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Jean M
06-13-2015, 11:47 AM
At the moment I'm adding the mtDNA results from Allentoft to my online tables, but would like to be able to add Y-DNA results too eventually.

I know that various people are working on the raw data to produce these, but the results seem to be scattered about. If anyone would like to place results here (with the RISE number), I would be very grateful.

Passa
06-13-2015, 11:52 AM
This is from Genetiker:

Below are the Y haplogroups for 47 of the 55 newly available male genomes from prehistoric Eurasia.

I’ll update this post as I process more of the samples.

RISE512 Russia Andronovo R1a1a1b-S224/Z645
RISE94 Sweden Battle Axe R1a1a1-Page7
RISE566 Czech Republic Bell Beaker R1b1a2a1a-P310/PF6546/S129
RISE560 Germany Bell Beaker R1b1a2-L150.1/PF6274.1/S351.1
RISE563 Germany Bell Beaker R1b1a2a1a2b-PF6570/S28/U152
RISE564 Germany Bell Beaker R1b1a2a1-L51/M412/PF6536/S167
RISE434 Germany Corded Ware P1
RISE436 Germany Corded Ware P1
RISE446 Germany Corded Ware R1a1a1-M417
RISE1 Poland Corded Ware CT
RISE431 Poland Corded Ware K(xLT)
RISE555 Russia EBA R1b1a2a2-CTS7340/Z2107
RISE492 Russia Iron Age R1
RISE600 Russia Iron Age Q1a1b-M25
RISE601 Russia Iron Age Q1a1b-M143
RISE494 Russia Karasuk R1a1a1-Page7
RISE397 Armenia LBA R1b1a2a2-Y4371/Z8128
RISE408 Armenia LBA J
RISE598 Lithuania LBA BT
RISE553 Russia LBA P
RISE554 Russia LBA I?
RISE374 Hungary Maros G2a2a1a-PF6308
RISE413 Armenia MBA R1b1-M415/PF6251
RISE416 Armenia MBA DE
RISE423 Armenia MBA E1b1b1b2a1-PF2020/Z1153
RISE524 Russia Meshovskaya R1b1a2-PF6494
RISE525 Russia Meshovskaya R1a1a1-Page7
RISE21 Denmark Nordic BA ?
RISE47 Denmark Nordic BA R1b1a2-M520/PF6410
RISE175 Sweden Nordic BA I
RISE207 Sweden Nordic BA I1-M450/S109
RISE276 Denmark Nordic LBA R1b1a2-L265/PF6431
RISE42 Denmark Nordic LN CT
RISE179 Sweden Nordic LN I
RISE61 Denmark Nordic MN B R1a1a1-Page7
RISE546 Russia Pit Grave R1b1a2-PF6482/YSC0000203
RISE547 Russia Pit Grave R1b1a2a2-CTS9416
RISE548 Russia Pit Grave R1b1a2a2-Z2105
RISE550 Russia Pit Grave R1b1a2(xL51)
RISE486 Italy Remedello I2a1a1a-L672/S327
RISE487 Italy Remedello I
RISE489 Italy Remedello I2a1a1a-L672/S327
RISE386 Russia Sintashta R1a1a1b2a2-Z2124
RISE392 Russia Sintashta R1a1a1b-S224/Z645
RISE139 Poland Unetice ?
RISE247 Hungary Vatya I2a2a-L368
RISE254 Hungary Vatya I2a2a-L59

https://genetiker.wordpress.com/2015/06/11/y-haplogroups-for-prehistoric-eurasian-genomes/

rms2
06-13-2015, 12:58 PM
Here (https://docs.google.com/spreadsheets/d/1HuNPykGuq2PbHkUOL5dCiwrveIy-OGO2qOklwfsayW8/edit?pli=1#gid=1195386997) is a spreadsheet of the y-dna haplogroups from Allentoft that gives a general breakdown (minus downstream subclades). I don't see RISE numbers on it, however.

Allentoft says one of the Corded Ware men was R1b, but I don't see that on genetiker's list. Perhaps that is one of the two he has as "P1" thus far.

Coldmountains
06-13-2015, 01:28 PM
bump.

ArmandoR1b
06-13-2015, 01:41 PM
This is from Genetiker:

Below are the Y haplogroups for 47 of the 55 newly available male genomes from prehistoric Eurasia.

I’ll update this post as I process more of the samples.

RISE512 Russia Andronovo R1a1a1b-S224/Z645
RISE94 Sweden Battle Axe R1a1a1-Page7
RISE566 Czech Republic Bell Beaker R1b1a2a1a-P310/PF6546/S129
RISE560 Germany Bell Beaker R1b1a2-L150.1/PF6274.1/S351.1
RISE563 Germany Bell Beaker R1b1a2a1a2b-PF6570/S28/U152
RISE564 Germany Bell Beaker R1b1a2a1-L51/M412/PF6536/S167
RISE434 Germany Corded Ware P1
RISE436 Germany Corded Ware P1
RISE446 Germany Corded Ware R1a1a1-M417
RISE1 Poland Corded Ware CT
RISE431 Poland Corded Ware K(xLT)
RISE555 Russia EBA R1b1a2a2-CTS7340/Z2107
RISE492 Russia Iron Age R1
RISE600 Russia Iron Age Q1a1b-M25
RISE601 Russia Iron Age Q1a1b-M143
RISE494 Russia Karasuk R1a1a1-Page7
RISE397 Armenia LBA R1b1a2a2-Y4371/Z8128
RISE408 Armenia LBA J
RISE598 Lithuania LBA BT
RISE553 Russia LBA P
RISE554 Russia LBA I?
RISE374 Hungary Maros G2a2a1a-PF6308
RISE413 Armenia MBA R1b1-M415/PF6251
RISE416 Armenia MBA DE
RISE423 Armenia MBA E1b1b1b2a1-PF2020/Z1153
RISE524 Russia Meshovskaya R1b1a2-PF6494
RISE525 Russia Meshovskaya R1a1a1-Page7
RISE21 Denmark Nordic BA ?
RISE47 Denmark Nordic BA R1b1a2-M520/PF6410
RISE175 Sweden Nordic BA I
RISE207 Sweden Nordic BA I1-M450/S109
RISE276 Denmark Nordic LBA R1b1a2-L265/PF6431
RISE42 Denmark Nordic LN CT
RISE179 Sweden Nordic LN I
RISE61 Denmark Nordic MN B R1a1a1-Page7
RISE546 Russia Pit Grave R1b1a2-PF6482/YSC0000203
RISE547 Russia Pit Grave R1b1a2a2-CTS9416
RISE548 Russia Pit Grave R1b1a2a2-Z2105
RISE550 Russia Pit Grave R1b1a2(xL51)
RISE486 Italy Remedello I2a1a1a-L672/S327
RISE487 Italy Remedello I
RISE489 Italy Remedello I2a1a1a-L672/S327
RISE386 Russia Sintashta R1a1a1b2a2-Z2124
RISE392 Russia Sintashta R1a1a1b-S224/Z645
RISE139 Poland Unetice ?
RISE247 Hungary Vatya I2a2a-L368
RISE254 Hungary Vatya I2a2a-L59

https://genetiker.wordpress.com/2015/06/11/y-haplogroups-for-prehistoric-eurasian-genomes/


Genetiker is posting some bad data such as the Corded Ware. His results should be ignored until more knowledgeable people have looked at the files.

ArmandoR1b
06-13-2015, 02:30 PM
Felix is analyzing the files and posting the Y-DNA and mtDNA results at http://www.y-str.org/p/ancient-dna.html

He is also uploading files to https://drive.google.com/folderview?id=0B4Ph8NJKscV6fnBqdnIxQVI4dmhYaFY3Tkh LTVBmR29VdldYMVlrVlEwenN2SnZfWE9PUEE&usp=sharing#list

George
06-13-2015, 02:47 PM
At the moment I'm adding the mtDNA results from Allentoft to my online tables, but would like to be able to add Y-DNA results too eventually.

I know that various people are working on the raw data to produce these, but the results seem to be scattered about. If anyone would like to place results here (with the RISE number), I would be very grateful.

In the large thread you started concerning the Allentoft paper (post #360) there is a report from a Belarusian analyst about the intriguing I2a result from the Yamna complex: RISE552 is allegedly L-699. I guess that would make the gentleman part of the complex I2 M223 group. You probably already have his MtDNA: T2a1a.

Jean M
06-13-2015, 03:04 PM
Felix is analyzing the files and posting the Y-DNA and mtDNA results at http://www.y-str.org/p/ancient-dna.html


I'll follow Felix. Thank you so much.

ArmandoR1b
06-13-2015, 03:11 PM
I couldn't remember if Felix had ever fixed his site to accurately reflect Hinxton-1 as being positive for Z245. He never did so we will have to be careful about what he reports as being the terminal SNP. There should be enough people checking what he posts and doing their own analysis to determine what he has missed just like jdean found with Hinxton-1.

MfA
06-13-2015, 03:33 PM
RISE423 Nerquin Getashen MBA 1402 BC 1211 BC E-L795+, PF6751- T2a


http://community.haplozone.net/index.php?topic=3961.msg37508#msg37508

T101
06-13-2015, 05:13 PM
Here (https://docs.google.com/spreadsheets/d/1HuNPykGuq2PbHkUOL5dCiwrveIy-OGO2qOklwfsayW8/edit?pli=1#gid=1195386997) is a spreadsheet of the y-dna haplogroups from Allentoft that gives a general breakdown (minus downstream subclades). I don't see RISE numbers on it, however.

Allentoft says one of the Corded Ware men was R1b, but I don't see that on genetiker's list. Perhaps that is one of the two he has as "P1" thus far.

Krefter has reported over at Eurogenes that "the single Corded Ware R1b is confirmed to be R1b1a2a-L23, but he is negative for the Eastern-branch Z2103 and western PF6543(parallel to L11). Although he wasn't tested for the ancestor of L11: L51."

rms2
06-13-2015, 05:25 PM
Krefter has reported over at Eurogenes that "the single Corded Ware R1b is confirmed to be R1b1a2a-L23, but he is negative for the Eastern-branch Z2103 and western PF6543(parallel to L11). Although he wasn't tested for the ancestor of L11: L51."

I wonder if he wasn't tested for L51 or just that they couldn't get a result either way for L51.

Motzart
06-13-2015, 05:40 PM
I'll follow Felix. Thank you so much.

I wouldn't have any hesitations about using Genetiker's data, people may not agree with his ideas but his data has always been fully accurate.

ArmandoR1b
06-13-2015, 05:42 PM
Krefter has reported over at Eurogenes that "the single Corded Ware R1b is confirmed to be R1b1a2a-L23, but he is negative for the Eastern-branch Z2103 and western PF6543(parallel to L11). Although he wasn't tested for the ancestor of L11: L51."

Yet he is using Genetiker's insane results for his spreadsheet at https://docs.google.com/spreadsheets/d/1HuNPykGuq2PbHkUOL5dCiwrveIy-OGO2qOklwfsayW8/edit#gid=2120948378 that don't show a single R1b1a2a-L23 in Corded Ware Germany

ArmandoR1b
06-13-2015, 05:54 PM
I wouldn't have any hesitations about using Genetiker's data, people may not agree with his ideas but his data has always been fully accurate.

4 out of the 5 results for Corded Ware that Genetiker posted above do not show R1 yet the Allentoft et al. figure 6 shows that all of he Corded Ware to be R1 http://www.nature.com/nature/journal/v522/n7555/fig_tab/nature14507_SF6.html and if you look at the Allentoft Supplementary Table 1: Sample information you will see that there are three German Corded Ware males and two Poland Corded Ware males.

That is just one example of Genetiker with insane results.

Do remember this post by yourself?

http://www.anthrogenica.com/showthread.php?3155-First-ancient-genomes-from-Britain-Celtic-and-Anglo-Saxon&p=55048&viewfull=1#post55048


Your information on ERS389795 contains information from two parties currently in disagreement.

Genetiker: ERS389795 - Unlikely to be R1b - K1a1 - Anglo Saxon - (Low Coverage)

Felix/Eurogenes: ERS389795 - R1b-L11 - K1a1b1b - Iron Age - (High Coverage)

Well guess who was right about R1b. Do you want to go through that whole Hinxton-1 Z245 discussion we had in that same thread all over again?

jdean
06-13-2015, 06:07 PM
RISE1 appears to be postive for Y435 (2934185 C to T) which according to Ybrowser is 'Approx. hg: R-M207'

(using Felix's data https://drive.google.com/folderview?id=0B4Ph8NJKscV6fnBqdnIxQVI4dmhYaFY3Tkh LTVBmR29VdldYMVlrVlEwenN2SnZfWE9PUEE&usp=sharing#list)

ArmandoR1b
06-13-2015, 06:09 PM
Here is where Genetiker tried to defend himself about the Hinxton-1 results -



$ samtools view -c ERR405822.bam Y:9170545-9170545
0
$ samtools view -c ERR405802.bam Y:18167403-18167403
0
$ samtools view -c ERR405812.bam Y:18167403-18167403
0
$ samtools view -c ERR405842.bam Y:8149348-8149348
0
$ samtools view -c ERR405842.bam Y:16492547-16492547
0

Again, the files you're using are GARBAGE.


and here is what Felix had on his site at one time -


Here's Felix's response -

Looking at what genetiker posted (screenshot), I can say for sure, he had neither realigned his BAM file nor used a variant caller to emit confident sites. Realignment is so important that bases mismatching the reference near the misalignment can easily be mistaken as SNPs.

(screenshot from anthrogenica.com)

I suggest genetiker to use all steps correctly and completely before criticizing someone's work as garbage. This post is only intended to reassure that the processed Ancient DNA uploads by me can be used with great confidence. By posting this blog, I am not only making the process transparent, you can verify the output results yourself.


http://www.fc.id.au/2014/10/convert-ancient-dna-sequence-reads-to.html

Jean M
06-13-2015, 06:17 PM
RISE1 appears to be positive for Y435 (2934185 C to T) which according to Ybrowser is 'Approx. hg: R-M207'

Thanks. At the moment Felix has RISE1 as C-IMS-JST029149, which certainly does not tally with the paper, which has the Corded Ware results (in the bar chart) as R1, R1a and R1b. Plus he is reporting CT in Bronze Age Sweden, which should be I1, I1a, R1a or R1b.

I'm starting to despair.

ArmandoR1b
06-13-2015, 06:20 PM
I wonder if he wasn't tested for L51 or just that they couldn't get a result either way for L51.
I am sure they just didn't get a result either way. I made the same mistake about Hinxton-1 thinking they hadn't tested it for some SNPs but it turned out to be a low quality specimen. Once Felix uploads all of the files I am sure that some of them will show negative results for L51.

ArmandoR1b
06-13-2015, 06:28 PM
Thanks. At the moment Felix has RISE1 as C-IMS-JST029149, which certainly does not tally with the paper, which has the Corded Ware results (in the bar chart) as R1, R1a and R1b. Plus he is reporting CT in Bronze Age Sweden, which should be I1, I1a, R1a or R1b.

I'm starting to despair.

However, jdean is able to find SNPs that place the specimens in the proper haplogroup using the data the Felix is uploading. So don't despair too much.

jdean
06-13-2015, 06:32 PM
Thanks. At the moment Felix has RISE1 as C-IMS-JST029149, which certainly does not tally with the paper, which has the Corded Ware results (in the bar chart) as R1, R1a and R1b. Plus he is reporting CT in Bronze Age Sweden, which should be I1, I1a, R1a or R1b.

I'm starting to despair.

Don't worry too much, there are going to be loads of folk crawling all over this data.

jdean
06-13-2015, 07:10 PM
Rise210 looks to be positive for FGC31441 (13481514 C to T) which Ybrowser lists as 'R1b (not listed)'

Looking through BigY files I have I'd say this is above L11, however RISE210 isn't suppose to have a Y Chromosome ???

(using Felix's data https://drive.google.com/folderview?id=0B4Ph8NJKscV6fnBqdnIxQVI4dmhYaFY3Tkh LTVBmR29VdldYMVlrVlEwenN2SnZfWE9PUEE&usp=sharing#list)[/QUOTE]

jdean
06-13-2015, 07:31 PM
Anybody any idea what RISE00 is ?

Seems to be positive for A125 (9992071 A to C) which is described as R1b-FGC5496 (is that Mark Jost's group ?) which is in the DF13 area !!!

According to supp data also supposed to lack a Y ???

David Mc
06-13-2015, 07:49 PM
RISE00 is supposed to Corded Ware from Estonia... if it turns out to be R1b (and DF13, at that), it will open up quite a few questions!

Anabasis
06-13-2015, 08:01 PM
Any idea whats the subsclade of RISE431 . Genetiker says K(xLT). Is it possible that its L-L595 or L-656 which is found in modern Estonia, Ireland and Germany.

Joe B
06-13-2015, 08:17 PM
Thanks. At the moment Felix has RISE1 as C-IMS-JST029149, which certainly does not tally with the paper, which has the Corded Ware results (in the bar chart) as R1, R1a and R1b. Plus he is reporting CT in Bronze Age Sweden, which should be I1, I1a, R1a or R1b.

I'm starting to despair.
The "early" R1b clades are getting an extreme look over by smal.
some updates...

RISE397_Kapan_LBA_Armenia L23/PF6534/S141+ > Y4371/Z8128+ > Z2106+ > PH4902+ > Y:18249219(A/C)+ CTS9219- (assigned to CTS7763 branch)

RISE547_Temrta IV_Yamnaya_Russia L478/PF6403+ > CTS9416+ > Z2106+ Y:9992926(T/C)-
RISE548_Temrta IV_Yamnaya_Russia PF6494+ > L23/PF6534/S141+ > Z8128/Y4371+ Z2105+ CTS9416+ CTS1843/Z2109- CTS9219- Y:22971205(G/C)- Y:7033880(C/T)- PH4503-
RISE550_Peshany V_Yamnaya_Russia PF6399/S10+ PF6494+ > Z8129/Y12537+ CTS8966-

RISE555_Stalingrad Quarry_EBA_Russia PF6399/S10+ > CTS7340/Z2107+ > Z2106+ Y:8025025(G/A)-

Please, look at the M269+ P312- U106- FTDNA project tree (http://www.kumbarov.com/ht35/R1b1a2_ht35_project_tree_16_05_25_2015.pdf) to find positions of these SNPs in Y Haplotree.
RISE397_Kapan_LBA_Armenia L23/PF6534/S141+ > Y4371/Z8128+ > Z2106+ > PH4902+ > Y:18249219(A/C)+ CTS9219- (assigned to CTS7763 branch)
R1b>M269>L23>Z2103>Z2106>CTS7763 or R1b>M269>L23>Z2103>Z2106>CTS7763>PH4902>Y:18249219(A/C)

RISE547_Temrta IV_Yamnaya_Russia L478/PF6403+ > CTS9416+ > Z2106+ Y:9992926(T/C)-
R1b>M269>L23>Z2103>Z2106>?

RISE548_Temrta IV_Yamnaya_Russia PF6494+ > L23/PF6534/S141+ > Z8128/Y4371+ Z2105+ CTS9416+ CTS1843/Z2109- CTS9219- Y:22971205(G/C)- Y:7033880(C/T)- PH4503-
R1b>M269>L23>Z2103>?

