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GailT
01-16-2014, 04:35 AM
U2 is a rare and interesting haplogroup. There was a U2 sample found in ancient remains dating to about 35,000 years ago at Kostenki, Russia. Around that time U2 appears to have spread both to Europe and to south Asia. Several suclades (U2a, U2b and U2c) are found most often in south Asia. U2d is found mostly in the Near East and southwest Asia, and U2e is found mostly in Europe. I'm uncertain of the migration history of U2e. It is estimated to be about 19,000 years old and it might have been among early Europeans, or it might have migrated to Europe with Neolithic farmers or herders.

There is a new U2e1 Chinese sample from a study by Jiang et al., which is in an unnamed subclade that I'm calling U2e1h, with an age estimate of about 5000 ybp. There are 10 samples in this group with ancestry from: China, India, Russia, Ukraine, France, Denmark, and 2 samples each from Italy and Spain. This is another group that seems to fit a possible Indo-European expansion, although other explanations could be possible for the unusual distribution.

parasar
01-16-2014, 04:50 AM
U2 is a rare and interesting haplogroup. There was a U2 sample found in ancient remains dating to about 35,000 years ago at Kostenki, Russia. Around that time U2 appears to have spread both to Europe and to south Asia. Several suclades (U2a, U2b and U2c) are found most often in south Asia. U2d is found mostly in the Near East and southwest Asia, and U2e is found mostly in Europe. I'm uncertain of the migration history of U2e. It is estimated to be about 19,000 years old and it might have been among early Europeans, or it might have migrated to Europe with Neolithic farmers or herders.

There is a new U2e1 Chinese sample from a study by Jiang et al., which is in an unnamed subclade that I'm calling U2e1h, with an age estimate of about 5000 ybp. There are 10 samples in this group with ancestry from: China, India, Russia, Ukraine, France, Denmark, and 2 samples each from Italy and Spain. This is another group that seems to fit a possible Indo-European expansion, although other explanations could be possible for the unusual distribution.

Aren't U2e and U2d related to U2c?

There is that Brahmin like (more likely a Shraman) Xiongnu sample who was R1a1/U2e1 from Duurlig Nars in North Eastern Mongolia.
"the autosomal profile of MNX3 West Eurasian male is 14 times more probable from a Brah-min Indian than from a modern Caucasian"
http://volgagermanbrit.us/documents/Kim_et_al.pdf

newtoboard
01-17-2014, 02:08 AM
Is there any U2d in Europe or South Adia?

parasar
01-17-2014, 03:47 AM
Is there any U2d in Europe or South Adia?

It is present in Europe.


The sequencing of the entire mitochondrial DNA belonging to haplogroup U2d reveals that this clade is defined by four coding-region mutations at positions 1700, 4025, 11893, and 14926. Phylogenetic analysis suggests that western Eurasian haplogroup U2d appears to be a sister clade with the Indo-Pakistani haplogroup U2c. Results of a phylogeographic analysis of published population data on the distribution of haplogroup U2d indicate that the presence of such mtDNA lineages in Europe may be mostly a consequence of medieval migrations of nomadic tribes from the Caucasus and eastern Europe to central Europe.http://digitalcommons.wayne.edu/humbiol/vol80/iss5/6/

BMG
01-21-2014, 09:04 AM
Aren't U2e and U2d related to U2c?

U2c and U2d is related and branches from U2c'd defined by C16234T . We have a U2c'd sample from jordan
http://www.ianlogan.co.uk/sequences_by_group/u2_genbank_sequences.htm

soulblighter
01-21-2014, 02:10 PM
I have the following "relatives" on 23andme who are U2:

U2a=8
U2b1=2
U2b2=3
U2c=7
U2e1=5

It appears that U2 may be widely distributed in South asia.

parasar
01-21-2014, 04:10 PM
U2c and U2d is related and branches from U2c'd defined by C16234T . We have a U2c'd sample from jordan
http://www.ianlogan.co.uk/sequences_by_group/u2_genbank_sequences.htm

And T152C! connects U2e and U2c'd.
http://www.mtdnacommunity.org/human-mtdna-phylogeny.aspx

GailT
01-22-2014, 07:35 AM
The relationship between U2c and U2d is very old - Behar estimates the age of U2c'd as 39 kya. The common ancestor of U2c'd'e would be slightly earlier than U2c'd.

