More aDNA - J2a

[Gravetto-Danubian]

Haplogroup J (x 2 samples) was found in Epipalaeolithic Georgia in the just released Pinhasi et al.

http://www.nature.com/ncomms/2015/151116/ncomms9912/full/ncomms9912.html

Great news indeed !

[Anabasis]

ANE=Caucasian theory collapsed. I am so happy that the "teal" tale end. So far nobody could argue that exsistence of "teal" as a component carried by so called PIE. Its just a native component of caucasia and associated with J2 rather then R. I dont want to say that but I was right!!!!!

[ADW_1981]

ANE=Caucasian theory collapsed. I am so happy that the "teal" tale end. So far nobady could argue that exsistence of "teal" as a component carried by so called PIE. Its just a native component of caucasia and associated with J2 rather then R. I dont want to say that but I was right!!!!!

A bit early to say on that really. Since EF and Teal form a cluster with WHG as the outgroup, it could be Teal was carried by eastern BMAC cultures. This isn't really different from what some other people were saying a few months ago. The unknown was that Teal seems to be heavily concentrated in the Caucasus during the Palaeolithic period.

[Agamemnon]

What I find interesting is that the Caucasus doesn't really stand out as a place of high J diversity, J2 and J1 both seem to be notoriously uniform in this part of the world and, judging from contemporary data, the preponderance of these lineages has often been tied to founder effects across the Caucasus.

[Leeroy Jenkins]

What I find interesting is that the Caucasus doesn't really stand out as a place of high J diversity, J2 and J1 both seem to be notoriously uniform in this part of the world and, judging from contemporary data, the preponderance of these lineages has often been tied to founder effects across the Caucasus.

We do have J2a from early Neolithic Anatolian farmers that lack the "teal" component (AFAIK) and J in an EHG context, so who knows where J, J1 or J2 originate. Any or all 3 of those haplogroups could have been widespread throughout the Caucasus, the Near East and other parts of West Eurasia since pre-Neolithic times.

[Agamemnon]

We do have J2a from early Neolithic Anatolian farmers that lack the "teal" component (AFAIK) and J in an EHG context, so who knows where J, J1 or J2 originate. Any or all 3 of those haplogroups could have been widespread throughout the Caucasus, the Near East and other parts of West Eurasia since pre-Neolithic times.

Indeed, seems to me that the more J we find the more complicated its history gets... At least that's my personal impression so far. Like I said in the other thread, this is just the beginning and we'll need a lot more ancient data from the Near East if we are to get a clear assessment of J's spread and dispersal throughout the ages.

[ADW_1981]

What I find interesting is that the Caucasus doesn't really stand out as a place of high J diversity, J2 and J1 both seem to be notoriously uniform in this part of the world and, judging from contemporary data, the preponderance of these lineages has often been tied to founder effects across the Caucasus.

I believe they are - let me dig up some papers. Here's one of the more recent ones. http://www.ncbi.nlm.nih.gov/pubmed/25397702

[Anabasis]

A bit early to say on that really. Since EF and Teal form a cluster with WHG as the outgroup, it could be Teal was carried by eastern BMAC cultures. This isn't really different from what some other people were saying a few months ago. The unknown was that Teal seems to be heavily concentrated in the Caucasus during the Palaeolithic period.

No way we are talking about 13 k year old ancient samples. In my opinion those teal people are endemic on the region from caucaus to iran and SCA. Thats the gene pool for "Teal". Not carried by R1b or any so called "PIE". They were native. BMAC people of course could be in same pool. What i argue is Teal should not be associeted with R1 clades. That ancient samples proved that.

[ADW_1981]

No way we are talking about 13 k year old ancient samples. In my opinion those teal people are endemic on the region from caucaus to iran and SCA. Thats the gene pool for "Teal". Not carried by R1b or any so called "PIE". They were native. BMAC people of course could be in same pool. What i argue is Teal should not be associeted with R1 clades. That ancient samples proved that.

That's exactly what I am saying. How can it be related to the spread of PIE when that language came from the steppes and either the Sintashta or Andronovo culture (I forget which) was low on Teal component. The discovery of an 13,000 ybp Caucasian hunter-gatherer carrying exorbitant amounts of Teal would only reinforce the theory that PIE was spread with EHG in the north.

