be pretty Sardinian-like in the D-statistics, but not as much as Gok4 and Otzi. In the admixture he seems to have post-Neolithic southwest Asian ancestry similar to modern Italians and Balkaners, but in the D-statistics and TreeMix analysis is shown to be more related to Sardinians than to Tuscans. Possibly Balkaners and Italians during the Neolithic and bronze age were very Sardinian-like, and admixture with more north European-like people(Indo Europeans?) and southwest Asian-like people occurred in the bronze and Iron age, and P192.1 is from an early stage of these admixture events.

I am not surprised that both the TreeMix analysis and F3-statistics show that there is likely Sub Saharan African ancestry in IBS(Iberian), but I am surprised they showed the same for TSI(Tuscan). The TreeMix analysis with Otzi estimates 2.7% Sub Saharan ancestry in the south European clade(IBS, TSI, Sardinian). In the F3-statistics using only modern populations, Tuscans fit as being admixed with any European or African population they tested with(only not listed was Finn, not sure if they tested Finn as a European source), but IBS(Iberian) only fit as being admixed between YRI and GBR. Another suprising thing about the F3-statistic results is that both TSI and IBS fit as being admixed between Sardinia and any of the three east Asian populations used(CHB, JPT, CHS). Maybe it's because Sardinians have more basal Eurasian ancestry(proposed in Laz 2013) and east Asian populations fit as IBS and TSI's extra mainstream Eurasian ancestry. The rest of the F3-statistic, like most of Underhill 2014, show what is already known.

Nobody1
11-05-14, 12:49
I am not surprised that both the TreeMix analysis and F3-statistics show that there is likely Sub Saharan African ancestry in IBS(Iberian), but I am surprised they showed the same for TSI(Tuscan). The TreeMix analysis with Otzi estimates 2.7% Sub Saharan ancestry in the south European clade(IBS, TSI, Sardinian). In the F3-statistics using only modern populations, Tuscans fit as being admixed with any European or African population they tested with(only not listed was Finn, not sure if they tested Finn as a European source), but IBS(Iberian) only fit as being admixed between YRI and GBR. Another suprising thing about the F3-statistic results is that both TSI and IBS fit as being admixed between Sardinia and any of the three east Asian populations used(CHB, JPT, CHS). Maybe it's because Sardinians have more basal Eurasian ancestry(proposed in Laz 2013) and east Asian populations fit as IBS and TSI's extra mainstream Eurasian ancestry. The rest of the F3-statistic, like most of Underhill 2014, show what is already known.

Im not sure how you get to most of your 'conclusions' from that study but than again im not sure how you derived your Puerto-Rican uncle to be a Mesolithic Hunter-gatherer either;

The Sub-Saharan values (1%-3%) are linked to Moorjani et al 2011 with the results from that study being 1.5% Tuscany (TSI) and 2.4% Spain / 3.2% Portugal (IBS); And the F3-statsistic shows the significance of the admixtures (Z=/) and maybe you should take a look at those significance (less minus = higher);

An interesting part of the study is shown in the TreeMix charts and that is that the same Neolithic Near East migration into Europe also migrated into east Africa (LWK) from the Near East (follow the arrows);

Fire Haired14
11-05-14, 13:14
Im not sure how you get to most of your 'conclusions' from that study but than again im not sure how you derived your Puerto-Rican uncle to be a Mesolithic Hunter-gatherer either;

If you're your so smart why don't you make your own thread? Don't just give snobby comments on threads others worked hard on.