RISE550_Peshany V_Yamnaya_Russia PF6399/S10+ PF6494+ > Z8129/Y12537+ CTS8966-
R1b>M269>L23>Z2103>?

RISE555_Stalingrad Quarry_EBA_Russia PF6399/S10+ > CTS7340/Z2107+ > Z2106+ Y:8025025(G/A)-
R1b>M269>L23>Z2103>Z2106>?

SNPs Z2103 Z2105 CTS9416 Z8129/Y12537 Z8128/Y4371 are on the same phylogenetic level.

RISE397_Kapan_LBA_Armenia R1b>M269>L23>Z2103>Z2106>CTS7763 is a good catch by smal. R1b-CTS7763 is a very specific branch of the R1b-Z2103 haplogroup. Most of us a year or two ago would have guessed Armemian R1b-Z2103 to be R1b-L584 or maybe R1b-L277.
The R1b-M269 (P312- U106-) DNA Project (aka ht35 Project) Phylogenetic Tree (https://www.familytreedna.com/groups/ht-3-5new/about/results) that smal has built has been very useful with these ancient samples.

rncambron
06-13-2015, 08:36 PM
Anybody any idea what RISE00 is ?

Seems to be positive for A125 (9992071 A to C) which is described as R1b-FGC5496 (is that Mark Jost's group ?) which is in the DF13 area !!!

According to supp data also supposed to lack a Y ???

But this is also J1-YSC76 according to the ISOGG Browser so this cannot be definitive evidence of the provenance of DF13.

Silesian
06-13-2015, 08:58 PM
The "early" R1b clades are getting an extreme look over by smal.

]RISE397_Kapan_LBA_Armenia R1b>M269>L23>Z2103>Z2106>CTS7763 is a good catch by smal. R1b-CTS7763 is very specific branch of the R1b-Z2103 haplogroup. Most of us a year or two ago would have guessed Armemian R1b to be R1b-L584 or maybe R1b-L277.
The R1b-M269 (P312- U106-) DNA Project (aka ht35 Project) Phylogenetic Tree (https://www.familytreedna.com/groups/ht-3-5new/about/results) that smal has built has been very useful with these ancient samples.[/I

Thanks Joe&Smal for all the work within our project. To give a quick visual, using mapping tools for tested positive- and possible possible positive R1b-CTS7763.
SAMEA3325367 RISE397 Kapan LBA Armenia Male 1048 BC 855 BC
4829
4830
4835


Out of Curiosity- are these old samples in anyway connected to China and Bhutan?
SAMEA3325417 RISE555 Stalingrad Quarry EBA Russia Male 2857 BC 2497 BC R1b1a2a2Male 2857 BC 2497 BC R1b1a2a2

]RISE397_Kapan_LBA_Armenia R1b>M269>L23>Z2103>Z2106>CTS7763 Male1048 BC 855 BC R1b1a2a2

http://oi58.tinypic.com/vgopvq.jpg

1KGP-NA18645 (Han Chinese in Beijing, China)
H2014-bhu-1953 (Bhutanese)
http://www.kumbarov.com/ht35/R1b1a2_ht35_project_tree_16_05_25_2015.pdf

GarethH
06-13-2015, 09:02 PM
If someone could send me the data for RISE431 I can have a look for any key SNPs for LxL1 or TxT1.
Thanks
Gareth

genetiker
06-13-2015, 10:45 PM
I'm now updating my Y haplogroups post based on analyses that include many more SNPs:

http://genetiker.wordpress.com/2015/06/11/y-haplogroups-for-prehistoric-eurasian-genomes/

Krefter
06-13-2015, 10:50 PM
I'm now updating my Y haplogroups post based on analyses that include many more SNPs:

http://genetiker.wordpress.com/2015/06/11/y-haplogroups-for-prehistoric-eurasian-genomes/

Thanks alot. I'll probably ask you later to tell which clades certain samples are negative for. For example a M417, I'll ask if it's negative for S224. Are you done uploading? I see there is still DE, P1, etc.

Chad Rohlfsen
06-13-2015, 11:05 PM
Nice. R1b(xL51) in Yamnaya, L51 and P310 in Beaker.

rms2
06-13-2015, 11:10 PM
Nice. R1b(xL51) in Yamnaya, L51 and P310 in Beaker.

Allentoft et al lists an R1b among their Corded Ware results, and someone somewhere here said he was L51xL11. Can we confirm that?

Chad Rohlfsen
06-13-2015, 11:11 PM
I'm now updating my Y haplogroups post based on analyses that include many more SNPs:

http://genetiker.wordpress.com/2015/06/11/y-haplogroups-for-prehistoric-eurasian-genomes/


How about the R1b Corded Ware?

Chad Rohlfsen
06-13-2015, 11:12 PM
Allentoft et al lists an R1b among their Corded Ware results, and someone somewhere here said he was L51xL11. Can we confirm that?

Still waiting on confirmation, but we have now have two Yamnaya at xL51 and now an L51 and P310 Beaker.

Krefter
06-13-2015, 11:27 PM
Allentoft et al lists an R1b among their Corded Ware results, and someone somewhere here said he was L51xL11. Can we confirm that?

I heard from Richard Rocca he's L23(xL11, Z2103), and L51 didn't get a call. Anyways he can't be ancestral to Bell Beaker P312 and U152, because he was xL11. There's no way L51 became U152 in 500 years or so, and all his L51* brothers died out. There's still L23(xL51) and L51(xL11) in Central-East Europe today. They're more likely to be descendants of this Corded Ware R1b.

jdean
06-13-2015, 11:49 PM
But this is also J1-YSC76 according to the ISOGG Browser so this cannot be definitive evidence of the provenance of DF13.

Yep saw that, however there's also Y435 (2934185 C to T, Ybrowser listed as Approx. hg: R-M207), FGC31441 (13481514 C to T, Ybrowser listed as R1b) and A621 (9981785 C to G Ybrowser listed as R1b) so it looks reasonably good. There is an E1b SNP in the mix though and I'm still curious as to why the supplementary info has RISE00 predicted female ?

jdean
06-13-2015, 11:53 PM
RISE00 is supposed to Corded Ware from Estonia... if it turns out to be R1b (and DF13, at that), it will open up quite a few questions!

Cheers David, where did you see that ?

Chad Rohlfsen
06-13-2015, 11:59 PM
I heard from Richard Rocca he's L23(xL11, Z2103), and L51 didn't get a call. Anyways he can't be ancestral to Bell Beaker P312 and U152, because he was xL11. There's no way L51 became U152 in 500 years or so, and all his L51* brothers died out. There's still L23(xL51) and L51(xL11) in Central-East Europe today. They're more likely to be descendants of this Corded Ware R1b.

That corded ware can be ancestral. We have L51 and P310 in Beakers.

David Mc
06-14-2015, 12:11 AM
Cheers David, where did you see that ?

Hi jdean. On page 42 of the Supplementary Information from Allentoft.

jdean
06-14-2015, 12:15 AM
Hi jdean. On page 42 of the Supplementary Information from Allentoft.

Cheers David : )

David Mc
06-14-2015, 12:15 AM
You can find it here, if you don't already have it: http://www.nature.com/nature/journal/v522/n7555/extref/nature14507-s1.pdf

jdean
06-14-2015, 12:25 AM
You can find it here, if you don't already have it: http://www.nature.com/nature/journal/v522/n7555/extref/nature14507-s1.pdf

I had it but apparently the txt search didn't reach into PDF files : )

Krefter
06-14-2015, 12:31 AM
That corded ware can be ancestral. We have L51 and P310 in Beakers.

Are they P310* and L51*?

Chad Rohlfsen
06-14-2015, 12:46 AM
Still waiting on that. I wouldn't doubt it.

R.Rocca
06-14-2015, 04:00 AM
I heard from Richard Rocca he's L23(xL11, Z2103), and L51 didn't get a call. Anyways he can't be ancestral to Bell Beaker P312 and U152, because he was xL11. There's no way L51 became U152 in 500 years or so, and all his L51* brothers died out. There's still L23(xL51) and L51(xL11) in Central-East Europe today. They're more likely to be descendants of this Corded Ware R1b.

Since the Corded Ware samples are extremely low coverage, I started manually looking at haplogroup R equivalent SNPs that are not found on the ISOGG tree (see below) Unfortuntely, it has muddied the classification substantially. In fact, most of the samples look like they are R1a and the only one that may be R1b (RISE1) is one of the worse quality samples in the dataset. I'll keep looking at more SNPs and see what else turns up.

R-M207 Equivalents:
SAMEA3325374 RISE431 = 15594523 ALT->REF (A->G); # of mutations in tree = 2 (weighted = 70); ['F295', 'M685'] <<< POSITIVE
SAMEA3325374 RISE431 = 17722802 ALT->REF (G->A); # of mutations in tree = 1 (weighted = 35); SITEOF(['CTS7876', 'PF6052']) <<< POSITIVE
SAMEA3325375 RISE434 = 9889199 ALT->REF (G->A); # of mutations in tree = 1 (weighted = 35); ['M651'] <<< POSITIVE
SAMEA3325375 RISE434 = 17334694 ALT->REF (G->T); # of mutations in tree = 1 (weighted = 35); ['M718'] <<< POSITIVE
SAMEA3325375 RISE434 = 17722802 ALT->REF (G->A); # of mutations in tree = 1 (weighted = 35); SITEOF(['CTS7876', 'PF6052']) <<< POSITIVE

R1b Equivalents:
SAMEA3325334 RISE1 = 21558298 ALT->REF (G->T); # of mutations in tree = 1 (weighted = 35); ['L1345', 'PF6266', 'YSC0000224'] <<< POSITIVE
SAMEA3325377 RISE436 = 23403749 ALT->REF (G->A); # of mutations in tree = 1 (weighted = 35); ['CTS11985', 'PF6523'] <<< NEGATIVE
SAMEA3325377 RISE436 = 22722580 ALT->REF (T->C); # of mutations in tree = 1 (weighted = 35); ['L1349', 'PF6268', 'YSC0000231'] <<< POSITIVE
SAMEA3325374 RISE431 = 22889018 ALT->REF (G->A); # of mutations in tree = 1 (weighted = 35); ['L754', 'PF6269', 'YSC0000022'] <<< POSITIVE
SAMEA3325375 RISE434 = 17400785 ALT->REF (G->A); # of mutations in tree = 1 (weighted = 35); ['L388', 'PF6468'] <<< NEGATIVE
SAMEA3325375 RISE434 = 7375015 ALT->REF (C->T); # of mutations in tree = 2 (weighted = 70); ['L774', 'PF6245', 'YSC0000277'] <<< NEGATIVE

R-L23 Equivalents:
SAMEA3325374 RISE431 = 14435818 REF->ALT (T->C); # of mutations in tree = 2 (weighted = 70); SITEOF(['CTS2704', 'PF6100']) <<< NEGATIVE
SAMEA3325377 RISE436 = 8149348 ALT->REF (A->G); # of mutations in tree = 2 (weighted = 70); ['L265', 'PF6431'] <<< NEGATIVE
SAMEA3325377 RISE436 = 8667179 ALT->REF (A->G); # of mutations in tree = 1 (weighted = 35); ['PF6435'] <<< NEGATIVE

R1a Equivalents:
SAMEA3325374 RISE431 = 13590915 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35) <<< Positive
SAMEA3325374 RISE431 = 14613372 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); ['CTS3004', 'M669'] <<< Positive
SAMEA3325374 RISE431 = 16414608 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); ['CTS5648', 'M695'] <<< Positive
SAMEA3325374 RISE431 = 16563407 REF->ALT (G->T); # of mutations in tree = 1 (weighted = 35); ['CTS5936', 'M698', 'PF6192'] <<< Positive
SAMEA3325374 RISE431 = 17883019 REF->ALT (AGGGGGG->AGGGGG); # of mutations in tree = 1 (weighted = 35) <<< Positive
SAMEA3325374 RISE431 = 18158155 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); ['CTS8710', 'M737'] <<< Positive
SAMEA3325374 RISE431 = 18920886 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); ['F2901', 'M742', 'PF6204'] <<< Positive
SAMEA3325374 RISE431 = 23050018 REF->ALT (C->G); # of mutations in tree = 1 (weighted = 35); ['F3398', 'PF7532'] <<< Positive
SAMEA3325374 RISE431 = 22803327 REF->ALT (G->C); # of mutations in tree = 1 (weighted = 35); ['CTS10847', 'M791', 'PF6221'] <<< Positive
SAMEA3325375 RISE434 = 16563407 REF->ALT (G->T); # of mutations in tree = 1 (weighted = 35); ['CTS5936', 'M698', 'PF6192'] <<< Positive
SAMEA3325375 RISE434 = 21225537 REF->ALT (C->A); # of mutations in tree = 1 (weighted = 35); ['F3159', 'M761'] <<< Positive
SAMEA3325375 RISE434 = 22897863 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); ['F3364', 'M794', 'PF6222'] <<< Positive
SAMEA3325375 RISE434 = 24454540 REF->ALT (T->G); # of mutations in tree = 1 (weighted = 35); ['F3644', 'M810'] <<< Positive
SAMEA3325377 RISE436 = 15686890 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); ['CTS4509', 'M687'] <<< Positive
SAMEA3325377 RISE436 = 16414608 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); ['CTS5648', 'M695'] <<< Positive

parasar
06-14-2015, 04:34 AM
https://genetiker.wordpress.com/2015/06/11/y-haplogroups-for-prehistoric-eurasian-genomes/

RISE512 Russia Andronovo R1a1a1b-S224/Z645
RISE94 Sweden Battle Axe R1a1a1-Page7
RISE566 Czech Republic Bell Beaker R1b1a2a1a-P310/PF6546/S129
RISE560 Germany Bell Beaker R1b1a2-L150.1/PF6274.1/S351.1
RISE563 Germany Bell Beaker R1b1a2a1a2b-PF6570/S28/U152
RISE564 Germany Bell Beaker R1b1a2a1-L51/M412/PF6536/S167
RISE434 Germany Corded Ware R1a1a1
RISE436 Germany Corded Ware R1a1a1
RISE446 Germany Corded Ware R1a1a1-M417(xZ647)
RISE1 Poland Corded Ware P
RISE431 Poland Corded Ware R1a1a1
RISE555 Russia EBA R1b1a2a2-CTS7340/Z2107
RISE492 Russia Iron Age R1a1a1(xZ283)
RISE600 Russia Iron Age Q1a1b-M25
RISE601 Russia Iron Age Q1a1b-M143
RISE602 Russia Iron Age J2a
RISE494 Russia Karasuk R1a1a1-Page7
RISE397 Armenia LBA R1b1a2a2-Y4371/Z8128
RISE408 Armenia LBA J2b2f
RISE598 Lithuania LBA R1a1a1
RISE553 Russia LBA R1a1a1
RISE554 Russia LBA IJK
RISE374 Hungary Maros G2a2a1a-PF6308
RISE413 Armenia MBA R1b1a2
RISE416 Armenia MBA E1b1b1
RISE423 Armenia MBA E1b1b1b2a1-PF2020/Z1153
RISE524 Russia Meshovskaya R1b1a2-PF6494
RISE525 Russia Meshovskaya R1a1a1-Page7(xZ283)
RISE21 Denmark Nordic BA ?
RISE47 Denmark Nordic BA R1b1a2-M520/PF6410
RISE175 Sweden Nordic BA I1a3a2
RISE207 Sweden Nordic BA I1-M450/S109
RISE276 Denmark Nordic LBA R1b1a2a
RISE42 Denmark Nordic LN R1a1a1
RISE179 Sweden Nordic LN I1a3a2
RISE61 Denmark Nordic MN B R1a1a1-Page7
RISE546 Russia Pit Grave R1b1a2-PF6482/YSC0000203
RISE547 Russia Pit Grave R1b1a2a2-CTS9416
RISE548 Russia Pit Grave R1b1a2a2-Z2105
RISE550 Russia Pit Grave R1b1a2(xL51)
RISE486 Italy Remedello I2a1a1a-L672/S327
RISE487 Italy Remedello I2a1a
RISE489 Italy Remedello I2a1a1a-L672/S327
RISE386 Russia Sintashta R1a1a1b2a2-Z2124
RISE392 Russia Sintashta R1a1a1b-S224/Z645
RISE139 Poland Unetice ?
RISE247 Hungary Vatya I2a2a-L368
RISE254 Hungary Vatya I2a2a-L59

All of Sintashta and Andronovo may turn out to be Z93 since at least one is now confirmed Z2124.

We can see it there even now:
http://3.bp.blogspot.com/-yo928Hon9Ww/UzN-U-aGWMI/AAAAAAAAJiM/3AE7m5bNwCY/s1600/ejhg201450f3.jpg

Almost at the exact same area:
http://www.nature.com/nature/journal/v522/n7555/images/nature14507-f1.jpg

ADW_1981
06-14-2015, 05:01 AM
According to genetiker RIS416 is male, and the Nordic Bronze Age samples seem different from the results in the paper.

Bernard
06-14-2015, 11:38 AM
Allentoft sent me these informations:
In this study we focus more on genome-wide data, so we haven't spent much effort on the Y-chromosome. But I attach here a list for the individuals where it could be determined.
sampleId groupA hg1
RISE1 baCw R1b
RISE47 baSca R1b
RISE61 baSca R1a
RISE94 baCw R1a
RISE98 baSca R1b
RISE175 baSca I1a
RISE179 baSca NA
RISE207 baSca I1
RISE247 baHu I2a
RISE254 baHu I2
RISE276 baSca R1b
RISE374 baHu G2a
RISE386 baSin R1a
RISE392 baSin R1a
RISE397 baArm R1b
RISE408 irArm J2b
RISE413 baArm R1b
RISE416 baArm NA
RISE423 baArm E1b
RISE431 baCw R1a
RISE434 baCw R1a
RISE436 baCw R1
RISE446 baCw R1a
RISE479 baHu I2
RISE486 baRem I2
RISE487 baRem I2
RISE489 baRem I2a
RISE492 baKarasuk R1a
RISE493 baKarasuk Q1a
RISE494 baKarasuk R1a
RISE495 baKarasuk R1a
RISE504 irRus J2
RISE512 baAndrov R1a
RISE524 baMezh R1b
RISE525 baMezh R1a
RISE546 baYam R1b
RISE547 baYam R1b
RISE548 baYam R1b
RISE550 baYam R1b
RISE552 baYam I2a
RISE553 baAfGo R1a
RISE554 baAfGo NA
RISE555 baStq R1b
RISE560 baBb R1b
RISE563 baBb R1b
RISE564 baBb R1b
RISE566 baBb R1b
RISE600 irAltai Q1a
RISE601 irAltai Q1a
RISE602 irAltai J2a

Krefter
06-14-2015, 12:28 PM
I added Allentoft's and Geneticker's analysis to my spreadsheet.

https://docs.google.com/spreadsheets/d/1HuNPykGuq2PbHkUOL5dCiwrveIy-OGO2qOklwfsayW8/edit#gid=1630708280

Jean M
06-14-2015, 12:36 PM
Allentoft sent me these informations:

Thank you so much Bernard. It is really, really appreciated. It was infuriating that we had Y-DNA results only in the bar chart, and so could not allocate them to specific samples. I will start to add them to my tables today.