[J Man]

Wowwwwwww!!!

[kingjohn]

now i think the natufians belonged also to j haplogroup not
only g2
if they were in such early date in georgia it is truly amazing
and it is not even an E but i am happy for all the j out there
best regards
adam

[Agamemnon]

^^ Possible, but as long as we don't have ancient data from the Levant this is just an educated guess.

[J Man]

now i think the natufians belonged also to j haplogroup not
only g2
if they were in such early date in georgia it is truly amazing
and it is not even an E but i am happy for all the j out there
best regards
adam

These Y-DNA haplogroup J results from these Caucasus/Caucasian hunter-gatherers have nothing to do with the Natufians.

[J Man]

We do have J2a from early Neolithic Anatolian farmers that lack the "teal" component (AFAIK) and J in an EHG context, so who knows where J, J1 or J2 originate. Any or all 3 of those haplogroups could have been widespread throughout the Caucasus, the Near East and other parts of West Eurasia since pre-Neolithic times.

Yes that is true but it is possible that the J2a sample found among the Neolithic Anatolians came from an assimilated Caucasus like hunter-gatherer population that inhabited parts of the Northern Near East/Anatolia that was there before Neolithic farmers made it up from the Levant. The Caucasus/Teal like autosomal ancestry could have been bred out within a few generations after being assimilated into a Neolithic culture. Of course I could be wrong though and this is just a guess. We still need a lot more

[Gravetto-Danubian]

I agree with Agamemnon's observations. The Trail of J is complex. But it does appear to be the equivalent of haplogroup I in Europe as a marker of an ice age population which drifted together.

It then must have dispersed widely and lost any one to one correspondence to autosomal components. Indeed unlike haploid markers, autosomal components are reticulating in the pattern of inheritance.

Even the these small samples of data from the near East raises a possibility of large-scale population replacements or turnovers in the near East as well, like Europe.

I'd bet that hg G was dominant in the refuge population which was Proto - Natufian, but now the Levant is dominated by Haplogroup J. Must be related to the fact that much of this early farm population just up and left for Europe. On the other hand G find some high frequencies in the caucuses nowadays, the timing of which is still yet to be determined. If I recall - the BA Armenian was R1b (x2) and E, no G or J.

Again, great news for our J cousins .

[Lank]

J2a (J-M410), according to YFull has a TMRCA of 18100 ybp, and the branch formed 27800 ybp. This new ancient J2a sample lived 13,000 years ago.

[Agamemnon]

J2a (J-M410), according to YFull has a TMRCA of 18100 ybp, and the branch formed 27800 ybp. This new ancient J2a sample lived 13,000 years ago.

Good point, that's a lot of time for J2a to spread around. I wonder which specific J2a branch "Kotias" carried.

[MfA]

If I recall - the BA Armenian was R1b (x2) and E, no G or J.


Little correction here, there were 2 R1b, 2 E-M84, 1J2b.

[kingjohn]

j man ,agamemnon
as you say time will tell the only problems
with this culture https://en.wikipedia.org/wiki/Natufian_culture is that it would be hard
to extract dna because of the warm climate
one of the skulls is from 11,300 bc it is in the same time as the natufians
and if it was that far north it is simple logic that it would be found farther south but as you say time will tell.
kind regards
adam

[J Man]

j man ,agamemnon
as you say time will tell the only problems
with this culture https://en.wikipedia.org/wiki/Natufian_culture is that it would be hard
to extract dna because of the warm climate
one of the skulls is from 11,300 bc it is in the same time as the natufians
and if it was that far north it is simple logic that it would be found farther south but as you say time will tell.
kind regards
adam

The Natufians may have carried Y-DNA haplogroup E among them as well. Time and more testing hopefully will tell some day.

[J Man]

There seems to have been a bit of a mix up when it comes to reporting the Y-DNA haplogroups of these CHG samples. In the paper itself it says.

''Continuity in the Caucasus is also supported by the mitochondrial and Y chromosomal haplogroups of Kotias (H13c and J2a, respectively) and Satsurblia (K3 and J), which are all found at high frequencies in Georgia today22, 23, 24 (Supplementary Note 8).''