I don't know of any U2c'd samples. Ian shows the branch point on his page but does not show a GenBank sample at that branch point.

FunkyWanderer
03-20-2014, 03:21 PM
Here's my Genographic results I just got back today.

Paternal Line: M42 > M168 > M89 > P128 > M45 > M207 > P231 > M343 > L278 > P310 > L21
Maternal Line: L3 > N > R > U > U2 > U2E > U2E1'2'3

MEDITERRANEAN
43%
NORTHERN EUROPEAN
39%
SOUTHWEST ASIAN
15%
NEANDERTHAL
1.9%
DENISOVAN
1.9%



YOUR FIRST REFERENCE POPULATION: BRITISH (UNITED KINGDOM)
YOUR SECOND REFERENCE POPULATION: GREEK



I find is curious there is no French reference population...

And myFTDNA gives:


Y-DNA R1b1a2a1a1b4 Shorthand R-L21 DF13
mtDNA U2e1b


I'm French Canadian, and I can track both Paternal and Maternal to France during the first colonization of Nouvelle France in the 1650's, and my paternal line to to 1033.

Paternal: Gen. Raphael de Podio, Commander of the Roman Cavalry & Grand Chamberlain of the Roman Republic, Governor of Provinces of Lanquedoc & Dauphiny of Southeastern France (b. bef. 1033)
Maternal: Marie Cholet, b.1602 and d. 1642

GailT
05-16-2014, 05:10 AM
Ian Logan has processed the 1041 mtDNA full sequence results from the Human Genome Diversity Project (link). (http://archiver.rootsweb.ancestry.com/th/read/GENEALOGY-DNA/2014-05/1400007181)

There are 9 U2 samples from Pakistan include 3 U2a, 2 U2b and 4 U2e1. One of the U2e1 samples is in U2e1h (the group I posted on above which is widely distributed across Eurasia) and the other 3 form a new subclade of U2e1 only found in Pakistan.

Based on the modern U2e distribution I still think a southwest Asian origin for U2e seems likely. In Mesolithic Europe there is the Blätterhöhle sample BLA3 dated at 11,200 ypb and identified as U2e based on HVR1 results. Then there are the two closely related Motala U2e1 samples dated at 8000 ybp, results still not published as far as I know. And then the Uznyi Oleni Ostrov U2e1 samples dated at 7500 ybp. So U2e was in Europe during the Mesolithic but I think it more likely that it originated in soutwest Asia or eastern Europe/Russia, and much of the present day European U2e1 could represent more recent migration from further east, perhaps with Indo European speakers. The only modern U2e* sample is from India.

GailT
07-04-2014, 02:54 PM
Here is an update on U2e3. There are 4 GenBank samples and 6 additional samples in the U2 FTDNA project, for a total of ten. All but two samples are in a very young branch of U2e3a found in Ireland that dates to about 1000 years ago. I estimate that U2e3 has a MRCA about 11,000 years ago, and that U2e3a has a MRCA about 6000 years ago (large uncertainty with the small number of samples).

U2e3a*1: 8 samples from Ireland, MRCA 2000 years ago.
U2e3a*2: 1 sample from the Middle East
U2e3*b: 1 sample from Italy

It might be possible that the Irish cluster descends from a Mediterranean woman who migrated to the British Isles during the Roman Empire era (also very speculative given the small number of samples).

parasar
07-04-2014, 03:41 PM
Kostenki has 4 extra mutations (at markers 542, 711, 13269, & 15262) so it forms its own subclade parallel to U2a, U2b, U2e etc. So this suggests that U2 was widespread, perhaps from Russia to India, with at least 6 different lineages surviving ca 35 kya. The ancestor of U2e was one of those lineages, but the MRCA of U2e probably lived around 20 kya almost certainly somewhere in southwest Asia.



