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isbara
25-01-15, 19:41
1.
At a forum professor Anatole Klyosov(rodstvo),wrote about the unusual phenomenon of the similarity of two basal haplotypes of Y-DNA haplogroups R1a and T1a.

There is a match of15/22 Y-STR markers between the following values:

12 12 13 - 11 11 - 11 - 11 8 16 16 8 10 8 12 10 12 12 8 12 11 11 12 (R1a)
11 12 13 - 11 13 - 9 - 11 8 17 17 8 10 8 1210 12 12 8 11 12 11 12 (T1a)

About this subject it is written by a user in thislink: eupedia

“Thefeeling that T - is an early R1a1, which mutated DYS426 12 -> 11,but DYS392 = 13 survived from ancient R1a1 (by the way, is the sameand R1b). Haplogroup T definitely does not fit into an existing tree haplogroups after a series of 2009-2011, side moves.”

I know the Y-SNP is different, but Haplogroup T(or K2) has now moved from places 2-3 times in the Y-tree, so is there a possibility there could be a connection between T and R? What if new SNP's would befound to proof this? Would this not clear the fact that haplogroup T is found rarely in all studies done till now?

What do you think about the Y-STR similarity between the basal haplotypes of R1a and T1a? Did anyone see same kind of results in other databases, when you compare R1a and T1 haplotypes?

2.
On the study paper named “Comparison of Y-chromosomal lineage datingusing either evolutionary or genealogical Y-STR mutation rates”, professor Hui Li gives the following information:

-The most important link between genetic diversity and human history istime, for instance, the time when a lineage originated or expanded, or when a population split from another and migrated.

-Haplogroup G is grouped with haplogroup C, and haplogroup T is placed in the same branch with Q and R in the network. Haplogroup R branches from haplogroup Q, with the SNP M242 that defines Q being assigned asrecurrent. The similar situation has also been observed in haplogroup D and E, I and J in the network tree.

-Figure 1a, 1b, 2a and 3a at biorxiv are graphs that put the haplogroups Q, R and T in the same branch.

In another study paper named “Convergence of Y chromosome STR haplotypes from different SNP haplogroups compromises accuracy of haplogroup prediction”, professor Hui Li gives the following information at arxiv:

-The three ancient haplogroup C, D, and E were clustered in branch I, representing the out of Africa migration. Haplogroup F, G, H, I, J were mainly clustered in branch II, which might indicate the possible population expansion in the Middle East and Europe. Haplogroup L, T, K, N, and O were clustered in branch III, representing the peopling of the Far East. Haplogroup P, Q, and R were mainly clustered in branch IV, demonstrating the population expansion from Central Eurasia and the migration through northern Eurasia into the Americas.

-Haplogroup O2b* and O2b1a were clustered with T* and T1a*, and also showed affinity with O3a* and O3a1c*. Haplogroup O3a2+s formed a tight cluster, indicating high similarities between those lineages, although haplogroup L+s have also been placed in the O3a2 cluster.

3.
Except the known Ftdna project databases, which databases can i publicly use or make a request to research the statistics of the haplogroup results for haplotypes with 23-23 values for Y-STR markers YCAII-a-b?

4.
-At the “The Y-chromosome tree bursts into leaf: 13,000 high-confidence SNPs covering the majority of known clades”study,the most basal branch of haplogroup T is of a Bhutanese person with ID Bhu-1892. Bhutan is a country within the borders of China and India. What do you guys think about this, what does this mean for the origin of haplogroup T?

-Also it is a known fact that Dravidians had more than 50%(“High Resolution Phylogeographic Map of Y-Chromosomes Reveal the Genetic Signatures of Pleistocene Origin of Indian Populations”) of haplogroup T.

-Also at the study “A Western Eurasian Male Is Found in 2000-Year-Old Elite Xiongnu Cemetery in Northeast Mongolia” this is written:

“Calculation by DNA#VIEW shows that the autosomal profile of Xiongnu Cemetery with ID MNX3(mt: U2e1, Y: R1a1) West Eurasian male is 14 times more probable from a Brahmin Indian than from a modern Caucasian (Table 6).”