But in the Supplementary Note 8 link it says.

http://www.nature.com/ncomms/2015/151116/ncomms9912/extref/ncomms9912-s1.pdf

''Supplementary Table 19. Y chromosome haplogroups for ancient male samples.
Sample Major haplogroup Maximum likelihood haplogroup Confidence haplogroup
Kotias J J J
Satsurblia J J2a J2
Bichon I I2a* I2
Haplogroups were determined by Yfitter13. The “maximum likelihood haplogroup” is described by 13, as being the best guess
haplogroup while the “confidence haplogroup” is described as the conservative guess haplogroup.''


Below this again in the Supplementary Note 8 link it says.

''Y-chromosomal haplogroups
Both Georgian hunter-gatherer samples were assigned to haplogroup J with Kotias belonging to
the subhaplogroup J2a (see methods). Haplogroup J is estimated to have arisen 31.7 kya in the
Middle East and is widely distributed in Eurasia, the Middle East and North Africa48,49. Patterns
of haplogroup frequency are consistent with an expansion from the Middle East towards Europe
which has been suggested to have accompanied the Neolithic transition in Europe48,50,51. In a
study exploring J haplogroups in 445 individuals from Eurasia, J2a was found at highest
frequency in Georgia and Iraq48. It is intriguing that both the mitochondrial and Y chromosome
haplogroups of our ancient Georgian samples have been associated with the Neolithization of
Europe. This tentatively suggests a genetic link between Georgian hunter-gatherers and early
European migrants from the Near East.''



So which is correct? Is Kotias J or J2a? Is Satsurblia J or J2a?

[Erik]

Aha, so my dad's family lived in Georgia as well ;)

[Viktor Reznov]

We really need those Natufian and and Khiamian results to see how old J2a is in the Levant.

[J Man]

We really need those Natufian and and Khiamian results to see how old J2a is in the Levant.

You mean to see if J2a was present among the Natufians and Khiamians?

[parasar]

There seems to have been a bit of a mix up when it comes to reporting the Y-DNA haplogroups of these CHG samples. In the paper itself it says.
...

So which is correct? Is Kotias J or J2a? Is Satsurblia J or J2a?

No way to figure out unless someone looks at the SNPs in detail (Genetiker has not looked at SNPs for some time now!).
I still think J entered the near-east from Upper Paleolithic Europe.
"WHG and CHG are the descendants of two ancient populations that appear to have persisted in Europe since the mid Upper Palaeolithic and survived the LGM separately."

[Viktor Reznov]

You mean to see if J2a was present among the Natufians and Khiamians?
Yes..

[MfA]

Kotias line: J2-Y12378
http://www.open-genomes.org/genomes/Jones%20(2015)%20Georgia/KK1/images/


EDIT: not sure why i posted here, but better to move it to proper thread: http://www.anthrogenica.com/showthread.php?5834-More-aDNA-J2a

[Agamemnon]

Kotias line: J2-Y12378
http://www.open-genomes.org/genomes/Jones%20(2015)%20Georgia/KK1/images/

According to YFull Y12378's TMRCA is around ~9200 yBP, it seemingly peaks in Georgia and North Ossetia and is also found in Chechnya, Brazil, Spain and Turkey.

[J Man]

According to YFull Y12378's TMRCA is around ~9200 yBP, it seemingly peaks in Georgia and North Ossetia and is also found in Chechnya, Brazil, Spain and Turkey.

Looks like this branch of J2a has been in the Caucasus since at least the Mesolithic.

[royking]

Yes, Ted Kandell from OGF found this sample to be J2a-Y12378. "The sample KK1 from Kotias Klde, Georgia, 9955-9589 ybp (cal BP+60) is
Y12630+ Y12628+ and therefore J-Y12378. However, he's also SK1314/Y12595-, Y12624-, CTS3089-, and therefore a "partial" J-Y12378.
http://www.open-genomes.org/…/Jones%20(2015)%20…/KK1/images/

This is a preliminary result from just 1 out of 5 sequences for KK1, but it seems to be consistent." CEPH also has an Adyghe who is likely from this cluster and ChrisR has several Georgians, a Chechen and an Adyghe from this group.