[Added] First lot up.

genetiker
06-14-2015, 01:00 PM
The idea that RISE1 can be declared to be R1b is ridiculous. Of all of the 101 genomes, it has the least amount of data.

Below is a list of all of the calls that I have for RISE1. Non-ISOGG SNPs are given by position. Positive calls are in bold.

I can tell you, after looking at the lists of calls for 48 genomes, that the non-ISOGG SNPs, while sometimes informative, are also often unreliable.

Genomes that are undoubtedly R1b have many non-ISOGG R1b SNPs that should be positive, but that are negative. And they have many non-ISOGG R1a SNPs that should be negative, but that are positive.

Likewise, genomes that are undoubtedly R1a have many non-ISOGG R1a SNPs that should be positive, but that are negative. And they have many non-ISOGG R1b SNPs that should be negative, but that are positive.

If one takes the below calls at face value, which Willerslev and his associates apparently do, then one would have to conclude that RISE1 is R1b1*(xM269), which is highly improbable for a sample as recent as it is.

The bottom line is that you need a lot more data that what's available for RISE1 to confidently assign a haplogroup.

(AB )T-16676762
(AB )T-21145418
(AB )T-21627877
A0a1-L1070
A0b-L1044
A1b1b2b-14405734
A1b1b2b-15726862
BT-M9080
BT-M9178
BT-M9334
C-IMS-JST029149
C2b1-F1788
CT-CTS109/M8948
CT-CTS5746/M5697
CT-M5717/PF844
CT-Y1465
D1b1d1a-Z14820
D1b2-CTS2712
DE-CTS9461/M5511/PF1770
DE-F1498/M5430/PF1428
E1a-CTS10067
E1a-CTS4268
E1a1-19241349
E1a2a2-Z15210
E1a2b-Z15089
E1a2b1a2-Z15003
E1a2b1a2-Z15021
E1b1a1a1c2-Z15943
E1b1a1a1c2c3c-Z16162
E1b1a1a1c2c3c-Z16195
E1b1b1-14448405
E1b1b1a1-21228969
E1b1b1a1-21627938
E1b1b1a1-22537242
E1b1b1a1b-14405763
E1b1b1a1b-16461066
E1b1b1b1-14089875
E1b1b1b1-16488587
E1b1b1b1-17672303
E1b1b1b1-22023773
E1b1b1b2a1a-17202886
E1b1b1b2a1a-17296108
E2-Z15767
F3-15845978
F3-21680010
G-CTS189/M3444
G-L204/PF2825
G-PF3134/U33
G2a-21069640
G2a-2795691
G2a1a-FGC608/Z6572
G2a1a-FGC635/Z6738
G2a1a1a1-Z6697
G2a2a1a2a1-Z6134
G2a2b-14881975
G2a2b-6702979
G2a2b2a1a2a-L1268
G2a3b1-28556572
G2a3b1-28789040
G2a3b1a1a-17104272
G2a3b1a2-16471001
H1a1d2-M2925/Z4618
H1b1-Z14185
H1b2-Z14273
H3-Z13614
H3a2b-Z12884
H3a2b-Z12937
H3b1-Z13738
I-17831226
I-PF3817
I1a3a2-21406999
I1a3a2b-CTS10345
I2-15354989
I2a1a-13909649
I2a1a-14334085
I2a1a-15352769
I2a1a-15576646
I2a1a-16729605
I2a1a-17512081
I2a1a-18584779
I2a1a-21096199
I2a1a1-19241365
I2c-2900158
J-F1181/PF4518/S35
J1c-14100585
J1c-6969181
J2a-15020309
J2a2-16611295
J2a2-7274947
J2a3b-17479242
J2a3b1-21115985
J2a3h2-14405748
J2b-15288201
O3a-F572
P-7340314
R1a1a1-6853286
R1b1-21558298
R1b1a2-13883384
R1b1a2a-17512118
R1b1a2a1a1b-2668940
R1b1a2a1a1b3-23332847
R1b1a2a1a2c1i8-BY166/Z18021
R1b1c-17214322
R1b1c-21703087
R1b1c3-28639708
R2a1-14334030
R2a1-22596622
R2a1-23233992
R2a1-23249508
T1-17229297
T1-7146873
T1a1-17158473

smal
06-14-2015, 01:54 PM
R1b1-21558298


21558298 (G->T) is a well known marker, L1345/PF6266/YSC0000224, positioned in the R-L754 node.

R.Rocca
06-14-2015, 02:13 PM
The idea that RISE1 can be declared to be R1b is ridiculous. Of all of the 101 genomes, it has the least amount of data.

Below is a list of all of the calls that I have for RISE1. Non-ISOGG SNPs are given by position. Positive calls are in bold.

I can tell you, after looking at the lists of calls for 48 genomes, that the non-ISOGG SNPs, while sometimes informative, are also often unreliable.

Genomes that are undoubtedly R1b have many non-ISOGG R1b SNPs that should be positive, but that are negative. And they have many non-ISOGG R1a SNPs that should be negative, but that are positive.

Likewise, genomes that are undoubtedly R1a have many non-ISOGG R1a SNPs that should be positive, but that are negative. And they have many non-ISOGG R1b SNPs that should be negative, but that are positive.

If one takes the below calls at face value, which Willerslev and his associates apparently do, then one would have to conclude that RISE1 is R1b1*(xM269), which is highly improbable for a sample as recent as it is.

The bottom line is that you need a lot more data that what's available for RISE1 to confidently assign a haplogroup.



I agree with the poor quality of RISE1. However, I don't agree with your point about it being "ridiculous" to label it R1b. I mean, you did label it "P" in your web-page, so why is that not any more or less "ridiculous" if you don't have any negative calls between P and R1b1-PF6266? Perhaps as a couationary measure, you should simply label it "Likely R1b1-PF6266"?

alan
06-14-2015, 02:17 PM
RISE1,Corded Ware if he is an L23 prob L51 is a very significant addition as it adds both a chronological and phylogenic intermediate point between the Samara L23 derived samples c. 3100-2900BC and our bell beaker samples in central Europe which probably dont long pre-date 2500BC. It sites right in the middle of the c. 400 year gap between Yamanya and Bell Beaker L23 derived samples. As CW dominates temperate Europe through much of that gap and we have got no R1b from the Alpine or Med pre-beaker samples yet then at the moment CW is looking the prime candidate as the intermediary zone between Yamnaya and Bell Beaker. Sample is still far too small to feel huge confidence yet though.

jdean
06-14-2015, 02:56 PM
RISE47 looks positive for A533 (13687378 T to A, Ybrowser entry R1b1a2a1a1c2b1b), could be the first U106 in aDNA !!

(using Felix's data)

alan
06-14-2015, 04:39 PM
RISE47 looks positive for A533 (13687378 T to A, Ybrowser entry R1b1a2a1a1c2b1b), could be the first U106 in aDNA !!

(using Felix's data)

That could be significant as the Nordic Bronze Age ultimately roots in beaker and corded ware with no other obvious significant intrusions although many contacts. I suppose the lack of U106 in beaker to date does hint U106 or an L11 ancestor of it came with Corded Ware to Scandinavia as has been contemplated many times based on modern populations. Too small a sample to reach any confident conclusions yet though.

Krefter
06-14-2015, 04:44 PM
RISE47 looks positive for A533 (13687378 T to A, Ybrowser entry R1b1a2a1a1c2b1b), could be the first U106 in aDNA !!

(using Felix's data)

Is it positive for any upstream mutations of R1b1a2a1a1c2b1b? Can you give a link to Ybrowser?

Krefter
06-14-2015, 04:47 PM
Ancient West Eurasian Y DNA. I added the Allentoft data.

https://docs.google.com/spreadsheets/d/12G2cfjG0wHWarsl5bB99ridFmvUWzqlZfZ6_e_R6oIA/edit?usp=drive_web

jdean
06-14-2015, 06:02 PM
Is it positive for any upstream mutations of R1b1a2a1a1c2b1b? Can you give a link to Ybrowser?

Bunch of stuff in the vaguely R, P, CT area but nothing very defining. I'm not looking for negative SNPs though which probably would be a good idea : )

Ybrowser is here at the mo.

http://ybrowse.org/gb2/gbrowse/chrY/?

Silesian
06-14-2015, 06:04 PM
Comparing EurogenesK15 with Rise sample M690970.
Eurogenes EUtest V2 K15 Oracle results:
Kit M690970-R1a

Admix Results (sorted):

# Population Percent
1 North_Sea 40.16
2 Atlantic 22.94
3 Eastern_Euro 14.68
4 Baltic 12.34
5 West_Asian 7.74
6 Sub-Saharan 2.14
4845
4846
Top three
North Europe
40.16%+/-
4847
Atlantic
22.94%+/-
4848
East Europe
14.68%+/-
4849

Baltic
12.34%+/-

http://bga101.blogspot.ca/2013/10/eurogenes-k15-now-at-gedmatch.html

Krefter
06-14-2015, 06:59 PM
Can someone please test the R1b from Late Neolithic Sweden(RISE98) for downstream SNPs?

Heber
06-14-2015, 07:52 PM
Here is my latest understanding of Allentoft R1b results
4850

Edit
I found 18 R1b samples and 101 total, 56 male and 45 female samples with associated BAM files.
It would be useful if YFull could use the BAM file (or its Y component) to create entries on its database.
This would allow us to benchmark the Y Tree against a published dataset, compare their estimated TMRCA against the c dates ages in the Allentoft study and better position these samples on the phylogenetic tree. I would also use a consistent (proven) BAM analysis process and automated YTree generation.
This would also contribute greatly to the usefulness of the YFull service.

https://www.pinterest.com/gerardcorcoran/european-bronze-age/

Krefter
06-14-2015, 08:21 PM
Here is my latest understanding of Allentoft R1b results
4850

I found 18 R1b samples and 101 samples with associated BAM files.
I will check the total number of male samples.
It would be useful if YFull could use the BAM file (or its Y component) to create entries on its database.
This would allow us to benchmark the Y Tree against a published dataset, compare their estimated TMRCA against the c dates ages in the Allentoft study and better position these samples on the phylogenetic tree. I would also use a consistent (proven) BAM analysis process and automated YTree generation.
This would also contribute greatly to the usefulness of the YFull service.

https://www.pinterest.com/gerardcorcoran/european-bronze-age/

Do you plan on tested for R1b subclade SNPs?

Radboud
06-14-2015, 08:23 PM
Comparing EurogenesK15 with Rise sample M690970.
Eurogenes EUtest V2 K15 Oracle results:
Kit M690970-R1a

Admix Results (sorted):

# Population Percent
1 North_Sea 40.16
2 Atlantic 22.94
3 Eastern_Euro 14.68
4 Baltic 12.34
5 West_Asian 7.74
6 Sub-Saharan 2.14
4845
4846
Top three
North Europe
40.16%+/-
4847
Atlantic
22.94%+/-
4848
East Europe
14.68%+/-
4849

Baltic
12.34%+/-

http://bga101.blogspot.ca/2013/10/eurogenes-k15-now-at-gedmatch.html

Silesian my friend, do you have a link to a list of Gedmatch kits?:)

ChrisR
06-14-2015, 09:17 PM
Ancient Kurgan Altai J2a RISE602 (http://j2-m172.info/2015/06/ancient-kurgan-altai-j2a-rise602-allentoft-et-al-2015/) (SAMEA3325434)

Y-DNA J2a2-PF5060(xP279,PF5048)

Heber
06-14-2015, 09:28 PM
Do you plan on tested for R1b subclade SNPs?

I will contact YFull to see if they will do this (At least for R1b).
They should be motivated to do it as it will improve their service

KSDA
06-14-2015, 09:36 PM
Took a glance at some of the Scandinavian R1a samples, the low coverage made it hard to discern clades but here's what I found:

RISE61 (Nordic MN B, Denmark): R-Z645 > Z648+, Z650+, CTS12179- (possible branch split?)
RISE94 (CW/Battle Axe, Sweden): R-Z645 > Z649+. Z651+; no calls at Z283 and Z282 levels, xPF6155 (Z2913-), xZ284 (Z289-), xZ280 (Z687-)
RISE42 (Nordic LN, Denmark): R-M417, no calls for downstream SNPs at branches Z645 and CTS4385

Hopefully Allentoft's next round of genomes from the Viking age will be more fruitful.

Krefter
06-14-2015, 09:45 PM
Took a glance at some of the Scandinavian R1a samples, the low coverage made it hard to discern clades but here's what I found:

RISE61 (Nordic MN B, Denmark): R-Z645 > Z648+, Z650+, CTS12179- (possible branch split?)
RISE94 (CW/Battle Axe, Sweden): R-Z645 > Z649+. Z651+; no calls at Z283 and Z282 levels, xPF6155 (Z2913-), xZ284 (Z289-), xZ280 (Z687-)
RISE42 (Nordic LN, Denmark): R-M417, no calls for downstream SNPs at branches Z645 and CTS4385

Hopefully Allentoft's next round of genomes from the Viking age will be more fruitful.

Most of those SNPs aren't on ISOGG's tree.

KSDA
06-14-2015, 09:52 PM
Most of those SNPs aren't on ISOGG's tree.

I should note that I used YFull's tree (which is finally back up).

Krefter
06-15-2015, 12:03 AM
R1b-U106, R1a1a1, and I1a3a1 in Sweden/Denmark 4,000 years ago. Note outside this I1 has only been found in Neolithic Hungary and Bell Beaker R1b is 2/2 P312 so far.

https://docs.google.com/spreadsheets/d/12G2cfjG0wHWarsl5bB99ridFmvUWzqlZfZ6_e_R6oIA/edit#gid=479090567

Geneticker's page.

https://genetiker.wordpress.com/2015/06/11/y-haplogroups-for-prehistoric-eurasian-genomes/

VinceT
06-15-2015, 12:49 AM
RISE47 looks positive for A533 (13687378 T to A, Ybrowser entry R1b1a2a1a1c2b1b), could be the first U106 in aDNA !!

(using Felix's data)

I think the Ybrowse entry for A533 is in error, and probably should be A>T, not T>A. A is the reference allele, and likely ancestral, which is the call that was given for RISE47. So RISE47 looks like a standard R1b1a2* for now.

My preliminary scan:

M520/PF6410+ (in R1b1a2-M269)
PF6438+ (in R1b1a2-M269)
A702/Z8137/rs67021730+ (Approx with R1b-M343 or R1b1-M415)
L388/PF6468+ (below R1b1)
CTS7659/FGC50/PF6470+ (Approx or below R-L388)
L62/M513/PF6200- (not in R1a)
P297/PF6398+ (in R1b1a)
P312/PF6547/S116- (not in R1b1a2a1a2-P312)
L754/PF6269/YSC0000022+ (Approx with R1b-M343 or R1b1-M415)

However genetiker (https://genetiker.wordpress.com/) recently tagged RISE98 as R-U106*, but with the BAM file at a pleasantly sized 14GB, I won't be able to check that until next evening.

MJost
06-15-2015, 01:43 AM
Anybody any idea what RISE00 is ?

Seems to be positive for A125 (9992071 A to C) which is described as R1b-FGC5496 (is that Mark Jost's group ?) which is in the DF13 area !!!

According to supp data also supposed to lack a Y ???


FYI:
comment: Found in a R1b-FGC5496 person. Also found in J1-YSC76.

MJost

felix
06-15-2015, 02:36 AM
RISE1 appears to be postive for Y435 (2934185 C to T) which according to Ybrowser is 'Approx. hg: R-M207'

(using Felix's data https://drive.google.com/folderview?id=0B4Ph8NJKscV6fnBqdnIxQVI4dmhYaFY3Tkh LTVBmR29VdldYMVlrVlEwenN2SnZfWE9PUEE&usp=sharing#list)

C haplogroup - IMS-JST029149, is the best I can get from the ISOGG Y-SNPs for RISE1. Where did you get Y435 mutation from? I can't find it in ISOGG tree.

R.Rocca
06-15-2015, 02:55 AM
R1b-U106, R1a1a1, and I1a3a1 in Sweden/Denmark 4,000 years ago. Note outside this I1 has only been found in Neolithic Hungary and Bell Beaker R1b is 2/2 P312 so far.

https://docs.google.com/spreadsheets/d/12G2cfjG0wHWarsl5bB99ridFmvUWzqlZfZ6_e_R6oIA/edit#gid=479090567

Geneticker's page.

https://genetiker.wordpress.com/2015/06/11/y-haplogroups-for-prehistoric-eurasian-genomes/

More specifically, including I0806 from the Haak study, 3 of 3 Bell Beaker that produced results have been P312+. Of course, going back to Lee (2012), 7 of 7 are R1b+.

Krefter
06-15-2015, 03:44 AM
More specifically, including I0806 from the Haak study, 3 of 3 Bell Beaker that produced results have been P312+. Of course, going back to Lee (2012), 7 of 7 are R1b+.

Wait, two of the Allentoft's are P312+?

jdean
06-15-2015, 08:24 AM
FYI:
comment: Found in a R1b-FGC5496 person. Also found in J1-YSC76.

MJost

Sorry Mark, this was a false alarm. For some odd reason there was Y-DNA information in Felix's variance files for female samples, I'm guessing this was something to do with regions of the X that are similar to the Y ?

jdean
06-15-2015, 09:00 AM
I think the Ybrowse entry for A533 is in error, and probably should be A>T, not T>A. A is the reference allele, and likely ancestral, which is the call that was given for RISE47. So RISE47 looks like a standard R1b1a2* for now.

My preliminary scan:

M520/PF6410+ (in R1b1a2-M269)
PF6438+ (in R1b1a2-M269)
A702/Z8137/rs67021730+ (Approx with R1b-M343 or R1b1-M415)
L388/PF6468+ (below R1b1)
CTS7659/FGC50/PF6470+ (Approx or below R-L388)
L62/M513/PF6200- (not in R1a)
P297/PF6398+ (in R1b1a)
P312/PF6547/S116- (not in R1b1a2a1a2-P312)
L754/PF6269/YSC0000022+ (Approx with R1b-M343 or R1b1-M415)

However genetiker (https://genetiker.wordpress.com/) recently tagged RISE98 as R-U106*, but with the BAM file at a pleasantly sized 14GB, I won't be able to check that until next evening.

Looking through my BigY collection (about 1400 kits) it seems T is the ancestral value for L11 but working out which of the small number of kits that don't get a call at this loci rather than having the referance value would be a bit of a pain in the bum. I can say that the greater majority of the U106 kits that don't get a call are L48 (however that's probably not unexpected).

PeterM has a piece of software that can check large numbers of bed files so I may ask him if he fancies running the numbers, though of course Thomas presumably Knows the answer and probably where on the tree A is ancestral (other than A533)

jdean
06-15-2015, 09:34 AM
C haplogroup - IMS-JST029149, is the best I can get from the ISOGG Y-SNPs for RISE1. Where did you get Y435 mutation from? I can't find it in ISOGG tree.