-Also there was a study about Xiaohe graves(3500-4000YBP), eurogenes. There was 11x R1a1a and 1x K*-M9. We know from older studies that marker M70 was the most closest SNP child existing from M9 marker, thats why it was called earlier K2. Is it possible that R1a and T1 could have a connection because of this situation in which 1 K-M9 isassociated with a group of 11x R1a? Maybe some groups of M9 marker stayed together in Central/East Asian regions before and after the mutations of some haplogroups occured?

-What do you think about all these points?

5.
At the study “Haplotype Diversity in mtDNA and Y-Chromosome in Populations of Altai–Sayan Region” Haplogroup K-M9(xL, N, O, P) is found with 38.8%. In an earlier study Haplogroup T was found within Altaian Kazakhs(Y-Chromosome Variation in Altaian Kazakhs Reveals a Common Paternal Gene Pool for Kazakhs and the Influence of Mongolian Expansions) again after a situation of K-M9(N, O, P) i think. Do you think that the 38.8% of K-M9(xL, N, O, P) could belong to Haplogroup T? I asked professor Gubina about this, and she told me marker of T was not typed, and she has no plans for this in the future. Is there someone that could try to test these K-M9(xL, N, O, P) samples further to seeif T is found among them?

6.
Inan Y-STR only study of 2003 of professor Keyser-Tracqui about Xiongnu graves of 2000 years ago in Mongolia, there is a there is a grave with number 76. The haplotype of this sample has 5 Y-STR markers tested, in which these results were found:

DYS392:13,DYS393:13, DYS19=14, YCAIIa-b:23-23.

The YCAIIa-b value of 23-23 is very unique, together with DYS14(14),DYS392(13), DYS393(13) it is found in only specificly haplogroups T-M70 and R1b. I have searched and analyzed all T-M70 and R1b haplotypes at Familytreedna.com, and found that 27/649 T-M70 haplotypes were a match(4,16%) and 21/5650 R1b haplotypes(0,37%) were a match. Looking at the YCAIIa-b values of the T-M70 and R1b haplotypes at Familytreedna.com, i saw that R1b haplotypes had mostly the following structure YCAIIa-b(19-...). T-M70 haplotypes had mostly the following structure YCAIIa-b(23-...). Also the fact that the haplotype prediction of grave number 84bis(and maybe also the haplotype of grave number 95) is specificly unique for haplogroup L-M20, do you think the outcome of grave number 76 has higher probabilities for T-M70 than R1b? Is there someone, maybe from the Ftdna T groups that can maybe test the Y-SNP haplogroup of this ancient grave number 76?

Also professor Keyser-Tracqui said that she was busy with a new project about Xiongnu graves in a cemetery with a new location in Mongolia. Does someone know what the status of this study is? Are there other new ancient dna projects going on about this subject?

7.
In the study of David K. Faux in 2007, “The Genetic Link of the Viking – Era Norse to Central Asia: An Assessment of the Y Chromosome DNA, Archaeological, Historical and Linguistic Evidence”,he said he found in Shetland project, haplogroups K2-M70, R1a and Q, and he also makes a connection between T and R1a and says these came together from Central Asia to Eurasian regions.

8.
At this page 221.145.178.204 there is a wide ancient dna study performed, with 1462 ancient samples in 2007 by professor Kijeong Kim from South Korean Chung-Ang University. 8 years have been passed, and the results are still not published. In 2010 there was only the result of a single sample of these 1462 ancient samples published within a paper named “A western Eurasian male is found in 2000-year-old elite Xiongnu cemetery in Northeast Mongolia.”, which showed the first occurence of R1a among Xiongnu grave samples.There are thousands of other Scythian(11th BC - 2th centuries AD),Xiongnu(3th-3th centuries BC), Hun(3th-6th centuries) and Turk(6th-8th centuries) graves in Eurasian regions. What if they all got tested and showed interesting results that could change all the conclusions made by scientists about dna migration routes?