[J Man]

Yes, Ted Kandell from OGF found this sample to be J2a-Y12378. "The sample KK1 from Kotias Klde, Georgia, 9955-9589 ybp (cal BP+60) is
Y12630+ Y12628+ and therefore J-Y12378. However, he's also SK1314/Y12595-, Y12624-, CTS3089-, and therefore a "partial" J-Y12378.
http://www.open-genomes.org/…/Jones%20(2015)%20…/KK1/images/

This is a preliminary result from just 1 out of 5 sequences for KK1, but it seems to be consistent." CEPH also has an Adyghe who is likely from this cluster and ChrisR has several Georgians, a Chechen and an Adyghe from this group.

The link does not work.

[parasar]

The link does not work.
http://www.open-genomes.org/genomes/Jones%20(2015)%20Georgia/KK1/images/
Same as MfA posted.

[Edward J]

Is that quote about CHG coming from Europe into the near east from the paper?

[ADW_1981]

Is that quote about CHG coming from Europe into the near east from the paper?

The term Europe is a bit misleading. The cluster formed as refugia in the Caucasus mountains, probably sourced from an earlier population residing in eastern Turkey. The paper might actually have some specific answer on this, but I would imagine it was south of the Caucasus mountains since EF is a closer node than WHG.

[parasar]

Is that quote about CHG coming from Europe into the near east from the paper?

No that is my opinion based on where I think the split in IJ happened and the near complete absence of Y-I in South Asia.

The quote -"WHG and CHG are the descendants of two ancient populations that appear to have persisted in Europe since the mid Upper Palaeolithic and survived the LGM separately." - is from the paper though.

[J Man]

I emailed the main author of this study/paper to clear something up. Here is her reply.

''I'm very sorry about the mix up in the supplementary material. The main text is correct - Kotias was assigned to haplogroup J2a and Satsurblia to J.''

[ChrisR]

Yes, Ted Kandell from OGF found this sample to be J2a-Y12378. "The sample KK1 from Kotias Klde, Georgia, 9955-9589 ybp (cal BP+60) is
Y12630+ Y12628+ and therefore J-Y12378. However, he's also SK1314/Y12595-, Y12624-, CTS3089-, and therefore a "partial" J-Y12378.
http://www.open-genomes.org/genomes/Jones%20%282015%29%20Georgia/KK1/images/

This is a preliminary result from just 1 out of 5 sequences for KK1, but it seems to be consistent." CEPH also has an Adyghe who is likely from this cluster and ChrisR has several Georgians, a Chechen and an Adyghe from this group.
Just to post this also here in this open forum my Facebook message of today (https://www.facebook.com/groups/j2.m172/permalink/10153704300987769/?comment_id=10153704502007769&offset=0&total_comments=13&comment_tracking={%22tn%22%3A%22R6%22})

This seems like another good confirmation of the YFull time estimates. In my research tree SK1321 is at the same level as Y12630 and Y12378:
http://tree.j2-m172.info/?Hg=J2a1b
This haplogroup seems genuinely Georgian/Caucasic.
If no (reliable) novel SNPs in KK1 exist this might be even the ancestor (or a near relative to him) of all SK1321,Y12630,Y12378+ men.
AFAIK we need to be open minded on the origin of the ancestral haplogroups Z6049<PF4610<M410 as long as no ancient DNA negative for all subclades is found.

[Agamemnon]

My personal feeling right now is that it'll be hard to make sense of these results until the we get our hands on the Mal'ta boy equivalent of J, that is to say a J sample which is over 20,000 years old... Just a thought.

[J Man]

What I actually find the most interesting about all of this is that there were Y-DNA haplogroup J2a men who were still technologically and culturally Mesolithic hunter-gatherers in the Caucasus even after farming had been around for a few thousand years.

[Agamemnon]

What I actually find the most interesting about all of this is that there were Y-DNA haplogroup J2a men who were still technologically and culturally Mesolithic hunter-gatherers in the Caucasus even after farming had been around for a few thousand years.

Indeed, it gives the lie to all the J2a=early farmers theories in a sense. Further proof that contemporary frequencies are utterly misleading.