The holes in ISOGG's tree are probably always going to be a problem when fishing about Swiss cheese aDNA for level defining SNPs, we had the same problem with Hinxton1 which showed positive for Z245, a very well known SNP equivalent to DF13, but ISOGG still don't have it on their tree. You can see it referenced in plenty of other places though, along with the other DF13 equivalent SNPs which are all also lacking from ISOGG.

This is compounded even further when all that can be found are referenced (often multiple times in Ybrowser with slightly different descriptions) as vaguely R etc..

However Smal had this to say about another of the variants in RISE01


21558298 (G->T) is a well known marker, L1345/PF6266/YSC0000224, positioned in the R-L754 node.

I will add that it may be 'well known' but it doesn't appear to be well documented : ) mind you Yfull wasn't up when I was trying to work out what could be made out of the smattering of information provided by these results so I think I'll have a poke about there to satisfy my curiosity.

smal
06-15-2015, 10:34 AM
I will add that it may be 'well known' but it doesn't appear to be well documented : ) mind you Yfull wasn't up when I was trying to work out what could be made out of the smattering of information provided by these results so I think I'll have a poke about there to satisfy my curiosity.

It is really very well documented : )
For example, see Karmin et al. 2015

Build37Position...Unique/recurring...No_individuals_with_derived_alleles... .Haplogroup_label...Marker......AltMarkerNames
21558298...............unique...............386... ........................................R1b1'14... ......L754_eq....L1345_PF6266_YSC0000224


Currently YFull do not even have a single sample which would allow them to show L754 level in Tree.

Krefter
06-15-2015, 11:23 AM
I think the Ybrowse entry for A533 is in error, and probably should be A>T, not T>A. A is the reference allele, and likely ancestral, which is the call that was given for RISE47. So RISE47 looks like a standard R1b1a2* for now.

My preliminary scan:

M520/PF6410+ (in R1b1a2-M269)
PF6438+ (in R1b1a2-M269)
A702/Z8137/rs67021730+ (Approx with R1b-M343 or R1b1-M415)
L388/PF6468+ (below R1b1)
CTS7659/FGC50/PF6470+ (Approx or below R-L388)
L62/M513/PF6200- (not in R1a)
P297/PF6398+ (in R1b1a)
P312/PF6547/S116- (not in R1b1a2a1a2-P312)
L754/PF6269/YSC0000022+ (Approx with R1b-M343 or R1b1-M415)

However genetiker (https://genetiker.wordpress.com/) recently tagged RISE98 as R-U106*, but with the BAM file at a pleasantly sized 14GB, I won't be able to check that until next evening.

So, xP312, What clade L388 in?

jdean
06-15-2015, 11:33 AM
It is really very well documented : )
For example, see Karmin et al. 2015

Build37Position...Unique/recurring...No_individuals_with_derived_alleles... .Haplogroup_label...Marker......AltMarkerNames
21558298...............unique...............386... ........................................R1b1'14... ......L754_eq....L1345_PF6266_YSC0000224


Currently YFull do not even have a single sample which would allow them to show L754 level in Tree.

OK it wasn't very well documented in places I looked : )

Thanks for the reference, very handy : )

Of course this is the problem with SNPs further upstream, around L11 isn't so hard as there are bags of U106 and P312 BigY results to examine, though I am very thin on the ground for U152 and DF99 of course

Jean M
06-15-2015, 03:04 PM
I am collating haplogroup findings and comments by the community in a document format:

[Added] Updated: https://drive.google.com/file/d/0B9vzsK0Ig1mNeml0YnU1WDhXNWM/view?usp=sharing

rms2
06-15-2015, 03:20 PM
If RISE98 really is R1b-U106 (and apparently it is), that is somewhat gratifying to me, since long ago I predicted that U106 would ultimately be found in Corded Ware rather than in Beaker. Of course, I could still be wrong about the Beaker part of that, if a U106 turns up in Beaker. Given the apparent affinity and proximity of the two cultures, anything is possible.

rms2
06-15-2015, 03:29 PM
If RISE98 really is R1b-U106 (and apparently it is), that is somewhat gratifying to me, since long ago I predicted that U106 would ultimately be found in Corded Ware rather than in Beaker. Of course, I could still be wrong about the Beaker part of that, if a U106 turns up in Beaker. Given the apparent affinity and proximity of the two cultures, anything is possible.

Think of the various results from Haak et al and now Allentoft et al that, all by themselves, as stand-alones, should be front page headline news. Now there are so many that our heads are spinning and we almost have too much to talk about, feast-or-famine, as the ancient y-dna situation seems to be.

Take this U106+ result for example. That could be really significant for the apparent connection between U106 and the evolution of Germanic, but is anyone talking about that?

Krefter
06-15-2015, 03:32 PM
If RISE98 really is R1b-U106 (and apparently it is), that is somewhat gratifying to me, since long ago I predicted that U106 would ultimately be found in Corded Ware rather than in Beaker. Of course, I could still be wrong about the Beaker part of that, if a U106 turns up in Beaker. Given the apparent affinity and proximity of the two cultures, anything is possible.

So, RISE98 according to archaeologist is strictly from Corded Ware? Think about it: R1b-U106 and R1b-P312 were already marking the territory they have today over 4,000 years ago. Although we mostly only have data from Central Europe. R1b-L11 may have spread later into France, Italy, Iberia, and the British isles.

rms2
06-15-2015, 03:38 PM
So, RISE98 according to archaeologist is strictly from Corded Ware? Think about it: R1b-U106 and R1b-P312 were already marking the territory they have today over 4,000 years ago. Although we mostly only have data from Central Europe. R1b-L11 may have spread later into France, Italy, Iberia, and the British isles.

It's listed as belonging to the "Swedish Battle Axe" culture, which is a Scandinavian Corded Ware subgroup.

Jean M
06-15-2015, 03:48 PM
If RISE98 really is R1b-U106 (and apparently it is), that is somewhat gratifying to me.

Me too. I not only felt that it was a Corded Ware type, but that it entered Scandinavia, rather than hanging about on the North European plain. But as you say, closely related and adjoining cultures are not rigidly separated. So no doubt the story will turn out to be as complex as any other in this game.

Radboud
06-15-2015, 04:16 PM
If RISE98 really is R1b-U106 (and apparently it is), that is somewhat gratifying to me, since long ago I predicted that U106 would ultimately be found in Corded Ware rather than in Beaker. Of course, I could still be wrong about the Beaker part of that, if a U106 turns up in Beaker. Given the apparent affinity and proximity of the two cultures, anything is possible.

YES, the first R1b U106 has been found in Corded Ware Sweden!:) I am now convinced that R1b U106 played a significant role in Proto-Germanic.

alan
06-15-2015, 04:29 PM
YES, the first R1b U106 has been found in Corded Ware Sweden!:) I am now convinced that R1b U106 played a significant role in Proto-Germanic.

What is also interesting is that it hasnt yet been found anywhere else in CW, beaker etc. So, that raises the issue of where and when U106 expanded from. It has been long suggested there was a north-south movement from Scandinavia to the Germanic 'mainland'. Their climate declined in stages.

alan
06-15-2015, 04:30 PM
U106 in CW does of course support the idea that L11 originated quite far east, perhaps Ukraine.

Heber
06-15-2015, 06:44 PM
I will contact YFull to see if they will do this (At least for R1b).
They should be motivated to do it as it will improve their service

Here is the prompt reply from Vadin Urasin of Yfull. The quality of the Y BAM files must be poor indeed if this talented team find it tough going.
It would make sense for the Allendoft team to work with the YFull team to get these BAM files processed and published. At $49 a pop retail and probably pro bono for a project such as this it is a tiny part of the overall project budget.
I would be happy to sponsor the first Iberian or Irish Bell Beaker R1b found.

"We have checked quality of several samples of this study. This is a very poor in part of Y chromosome. But we continue to check quality of some other samples. May be we will find something with enough quality."

ChrisR
06-15-2015, 09:35 PM
UPDATE: Two J2a2 Iron Age Altai (http://j2-m172.info/2015/06/j2a2-ph3085-sk1403-ancient-altai-modern-uygur-turkish/)

Sary-Bel Kurgan burial sample (RISE602, SAMEA3325434, ERX925332) ~ II c. BC – I century AD.
Kytmanovo 721-889 AD (RISE504, SAMEA3325397, ERX925295)
Haplogroup J2a2-PF5050>PF5058>PF5000>PF5056>PH3085,SK1403 or shorter form J2a2-PH3085,SK1403 shared with modern Uygur and Turkish samples.

Heber
06-15-2015, 10:02 PM
Here is my latest understanding of Allentoft R1b results
4850

Edit
I found 18 R1b samples and 101 total, 56 male and 45 female samples with associated BAM files.
It would be useful if YFull could use the BAM file (or its Y component) to create entries on its database.
This would allow us to benchmark the Y Tree against a published dataset, compare their estimated TMRCA against the c dates ages in the Allentoft study and better position these samples on the phylogenetic tree. I would also use a consistent (proven) BAM analysis process and automated YTree generation.
This would also contribute greatly to the usefulness of the YFull service.

https://www.pinterest.com/gerardcorcoran/european-bronze-age/

Here is my latest understanding of Allentoft R1b results

RISE HG Branch SNP
RISE1 baCw R1 M207
RISE47 baSca R1b M269 P146
RISE98 baSca R1b U106
RISE276 baSca R1b M269
RISE397 baArm R1b L23
RISE413 baArm R1b M269
RISE524 baMezh R1b M269
RISE546 baYam R1b M269
RISE547 baYam R1b M269 Z2106
RISE548 baYam R1b M269 CTS9416
RISE550 baYam R1b M269 Z8129
RISE553 baAfGo R1b ?
RISE555 baStq R1b M269 Z2106
RISE560 baBb R1b L11
RISE563 baBb R1b U152
RISE564 baBb R1b L51
RISE566 baBb R1b L11

4881

Jean M
06-15-2015, 10:22 PM
UPDATE: Two J2a2 Iron Age Altai (http://j2-m172.info/2015/06/j2a2-ph3085-sk1403-ancient-altai-modern-uygur-turkish/)

Thanks. Have updated https://drive.google.com/file/d/0B9vzsK0Ig1mNeml0YnU1WDhXNWM/view?usp=sharing

VinceT
06-16-2015, 01:32 AM
So, xP312, What clade L388 in?
L388 is equivalent with L389, positioned under R-M343 and M415 but above R-P297, peer to R-V88. See the R1b1* project: https://www.familytreedna.com/public/R1b1Asterisk/

(The split shown in the ISOGG tree between M343 and P25/M415 might not exist, and may be a legacy from P25 back-mutations observed from earlier studies. We need more data from samples branching off at these early nodes to better resolve SNP placement on the tree, but said samples are very rare.)

L388 and L389 were originally identified from 23andMe results that were submitted to Adriano Squecco's comparative spreadsheet. http://daver.info/ysub/

KSDA
06-16-2015, 02:40 AM
Took a glance at some of the Scandinavian R1a samples, the low coverage made it hard to discern clades but here's what I found:

RISE61 (Nordic MN B, Denmark): R-Z645 > Z648+, Z650+, CTS12179- (possible branch split?)
RISE94 (CW/Battle Axe, Sweden): R-Z645 > Z649+. Z651+; no calls at Z283 and Z282 levels, xPF6155 (Z2913-), xZ284 (Z289-), xZ280 (Z687-)
RISE42 (Nordic LN, Denmark): R-M417, no calls for downstream SNPs at branches Z645 and CTS4385

Hopefully Allentoft's next round of genomes from the Viking age will be more fruitful.

Based the RISE42 call of R-M417 on genetiker's blog post placing it at R1a1a1 (M417), but I looked at all 31 of the R-M417 level SNPs from YFull and none of those SNPs were covered. Shouldn't really be surprised since the bam file for the entire genome is less than 50 MB. Not sure what his call was based on.

Now, on to the other Corded Ware samples:

RISE431 (CW, Poland): R-M417 (PF7532+, CTS5648+)
RISE434 (CW, Tiefbrunn, Germany): R-M417 (F3159+), xL664 (Y2895-)
RISE436 (CW, Tiefbrunn, Germany): R-M417 (CTS5648+)
RISE446 (CW, Bergheinfeld, Germany): R-M417 (CTS7278+, CTS10993+, FGC2547+, FGC2550+), xCTS4385 (Z2461-), xZ645 (Z647-)

Jean M
06-16-2015, 10:44 AM
Thank you : have updated: https://drive.google.com/file/d/0B9vzsK0Ig1mNeml0YnU1WDhXNWM/view?usp=sharing

Cofgene
06-16-2015, 11:37 AM
Greg Magoon has been working very hard on this one, backed by Vince Tilroe and others. RISE98 appears negative for all known downstream clades within U106. Namely:
Z381-
Z18- Z19- Z368-
FGC7915- FGC3854- (no call for FGC3861 itself)
FGC396- FGC400- FGC408- A278- FGC416- FGC424- FGC425- FGC426- FGC427-
S12025- S19739-
8464434- 13989289- 17360032- 21719747- 23282505- 24410775-
16670061- 17951958- 18945748-
6823524- 7747602- 9849392- 18764397- 18910212- 18930965-

It has also been checked against the FGC variant database, with no report of known variants. Five candidate novel variants, labelled FGC36477-FGC36481, have been identified at comparatively high quality. They have been consistently checked negative or no call across other U106 samples.

U106 directly downstream branches defined only by Big-Y results will need to test for FGC36479-81 so that we can position these RISE98 novel variants.

Krefter
06-16-2015, 11:48 AM
Greg Magoon has been working very hard on this one, backed by Vince Tilroe and others. RISE98 appears negative for all known downstream clades within U106. Namely:
Z381-
Z18- Z19- Z368-
FGC7915- FGC3854- (no call for FGC3861 itself)
FGC396- FGC400- FGC408- A278- FGC416- FGC424- FGC425- FGC426- FGC427-
S12025- S19739-
8464434- 13989289- 17360032- 21719747- 23282505- 24410775-
16670061- 17951958- 18945748-
6823524- 7747602- 9849392- 18764397- 18910212- 18930965-

It has also been checked against the FGC variant database, with no report of known variants. Five candidate novel variants, labelled FGC36477-FGC36481, have been identified at comparatively high quality. They have been consistently checked negative or no call across other U106 samples.

U106 directly downstream branches defined only by Big-Y results will need to test for FGC36479-81 so that we can position these RISE98 novel variants.

Is U106* commonly found today?

Jean M
06-16-2015, 01:43 PM
Greg Magoon has been working very hard on this one, backed by Vince Tilroe and others..

Thank you. With Genetiker's result backed by Greg Magoon and Vince Tilroe, I think U106 for RISE98 can now go into http://www.ancestraljourneys.org/ancientdna.shtml . I will put the community's results in the 'additional information' column.

T101
06-16-2015, 04:37 PM
YES, the first R1b U106 has been found in Corded Ware Sweden!:) I am now convinced that R1b U106 played a significant role in Proto-Germanic.

It's an excellent result. It puts U106 in the perfect location for it to be a key part of the Nordic Bronze Age (1700 - 500 BC,) the Jastorf Culture, and Proto-Germanic around 500 BC.

I however don't agree with the Corded Ware or Battle Axe designation. The dating for RISE98 fall outside of all accepted dates for Corded Ware. On the contrary this looks like the group that helped bring about the demise of Corded Ware, and pushed R1a Z284 further north up the Scandinavian peninsula, so that R1a-Z284 didn't play apart in the later settlement of continental Europe. I would not be surprised if this group RISE98 is associated with a Beaker push from southern Germany, or the Czech Republic through the Moravian gate.

Cofgene
06-16-2015, 04:44 PM
Is U106* commonly found today? Not any more. The star designation basically means someone has not completed testing available SNPs or done y-DNA sequencing to establish their specific branch and terminal haplogroup. More structure directly under U106 is being defined as additional Big-Y or FGC Elite results are completed.

R.Rocca
06-16-2015, 05:10 PM
It's an excellent result. It puts U106 in the perfect location for it to be a key part of the Nordic Bronze Age (1700 - 500 BC,) the Jastorf Culture, and Proto-Germanic around 500 BC.

I however don't agree with the Corded Ware or Battle Axe designation. The dating for RISE98 fall outside of all accepted dates for Corded Ware. On the contrary this looks like the group that helped bring about the demise of Corded Ware, and pushed R1a Z284 further north up the Scandinavian peninsula, so that R1a-Z284 didn't play apart in the later settlement of continental Europe. I would not be surprised if this group RISE98 is associated with a Beaker push from southern Germany, or the Czech Republic through the Moravian gate.

The youngest Corded Ware dates are from 2200–2000 BC, so this sample falls within that time frame. Also, it is very easy to distinguish a Corded Ware grave from a Bell Beaker grave, so the archaeologists would have labeled them as such if they were Bell Beaker.

T101
06-16-2015, 05:51 PM
The youngest Corded Ware dates are from 2200–2000 (tel:2200–2000) BC


What is your source for that date?

And do we have any information regarding the burial?

vettor
06-16-2015, 05:58 PM
Thank you. With Genetiker's result backed by Greg Magoon and Vince Tilroe, I think U106 for RISE98 can now go into http://www.ancestraljourneys.org/ancientdna.shtml . I will put the community's results in the 'additional information' column.

thanks

Can you explain your method of sorting between European Neolithic and Copper-Bronze as some parts of the time scales cover both groups?

rms2
06-16-2015, 06:34 PM
What is your source for that date?

And do we have any information regarding the burial?

As Jean M pointed out in a post in another thread (http://www.anthrogenica.com/showthread.php?4710-R1b-U106-in-Swedish-Battle-Axe-Culture-%28a-Corded-Ware-subgroup%29&p=90019&viewfull=1#post90019), RISE98 comes from Lilla Bedinge in southern Sweden, the largest Swedish Battle Axe culture cemetery currently known.

I don't believe there are any Bell Beaker burials in Sweden that we know about.

T101
06-16-2015, 06:51 PM
As Jean M pointed out in a post in another thread (http://www.anthrogenica.com/showthread.php?4710-R1b-U106-in-Swedish-Battle-Axe-Culture-%28a-Corded-Ware-subgroup%29&p=90019&viewfull=1#post90019), RISE98 comes from Lilla Bedinge in southern Sweden, the largest Swedish Battle Axe culture cemetery currently known.


Thanks. That's good burial info from Jean as always. I however still question the date. RISE98 at (2275 - 2032BC) is too late for Battle Axe. Great result tho - congrats!

T101
06-16-2015, 06:58 PM
I didn't mean a beaker burial in Scandinavia but was indicating a Beaker push from possibly Southern Germany, the Czech Republic, and perhaps even north of the Carpathians starting with L11.

T101
06-16-2015, 07:38 PM
it is very easy to distinguish a Corded Ware grave from a Bell Beaker grave,

Not necessarily, there are a lot of similarities and shared traditions between Bell Beaker and Battle Axe graves. They both have flat graves, similar body flexing and positioning with gender divisions, and similar added grave items.

Radboud
06-16-2015, 07:46 PM
I think at this point we can't exclude the possibility that R1b U106 is not a bell beaker marker but the option is still open.