I have contacted Kijeong Kim about this situation, and he persists onnot sharing the Y-SNP haplogroup results. As a reason he says they have not performed repeat analysis. But even if a part of the results could be wrong, for example maybe 0 - 5% of the 1462 ancient samples, isnt it really useful to have at least a good preview picture whatcan let other dna project investors to invest in reanalyses of partsof these samples? Why should such a massive pre study be kept private? Do you think there could be a political pressure to not publish these results? I dont understand what they could loose if they publish results of such an important study? Who does agree with me on this subject? Are there academics on this forum that could convince professor Kijeong Kim to publish these pre results?

9.
Until now, i find that the level of sample count(in academic dna studies) is very low and unreliable. In time when more seriously projects are being performed, we will see different results.

For example, a couple of years ago who would have thought that Y-haplogroup G would be found in Kazakhs with such high frequency?For example there is found 87% of haplogroup G in Bíró et. al. 2009 and in some other studies haplogroup C is found with 40-60%. In the newest study "Y-chromosome descent clusters and male differential reproductive success: young lineage expansions dominate Asian pastoral nomadic populations" there was found 26% of G in Karakalpaks. There are other studies that show similar results. And about haplogroup T, there are tons of studies with high frequncy K* that were not taken serious enough to test more markers. I keep reading articles and posts about T being found with high frequencies in the Middle-East, what do we mean by high actually? T results are showed in really few studies, and does not go higher than 0-15%. For example i find the conclusions made in the following study "Increased Resolution of Y Chromosome Haplogroup T Defines Relationships among Populations of the Near East, Europe, and Africa" very funny and not deserved to be called academic. The highest frequency in table 1 is only 12,5%, based upon this they declare the origin of T Jewish. This is not scientific, because 12,5% of haplogroup T is also found in the Xibe population of Xinjiang. Also the Phoenician connection of Genographics, on which facts do you base this on? Are there data relating to ancient dna studies of Phoenicians? No! Thats why this is not scientific, and these are the methods of non scientific companies that earn money out of these lies. For example, how can someone make a Phoenician connection with Thomas jefferson(ancient dna, born 1743)?

And also, i really doubt the reliability and seriousness of the majority of dna studies. Tell me something, how many academic Y-dna studies are there, whom have researched carefully and very strict the historical documents of the participants of their projects? What if in the majority of the dna studies, the samples that are collected belong to people from one village, or yet evenbelong to people from the same villages that belong to only a couple of families that are relatives to each other in the close history? Is this enough to make a valid generalization of the haplogroups found in specific countries? The solution is to conduct Y-DNA studies in which the paternal historical documents of each participant is recorded very carefully, so that the studies may be counted as scientific to assign general haplogroups to specific groups of populations.

Ancient dna projects are the most important piece of the puzzle that needs to solved right now. Think of it like this, what if in between 1200 and 1300 AD, specific groups of people migrated completely from Mongolia to Iran? What if ancient dna will proof this? And for example did you know that the population numberin modern Mongolia is less than 3 million. Do you think that it is scientific and also true to assign a haplogroup to the ancient Mongol tribes based on the Y-DNA tests done on nowadays Mongolian population with less than 3 million inhabitants? Did you know that in the beginof 1300's there was a massive migration from Mongolia to China,Afghanistan, Iran and Türkiye. Do you know of the existance of the Ilkhanid Mongol state in Iran and Türkiye?