[J Man]

Wohhhhh! Stop the presses! Check this out.

http://j2-m172.info/links/scientific-papers/

11300 BC Late Upper Palaeolithic Caucasus (Satsurblia cave, Western Georgia) in Jones et al 2015 is
J(1/2a)?;
7940-7574 BC Mesolithic Caucasus (Kotias Klde cave, Western Georgia, sample KK1) in Jones et al 2015 (OG) is
J2a1b-Z6049>Y12630(xSK1314);

[J Man]

Just to post this also here in this open forum my Facebook message of today (https://www.facebook.com/groups/j2.m172/permalink/10153704300987769/?comment_id=10153704502007769&offset=0&total_comments=13&comment_tracking={%22tn%22%3A%22R6%22})

So Kotias Klde then is positive for the M410 mutation that defines J2a correct?

[Viktor Reznov]

Wohhhhh! Stop the presses! Check this out.

http://j2-m172.info/links/scientific-papers/

11300 BC Late Upper Palaeolithic Caucasus (Satsurblia cave, Western Georgia) in Jones et al 2015 is
J(1/2a)?;
7940-7574 BC Mesolithic Caucasus (Kotias Klde cave, Western Georgia, sample KK1) in Jones et al 2015 (OG) is
J2a1b-Z6049>Y12630(xSK1314);

He was J2a1b?:eek:

[J Man]

He was J2a1b?:eek:

Not sure really. Different people seem to be thinking different things. One thing for sure is that he was J2 and most likely some sort of J2a.

[Agamemnon]

Nah, he wasn't J2a1b-M67, Y12630 is a pretty basal branch of J2a anyway.

[J Man]

Nah, he wasn't J2a1b-M67, Y12630 is a pretty basal branch of J2a anyway.

Looking at this page on open genomes he is part of the J-Y12378 branch. It looks like it is downstream of J-M410. J-M410 as I am sure you know is J2a.

http://www.open-genomes.org/genomes/Jones%20%282015%29%20Georgia/KK1/images/J2a-M410%20YFull%20tree%20at%2013,100%20ybp%20showing% 20Kotias%20Klde%201%20J-Y12378.png

[parasar]

Ancient J/J2 is essentially filling out the regions where it is present today. So I expect if/when we get ancient DNA results from Iran, South Asia, Arabia, it will show some J.

https://www.google.com/maps/d/viewer?mid=z_sglqYam1DA.krc3YkMRD7Wo

http://j2-m172.info/links/scientific-papers/

Ancient J/J2 DNA
See Ancient J2 Map (Ancient J2 Samples) by Ilhan Cengiz

11300 BC Late Upper Palaeolithic Caucasus (Satsurblia cave, Western Georgia) in Jones et al 2015 is
J(1/2a)?;
7940-7574 BC Mesolithic Caucasus (Kotias Klde cave, Western Georgia, sample KK1) in Jones et al 2015 (OG) is
J2a1b-Z6049>Y12630(xSK1314);
6500-6200 BC Neolithic Anatolia (Barcın, Northwestern Turkey, sample I0708/BAR6/L11-439) in Mathieson et al 2015 is
J2a-M410;
5500-5000 BC Karelian-Finno Ugric hunter gatherer near Finland (EHG, Yuzhnyy Oleni Ostrov, Karelia, sample I0211/UzOO40) in Mathieson et al 2015 is
J-PF4521;
5030-4840 BC Neolithic Sopot Culture in Hungary (sample ALE14) in Szecsenyi-Nagy 2015 is
J2-M172;
5000-4300 BC? Neolithic Lengyel Culture in Hungary (sample FEB3) in Szecsenyi-Nagy 2015 is
J2-M172;
1270-1110 calBC late Bronze Age Kyjatice Culture boy in Hungary (sample BR2) in Gamba et al. 2014 (OG>AM) is
J2a1a1a1b1-M67/S51>Z7671>CTS900>Y11202>Z30695>Z30685;
in the study autosomally he clusters with modern Western Europeans (mainly French) so his near ancestry should be not from Caucasus or Anatolia (West Asia).
1209-1009 BC late Bronze Age Norabak Culture in Armenia (sample RISE408) in Allentoft et al. 2015 is
J2b2a-M241>L283>Z600(xYP1,YP6)
~50 AD (900 BC to 1000 AD) Iron age Sary-Bel Kurgan Altai (sample RISE602) looks like complexes (II c. BC – I century AD) Bulan-Koba culture, which has been following the Scythian-Saka epoch in the Russian Altai (near border to Kazakhstan, China, Mongolia) in Allentoft et al. 2015.
J2a2-PF5050>PF5058>PF7384>PF5056>PH3085,SK1403
400-600 AD Merovingian buriel site Roman-Frankish transitional period in Lauwerier, De Kort 2014:
2 J2a1a1a1b1-M67? and one J2b?
~ 805 AD late Iron age Kytmanovo Altai (sample RISE504) in Allentoft et al. 2015.
J2a2-PF5050>PF5058>PF7384>PF5056>PH3085,SK1403
8-9th centuries AD Saltovo-Mayaki culture (Khazars period, sample A80411) in Afanas’ev et al 2015 (updates expected)