So that seems to confirm multiple waves of migration of U2e into Europe. We know that U2e was in Europe by 11 kya, but U2e almost certainly did not arrive in Europe until after the LGM (unless the age estimate for U2e is significantly wrong).

It would be very helpful to have the full sequence for the Blätterhöhle sample to see if it is extinct or if it is ancestral to any of the U2e subclades in Europe. My guess is that U2e1, U2e2 and U2e3 all originated in southwest Asia and spread with Indo-European migrations. They could have also spread before that time, but it seems likely that this would have been a major event in in the spread of U2e.

The U2e* samples from India is AY714026. It is difficult to say anything from a single sample. This could represent a U2e subclade that migrated from southwest Asia at any time after 20 kya. The fact that it has not yet been found outside of India might indicate a more ancient migration rather than an Indo-European migration.

edit: I'll post some additional info on U2e in the U2 dicussion forum.

I doubt that U2e has anything to do with SW* Asia. U2 overall correlates best to the ANE (WHG, IMO, is related but later) component present in Europe. ANE significantly overlaps India and Europe, the two places where U2 is also present. ANE shows no affinity to the SW Asian components (part EEF, and something termed basal Eurasian). ANE did enter northern parts of West Asia, especially the Caucasus, but that is in the post-Neolithic timeframe - as Stuttgart has no ANE.

The provenance of the ancient U2 (from Jean's compilation) are in concordance with the ANE scenario:

Russia Kostenki 14 U2 11467, 12308, 12372, 1811, 16051

Germany Blätterhöhle, Hagen 11000ybp U2e
Sweden Motala 2 8000ybp U2e1
Russia 7500 ybp U2e 2 samples
Sweden Motala 12 8000ybp U2e

In Jean's DNA from the European and Mid-East Neolithic compilations there is not one U2.

So U2e was present in European hunter-gatherers but not in the neolithics.
That its presence is hunter-gathers correlates to ANE (see Motala 12 who per Lazaridis et al had 19% ANE) is also possible.

*Edit

GailT
07-04-2014, 06:03 PM
In Jean's DNA from the European and Mid-East Neolithic compilations there is not one U2. So U2e was present in European hunter-gatherers but not in the neolithics. That its presence is hunter-gathers correlates to ANE (see Motala 12 who per Lazaridis et al had 19% ANE) is also possible.

Perhaps U2e originated in the Black Sea/Caspian Sea refuge 20 kya, and then expanded into India and western Europe after the LGM. The Mesolithic European U2e might have been mostly replaced during the Neolithic, and another wave of U2e associated with Indo-Europeans expanded into Europe in the Bronze age.

U4 is another group that seems to have expanded from the East European plain after the LGM, and U5 seems to have expanded from western Europe to the east after the LGM. As the ice retreated and bands of hunter-gatherers expanded northward in both western and eastern Europe, it seems possible that there could have been east-west diffusion of U5, U4 and U2e. But the LGM origin of U2e would have been in a southern refuge, perhaps around the Black Sea and Caspian Sea, and this could also explain its early arrival in India and Pakistan.

I don't see any evidence of U2e in SE Asia but there is in southwest Asia. It might be confusing as to whether the Black Sea and Caspian Sea region should be called eastern Europe or southwest Asia - it seems that both of these names are used for the same region.

GailT
07-04-2014, 06:26 PM
Here is a summary of the 17 U2d FMS samples. The age estimate for U2d is 23 kya.

U2d1, 15,000 years, 6 samples: 2 Iran, Turkey, Kuwait, N Caucasus, ?,
U2d2, 9000 years, 8 samples: 2 Iran, 2 N Caucasus, Turkey, Tatar, Denmark, Jordan
U2d3, 6500 years, 2 samples: 2 N Caucasus
U2d*: 1 sample from Spain

parasar
07-04-2014, 06:51 PM
Perhaps U2e originated in the Black Sea/Caspian Sea refuge 20 kya, and then expanded into India and western Europe after the LGM. The Mesolithic European U2e might have been mostly replaced during the Neolithic, and another wave of U2e associated with Indo-Europeans expanded into Europe in the Bronze age.