10.
Another mistake i saw recently in an academic paper("Title:Present Y chromosomes support the Persian ancestry of Sayyid Ajjal Shamsal-Din Omar and Eminent Navigator Zheng He"), in which theancient dna of Sayyid Ajjal Shams al-Din Omar was found to belong to haplogroup L-M20. In the paper it is written that he is of Khwarezmian tribe, and they conclude he is of Persian origin(with the doubts they write). This is totally not scientific and not true. Every historian that is associated with medieval history knows that the dynasty of Khwarazm Shahs and their state is of Turkish origin(Mamlukids, Kipchaks, etc...), and we also know that the borders of Khwarezmia lies within Central Asia, the land of the Turks(6th-8th centuries). We also know that in the Gokcumen 2008 study, there was found 57% of L-M20 in Afshar Turks in Türkiye. But still, Sayyid Ajjal Shams al-Din Omar is concidered to be of Persian origin, is this scientific? No. What if an important group of ancient Turks with L-M20 migrated between 1200 and 1500 AD from Mongolia, China and Central Asia to Iran and Türkiye countries? Do the academicians bother to think about this?

Facts about the Turkish origin of Sayyid Ajjal Shams al-Din Omar:

-Some other genealogies even pointed to that the ancestors of Sayyid Ajjal had already arrived in China in the Song Dynasty. Therefore, whether Sayyid Ajjal has a Persian ancestry or not is yet to be validated.

-Foremost amongst these soldier-administrators was Sayyid al-Ajall Shams al-DinUmar al-Bukhari (Ch. Sai-tien-ch'ih shan-ssu-ting). a court official and general of Turkic origin who participated in the Mongol invasion of Szechwan. Source:Institute of Muslim Minority Affairs, Jāmiʻat al-Malik ʻAbdal-ʻAzīz. Maʻhad Shuʻūn al Aqallīyat al-Muslimah (1986)

-The Khwarazmian dynasty, also known as the Khwarezmid dynasty, dynasty of Khwarazm Shahs, was a Persianate Sunni Muslim dynasty of Turkic mamluk origin.

The dynasty ruled large parts of Greater Iran during the High Middle Ages, in the approximate period of 1077 to 1231,first as vassals of the Seljuqs and Kara-Khitan, and later as independent rulers, up until the Mongol invasion of Khwarezmia inthe 13th century.

-The Mamluk Sultanate was an Arabized Turkic state inmedieval Egypt, the Levant, and Hejaz.

Mamluk Dynasty (Delhi) (1206–1290)
Mamluk Sultanate (Cairo) (1250–1517)

Also, the same situation with haplogroup T, the haplotypes of T and R1a-R1b really look similar. If you look at the Y-STR markers one by one, you will see what i mean, so what does this point out? Could it be possible that T is defined not correctly in the Y-tree? Can you guys also answer the questions i asked in the first post? We know of the sudden new discoveries of markers like M184 that changed the position of older K2-M70 fundamentally. What if the reason of the rare low frequencies of T in whole world is because there are still undiscovered SNP's that cause for the wrong classification of it in the Y-Tree?

LeBrok
25-01-15, 20:36
Interesting and intriguing. Welcome to Eupedia isbara.

isbara
25-01-15, 22:00
Interesting and intriguing. Welcome to Eupedia isbara.
Thanks LeBrok.

Sile
26-01-15, 00:58
@isbara

good read to your post

I have seen most of these ...........in regards to your point 1 - he stated IIRC ...what he called the T was a pre-R1a marker . But 2 things have happened since this paper was written in 2011/2012......BTW, the russians are heavily involved with the T marker.

1 - They found a LT-P326 marker which most of T and L people have ( I have it). this marker's origins are stated between coastal east iran ( ancient gedrosian-ariana ) and northern afghan lands ( ancient bactria ). And this marker is before T

2- M70 does not designate T1 anymore , it designates T1a.............for your point 1 to work, you will need to have no M70 in the person ( they do exist, Germany, ossetian zone, Armenia and Syria )

Anyway there is a T ydna forum in this site ...check it out


Are you also a T marker ?

regards

isbara
26-01-15, 02:51
BTW, the russians are heavily involved with the T marker.

Thanks for your message. Do you know of other data of Russian academicians like Klyosov relating to T?


They found a LT-P326 marker which most of T and L people have ..