[J Man]

Ancient J/J2 is essentially filling out the regions where it is present today. So I expect if/when we get ancient DNA results from Iran, South Asia, Arabia, it will show some J.

https://www.google.com/maps/d/viewer?mid=z_sglqYam1DA.krc3YkMRD7Wo

http://j2-m172.info/links/scientific-papers/

Well J will show up sure but the important thing is the time periods that J shows up in.

[RCO]

Arabia J is quite "new" just like R1b in Ireland. Northern Near East is the core area of basal types of J. Iran will be the J basal breakthrough because is the region with the most basal diversity.

[Agamemnon]

Arabia J is quite "new" just like R1b in Ireland. Northern Near East is the core area of basal types of J. Iran will be the J basal breakthrough because is the region with the most basal diversity.

Most of the J in the Caucasus also happens to be quite recent (like I said, its predominance is often attributed to founder effects), so that's not really convincing, though J1's phylogeny does indicate a north-to-south spread. More data is needed at this point.

[RCO]

When we investigate a line from Eastern Anatolia, the Caucasus, the Caspian Plains and the Iranian Plateau we can find a continuum of all J basal types. The last article was "Afghan Hindu Kush: Where Eurasian Sub-Continent Gene Flows Converge". Julie Di Cristofaro et al. PLOS. October 2013. Figure S7 . They sampled the Iranian diversity, including J1. Unfortunately they only used M267, P58 and 388=13. Iran, Gilan - More than 10% of Gilaki, Caspian Sea is J-M267*(xPage08, xDYS388-13). They refused to test M365 there. Now we have the NGS and the J diversity there is very big in terms of different basal SNPs and different overall frequencies of J1 and J2 types.

[J Man]

I emailed Eppie Ruth Jones about the M410 SNP status (which defines Y-DNA haplogroup J2a) of the Kotias Klde sample and here is her reply.

''Yes Kotias does seem to have the M410 mutation (6Gs at position 2751678 in hg19 orientation).''

[ChrisR]

He was J2a1b?:eek:
I know it is confusing but keep in mind that in the last years the hierarchical nomenclature below J1, J2a and J2b2 has changed dramatically. In general you always need to look for the Name Version of the source.
http://www.isogg.org/wiki/Y-DNA_project_help#Nomenclature_System_.28YCC.29
This nomenclature is not yet certified by ISOGG but should comply to the "pride of place":
http://j2-m172.info/research/basic-tree-subclades/
I always try to use at least one SNP which is more telling then the hierarchical name.
So the old J2a1b/J2a4b in J2-M172 Hg research is now J2a1a1a1b1-M67 and the old J2a*(xL26) is now J2a1b-Z6049 and J2a2-PF5050.

[J Man]

I know it is confusing but keep in mind that in the last years the hierarchical nomenclature below J1, J2a and J2b2 has changed dramatically. In general you always need to look for the Name Version of the source.
http://www.isogg.org/wiki/Y-DNA_project_help#Nomenclature_System_.28YCC.29
This nomenclature is not yet certified by ISOGG but should comply to the "pride of place":
http://j2-m172.info/research/basic-tree-subclades/
I always try to use at least one SNP which is more telling then the hierarchical name.
So the old J2a1b/J2a4b in J2-M172 Hg research is now J2a1a1a1b1-M67 and the old J2a*(xL26) is now J2a1b-Z6049 and J2a2-PF5050.