U4 is another group that seems to have expanded from the East European plain after the LGM, and U5 seems to have expanded from western Europe to the east after the LGM. As the ice retreated and bands of hunter-gatherers expanded northward in both western and eastern Europe, it seems possible that there could have been east-west diffusion of U5, U4 and U2e. But the LGM origin of U2e would have been in a southern refuge, perhaps around the Black Sea and Caspian Sea, and this could also explain its early arrival in India and Pakistan.

I don't see any evidence of U2e in SE Asia but there is in southwest Asia. It might be confusing as to whether the Black Sea and Caspian Sea region should be called eastern Europe or southwest Asia - it seems that both of these names are used for the same region.

I meant SW Asia - corrected my post.
Though, I agree that there is no evidence of U2e or even U from SE Asia. For that we would need to go to the R level.

parasar
07-05-2014, 03:40 PM
Here is a summary of the 17 U2d FMS samples. The age estimate for U2d is 23 kya.

U2d1, 15,000 years, 6 samples: 2 Iran, Turkey, Kuwait, N Caucasus, ?,
U2d2, 9000 years, 8 samples: 2 Iran, 2 N Caucasus, Turkey, Tatar, Denmark, Jordan
U2d3, 6500 years, 2 samples: 2 N Caucasus
U2d*: 1 sample from Spain

Kivisild et al 1999 had a couple of 51 234 samples (only HVS-I)
Lam67 AP 51 234 U2i +12308 HinfI; –11465 Tru1I
Y36 AP 51 234 U2i +12308 HinfI
http://www.researchgate.net/publication/12726008_Deep_common_ancestry_of_indian_and_wester n-Eurasian_mitochondrial_DNA_lineages/file/d912f50995658d70b3.pdf

parasar
07-06-2014, 04:32 PM
I don't think that the hyper-Hypervariable region markers like 152 are useful for phylogentics, especially very deep in the tree, but even if you do assume that T152C! has some value for indicating a closer relationship among U2c, U2d and U2e, it might suggest that they share a common ancestor around 40 kya instead of 42 kya, so T152C! doesn't seem to add value.

I think it seems very likely that U2 was widespread from Russia to south Asia around 40 kya, given that we have 5 surviving lines that date from time, and also the Kostenki U2* sample.

U2e is interesting because it undergoes a bottleneck from 40 kya to 20 kya before it begins to expand in Asia and Europe. It seems possible that U2e expanded with Indo-European speakers given that it is found today from Europe to India, but that it also arrived in Europe as early as 11 kya, based on the Blätterhöhle sample. I would guess that U2e expanded from southwest Asia into south Asia after 20 kya and into Europe after the LGM, and then there might have been additional waves of expansion of U2e from SW Asia during the Neolithic. But we need more ancient mtDNA. I don't think we can reconstruct the complexity of multiple waves of migration from present day distributions because the time resolution ability of mtDNA is very poor.


There are 4 lineages of U2e:

U2e1 - found from Europe to India.
U2e2 - found from Europe to India.
U2e3 - just a few FMS samples found in Italy, Ireland and the Middle East
U2e* - a single sample from India

How about 16189? Do you think this is shared between U2e and U2d?


[U2d]might share the 16189 mutation with U2e by ancestry.

T16189C! is also seen in T1 and U1 among others.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1182158/

There was an article about how 16189C may have been misread. http://onlinelibrary.wiley.com/doi/10.1111/j.1529-8817.2005.00234.x/full

GailT
07-06-2014, 06:07 PM
16189 was the 6th most common mutation in the Soares et al 2009 study and is also found in several people in U2c. So you could suppose that it was ancestral to U2c'd'e (and there was an early back mutation in U2c), or that it occurred independently in U2d and U2e (and in a few U2c samples). Maybe the former is more likely, but I don't think we can know for certain, and it does not seem very useful for the deep structure.