At the site of isogg there is a text "M1205, L405/PF5990 may comprise a new MP or MPS subgroup" under the "SNPs under Investigation" heading. It means there are still many question marks regarding the Y-SNP tree... Look at figure 1b of “Comparison of Y-chromosomal lineage datingusing either evolutionary or genealogical Y-STR mutation rates” of Hui Li. In here T1a, Q1a2a1, R1a and R1b1a2a1a2 are put in the same branch. Also G2a3b, C3e and C1a are put in the same branch. Like i wrote in my first post, C and G are found with high percentages in Kazakhs. This shows their could be a relation between the 2 haplogroups. Maybe later the complete Y-tree will change, but i still think there are too few ancient dna studies done and dont forget the contamination problems, to define a healthy Y-Tree and Y migration and origins route. I think that serious studies of ancient dna of the past 2000 years combined with seriously historical facts will give a much more realistic picture of the history, and many question, marks regarding the similarities between Y-STR haplotypes and the question marks regarding the not solved Y-SNP tree puzzle pieces, will be answered.

sparkey
26-01-15, 19:32
There are a lot of topics to address here, so I'll just give a brief response to the main topic. There's not really any chance that Haplogroup T is at the wrong place in the Y tree at this point. There are too many SNPs (dozens) that separate T from R's branch to suggest that they're actually closer. Certainly, fast-mutating SNPs can appear at multiple places in the Y tree, but odds are definitely against anything of the sort throwing off the currently understood Y tree. What we're seeing instead is simply STR convergence. Covergence happens randomly absent any push factors, so the fact that there's convergence between T and R on certain STRs probably doesn't say anything. But if, for example, Klyosov or someone else expands the analysis and shows convergence of certain STRs across the Y tree, or local to certain geographic locations, we could be seeing evolutionary factors at play. I'm not aware of any such effect being conclusively demonstrated as of yet, though.

isbara
26-01-15, 22:41
There are a lot of topics to address here, so I'll just give a brief response to the main topic. There's not really any chance that Haplogroup T is at the wrong place in the Y tree at this point. There are too many SNPs (dozens) that separate T from R's branch to suggest that they're actually closer. Certainly, fast-mutating SNPs can appear at multiple places in the Y tree, but odds are definitely against anything of the sort throwing off the currently understood Y tree. What we're seeing instead is simply STR convergence. Covergence happens randomly absent any push factors, so the fact that there's convergence between T and R on certain STRs probably doesn't say anything. But if, for example, Klyosov or someone else expands the analysis and shows convergence of certain STRs across the Y tree, or local to certain geographic locations, we could be seeing evolutionary factors at play. I'm not aware of any such effect being conclusively demonstrated as of yet, though.

What do you think about the study paper at ht tp:// biorxiv.org/content/biorxiv/early/2014/05/03/004705.full.pdf ? Look at the text in page 3 and the graphs at figure 1.

Sile
27-01-15, 19:17
What do you think about the study paper at ht tp:// biorxiv.org/content/biorxiv/early/2014/05/03/004705.full.pdf ? Look at the text in page 3 and the graphs at figure 1.

If you are refering to the wang paper with T1 sitting next to O and R1 sitting next to S ......then yes this is possible, but for the rest I doubt it

sparkey
29-01-15, 00:23
What do you think about the study paper at ht tp:// biorxiv.org/content/biorxiv/early/2014/05/03/004705.full.pdf ? Look at the text in page 3 and the graphs at figure 1.

I have mixed opinions of that one. It seems that the results they're getting when using genealogical mutations rates are too low when compared to most other estimates I've seen, which of course makes evolutionary mutation rates seem more accurate than they actually are. 21 STRs is also too few; naturally, more STRs will mean more accuracy. There are calculations out there in the hobbyist community using methodologies from the likes of Klyosov and Nordtvedt (both using genealogical rates FWIW) that match the SNP estimates much more closely than what this paper is getting for either mutation rate. I think that Nordtvedt's and Klyosov's methods both tend to dip a little under the SNP estimates, which may get at a point that this paper is trying to get at, but not to the same degree that this paper shows.