I noticed that Ilhan Cengiz has mixed up the haplogroup results of the Kotias Klde and Satsurblia samples on his map. Kotias Klde is J2a and Satsurblia is J.

[Gravetto-Danubian]

Has anyone attempted to collate than up to date collation of J lineages in Europe ?

[Viktor Reznov]

I know it is confusing but keep in mind that in the last years the hierarchical nomenclature below J1, J2a and J2b2 has changed dramatically. In general you always need to look for the Name Version of the source.
http://www.isogg.org/wiki/Y-DNA_project_help#Nomenclature_System_.28YCC.29
This nomenclature is not yet certified by ISOGG but should comply to the "pride of place":
http://j2-m172.info/research/basic-tree-subclades/
I always try to use at least one SNP which is more telling then the hierarchical name.


Yes it is quite confusing to have to keep with it all the time.


So the old J2a1b/J2a4b in J2-M172 Hg research is now J2a1a1a1b1-M67 and the old J2a*(xL26) is now J2a1b-Z6049 and J2a2-PF5050.
I suppose that sounds cooler for us in some ways :)

[ChrisR]

Yes it is quite confusing to have to keep with it all the time.
I suppose that sounds cooler for us in some ways :)
Hierarchical names IMO should be used only to see the chronology and for ordering purposes (in tables/sheets/databases etc.). A primary SNP name is a much better marker to name a specific haplogroup. If you and those with which you communicate all know about the SNPs you can also just use shorthand versions like J-M92* or J2a-M92*

[J Man]

Hierarchical names IMO should be used only to see the chronology and for ordering purposes (in tables/sheets/databases etc.). A primary SNP name is a much better marker to name a specific haplogroup. If you and those with which you communicate all know about the SNPs you can also just use shorthand versions like J-M92* or J2a-M92*

Check your email. :)

[lgmayka]

Kotias line: J2-Y12378
http://www.open-genomes.org/genomes/Jones%20(2015)%20Georgia/KK1/images/
Notice that the sibling of J-Y12378 is J-Z6050 (http://yfull.com/tree/J-Z6046/), for which YFull has modern Austrian and Punjabi examples. But J-Y12378 and J-Z6050 diverged over 15,000 years ago.

[J Man]

Notice that the sibling of J-Y12378 is J-Z6050 (http://yfull.com/tree/J-Z6046/), for which YFull has modern Austrian and Punjabi examples. But J-Y12378 and J-Z6050 diverged over 15,000 years ago.

Yes both J-Y12378 and J-Z6050 seem to be very old subclades of J2a.

[ChrisR]

EDIT: post moved to ancient J1b-F4306(xZS80) Satsurblia Late Upper Palaeolithic Caucasus (http://www.anthrogenica.com/showthread.php?5855-ancient-J1b-F4306%28xZS80%29-Satsurblia-Late-Upper-Palaeolithic-Caucasus&p=121614#post121614)

[ChrisR]

I published files and data regarding the Jones et al 2015 (http://www.nature.com/ncomms/2015/151116/ncomms9912/full/ncomms9912.html) J-samples analysis in this Google Drive folder:
ancient-Caucasus_J2a1b2-J1b_Jones-et-al-2015 (https://drive.google.com/folderview?id=0B7PnxbT9P49hSmNydS0xRU1ZU2s&usp=sharing)
From the original WGS BAM file (http://www.ebi.ac.uk/ena/data/view/ERP012743) the chrY BAM file was extracted and checked with IGV Viewer (http://www.broadinstitute.org/software/igv/home) for the relevant SNP information by using the included Region Navigator (importing regions using the bed.csv files)

Ted's analysis for Mesolithic genome (‘Kotias’ from Kotias Klde cave) is confirmed: this sample is genuinely J2a1->Z6049>SK1321(xSK1314) so a not completely evolved J2a1b2.