Jean M
06-16-2015, 07:53 PM
With the help all round, some other results have gone into my http://www.ancestraljourneys.org/ancientdna.shtml

They are highlighted in yellow on the collating table, now updated: https://drive.google.com/file/d/0B9vzsK0Ig1mNYUZZLW4tMzFEbkE/view?usp=sharing

Jean M
06-16-2015, 08:00 PM
Can you explain your method of sorting between European Neolithic and Copper-Bronze as some parts of the time scales cover both groups?

I explain some decisions on the page:


Bell Beaker is classed here as Copper Age, though described as Neolithic in Melchior and Late Neolithic in Lee.

Bell Beaker is very definitely associated with metallurgy. That's my criterion. Traditionally northern European archaeologists have not recognised a separate Copper Age. One can understand why. The period during which copper only, not bronze, was worked in Northern Europe was comparatively short. So their classification goes from Late Neolithic to Bronze Age.

In terms of chronology, copper was being cast in the Balkans around 5000 BC, before farming had arrived in places like Denmark and the British Isles. So there is considerable overlap, as you say.

R.Rocca
06-16-2015, 08:18 PM
Not necessarily, there are a lot of similarities and shared traditions between Bell Beaker and Battle Axe graves. They both have flat graves, similar body flexing and positioning with gender divisions, and similar added grave items.

It is not really a matter of opinion. There are very distinct dissimilarities between the two.

T101
06-16-2015, 08:30 PM
It is not really a matter of opinion.

Please you're assertion is ridiculous. I never said it was a Beaker grave nor did I imply it was a matter of opinion. Your words not mine.

where is your evidence as to the youngest age of Corded Ware being from 2200 - 2000BC.

R.Rocca
06-16-2015, 08:45 PM
Please you're assertion is ridiculous. I never said it was a Beaker grave nor did I imply it was a matter of opinion. Your words not mine.

where is your evidence as to the youngest age of Corded Ware being from 2200 - 2000BC.

I didn't say that you said it was a Bell Beaker grave either, so I'm not sure what you are getting all bent out of shape about. And here are some late radiocarbon Corded Ware dates from 2200-2000 BC...

https://journals.uair.arizona.edu/index.php/radiocarbon/article/download/3530/3045

T101
06-16-2015, 09:30 PM
Thanks Richard I'll take a look at it.

I still feel though the arrival of U106 at this late date heralds the end, or decline of Corded Ware and the push of R1a z282/ z284 northward from southern Scandinavia. Although perhaps this U106 is negative for all basal subclades and a dead end. We just need more aDna from eastern Hungary, East Germany, Poland, and Scandinavia.

lgmayka
06-16-2015, 11:37 PM
I still feel though the arrival of U106 at this late date heralds the end, or decline of Corded Ware and the push of R1a z282/ z284 northward from southern Scandinavia.
YFull estimates the TMRCA of R-Z284 at 4200 ybp (http://yfull.com/tree/R-Z284/).

Jean M
06-17-2015, 11:37 AM
Smal's results now added to http://www.ancestraljourneys.org/ancientdna.shtml
Chris R's have gone into http://www.ancestraljourneys.org/ironagedna.shtml

Many thanks.

[added] Collating table updated: https://drive.google.com/file/d/0B9vzsK0Ig1mNalpycWhvbWx2Zlk/view?usp=sharing

jdean
06-17-2015, 12:46 PM
Felix has the variance files for RISE174 now.

There is a mixed bag of SNPs for E, G, J and R which is probably why they decided not to assign a Y haplogroup for this sample.

Michał
06-17-2015, 01:05 PM
The youngest Corded Ware dates are from 2200–2000 BC, so this sample falls within that time frame.
Right, but it is also worth noting that in most Corded Ware cemeteries, the typical CWC burials are discontinued after 2200 BC (as nicely shown in the paper you have recommended to T101), which makes any non-typical burials from such a late period much more likely to represent a new non-CWC population that just happened to take over the same cemetery.



Also, it is very easy to distinguish a Corded Ware grave from a Bell Beaker grave, so the archaeologists would have labeled them as such if they were Bell Beaker.
It should be indeed quite easy to distinguish between CWC and BB, but only when comparing the typical CWC and BB burials. However, in this specific case of Grave 49 from Lilla Bedinge, all we can securely say about its cultural identity is that this is not a typical Corded Ware (Battle Axe) burial by any standards. In fact, if Allentoft et al. were strongly convinced that this is a typical Battle Axe grave (like they were in the case of another Swedish burial in Viby that turned out to be R1a-M417), they wouldn’t mark this sample as “Battle Axe/Nordic LN” (while classifying the Viby remains simply as “Battle Axe”).

Firstly, Grave 49 included no grave goods that would indicate any strong association with CWC/BA. More specifically, there was no corded pottery at all. Also, quite importantly, there were no battle axes, even though this particular skeleton (RISE98) belonged to a male person. As pointed out by JeanM in her above post, “the only recovered find is a bone needle deposited next to the northern skeleton” (and it should be noted that RISE98 was a southern skeleton).

Secondly, the CWC graves were rarely containing more than two people. By contrast, there are as many as seven people buried in Grave 49, including four adults and three children.

Thirdly, both the CWC and BB people were usually buried lying on their sides, while the skeletons from Grave 49 were found in the sitting crouched position, facing south-west, which hardly resembles a position typical for Corded Ware.

felix
06-18-2015, 02:34 AM
I couldn't remember if Felix had ever fixed his site to accurately reflect Hinxton-1 as being positive for Z245. He never did so we will have to be careful about what he reports as being the terminal SNP. There should be enough people checking what he posts and doing their own analysis to determine what he has missed just like jdean found with Hinxton-1.

I tried to fix Hinxton-1 being positive for Z245, but I cannot find the mutation in ISOGG Y-DNA (R haplogroup). The best I can come up with is still R-L151 unless I am missing something.

Edit: got the answer - http://www.anthrogenica.com/showthread.php?4664-Request-Y-DNA-haplogroup-results-from-Allentoft-2015&p=89837&viewfull=1#post89837

Jean M
06-18-2015, 11:35 AM
May as well put the Hinxton 1 and 4 results online, while I'm at it. Don't hesitate to tell me if I've got it wrong, folks. ;)
http://www.ancestraljourneys.org/ironagedna.shtml

alan
06-18-2015, 06:42 PM
Right, but it is also worth noting that in most Corded Ware cemeteries, the typical CWC burials are discontinued after 2200 BC (as nicely shown in the paper you have recommended to T101), which makes any non-typical burials from such a late period much more likely to represent a new non-CWC population that just happened to take over the same cemetery.



It should be indeed quite easy to distinguish between CWC and BB, but only when comparing the typical CWC and BB burials. However, in this specific case of Grave 49 from Lilla Bedinge, all we can securely say about its cultural identity is that this is not a typical Corded Ware (Battle Axe) burial by any standards. In fact, if Allentoft et al. were strongly convinced that this is a typical Battle Axe grave (like they were in the case of another Swedish burial in Viby that turned out to be R1a-M417), they wouldn’t mark this sample as “Battle Axe/Nordic LN” (while classifying the Viby remains simply as “Battle Axe”).

Firstly, Grave 49 included no grave goods that would indicate any strong association with CWC/BA. More specifically, there was no corded pottery at all. Also, quite importantly, there were no battle axes, even though this particular skeleton (RISE98) belonged to a male person. As pointed out by JeanM in her above post, “the only recovered find is a bone needle deposited next to the northern skeleton” (and it should be noted that RISE98 was a southern skeleton).

Secondly, the CWC graves were rarely containing more than two people. By contrast, there are as many as seven people buried in Grave 49, including four adults and three children.

Thirdly, both the CWC and BB people were usually buried lying on their sides, while the skeletons from Grave 49 were found in the sitting crouched position, facing south-west, which hardly resembles a position typical for Corded Ware.

In southern Sweden and north Poland CW/battle axe orientation is typically north-south with the male on his right side with head south looking east, female usually north-south head to north on left side also looking east. It is weirdly like a gender reversed beaker burial in terms of orientation but they share the north-south axis of the bordies, the flexed/crouched on side position, the facing east. There surely is some ancestral shared beliefs between the two cultures.

alan
06-18-2015, 06:49 PM
Right, but it is also worth noting that in most Corded Ware cemeteries, the typical CWC burials are discontinued after 2200 BC (as nicely shown in the paper you have recommended to T101), which makes any non-typical burials from such a late period much more likely to represent a new non-CWC population that just happened to take over the same cemetery.



It should be indeed quite easy to distinguish between CWC and BB, but only when comparing the typical CWC and BB burials. However, in this specific case of Grave 49 from Lilla Bedinge, all we can securely say about its cultural identity is that this is not a typical Corded Ware (Battle Axe) burial by any standards. In fact, if Allentoft et al. were strongly convinced that this is a typical Battle Axe grave (like they were in the case of another Swedish burial in Viby that turned out to be R1a-M417), they wouldn’t mark this sample as “Battle Axe/Nordic LN” (while classifying the Viby remains simply as “Battle Axe”).

Firstly, Grave 49 included no grave goods that would indicate any strong association with CWC/BA. More specifically, there was no corded pottery at all. Also, quite importantly, there were no battle axes, even though this particular skeleton (RISE98) belonged to a male person. As pointed out by JeanM in her above post, “the only recovered find is a bone needle deposited next to the northern skeleton” (and it should be noted that RISE98 was a southern skeleton).

Secondly, the CWC graves were rarely containing more than two people. By contrast, there are as many as seven people buried in Grave 49, including four adults and three children.

Thirdly, both the CWC and BB people were usually buried lying on their sides, while the skeletons from Grave 49 were found in the sitting crouched position, facing south-west, which hardly resembles a position typical for Corded Ware.

Do you mean a steppe type on your back with your knees up? Also is the RC date from the U106 guy himself?

I suppose there are only limited cultures who are likely to have left a U106 line in Sweden by the 3rd millenium.

R.Rocca
06-18-2015, 07:12 PM
Genetiker found that the RISE560 Bell Beaker sample is M12124+, which is below DF27 as per Underhill 2015.

Source: https://genetiker.wordpress.com/2015/06/11/y-haplogroups-for-prehistoric-eurasian-genomes/

vettor
06-18-2015, 07:23 PM
Genetiker found that the RISE560 Bell Beaker sample is M12124+, which is below DF27 as per Underhill 2015.

Source: https://genetiker.wordpress.com/2015/06/11/y-haplogroups-for-prehistoric-eurasian-genomes/

Genetiker and Felix are getting different results, is this because felix seems to be using the yfull format and genetiker is not?

R.Rocca
06-18-2015, 07:44 PM
Genetiker and Felix are getting different results, is this because felix seems to be using the yfull format and genetiker is not?

Felix seems to be running a program that only checks for ISOGG listed SNPs. Genetiker seems to be checking ISOGG SNPs and also unlisted SNP positions within the raw data files.

Jean M
06-18-2015, 08:56 PM
Genetiker found that the RISE560 Bell Beaker sample is M12124+, which is below DF27 as per Underhill 2015.


Thanks. He must have updated.

Krefter
06-18-2015, 09:07 PM
Genetiker found that the RISE560 Bell Beaker sample is M12124+, which is below DF27 as per Underhill 2015.

Source: https://genetiker.wordpress.com/2015/06/11/y-haplogroups-for-prehistoric-eurasian-genomes/

Awesome news, I hope it's confirmed. So, DF27 and U152 already existed over 4,000 years ago. Helps explain DF27 outside of Iberia today.

Jean M
06-18-2015, 10:10 PM
Genetiker found that the RISE560 Bell Beaker sample is M12124+, which is below DF27 as per Underhill 2015.


OK I give up. The only Underhill 2015 I know was on R1a. I can't find M12124 on YFull. In any case Genetiker has in other cases given the ISOGG haplogroup. In this case he says it is R1b1a2a1a2 (i.e. P312). Help!

Michał
06-18-2015, 10:23 PM
Do you mean a steppe type on your back with your knees up?
I guess "sitting" excludes "lying on his back".


Also is the RC date from the U106 guy himself?

See the earlier post by JeanM (http://www.anthrogenica.com/showthread.php?4710-R1b-U106-in-Swedish-Battle-Axe-Culture-%28a-Corded-Ware-subgroup%29&p=90019&viewfull=1#post90019) for further references. She gives a link to a paper in which "the S skeleton" from Grave 49 is radiocarbon-dated to 2476–2141 BC, but this is not consistent with the dates provided by Allentoft et al. (2275-2032 BC).

ArmandoR1b
06-18-2015, 10:33 PM
I tried to fix Hinxton-1 being positive for Z245, but I cannot find the mutation in ISOGG Y-DNA (R haplogroup). The best I can come up with is still R-L151 unless I am missing something.

Edit: got the answer - http://www.anthrogenica.com/showthread.php?4664-Request-Y-DNA-haplogroup-results-from-Allentoft-2015&p=89837&viewfull=1#post89837

Thank you for looking for that. I hope you are just as receptive for the other samples. There are a lot of SNPs that are known about that haven't made it to the ISOGG tree that are reliable and can be found in the files you have or the HGDP and 1,000 Genomes files. The YFull tree has most of them and in the order they found them in those files as well as customer files. The new YHDS database makes it easy to look up SNPs also. It's at http://www.semanticgen.net/ydhs/

By the way, any idea what can be done for recurrent SNPs for your programs?

razyn
06-18-2015, 10:43 PM
OK I give up. The only Underhill 2015 I know was on R1a. I can't find M12124 on YFull. In any case Genetiker has in other cases given the ISOGG haplogroup. In this case he says it is R1b1a2a1a2 (i.e. P312). Help!

I hope this isn't another one of those things Rich has to recant. The last one came in just as I was leaving for a Wednesday rehearsal. This week the conductor's kid graduated so we moved the rehearsal to Thursday -- and this one came in. Or hit the fan, as the case may be.

ArmandoR1b
06-18-2015, 10:47 PM
OK I give up. The only Underhill 2015 I know was on R1a. I can't find M12124 on YFull. In any case Genetiker has in other cases given the ISOGG haplogroup. In this case he says it is R1b1a2a1a2 (i.e. P312). Help!

It's not in the new YDHS database either. http://www.semanticgen.net/ydhs/

GabeGibeau
06-18-2015, 11:21 PM
Dick,

M12124 Details (ybrowse.org)

http://ybrowse.org/gb2/gbrowse_details/chrY?ref=ChrY;start=22161863;end=22161863;name=M12 124;class=Sequence;feature_id=159109;db_id=chrY%3A database

felix
06-18-2015, 11:27 PM
Thank you for looking for that. I hope you are just as receptive for the other samples. There are a lot of SNPs that are known about that haven't made it to the ISOGG tree that are reliable and can be found in the files you have or the HGDP and 1,000 Genomes files. The YFull tree has most of them and in the order they found them in those files as well as customer files. The new YHDS database makes it easy to look up SNPs also. It's at http://www.semanticgen.net/ydhs/

By the way, any idea what can be done for recurrent SNPs for your programs?

I currently check only ISOGG ytree and I believe it is reasonably accurate. I am a bit cautious in using any other due to some of the lessons learnt in the past including my own Y-haplogroup and the way BigY conflited with morleydna Ytree couple of years back.

ArmandoR1b
06-18-2015, 11:36 PM
I currently check only ISOGG ytree and I believe it is reasonably accurate. I am a bit cautious in using any other due to some of the lessons learnt in the past including my own Y-haplogroup and the way BigY conflited with morleydna Ytree couple of years back.

ISOGG is accurate but the issue is more about the SNPs not in the ISOGG tree which should be included. I guess we'll have to wait until ISOGG catches up.

Jean M
06-18-2015, 11:41 PM
M12124 Details (ybrowse.org)

Thanks, but that just says ISOGG haplogroup: R1b1a2a1a2 (as reported by Genetiker) and gives this mysterious Underhill 2015 ref.

jdean
06-19-2015, 01:18 AM
Thanks, but that just says ISOGG haplogroup: R1b1a2a1a2 (as reported by Genetiker) and gives this mysterious Underhill 2015 ref.

I'm guessing

http://genome.cshlp.org/content/25/4/459 ??

Which I think is what smal referred to as ' Karmin et al. 2015' in reply to my comment about L754

http://www.anthrogenica.com/showthread.php?4664-Request-Y-DNA-haplogroup-results-from-Allentoft-2015&p=89845&viewfull=1#post89845

That said I couldn't find M12124 in it when I had a quick look earlier and I may have the complete wrong end of the stick, It’s very late for me and I'm only up because I'm tired of the insomnia and thought a glass of water may help : )

R.Rocca
06-19-2015, 01:23 AM
OK I give up. The only Underhill 2015 I know was on R1a. I can't find M12124 on YFull. In any case Genetiker has in other cases given the ISOGG haplogroup. In this case he says it is R1b1a2a1a2 (i.e. P312). Help!

Hope this helps...
http://thebigone.stanford.edu/papers/Underhill_phylogenetic_March-2014.pdf

You can see sample SUFG001 on page 6. On the tree, it is marked as R1b-S250 (aka DF27). Thomas Krahn has M12124 associated to sample SUFG001 here...
http://ybrowse.org/gb2/gbrowse_details/chrY?ref=ChrY;start=22161863;end=22161863;name=M12 124;class=Sequence;feature_id=159109;db_id=chrY%3A database

Tomenable
06-19-2015, 01:34 AM
So, in the end, Genetiker is right that RISE560 is DF27 ???

razyn
06-19-2015, 02:40 AM
So, in the end, Genetiker is right that RISE560 is DF27 ???

The way I read it, Genetiker calls RISE560 M12124; and Rich Rocca is right that that is a DF27 (S250) marker -- per Underhill et al. whatever-year. Though the rest of the phylogeny is a bit unclear. Maybe M12124 is in that Feb. 2014 Geno2 spreadsheet -- the manipulation of which tends to hang up my MacBook (which doesn't really like Microsoft Excel, and especially humongous files displayed in it). But that's my cross of pain to bear. Knowing its position and mutation doesn't really help me place it in the DF27 tree, so I'm still feeling my way, a bit. Still, it's important news, and I for one consider it good news.

So just for purposes of discussion, the earliest U152 aDNA sample (RISE563 from Osterhofen) and the earliest DF27 aDNA sample (RISE560 from Augsburg), in hand and tested to date, are about 200 km or 125 miles apart:

4954

That's a detail from the handy map of aDNA samples created by Rozenfeld: http://www.anthrogenica.com/showthread.php?4640-Population-genomics-of-Bronze-Age-Eurasia-%28Allentoft-et-al-2015%29&p=89868&viewfull=1#post89868

alan
06-19-2015, 07:04 AM
The way I read it, Genetiker calls RISE560 M12124; and Rich Rocca is right that that is a DF27 (S250) marker -- per Underhill et al. whatever-year. Though the rest of the phylogeny is a bit unclear. Maybe M12124 is in that Feb. 2014 Geno2 spreadsheet -- the manipulation of which tends to hang up my MacBook (which doesn't really like Microsoft Excel, and especially humongous files displayed in it). But that's my cross of pain to bear. Knowing its position and mutation doesn't really help me place it in the DF27 tree, so I'm still feeling my way, a bit. Still, it's important news, and I for one consider it good news.