It would be nice to have full sequences from Kivisild et al 1999. It looks like the 16051 & 16234 are probably U2c.

parasar
11-12-2014, 03:40 AM
Ian Logan has processed the 1041 mtDNA full sequence results from the Human Genome Diversity Project (link). (http://archiver.rootsweb.ancestry.com/th/read/GENEALOGY-DNA/2014-05/1400007181)

There are 9 U2 samples from Pakistan include 3 U2a, 2 U2b and 4 U2e1. One of the U2e1 samples is in U2e1h (the group I posted on above which is widely distributed across Eurasia) and the other 3 form a new subclade of U2e1 only found in Pakistan.

Based on the modern U2e distribution I still think a southwest Asian origin for U2e seems likely. In Mesolithic Europe there is the Blätterhöhle sample BLA3 dated at 11,200 ypb and identified as U2e based on HVR1 results. Then there are the two closely related Motala U2e1 samples dated at 8000 ybp, results still not published as far as I know. And then the Uznyi Oleni Ostrov U2e1 samples dated at 7500 ybp. So U2e was in Europe during the Mesolithic but I think it more likely that it originated in soutwest Asia or eastern Europe/Russia, and much of the present day European U2e1 could represent more recent migration from further east, perhaps with Indo European speakers. The only modern U2e* sample is from India.

Do we have any sample 1811+ 16051- in the U branch?

GailT
11-12-2014, 04:01 AM
Do we have any sample 1811+ 16051- in the U branch?

A1811G defines U2'3'4'7'8'9 and these are all 16051- except for U2 and U9a.

parasar
11-12-2014, 04:53 AM
A1811G defines U2'3'4'7'8'9 and these are all 16051- except for U2 and U9a.

My mistake I should have asked 1811* in the U branch..
I had another question - about Ust-Ishim's R - I could not figure out three of his mutations - 73G non H, but R, 263G non H, 750G non H, 1438G non H, 2706G non H, 3107d non H, 4769G non H, 7028T non H, 8860G non H, 11719A non H, but R, 14766T non H, but R, 15326G non H, 16150. Are they or the R branch or earlier? Thanks.

GailT
11-12-2014, 05:11 AM
My mistake I should have asked 1811* in the U branch..

To date everyone who has tested the FMS is in one of the 9 named U haplogroups. There are a few interesting HVR test results in the U* project that might possibly be a new U branch, but I expect if they test the full sequence they might turn out to be in one of the named groups.

Ust-Ishim is R plus an extra mutation at 16150, The path from R to H2a2a1 is copied below. The results are reported relative to the rCRS, so R is the opposite of this list. 3107d is a dummy to account for an error in the original CRS and should be ignored.

R0 73A
H2a2a1 263A
H2a2 750A
H2 1438A
H 2706A
H2a 4769A
H 7028C
H2a2a 8860A
R0 11719G
HV 14766C
H2a2a 15326A

parasar
11-13-2014, 01:00 AM
To date everyone who has tested the FMS is in one of the 9 named U haplogroups. There are a few interesting HVR test results in the U* project that might possibly be a new U branch, but I expect if they test the full sequence they might turn out to be in one of the named groups.

Ust-Ishim is R plus an extra mutation at 16150, The path from R to H2a2a1 is copied below. The results are reported relative to the rCRS, so R is the opposite of this list. 3107d is a dummy to account for an error in the original CRS and should be ignored.

R0 73A
H2a2a1 263A
H2a2 750A
H2 1438A
H 2706A
H2a 4769A
H 7028C
H2a2a 8860A
R0 11719G
HV 14766C
H2a2a 15326A

Thanks. Getting the hang of it. Why was this convoluted a system not rectified earlier?!

I'm a U2b2 derivative, and comparing to Ust-Ishim I was not able to figure out why my rCRS has no 2706 listed but my RSRS has 2706 listed. Obviously I could not find 3107d and 16150 in my data.