Rough genetic time estimate comparison:
J2a1b2 age ybp according to Yfull YTree v3.17: 15400 to 9200
% of derived J2a1b2 variants: 67% of 43
time by derived variants and Yfull estimate: 4181
age since formation: 11218
ybp median 9,529–9,895 cal. BP: 9712
difference estimate/archeological age: 1507 years
So this looks very good and if YFull will include this good quality sample (15.4-fold WGS) the estimate will improve further.
Off course novel SNPs can account for the 1500 years of difference.

[ChrisR]

SNP status from the analysis for haplogroup J2a-M410>PF4610>Z6049>SK1321(xSK1314):
POSITIVE: SK1312/Y12601, SK1316/Y12379, SK1321/Y12622, Y12401, Y12579, Y12580, Y12582, Y12585, Y12589, Y12590, Y12594, Y12600, Y12603, Y12604, Y12605, Y12610/Z35797, Y12619, Y12621, Y12623, Y12625, Y12630;
POSITIVE (SNPs under investigation): SK1313/Y12593, Y12592, Y12606, Y12611, Y12628, Y12629, Y13127, Z28350;
NO CALL: Y12627; NO CALL (SNPs under investigation): Y12633;
NEGATIVE: SK1314/Y12595, Y12378, Y12391, Y12397, Y12399, Y12583, Y12598, Y12607, Y12631, Z35798;
NEGATIVE (SNPs under investigation): CTS3089, Y12389, Y12617, Y12624;

[lgmayka]

Notice that the sibling of J-Y12378 is J-Z6050 (http://yfull.com/tree/J-Z6046/), for which YFull has modern Austrian and Punjabi examples. But J-Y12378 and J-Z6050 diverged over 15,000 years ago.
The Austrian and Punjabi J-Z6050 have been joined by an Italian (http://yfull.com/tree/J-Z6046/). But his analysis is not complete, so we'll have to wait for the next tree version to find out whether he forms a subclade with one or the other.

[ChrisR]

The Austrian and Punjabi J-Z6050 have been joined by an Italian (http://yfull.com/tree/J-Z6046/). But his analysis is not complete, so we'll have to wait for the next tree version to find out whether he forms a subclade with one or the other.
This is a sample from the Sardinian (Francalacci) dataset which YFull announced to gradually include in their analysis. The Sardinians are nearer to the Austrian then to the Punjabi:
http://tree.j2-m172.info/?Hg=J2a1b

[ChrisR]

lucky Z6049 guys: they have their second ancient DNA sample. I0708 ancient Neolithic NW.Anatolia ~6350 BC is J2a-M410>PF4610>Z6049>Z6048(xS20392)
Have not yet looked if he shares more SNPs with HG02774 Punjabi. For a comparison with 399585 Puerto Rico his YFull novel SNPs would be very helpful.
He is also negative for one SNP at the Z6048 level: Z6050 (single read), so possibly an extinct branch since Z6048 should be 13100 ybp (11100 BC).
http://tree.j2-m172.info/?Hg=J2a1b
http://www.yfull.com/tree/J-Z6046/

Given the Z6048>S23891 Sardinian diversity the speculation of a Neolithic Western Anatolian (or Aegean?) origin becomes very valid. At the same time one wonders why no ancient DNA of this type in Europe was found and the Z6048 mutation is also not very common in modern Europe's J2a.

SNP check

Z6049+ Z6047+
Z6048+ S18075+ S9634+ S10343+ S24092+ Y12410+ Y12411/Z28458+ Y12412/Z28495+ Z6054+ SK646/Y12712+ Y12407? Y12408? Y12409/Z28463? Y12707? Z6050-
S20392- S21433- S24758- S9519? S20696? S20731? S22011? S22218? S23560? S23891?

[Gravetto-Danubian]

J2b found in Bronze Age Ireland
Outrageous !

http://m.pnas.org/content/early/2015/12/22/1518445113

[Leeroy Jenkins]

J2b found in Bronze Age Ireland
Outrageous !

http://m.pnas.org/content/early/2015/12/22/1518445113

That's mtDNA J2b, no?

[Gravetto-Danubian]

That's mtDNA J2b, no?

Yes. My error !
Sorry everyone ")