So just for purposes of discussion, the earliest U152 aDNA sample (RISE563 from Osterhofen) and the earliest DF27 aDNA sample (RISE560 from Augsburg), in hand and tested to date, are about 200 km or 125 miles apart:

4954

That's a detail from the handy map of aDNA samples created by Rozenfeld: http://www.anthrogenica.com/showthread.php?4640-Population-genomics-of-Bronze-Age-Eurasia-%28Allentoft-et-al-2015%29&p=89868&viewfull=1#post89868

Are they both bell beaker and are there radiocarbon dates? I am getting confused

Net Down G5L
06-19-2015, 08:16 AM
Are they both bell beaker and are there radiocarbon dates? I am getting confused

Yes, Bell Beaker, and No available RC dates - extract from Krefter's spreadsheet: (Df27 / U152 added)

Bell Beaker
Sample Name Sample Name Site Culture Location Sex 14C Date BP cal BC low
SAMEA3325418 RISE559 Augsburg Bell Beaker Germany Female nd nd
SAMEA3325419 RISE560 Augsburg Bell Beaker Germany Male nd nd DF27
SAMEA3325420 RISE562 Landau an der Isar Bell Beaker Germany Female nd nd
SAMEA3325421 RISE563 Osterhofen-Altenmarkt Bell Beaker Germany Male nd nd U152
SAMEA3325422 RISE564 Osterhofen-Altenmarkt Bell Beaker Germany Male nd nd
SAMEA3325423 RISE566 Knezeves Bell Beaker Czech Republic Male nd nd
SAMEA3325424 RISE567 Knezeves Bell Beaker Czech Republic Female nd nd
SAMEA3325425 RISE568 Brandysek Bell Beaker Czech Republic Female nd nd
SAMEA3325426 RISE569 Brandysek Bell Beaker Czech Republic Female nd nd

Jean M
06-19-2015, 09:23 AM
I'm guessing

http://genome.cshlp.org/content/25/4/459 ??

Which I think is what smal referred to as ' Karmin et al. 2015'

I thought of that, but it did not seem to be the one.

Jean M
06-19-2015, 09:40 AM
Hope this helps...
http://thebigone.stanford.edu/papers/Underhill_phylogenetic_March-2014.pdf

You can see sample SUFG001 on page 6. On the tree, it is marked as R1b-S250 (aka DF27).

That is very helpful Richard, but sample SUFG001 is actually marked as R1b-S116 aka R1b1a2a1a2 (P312). The line above (another branch) is marked as R1b-S250. That is sample HG01173, with R1b-Z195 as the most derived commonly known SNP observed in the corresponding sample. I can understand the confusion.

4955

Jean M
06-19-2015, 09:41 AM
The way I read it, Genetiker calls RISE560 M12124; and Rich Rocca is right that that is a DF27 (S250) marker -- per Underhill et al.

Afraid not.


So, in the end, Genetiker is right that RISE560 is DF27 ???

Genetiker did not identify RISE560 as DF27. He identified it as R1b1a2a1a2 (P312), which is correct if we regard M12124 as equivalent to P312, which no-one seems to have established. As I understand it now, M12124 is simply an SNP that appeared in one sample otherwise identified as P312*.

It would be good for someone else to check it.

alan
06-19-2015, 09:47 AM
Yes, Bell Beaker, and No available RC dates - extract from Krefter's spreadsheet: (Df27 / U152 added)

Bell Beaker
Sample Name Sample Name Site Culture Location Sex 14C Date BP cal BC low
SAMEA3325418 RISE559 Augsburg Bell Beaker Germany Female nd nd
SAMEA3325419 RISE560 Augsburg Bell Beaker Germany Male nd nd DF27
SAMEA3325420 RISE562 Landau an der Isar Bell Beaker Germany Female nd nd
SAMEA3325421 RISE563 Osterhofen-Altenmarkt Bell Beaker Germany Male nd nd U152
SAMEA3325422 RISE564 Osterhofen-Altenmarkt Bell Beaker Germany Male nd nd
SAMEA3325423 RISE566 Knezeves Bell Beaker Czech Republic Male nd nd
SAMEA3325424 RISE567 Knezeves Bell Beaker Czech Republic Female nd nd
SAMEA3325425 RISE568 Brandysek Bell Beaker Czech Republic Female nd nd
SAMEA3325426 RISE569 Brandysek Bell Beaker Czech Republic Female nd nd

I would say in all probability the Kromsdorf M269xU106 guy was P312 too and virtually certainly L11 anyway. Its a shame he wasnt resolved further because he was an exceptionally early beaker guy. If he is definately beaker then AFAIK he has the earliest reliable context/material RC date in central Europe for beaker.

It cannot be coincidence that all the ancient beaker DNA that has resolved to a more fine grained degree is P312 in what is a very small sample. That essentially proves that central European beaker was very P312 dominated. However we are never going to fully understand the origins and trajectory of beaker unless western Europe is sampled for ancient DNA OR we start finding it in pre-beaker cultures.

alan
06-19-2015, 09:56 AM
One thing that strikes me about the beaker people and their origins and travels is that given the skills they demonstrate in prospecting and mining they must have come from or passed through a zone where prospecting mining knowledge existed. AFAIK the metal mines in central Europe seem to have been in the Carpathians and also it has been suggested central Germany on the basis of analysis of CW copper sources. So if they came from central Europe and had this knowledge then there are only a very limited amount of areas they could pick up that knowledge. Alternatively they would not have picked up the knowledge until they reached Iberia - the north Italian mines closing down around the time beaker people arrived there and the Trielles folk apparently not being interested in trading.

Jean M
06-19-2015, 10:08 AM
Alan - you started a thread specifically for the R1b discoveries in Allentoft 2015 over here: http://www.anthrogenica.com/showthread.php?4657-R1b-findings-by-%28Allentoft-et-al-2015%29 . So I will update my list over there.

jdean
06-19-2015, 01:23 PM
That is very helpful Richard, but sample SUFG001 is actually marked as R1b-S116 aka R1b1a2a1a2 (P312). The line above (another branch) is marked as R1b-S250. That is sample HG01173, with R1b-Z195 as the most derived commonly known SNP observed in the corresponding sample. I can understand the confusion.

4955

To be fair it's not absolutely clear but I think you're right.

Ybrowser lists 34 SNPs as 'Found in SUFG001 Genomic Blood', M12097 - M12130

At least two of these have turned up outside of R1b

M12111 Z16684
M12115 ZS2496


Either way it'd be interesting to see if any of the other M SNPs had coverage for RISE560

razyn
06-19-2015, 01:25 PM
Afraid not.

Afraid so.


Genetiker did not identify RISE560 as DF27. He identified it as R1b1a2a1a2 (P312), which is correct if we regard M12124 as equivalent to P312, which no-one seems to have established. As I understand it now, M12124 is simply an SNP that appeared in one sample otherwise identified as P312*.

As I understand it -- from the same chart you copied into post #147 -- the captions in black refer to the group, and this sample SUFG001 is one of the two that are S250 (not just the Z196 one above it on the chart). The bracket line above those two refers to P312/S116 more broadly, and is so captioned in black.

Whether Underhill's chart is right, I don't know, but that's still how I read it (as I did last night); and I still think it was Rich, not Genetiker, who pointed that out.

I also still have no idea where under S250 M12124 might lie. I checked the YFull DF27 group, nobody in it so far has that mutation (22161863, G-A), and it is not being called equivalent to S250 -- just a subclade of it, as Z196 is. If Underhill's chart be correct.

R.Rocca
06-19-2015, 01:34 PM
Afraid so.



As I understand it -- from the same chart you copied into post #147 -- the captions in black refer to the group, and this sample SUFG001 is one of the two that are S250 (not just the Z196 one above it on the chart). The bracket line above those two refers to P312/S116 more broadly, and is so captioned in black.

Whether Underhill's chart is right, I don't know, but that's still how I read it (as I did last night); and I still think it was Rich, not Genetiker, who pointed that out.

I also still have no idea where under S250 M12124 might lie. I checked the YFull DF27 group, nobody in it so far has that mutation (22161863, G-A), and it is not being called equivalent to S250 -- just a subclade of it, as Z196 is. If Underhill's chart be correct.

You are reading it correctly razyn. For the time being, we can say that M12124 has been found in a DF27+ sample (SUFG001) and in an ancient sample of at least L51.

Jean M
06-19-2015, 01:36 PM
As I understand it -- from the same chart you copied into post #147 -- the captions in black refer to the group, and this sample SUFG001 is one of the two that are S250.

That I'm sure is how Rich read it, hence the confusion. But SUFG001 is actually marked as R1b-S116. I'm sorry that I managed to miss off the caption, which makes it clear (or clearer, anyway!):


Figure 5 Y-chromosome phylogeny inferred from 13 B10-Mb sequences of hg R individuals. Branches are drawn proportional to the number of derived variants. Each of the 24 branches is labeled by an index, and the number of SNPs assigned to the branch is shown in brackets. The tips of the tree are labeled with sequencing coverage, population, ID, and the most derived commonly known SNP observed in the corresponding sample.

The corresponding sample = SUFG001. The most derived commonly known SNP observed in it was S116.

I'm so sorry to disappoint you and other DF27 men.

Jean M
06-19-2015, 01:39 PM
You are reading it correctly razyn.

I'm afraid not Rich. I really am terribly sorry to contradict you. But the caption makes it clear what is meant, despite the confusing tree.

jdean
06-19-2015, 01:42 PM
Afraid so.


That being the case you would have expected it to be labeled

European SUFG001 R1b-S250

rather than

European SUFG001 R1b-S116

R.Rocca
06-19-2015, 01:42 PM
That I'm sure is how Rich read it, hence the confusion. But SUFG001 is actually marked as R1b-S116. I'm sorry that I managed to miss off the caption, which makes it clear (or clearer, anyway!):

Now I see what you mean. Underhill split U152 off from S116 and then the other two share the same branch to the exclusion of U152. So, either the branching is wrong, or the labeling is wrong. Without the raw data, the only way to know for sure is to ask Underhill to check.

ArmandoR1b
06-19-2015, 02:00 PM
That I'm sure is how Rich read it, hence the confusion. But SUFG001 is actually marked as R1b-S116. I'm sorry that I managed to miss off the caption, which makes it clear (or clearer, anyway!):



The corresponding sample = SUFG001. The most derived commonly known SNP observed in it was S116.

I'm so sorry to disappoint you and other DF27 men.

Underhill et al. sure did a bad job with that tree because the black text and branching contradict the green text.

jdean
06-19-2015, 02:07 PM
I currently check only ISOGG ytree and I believe it is reasonably accurate. I am a bit cautious in using any other due to some of the lessons learnt in the past including my own Y-haplogroup and the way BigY conflited with morleydna Ytree couple of years back.

From memory the morleydna Ytree was more of an (unsuccessful) experiment ?

Anyhow Z245 is genuinly a very well known SNP (at least amoungst folk reasurching P312 and L21

You can see the varius plus and minus results at the P312 project

https://www.familytreedna.com/public/atlantic-r1b1c?iframe=ysnp

and the L21 project of course

https://www.familytreedna.com/public/r-l21?iframe=ysnp

Over the years there have been a few folk turn up who were negative for one of the L21 equivalent SNPs (can't remember if this ever happened with Z245) whist having tested positive for L21, which created a bit of excitement, but it's always turned out their L21 results were wrong.

jdean
06-19-2015, 02:36 PM
May as well put the Hinxton 1 and 4 results online, while I'm at it. Don't hesitate to tell me if I've got it wrong, folks. ;)
http://www.ancestraljourneys.org/ironagedna.shtml

Sorry Jean, should have noticed before but Z245 is equivalent to L21 not DF13.

Also (and a very minor point) I’ve always written my moniker with no upper case or space which makes it look a bit like a name : )

Jean M
06-19-2015, 03:09 PM
Sorry Jean, should have noticed before but Z245 is equivalent to L21 not DF13.

Thank you - fixed, but was this sample derived for DF13 as well? Or not? Where did I get that idea? Is the list of calls anywhere?

[Added] It's OK. Found it: https://drive.google.com/folderview?id=0B7vzRsRM2aOQR1BLbHduVUUxcjQ&usp=sharing&tid=0B7vzRsRM2aOQTENJUlB4OVVWeUE#list

jdean
06-19-2015, 03:23 PM
Thank you - fixed, but was this sample derived for DF13 as well? Or not? Where did I get that idea? Is the list of calls anywhere?

Hinxton1 was pretty holey compared to Hinxton5 so it was lucky Z245 turned up. I had another look at it last night to see if I could spot any newer SNPs but no luck.

Felix's variance files are available here

https://drive.google.com/folderview?id=0B7vzRsRM2aOQTENJUlB4OVVWeUE&usp=sharing#list

They came out in slowly in separate runs, I'd pegged Hinxton5 as DF21 but got piped to DF25 which only turned up in the last batch : )

Jean M
06-19-2015, 03:35 PM
Hinxton1 was pretty holey compared to Hinxton5 so it was lucky Z245 turned up. I had another look at it last night to see if I could spot any newer SNPs but no luck.

Sorted. Thanks. I just had a look for DF13 and equivalents and couldn't find them positive or negative, so the haplogroup has been changed. Wish I'd noted all this down at the time. I normally stick to published papers in my tables, but it looks like some of them are just not bothering much with haplogroup allocation these days, as all the attention is focused on genome-wide comparisons.

jdean
06-19-2015, 03:46 PM
Sorted. Thanks. I just had a look for DF13 and equivalents and couldn't find them positive or negative, so the haplogroup has been changed. Wish I'd noted all this down at the time. I normally stick to published papers in my tables, but it looks like some of them are just not bothering much with haplogroup allocation these days, as all the attention is focused on genome-wide comparisons.

So much easer to just post the BAM files then sit back and let the enthusiastic amateur community poor over it for you : )

razyn
06-19-2015, 05:02 PM
The corresponding sample = SUFG001. The most derived commonly known SNP observed in it was S116.

I'm so sorry to disappoint you and other DF27 men.

I'm not disappointed, in that I still read it differently -- and still perceive Underhill's variously colored [coloured] captions as internally consistent. The most derived commonly known SNP in that DF27/S250 sample is S116. He had, but declined, the option of calling it M12124 -- which, clearly, is not commonly known. That doesn't mean it's unknown. It's unknown (to me, anyway) where it may lie; but it's not upstream of DF27, in that the YFull DF27 project has I believe 116 samples that call that locus, and they are all called G; whereas the M12124 mutation has A. The YFull group has 15 no-calls at that locus, all from 1000 Genomes (low coverage) sequencing.

So this may be a rare subclade, one we haven't yet found in high resolution sequencing of modern men -- or even one that has daughtered out (I don't know the age, or other details, of SUFG001).

And it may not be under S250. But Underhill says it is.

Jean M
06-19-2015, 05:26 PM
The most derived commonly known SNP in that DF27/S250 sample is S116.

Razyn - Forgive me, but you are not making sense. S116 is upstream of DF27. There is no way to make it downstream. If SUFG001 had been derived for DF27 or equivalent, then the last commonly known SNP would be DF27 or equivalent. This has already been pointed out above by another poster.

None of us has the faintest idea where M12124 fits into the phylogeny. Underhill did not propose a position for it. Thomas Krahn has not proposed a position for it. There is no earthly reason to suppose that it is below DF27. The only way to even begin to think in that direction would be if Underhill had found SUFG001 derived for DF27, which he didn't. Then of course we would need to find several samples ancestral or derived for it at different positions in the phylogeny. We don't have that data.

Krahn simply notes that M12124 exists in the SUFG001 sample that that Underhill used which was allocated to R1b1a2a1a2 (P312/PF6547/S116). If you want to contact Thomas Krahn to check whether he correctly understands Underhill 2015, that's up to you.

razyn
06-19-2015, 05:50 PM
Razyn - Forgive me, but you are not making sense.

I forgive you, but I know as much about this as you do, and am indeed making sense. It may really be more of an argument with Underhill's 7th grade English teacher, that I cannot say. I'm painfully aware that S116 is upstream of S250; and Underhill has a bracket for it (including U152 on one branch, Z196 and this other S250 guy we are disputing on the other. That's on the chart. S250 is also on the chart. Underhill has grouped the SUFG001 sample as one of its two members (for reasons unknown to either of us, or probably to Thomas -- but perhaps known to Jim Wilson, or some other lab guy who plays his cards a little closer to his vest). S250 (aka DF27) is commonly missed by the BigY test, and I believe always missed by chip tests. So the tag at the end, on which you base your well-intentioned and sympathetic corrections of me, is S116. I'm OK with calling a sample known to belong to an obscure DF27 subclade "S116." Or M269. Hundreds of people in my DF27 haplogroup project are still called M269 by FTDNA; I am very used to living with this. I think it's kind of dumb, but true, as far as it goes. Some designated "Reader" of Underhill's paper may have made that choice, before allowing it to be published, because he was looking at a 2011 ISOGG tree or whatever (w/o S250/DF27 on it).

Also, M12124 is not upstream of S116, as that would also make my 116 sequenced DF27 samples derived for it (with 22161863=A).

Jean M
06-19-2015, 05:58 PM
Underhill has grouped the SUFG001 sample as one of its two members

No - it only looks like that at first glance. Not all trees are as easy to follow as those of ISOGG and Y-Full. Unfortunately. We can blame it on the person who did the graphics if you like. I have had problems with the graphic reproductions of trees in every single publication of mine in which any tree appears, be it a family tree or a genetic phylogeny. Because they have to be redrawn, you can bet that a line will get shifted or missed out or something, and I won't notice until the thing is in print. There was a missing line in one tree in AJ.


Also, M12124 is not upstream of S116, as that would also make my 116 sequenced DF27 samples derived for it (with 22161863=A).

I imagine that it is a private mutation.

nuadha
06-19-2015, 06:16 PM
Thanks. At the moment Felix has RISE1 as C-IMS-JST029149, which certainly does not tally with the paper, which has the Corded Ware results (in the bar chart) as R1, R1a and R1b. Plus he is reporting CT in Bronze Age Sweden, which should be I1, I1a, R1a or R1b.

I'm starting to despair.

If someone hasn't already told you. go to davids site. in the first few hundred comments he posts a link to the list of ydna's that the authors used, matching sample to ydna.

Jean M
06-19-2015, 06:25 PM
If someone hasn't already told you. go to davids site. in the first few hundred comments he posts a link to the list of ydna's that the authors used, matching sample to ydna.

You may be referring to this list http://www.anthrogenica.com/showthread.php?4664-Request-Y-DNA-haplogroup-results-from-Allentoft-2015&p=89569&viewfull=1#post89569
helpfully posted on this thread by Bernard, who had emailed the authors for clarification. Those are the short haplogroup names in my collating table. Members of the community have been running though the original files to get a more detailed haplogroup assignment. There are a couple of lists online by members of the community: one by Felix and the other by Genetiker.

vettor
06-19-2015, 06:39 PM
You may be referring to this list http://www.anthrogenica.com/showthread.php?4664-Request-Y-DNA-haplogroup-results-from-Allentoft-2015&p=89569&viewfull=1#post89569
helpfully posted on this thread by Bernard, who had emailed the authors for clarification. Those are the short haplogroup names in my collating table. Members of the community have been running though the original files to get a more detailed haplogroup assignment. There are a couple of lists online by members of the community: one by Felix and the other by Genetiker.