My uncle is not Puerto Rican, he is 25% Puerto Rican and 75% northwest European. He was missing many light skin mutations most Mesolithic European samples are, and at the time he was the only person with a significant amount of Mesolithic European ancestry i knew of who was missing those mutations. I later found many Latinos and European-none west Eurasian admixed people have the same alleles as him. I also, found a pure-northwest European with the same alleles as him, but this guy was a totally light skinned. I never said my uncle has the same skin color as did most Mesolithic Europeans, i said it's possible he does


The Sub-Saharan values (1%-3%) are linked to Moorjani et al 2011 with the results from that study being 1.5% Tuscany (TSI) and 2.4% Spain / 3.2% Portugal (IBS); And the F3-statsistic shows the significance of the admixtures (Z=/) and maybe you should take a look at those significance (lower/higher);

An interesting part of the study is shown in the TreeMix charts and that is that the same Neolithic Near East migration into Europe also migrated into east Africa (LWK) from the Near East (follow the arrows);

There are two possible explanations in my opinion: Basal Eurasian is an African-west Eurasian mix or recent Sub Saharan African ancestry. Basal Eurasian ancestry being the source seems unlikely to me because Tuscans can be fit as being part Sardinian and part Sub Saharan African(LWK and YRI) even though Sardinians have more basal Eurasian ancestry. Plus, only south European populations Sardinian, TSI, and IBS were fit as being part Sub Saharan African.

It would be very interesting to see what early European farmer's relatives in west Asia and Africa were doing, and understand why their mtDNA is so rare in the middle east today. Neolithic European-like or just middle eastern people could be the source of LWK's west Eurasian ancestry.

Nobody1
11-05-14, 15:27
http://www.plosgenetics.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pgen.1004353.g003&representation=PNG_M

This is the chart for you (Figure 3);
TSI (Tuscans) is on the same branch as Sardinian and Iceman with additional 'ancestral European ancestry'; K=8 admixture was 0% Mozabite in TSI and high amount of Sardinian ancestry; The F3-statsistic is given in Table S4 with max -4.4 (to Sardinian) IBS significant -3.4 to GBR; And in the 1%-3% ssa for South Europe Tuscany was 1.5% (Study link: Moorjani et al); And the LWK west Eurasian ancestry is explained by an input of Near East Neolithic the same as the source for European Neolithic;

PS: as for your "hard work" : just post the link (as Angela did in the already existing thread);

Luan
11-05-14, 15:44
Interesting read on this topic.

Sile
11-05-14, 20:36
Since its acknowledged that 192.1 is a commoner and K8 is a "royal", the fact is that 192.1 is 300 plus years older in years than K8 which gives clear indication that 192.1 is more a common thracian person.
Since K8 is highly contaminated in modern DNA........why is he discussed even?

Also, note, they have tested 192.1 for mtDna and he is U3b ..................where is this from in the scheme of things?


http://forwhattheywereweare.blogspot.com.au/2014/05/ancient-thracians-otzi-and-origins-of.html

as per link , figure S1
my opinion is 192.1 more tuscan than anything else
K8 more french

Maybe the french derives from the gallic/celtic invasion of the balkans and anatolia , pre-roman times

Fire Haired14
11-05-14, 21:27
Sile, K8 has clear north European affinities in multiple tests, contamination can't explain that.

Fire Haired14
11-05-14, 21:34
http://www.plosgenetics.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pgen.1004353.g003&representation=PNG_M

This is the chart for you (Figure 3);
TSI (Tuscans) is on the same branch as Sardinian and Iceman with additional 'ancestral European ancestry'; K=8 admixture was 0% Mozabite in TSI and high amount of Sardinian ancestry; The F3-statsistic is given in Table S4 with max -4.4 (to Sardinian) IBS significant -3.4 to GBR; And in the 1%-3% ssa for South Europe Tuscany was 1.5% (Study link: Moorjani et al); And the LWK west Eurasian ancestry is explained by an input of Near East Neolithic the same as the source for European Neolithic;

I have acknowledged all of this.


PS: as for your "hard work" : just post the link (as Angela did in the already existing thread);

If I don't write down my thoughts i easily forget them, that's a big reason why i make long threads. Our conversation started off on the wrong foot, lets both be done with the snippy insults.

Greying Wanderer
11-05-14, 21:43
Those Kazanlak murals are interesting. Seems more and more to me that the area west of the Black Sea is a lot bigger deal than I personally realized.