If I understand you correctly 2706 is A (for H through H2a2a1) for rCRS, and RSRS is G. Since I'm not H, I should be G at 2706. But then 2706 should have been listed on my rCRS. So 2706 must have mutated in my line too.

GailT
11-13-2014, 04:49 AM
Thanks. Getting the hang of it. Why was this convoluted a system not rectified earlier?!

I'm a U2b2 derivative, and comparing to Ust-Ishim I was not able to figure out why my rCRS has no 2706 listed but my RSRS has 2706 listed. Obviously I could not find 3107d and 16150 in my data.

If I understand you correctly 2706 is A (for H through H2a2a1) for rCRS, and RSRS is G. Since I'm not H, I should be G at 2706. But then 2706 should have been listed on my rCRS. So 2706 must have mutated in my line too.

U2b is defined by T146C! G2706A A5186t C12106T G13194A C15049T, so 2706A occurred independently in U2b and H, and thus no mutation is shown in the rCRS results.

Are you in the FTDNA U2 project? There is some structure in U2b2 that is not yet in phylotree, and if you send me your results or join the project I might be able to place you in a new subclade of U2b2.

miryag1
06-03-2015, 11:21 PM
I have the following "relatives" on 23andme who are U2:

U2a=8
U2b1=2
U2b2=3
U2c=7
U2e1=5

It appears that U2 may be widely distributed in South Asia.

According to 23&Me I am also U2e1.
My family has been in the US back to the late 1700's and the only line I am stuck on, oddly enough, is y mothers maternal line. It stops at Jane Campbell born 1798 who married Arthur Houston and had daughter Sarah An Catherine Houston born 1841. None of our family is from Asia or India.

miryag1
06-03-2015, 11:25 PM
Ian Logan has processed the 1041 mtDNA full sequence results from the Human Genome Diversity Project (link). (http://archiver.rootsweb.ancestry.com/th/read/GENEALOGY-DNA/2014-05/1400007181)

There are 9 U2 samples from Pakistan include 3 U2a, 2 U2b and 4 U2e1. One of the U2e1 samples is in U2e1h (the group I posted on above which is widely distributed across Eurasia) and the other 3 form a new subclade of U2e1 only found in Pakistan.

Based on the modern U2e distribution I still think a southwest Asian origin for U2e seems likely. In Mesolithic Europe there is the Blätterhöhle sample BLA3 dated at 11,200 ypb and identified as U2e based on HVR1 results. Then there are the two closely related Motala U2e1 samples dated at 8000 ybp, results still not published as far as I know. And then the Uznyi Oleni Ostrov U2e1 samples dated at 7500 ybp. So U2e was in Europe during the Mesolithic but I think it more likely that it originated in soutwest Asia or eastern Europe/Russia, and much of the present day European U2e1 could represent more recent migration from further east, perhaps with Indo European speakers. The only modern U2e* sample is from India.

I am U2e1 and none of my family is from there. It is also in the US.

Macura
06-04-2015, 08:26 PM
U2e1b1 from Balkan, South-Slavic origin.

FunkyWanderer
06-10-2015, 01:01 PM
I'm U2e1b from Canada, French heritage.

GailT
06-10-2015, 02:36 PM
According to 23&Me I am also U2e1.
My family has been in the US back to the late 1700's and the only line I am stuck on, oddly enough, is y mothers maternal line. It stops at Jane Campbell born 1798 who married Arthur Houston and had daughter Sarah An Catherine Houston born 1841. None of our family is from Asia or India.


For people who tested at 23andMe, you can upload your results to James Lick's mthap tool to check for any extra mutations that might define a more specific subclade. For people who tested at FTDNA, you can join the FTDNA U2 project, and if you tested the full mtDNA sequence (FMS) please share the coding region results with the project admin and I'll try to place you in a more specific subclade.

U2e1 is widely distributed from Europe to India. My guess is that it originated in southwest Asia about 15,000 years ago and spread from there.