Thanks

I am surprised felix has not done the Haak samples or the neolithic mtdna bulgarian and romanian ones ( recent paper ).............maybe the system is too time consuming, oh well.

nuadha
06-19-2015, 06:46 PM
RISE1,Corded Ware if he is an L23 prob L51 is a very significant addition as it adds both a chronological and phylogenic intermediate point between the Samara L23 derived samples c. 3100-2900BC and our bell beaker samples in central Europe which probably dont long pre-date 2500BC. It sites right in the middle of the c. 400 year gap between Yamanya and Bell Beaker L23 derived samples. As CW dominates temperate Europe through much of that gap and we have got no R1b from the Alpine or Med pre-beaker samples yet then at the moment CW is looking the prime candidate as the intermediary zone between Yamnaya and Bell Beaker. Sample is still far too small to feel huge confidence yet though.

northwest europeans (Scottish, Icelandic, Norwegian) have more yamnaya like heritage and more EHG than East Central Europeans (Belarusians, Czechs), but the later group has more true Corded Ware Heritage. Therefore, Corded Ware could not be the primary vector for bringing Yamnaya like heritage and EHG to Northwest Europe.

There is also ydna to be considered and the massive number of bell beakers were probably dominated by r1b, which is mostly lacking in Corded Ware. A founder effect can not explain the quick jump in r1b from being a small minority among Corded Ware to a large majority among Bell Beakers.

Also, how could Italo-Celtic r1b derive from Corded Ware Culture?

The obvious source of western r1b is hungarian yamnaya, who's brothers keep showing up as r1b. There isn't even decent evidence that CW r1a came from the yamnaya (frankly, i don't think it did)

nuadha
06-19-2015, 07:09 PM
Think of the various results from Haak et al and now Allentoft et al that, all by themselves, as stand-alones, should be front page headline news. Now there are so many that our heads are spinning and we almost have too much to talk about, feast-or-famine, as the ancient y-dna situation seems to be.

Take this U106+ result for example. That could be really significant for the apparent connection between U106 and the evolution of Germanic, but is anyone talking about that?

I predicted the r1b and r1a results of haak but this study is something else. I didn't have any premonition that e would be so prominent in armenians nor that j would make a big move into central asia around the iron age. Ive mostly focused on the movement of r1a from europe into the steppe after the yamnaya left but i wonder if j moved into central asia in the wake of the early IE cultures there. Did this j group dilute the original yamnaya heritage in central asia before the iranians and indic people moved south?

also, what can we say about the contrast of E and J in the eurasian neolithic context? is j from mesopotamia but never made its way to europe is the neolithic? how far east did j go during the neolihtic.

ArmandoR1b
06-20-2015, 02:27 AM
Thanks

I am surprised felix has not done the Haak samples or the neolithic mtdna bulgarian and romanian ones ( recent paper ).............maybe the system is too time consuming, oh well.

Once you see that he is done with the Allentoft samples you can ask him to.

R.Rocca
06-20-2015, 04:19 AM
Thanks

I am surprised felix has not done the Haak samples or the neolithic mtdna bulgarian and romanian ones ( recent paper ).............maybe the system is too time consuming, oh well.

Haak tested a large mount of SNPs, but did not sequence the entire genome like Allentoft, so I'm not sure what you were expecting from Felix or anyone???

parasar
06-20-2015, 05:55 AM
Kudos to Genetiker.


Below are the Y haplogroups for the 55 newly available male genomes from prehistoric Eurasia.
RISE512 Russia Andronovo R1a1a1b-S224/Z645
RISE94 Sweden Battle Axe R1a1a1-Page7
RISE566 Czech Republic Bell Beaker R1b1a2a1a-P310/PF6546/S129
RISE560 Germany Bell Beaker R1b1a2a1a2-M12124(xM12050)
RISE563 Germany Bell Beaker R1b1a2a1a2b-PF6570/S28/U152
RISE564 Germany Bell Beaker R1b1a2a1-L51/M412/PF6536/S167
RISE434 Germany Corded Ware R1a1a1
RISE436 Germany Corded Ware R1a1a1
RISE446 Germany Corded Ware R1a1a1-M417(xZ647)
RISE1 Poland Corded Ware R
RISE431 Poland Corded Ware R1a1a1
RISE555 Russia EBA R1b1a2a2-CTS7340/Z2107
RISE492 Russia Iron Age R1a1a1(xZ283)
RISE504 Russia Iron Age J2a2-L581/PF5026/S398
RISE600 Russia Iron Age Q1a1b-M25
RISE601 Russia Iron Age Q1a1b-M143
RISE602 Russia Iron Age J2a2
RISE174 Sweden Iron Age ?
RISE493 Russia Karasuk Q1a1b1-L712
RISE494 Russia Karasuk R1a1a1-Page7
RISE495 Russia Karasuk R1a1a1b2a2-YP349
RISE397 Armenia LBA R1b1a2a2-Y4371/Z8128
RISE408 Armenia LBA J2b2f
RISE598 Lithuania LBA R1a1a1
RISE553 Russia LBA R1a1a1
RISE554 Russia LBA IJK
RISE374 Hungary Maros G2a2a1a-PF6308
RISE413 Armenia MBA R1b1a2
RISE416 Armenia MBA E1b1b1
RISE423 Armenia MBA E1b1b1b2a1-PF2020/Z1153
RISE524 Russia Meshovskaya R1b1a2-PF6494
RISE525 Russia Meshovskaya R1a1a1-Page7(xZ283)
RISE21 Denmark Nordic BA ?
RISE47 Denmark Nordic BA R1b1a2-M520/PF6410
RISE175 Sweden Nordic BA I1a
RISE207 Sweden Nordic BA I1-M450/S109
RISE276 Denmark Nordic LBA R1b1a2a
RISE42 Denmark Nordic LN R1a1a1
RISE179 Sweden Nordic LN I1
RISE98 Sweden Nordic LN R1b1a2a1a1-M405/S21/U106*
RISE61 Denmark Nordic MN B R1a1a1-Page7
RISE546 Russia Pit Grave R1b1a2-PF6482/YSC0000203
RISE547 Russia Pit Grave R1b1a2a2-CTS9416
RISE548 Russia Pit Grave R1b1a2a2-Z2105
RISE550 Russia Pit Grave R1b1a2a2-M12145
RISE552 Russia Pit Grave? I2a2a1b1b2-S12195
RISE486 Italy Remedello I2a1a1a-L672/S327
RISE487 Italy Remedello I2a1a
RISE489 Italy Remedello I2a1a1a-L672/S327
RISE386 Russia Sintashta R1a1a1b2a2-Z2124
RISE392 Russia Sintashta R1a1a1b-S224/Z645
RISE139 Poland Unetice ?
RISE247 Hungary Vatya I2a2a-L368
RISE254 Hungary Vatya I2a2a-L59
RISE479 Hungary Vatya I2a2a1a2a2-SK1247/Y4915

Krefter
06-20-2015, 06:12 AM
Kudos to Genetiker.

I've got it organized here.

https://docs.google.com/spreadsheets/d/12G2cfjG0wHWarsl5bB99ridFmvUWzqlZfZ6_e_R6oIA/edit?usp=drive_web

Helgenes50
06-20-2015, 07:12 AM
RISE577 Czech baUne DIY

Steppe

( 0.492892 genotype rate )


28.91% Near_Eastern
0.00% East_Asian
0.00% Siberian
0.00% Oceanian
39.92% WHG-UHG
0.46% Sub-Saharan
4.62% Hindu_Kush
26.09% Steppe
0.01% Amerindian
0.00% Southeast_Asian

K17 MDLP

(0.474867 genotype rate)

13.11% Caucasian-Basal
0.00% Melano-Austronesian
4.63% Uralic
0.00% Ancestral_East_Siber
0.90% Ancestral_West_Siber
3.02% Ancestral_North_Indi
0.23% Ancestral_South_Indi
38.97% West_European_HG
2.53% Ancestral_Sami-Finni
0.00% South_East_Asian
0.00% Archaic_African
10.44% Ancestral_Mediterran
0.00% Circumpolar
0.00% Near-East-Basal
25.49% Ancestral_East_Europ
0.00% African_Sub_Saharian
0.66% Amerindian

K8Ami ( Eurogenes)

( 0.492892 genotype rate)

0.01% Amerindian
0.00% Siberian
56.27% Euro_HG
0.00% Oceanian
0.50% Sub-Saharan
0.00% Southeast_Asian
29.03% LBK
14.20% South-Central_Asian

Harappa


( 0.479830 genotype rate)

0.00% S-Indian
10.29% Baloch
7.04% Caucasian
51.08% NE-Euro
0.14% SE-Asian
0.00% Siberian
0.00% NE-Asian
0.00% Papuan
0.00% American
0.00% Beringian
30.87% Mediterranean
0.01% SW-Asian
0.00% San
0.00% E-African
0.00% Pygmy
0.57% W-African

Megalophias
06-20-2015, 08:10 AM
So... where the heck is Z283 hiding?

Helgenes50
06-20-2015, 08:46 AM
RISE577's (Unetice) results are very close to those of the modern NW Europeans

K36 ( Eurogenes)

Basque 2.72%
Central_Euro 1.77%
East_Balkan 4.58%
East_Central_Euro 3.57%
Eastern_Euro 3.66%
Fennoscandian 9.21%
French 10.22%
Iberian 14.81%
Italian 5.07%
North_Atlantic 18.45%
North_Sea 21.42%
West_Med 4.53%

Generalissimo
06-20-2015, 08:49 AM
So... where the heck is Z283 hiding?

I'm not sure we'll see Z283 being tested. Z282 is more likely, and that's younger than Z283 and Z93, so it's probably too young for the Corded Ware period, and European specific, so it's unlikely to be seen in Asia.

One of the Late Bronze Age German samples from Haak et al. was Z280, which obviously also means Z282. It was one of the Urnfield genomes, I think.

Jean M
06-20-2015, 10:20 AM
I've got it organized here.

That's very handy Krefter.

PS Could you please remove my name from RISE94? I'm not a separate source. I'm just a collator. I have been noting results from other members of the community in addition to Felix and Genetiker. That's all. When I have confirmation from at least two people, I'm putting the result into my usual online aDNA tables. I give preference to people who can be identified by real name. That's pretty much a minimum in scholarly work. Reputation counts too.

rms2
06-20-2015, 11:58 AM
. . .

The obvious source of western r1b is hungarian yamnaya, who's brothers keep showing up as r1b . . .

That is my suspicion, as well, although I am open to the possibility that R1b got into Beaker via Corded Ware, particularly if Don Ringe is right and Italo-Celtic and Germanic belonged to the same early branch off of PIE.

I also think it unlikely that R1b-U106 was ever part of Beaker but instead was a kind of fellow traveler with R1a around the east and north sides of the Carpathians and onto the North European Plain.

Anyway, I think P312 at least stemmed directly from Yamnaya in the Carpathian Basin via one of its hybrid spin-off cultures, some of whom no doubt were there before or contemporaneously with Yamnaya but who received Yamnaya input, both cultural and genetic. Gimbutas, for example, attributed the genesis of Beaker to Vucedol, Somogyvar, and Zok-Mako. Here are a couple of pics that I think make things a bit more clear.

4990

4991

Jean M
06-20-2015, 12:57 PM
One of the Late Bronze Age German samples from Haak et al. was Z280, which obviously also means Z282. It was one of the Urnfield genomes, I think.

That's right. Halberstadt [HAL 36].

Tomenable
06-20-2015, 12:58 PM
One of the Late Bronze Age German samples from Haak et al. was Z280, which obviously also means Z282. It was one of the Urnfield genomes, I think.
That's right. Halberstadt [HAL 36].

Yes that R1a Z280 was a sample from one of westernmost sites of the Lusatian Culture, near Halberstadt.

The Lusatian Culture was part of the Urnfield horizon (one of Urnfield cultures):

http://s23.postimg.org/ejjquv6d7/Lusatian_Culture.png

Perhaps the most impressive of all sites of the Lusatian Culture discovered so far, is Biskupin in Poland:

http://www.biskupin.pl/asp/en_start.asp?typ=13&menu=143&strona=1&m=10&nazwa=303&schemat=0

A documentary about Biskupin (in English): https://www.youtube.com/watch?v=mc_KLJrD054


https://www.youtube.com/watch?v=mc_KLJrD054

Jean M
06-20-2015, 01:07 PM
Yes that R1a Z280 was a sample from one of westernmost sites of the Lusatian Culture, near Halberstadt.

In fact we have no evidence whatever that this was a Lusatian burial. The claim that it was seems extremely popular among parts of the online community, but it is not supported by a single fact. The location of Halberstadt might place this sample just on the edge of the Lausitz zone, but without specific identifying characteristics with the remains, we cannot allocate it to any particular Urnfield zone.

Furthermore, though the burial was described as Urnfield in Haak 2015, because its date falls in that period, it is completely atypical. Urnfield is characterised by cremation burials in urns. HAL 36 was an inhumation in a former LBK graveyard. So it was most likely the burial of a non-Urnfield wanderer whose companions recognised the site as an old graveyard. Some Baltic-speaker trading amber or other goods far from home would fit the picture.

From Haak 2015, supplement:


I0099/HAL36C (grave 40, feature 1114, 1113-1021 calBCE, MAMS 21484)
was buried in right-handed flexed position, head SSW, facing SE. Two decorated LBK pots and two undecorated globular pots were found above the grave but it was not clear whether they were part of the burial or the back filling. Thus, the skeleton was also originally thought to be part of the LBK burial series found at the same site, but subsequent radiocarbon dating performed for this study indicated a much younger date, placing this individual within the Late Bronze Age Urnfield culture of the Mittelelbe-Saale region.

Tomenable
06-20-2015, 01:26 PM
Thanks for the info. But Baltic language did not exist 3100 years ago, rather it was Proto-Balto-Slavic.

According to Chang et al. 2015, Proto-Balto-Slavic split into Proto-Baltic and Proto-Slavic about 2600 years ago:

www.linguisticsociety.org/files/news/ChangEtAlPreprint.pdf

http://s17.postimg.org/p76vh6k8f/Slavic_split.png

Though of course such estimates are always highly speculative and very approximate at best.

Tomenable
06-20-2015, 01:55 PM
it is completely atypical. Urnfield is characterised by cremation burials in urns.

On the other hand, inhumation burials were found in Lusatian cultural context already before (even though cremation was more frequent). Especially in the "Upper Silesia - Lesser Poland Group" (Czestochowa-Gliwice) of the Lusatian Culture inhumation burials were very frequent.

I guess we need to wait for more samples from the Lusatian Culture to see if more Z280 (and M458) shows up.

MJost
06-20-2015, 02:50 PM
Thank you for making this consolidation list. I see now that there are 31 R1b Samples. Its almost a magical feeling!

MJost

I've got it organized here.

https://docs.google.com/spreadsheets/d/12G2cfjG0wHWarsl5bB99ridFmvUWzqlZfZ6_e_R6oIA/edit?usp=drive_web

Leeroy Jenkins
06-20-2015, 03:06 PM
RISE577's (Unetice) results are very close to those of the modern NW Europeans

K36 ( Eurogenes)

Basque 2.72%
Central_Euro 1.77%
East_Balkan 4.58%
East_Central_Euro 3.57%
Eastern_Euro 3.66%
Fennoscandian 9.21%
French 10.22%
Iberian 14.81%
Italian 5.07%
North_Atlantic 18.45%
North_Sea 21.42%
West_Med 4.53%

Yeah, I noticed this too.

When comparing my Eurogenes K7 values to the currently available RISE samples from Felix, RISE 577 (Unetice) is my closest match with a least squares distance of 3.23718979. The Swedish Battle Axe sample, RISE 94, is close at 4.7329577969 as well as the other Unetice sample, RISE 150, at 5.1676703305.

Afshar
06-20-2015, 11:09 PM
Is there any easy way to extract str data from these files, especially Rise493. Or can we find them anywhere?

nuadha
06-20-2015, 11:43 PM
That is my suspicion, as well, although I am open to the possibility that R1b got into Beaker via Corded Ware, particularly if Don Ringe is right and Italo-Celtic and Germanic belonged to the same early branch off of PIE.

I also think it unlikely that R1b-U106 was ever part of Beaker but instead was a kind of fellow traveler with R1a around the east and north sides of the Carpathians and onto the North European Plain.

Anyway, I think P312 at least stemmed directly from Yamnaya in the Carpathian Basin via one of its hybrid spin-off cultures, some of whom no doubt were there before or contemporaneously with Yamnaya but who received Yamnaya input, both cultural and genetic. Gimbutas, for example, attributed the genesis of Beaker to Vucedol, Somogyvar, and Zok-Mako. Here are a couple of pics that I think make things a bit more clear.

4990

4991

Its interesting to contemplate the unusual idea of Celtic and Germanic coming via Corded Ware. I think that Corded Ware was probably multilingual and that they weren't, as a whole proto balto slavic. Also, there is a decent change that the enthnogenesis of the slavs happened around ukraine and not Poland which kind of opens up the west. To me, I think the lineages that led to Balto-Slavic and other Satem languages come from some interaction of eastern CW, CT, and yamnaya (more cultural than genetic), similar to what David Anthony himself suggested, which again opens up the western CW region.

However, I just can't place (pre) celtic with CW. Celtic is tied to BB and BB is too plentiful in r1b for it to have come from a minority of CW people. And when i say r1b, i really should say non r1b u106. There is a very good change that u106 did come with CW.

nuadha
06-21-2015, 12:23 AM
I think I should remind people of what yamnaya horizon actually is.

4997

4998

You can see that there is not a whole lot of land to the west of the sampled yamnaya. Surely, we also need to stick west european type r1b in there. So even if i ignore my theory, and look at these recent studies, I don't see a whole lot of room for r1a to come from the yamnaya, which is what many are holding out on.

Silesian
06-21-2015, 03:03 AM
I think I should remind people of what yamnaya horizon actually is.

4997

4998


You can see that there is not a whole lot of land to the west of the sampled yamnaya. Surely, we also need to stick west european type r1b in there. So even if i ignore my theory, and look at these recent studies, I don't see a whole lot of room for r1a to come from the yamnaya, which is what many are holding out on.

Yamnaya horizon-
1- I2 sample+1- r1b sample from Haak et al 2015 + 1- r1b sample from Allentoft 2015 compared with interval-1900km/3500km+/- Rise sample 509
http://umap.openstreetmap.fr/en/map/ancient-human-dna_41837#4/53.17/91.01

MDLP World-22 4-Ancestors Oracle Kit Num: F999946-Rise552
Admix Results (sorted):
# Population Percent
1 North-East-European 51.67
2 West-Asian 26.26
3 Samoedic 9.84
4 North-European-Mesolithic 5.18
5 Indo-Iranian 3.99
6 Indian 1.92
Using 4 populations approximation:
1 West-Asian + North-East-European + Russian_North + Udmurd @ 6.405675
4999

MDLP World-22 4-Ancestors Oracle-Kit Num: M020637
Admix Results (sorted):
# Population Percent
1 North-East-European 52.63
2 West-Asian 22.05
3 Samoedic 8.95
4 Indo-Iranian 5.99
5 North-European-Mesolithic 3.33
6 Atlantic_Mediterranean_Neolithic 3.04
7 South-America_Amerind 1.38
8 Arctic-Amerind 1.34
9 North-Amerind 1.09
Using 4 populations approximation:
1 West-Asian + North-East-European + Estonian + Mansi @ 7.687467


---------------------------------------------------------------------
MDLP World-22 4-Ancestors Oracle-Kit Num: M951285
Admix Results (sorted):
# Population Percent
1 North-East-European 52.70
2 West-Asian 23.45
3 Samoedic 7.69
4 North-European-Mesolithic 7.55
5 Indo-Iranian 3.30
6 North-Amerind 3.20
7 Atlantic_Mediterranean_Neolithic 1.85
Using 4 populations approximation:
1 West-Asian + North-East-European + Mari + Vepsa @ 6.140025
5000
Gedmatch.Com
MDLP World-22 4-Ancestors Oracle-Kit Num: F999942- Rise sample 509
Admix Results (sorted):
# Population Percent
1 North-East-European 55.29
2 West-Asian 25.40
3 North-European-Mesolithic 7.29
4 Indo-Iranian 3.55
5 North-Amerind 3.40
6 Samoedic 3.05
7 Atlantic_Mediterranean_Neolithic 1.41
Using 4 populations approximation:
1 West-Asian + North-East-European + Komi + Vepsa @ 6.028195

5001

nuadha
06-21-2015, 08:05 AM
Yamnaya horizon-
1- I2 sample+1- r1b sample from Haak et al 2015 + 1- r1b sample from Allentoft 2015 compared with interval-1900km/3500km+/- Rise sample 509
http://umap.openstreetmap.fr/en/map/ancient-human-dna_41837#4/53.17/91.01


Thanks, thats a beautiful map.

Coldmountains
06-21-2015, 10:34 AM
I think I should remind people of what yamnaya horizon actually is.

4997

4998

You can see that there is not a whole lot of land to the west of the sampled yamnaya. Surely, we also need to stick west european type r1b in there. So even if i ignore my theory, and look at these recent studies, I don't see a whole lot of room for r1a to come from the yamnaya, which is what many are holding out on.
As long as we have no DNA from Western Yamnaya it is more or less just speculation to make any claims about the non-existence of R1a there. It is basically no different from prior claims of the non-existence of R1b there based on entirely R1a-dominated steppe samples of Central Asia. It is certain that R1b was frequent there (likely the great majority) but R1a and I2 could also be relatively frequent in Western Yamnaya . Western Yamnaya is really close to important Corded Ware regions and i would be really surprised if there was a sharp genetic border between both cultures. They were genetically really close and not two different "races"

Coldmountains
06-21-2015, 10:42 AM
northwest europeans (Scottish, Icelandic, Norwegian) have more yamnaya like heritage and more EHG than East Central Europeans (Belarusians, Czechs), but the later group has more true Corded Ware Heritage. Therefore, Corded Ware could not be the primary vector for bringing Yamnaya like heritage and EHG to Northwest Europe.

There is also ydna to be considered and the massive number of bell beakers were probably dominated by r1b, which is mostly lacking in Corded Ware. A founder effect can not explain the quick jump in r1b from being a small minority among Corded Ware to a large majority among Bell Beakers.

Also, how could Italo-Celtic r1b derive from Corded Ware Culture?

The obvious source of western r1b is hungarian yamnaya, who's brothers keep showing up as r1b. There isn't even decent evidence that CW r1a came from the yamnaya (frankly, i don't think it did)

Belarusians have more ANE/Teal/WHG and nuch less EEF than Norwegians so I really doubt that Norwegians have more Yamnaya ancestry than them. Haaks figures don't look accurate in my opinion and Yamnaya-like ancestry in Eastern Europe is slightly higher than in Scandinavia. Volga Finns/Baltic Finns are closest to Yamnaya by far and after them Lithuanians/Russians/Belarusians/Poles/ Ukrainians. But of course Scandinavians and NW Europeans have much Yamnaya-like ancestry (40% - 50%)

Untill now all ancient samples from Hungary/Carpathian basin showed quite low Yamnaya-admixture results much lower than among modern North Europeans so it seems more and more unlikely that Bell Beakers and NW Europeans got their Yamnaya ancestry from Hungarian Yamnaya. Maybe they overlooked something but much if not most of R1b in Northern Europe could originate from Corded Ware. Western Yamnaya R1b tribes had maybe only a direct impact in the Balkan and were quickly assimilated by local farmers without leaving such much genetic traces

Jean M
06-21-2015, 10:50 AM
Sorted. Thanks. I just had a look for DF13 and equivalents and couldn't find them positive or negative, so the haplogroup has been changed. Wish I'd noted all this down at the time. I normally stick to published papers in my tables, but it looks like some of them are just not bothering much with haplogroup allocation these days, as all the attention is focused on genome-wide comparisons.

Just realised that I uploaded the wrong page, so this issue was fixed on my computer, but not online. Now it's really fixed. :)

Helgenes50
06-21-2015, 11:04 AM
Belarusians have more ANE/Teal/WHG and nuch less EEF than Norwegians so I really doubt that Norwegians have more Yamnaya ancestry than them. Haaks figures don't look accurate in my opinion and Yamnaya-like ancestry in Eastern Europe is slightly higher than in Scandinavia. Volga Finns/Baltic Finns are closest to Yamnaya by far and after them Lithuanians/Russians/Belarusians/Poles/ Ukrainians. But of course Scandinavians and NW Europeans have much Yamnaya-like ancestry (40% - 50%)

Untill now all ancient samples from Hungary showed quite low Yamnaya-admixture results much lower than among modern North Europeans so it looks more and more unlikely that Bell Beakers and NW Europeans got their Yamnaya ancestry from Hungarian Yamnaya. Maybe they overlooked something but much if not most of R1b in Northern Europe could originate from Corded Ware.
What increases the Yamnaya in the Norwegians in the Haak's paper is probably due to an SHG Ancestry like the Pitted ware or Motala-like or both

Silesian
06-21-2015, 01:20 PM
I think I should remind people of what yamnaya horizon actually is.
4997
4998


Just for fun used 2cM setting for matches. 2 R1b samples within Yamnaya horizon- 2 samples outside.
Yamna 2 (Yamnaya I0231) M020637 even has small match with Ust-Ishim 45k Siberia. Take results with a grain of salt, interesting though.
5010
Yamna 1 (Yamnaya_Sok_River I0443) M951285
5006
Yamna 2 (Yamnaya I0231) M020637
5007
Karelian-HG (EHG_Oleniy_Ostrov I0061) M652848
5008
M690970
5009
Rise-#493 heat map
http://f-picture.net/fp/891a1300dd0741cf86cc76e3e4a9898b

Anabasis
06-21-2015, 01:43 PM
Its sad that there arent any Ancient Armenia sample in Gedmatch heatmap.

Artmar
06-21-2015, 03:34 PM
YFull's analysis, first "batch". Published by Vladimir Tagankin on Facebook group.

RISE494. Karasuk. Z93>Z94>Z2124>Z2125>Z2123>Y934>YP520+
RISE392. Stepnoe VII. Sintashta, Z93>Z94>Z2124>Z2125>Z2123>Y877+ Y939-
RISE512. Kytmanovo. Andronovo Z2121+ (level Z2124) Y877-
RISE386. Bulanovo. Sintashta Z93>Z94>Z2124>Z2125>S23592>YP1456 (YP1460 level YP1456)
Kapova cave.

And the controversial one.
RISE525. Meshovskaya. Z283(-? false negative)>Z282>Z280>CTS1211>YP343>YP340>YP371>Y11162 (Y11175 level Y11162)
Y11175+ Y11171-
This Meshovskaya sample wasn't dated. Maybe that was a Slavic skeleton from that cave examined by chance? Someone should check it more carefully.

Jean M
06-21-2015, 04:05 PM
YFull's analysis, first "batch". Published by Vladimir Tagankin on Facebook group.

Really appreciated Artur. I thought the efforts to get something out of the raw data had tailed off. Hope rises again. :) I can't see these results on the Facebook page for YFull. Is that because it is a closed group? You can see it because you are a member?

Artmar
06-21-2015, 04:18 PM
Really appreciated Artur. I thought the efforts to get something out of the raw data had tailed off. Hope rises again. :) I can't see these results on the Facebook page for YFull. Is that because it is a closed group? You can see it because you are a member?
It was posted in "R1a Y-DNA haplogroup" group available under this link: https://www.facebook.com/groups/R1a1a/ in form of replies to my post.

Jean M
06-21-2015, 04:23 PM
It was posted in "R1a Y-DNA haplogroup" group available under this link: https://www.facebook.com/groups/R1a1a/ in form of replies to my post.

I wondered why it was all R1a. All is explained.

nuadha
06-21-2015, 04:46 PM
Western Yamnaya is really close to important Corded Ware regions and i would be really surprised if there was a sharp genetic border between both cultures.

So you would rather draw a sharp genetic border between the yamnaya themselves? Can you please justify that? People are only drawing that line within the yamnaya because of what has been sampled. Thats not how science works. You don't just say, well, the stuff we didn't test is going to be different.


It is basically no different from prior claims of the non-existence of R1b there based on entirely R1a-dominated steppe samples of Central Asia.

The situations are fundamentally different. We have one culture, one time period, and 2 different regions within that culture which were sampled.

Coldmountains
06-21-2015, 04:56 PM
So you would rather draw a sharp genetic border between the yamnaya themselves? Can you please justify that? People are only drawing that line within the yamnaya because of what has been sampled. Thats not how science works. You don't just say, well, the stuff we didn't test is going to be different.



The situations are fundamentally different. We have one culture, one time period, and 2 different regions within that culture which were sampled.

I don't think that there was any sharp border between various Yamnaya subcultures and between various Late PIE cultures. There was some R1b in Corded Ware so why should there be no R1a in Yamnaya? I am not claiming that R1a was dominant there or that most modern IE R1a is derived from there but it sounds very speculative for me to say that there was zero R1a in Yamnaya.

Jean M
06-21-2015, 04:58 PM
This Meshovskaya sample wasn't dated. Maybe that was a Slavic skeleton from that cave examined by chance? Someone should check it more carefully.

I'm afraid that this will need someone who can read Russian. I have only an abstract in English of V. Zhitenev, Kapova Cave – a multilayer archaeology site: a preliminary report, Prehistoric Eurasia (2012), pp. 155-178. https://www.academia.edu/9304055/Prehistoric_Eurasia


The article is devoted to results of archaeological researches which took place in Kapova cave in 2009-2011. Many confirmations of numerous human visits in Kapova cave during different historical and geological ages have been found in the Kupol’nyi (Dome) chamber. The culture layer of Late Bronze Age (Mezhovskaya culture) was the most powerful one, and contained some paleoantropological materials. Re-mains of a secondary burial in situ in this culture layer have been investigated. Upper Paleolithic horizons of visit have been also researched. Use of stalactites and stalagmite fragments, which were brought from the other cave areas, have been fixed. Questions about a place of Kapova cave in a circle of the Upper Paleolithic cave monuments of the Southern Ural are discussed in this article.

Vladislav Zhitenev is a co-author of Allentoft 2015 and presumably supplied the samples from Kapova Cave.

Michał
06-21-2015, 05:03 PM
RISE392. Stepnoe VII. Sintashta, Z93>Z94>Z2124>Z2125>Z2123>Y877+ Y939-
[...]
RISE386. Bulanovo. Sintashta Z93>Z94>Z2124>Z2125>S23592>YP1456 (YP1460 level YP1456)

If true, this would mean that the current YFull TMRCA estimates are likely underestimates (by at least 10-20%), which is actually what I have suspected from the very beginning.


And the controversial one.
RISE525. Meshovskaya. Z283(-? false negative)>Z282>Z280>CTS1211>YP343>YP340>YP371>Y11162 (Y11175 level Y11162)
Y11175+ Y11171-
This Meshovskaya sample wasn't dated. Maybe that was a Slavic skeleton from that cave examined by chance? Someone should check it more carefully.
Seems like an error (or recurrent mutation/contamination with modern DNA?). Mutation Y11175 under YP371 is younger than 2500 years.

nuadha
06-21-2015, 05:05 PM
Belarusians have more ANE/Teal/WHG and nuch less EEF than Norwegians so I really doubt that Norwegians have more Yamnaya ancestry than them. Haaks figures don't look accurate in my opinion and Yamnaya-like ancestry in Eastern Europe is slightly higher than in Scandinavia. Volga Finns/Baltic Finns are closest to Yamnaya by far and after them Lithuanians/Russians/Belarusians/Poles/ Ukrainians.


Why do you think they weren't accurate and where are you getting your estimates? Unless i have a really good reason, I would trust the highly competent authors who created the paper over the work done by bloggers.


Untill now all ancient samples from Hungary/Carpathian basin showed quite low Yamnaya-admixture results much lower than among modern North Europeans so it seems more and more unlikely that Bell Beakers and NW Europeans got their Yamnaya ancestry from Hungarian Yamnaya.

You are talking about a different culture 1000 years later...


Maybe they overlooked something but much if not most of R1b in Northern Europe could originate from Corded Ware. Western Yamnaya R1b tribes had maybe only a direct impact in the Balkan and were quickly assimilated by local farmers without leaving such much genetic traces

Seriously doubt that, apart from r1b u106 of course.

It takes a huge amount of special pleading to say that r1b in northwest europe developed out of an r1a dominated landscape and that the r1a landscape developed out of an r1b dominated landscape (yamnaya steppe).

Do you then suspect that the irish who came to america were r1a dominant?

Jean M
06-21-2015, 05:07 PM
Seems like an error (or recurrent mutation/contamination with modern DNA?). Mutation Y11175 under YP371 is younger than 2500 years.

It may not be an error if the burial was dug into the Meshovskaya layer, but is much more recent, as Artmar suggested. The skeleton itself was not dated. That's why I need a Russian reader to get to the bottom of this. The alternative would be contamination, I agree.

nuadha
06-21-2015, 05:15 PM
What increases the Yamnaya in the Norwegians in the Haak's paper is probably due to an SHG Ancestry like the Pitted ware or Motala-like or both

I definitely think that is part of it. But even in such a case I would say that the estimated yamnaya thats left in Northwest Eurpeans is still close to East Central Europe but East Central Europe has much more true Corded Ware heritage, implying that there is a strong alternative source for yamnaya like dna (not SHG) in NW Europe.

nuadha
06-21-2015, 05:20 PM
I don't think that there was any sharp border between various Yamnaya subcultures and between various Late PIE cultures. There was plenty R1b in Corded Ware so why should there be no R1a in Yamnaya? I am not claiming that R1a was dominant there or that most modern IE R1a is derived from there but it sounds very speculative for me to say that there was zero R1a in Yamnaya.

I don't actually think there was zero r1a in yamnaya and thats not something we could really disprove anyways. What I'm claiming is that the yamnaya were r1b dominant and the bulk of CW r1a does not come from yamnaya.

Michał
06-21-2015, 05:20 PM
There was plenty R1b in Corded Ware
Isn't this a kind of exaggeration? I wouldn' count that Swedish R1b-U106 sample, as it apparently shows no relationship to CWC/BA (other than location in a former BA cemetery), so we just have one very doubtful case of R1b in Corded Ware (RISE1, a sample of extremely low quality with probably just one positive read for a mutation known to be positioned downstream of M343), as opposed to at least eight secure R1a samples from different locations (Germany, Poland, Sweden).

ADW_1981
06-21-2015, 05:25 PM
Can any native Russian speaker confirm that excavations by Kovalev team have Afanasievo results forthcoming?

Coldmountains
06-21-2015, 05:33 PM
Why do you think they weren't accurate and where are you getting your estimates? Unless i have a really good reason, I would trust the highly competent authors who created the paper over the work done by bloggers
Belarusians have more ANE, Teal and less EEF so I don't understand how they can score lower in Yamnaya-like ancestry. Haak figures are not totally off but not totally accurate. North Europeans no matter if NW or East Europeans are extremely similar to each other in terms of Yamnaya-like ancestry but it is slightly higher among East Europeans. Only far eastern Europeans like Finno-Ugrians are outliners and have significantly more Yamnaya-like ancestry. But nevertheless it is not true that Yamnaya-like ancestry peaks in NW Europe because it peaks among far eastern Europeans like Udmurts (they also don't live in the Yamnaya steppe) by far.





Seriously doubt that, apart from r1b u106 of course

It takes a huge amount of special pleading to say that r1b in northwest europe developed out of an r1a dominated landscape and that the r1a landscape developed out of an r1b dominated landscape (yamnaya)
A founder effect is still a possibility but we need more ancient genomes to understand where the IE Bell Beakers came from. We have now good evidences that at least some of R1b in Northern Europe is from Corded Ware and Bell Beakers indeed show similarities to Corded Ware. They had contact and mixed but the question is if they just exchanged women or if there was a western migration from Corded Ware. I have also no hard opinion on that and maybe you are totally right about the direct Yamnaya origin of Bell Beakers but the low in Yamnaya-like ancestry scoring samples from the Carpathian basin forced me to be very skeptical about that.

Silesian
06-21-2015, 05:35 PM
K13 for rough guide for difference between samples[-3300-2700 BCE-R1b1a2a+2298 BC 2045 BC-R1a1a1b2a2, time&- shift in Atlantic from West Asian shift.Northwest Eurasions & map hotspot

For instance, the new K13 should be more useful for Central and South Asians than any of the others, because it features new reference samples relevant to them.
http://bga101.blogspot.ca/2013/11/updated-eurogenes-k13-at-gedmatch.html
http://www.ancestraljourneys.org/ancientdna.shtml
https://genetiker.wordpress.com/2015/06/11/y-haplogroups-for-prehistoric-eurasian-genomes/
http://biorxiv.org/content/early/2015/02/10/013433
http://www.nature.com/nature/journal/v522/n7555/full/nature14507.html

Kit Num: M690970
Population
North_Atlantic 47.98%
Baltic 33.64%
West_Med 1.44%
West_Asian 14.27%
East_Med -
Red_Sea -
South_Asian -
East_Asian -
Siberian -
Amerindian -
Oceanian -
Northeast_African -
Sub-Saharan 2.67%

K13 Oracle ref data revised 21 Nov 2013

Admix Results (sorted):

# Population Percent
1 North_Atlantic 47.98
2 Baltic 33.64
3 West_Asian 14.27
4 Sub-Saharan 2.67
5 West_Med 1.44
SAMEA3325361 RISE386 Bulanovo Sintashta Russia Male 2298 BC 2045 BC-R1a1a1b2a2- Z2124
---------------------------------------------------------------------------------------------
M951285

K13 Oracle ref data revised 21 Nov 2013
Population
North_Atlantic 20.51%
Baltic 41.42%
West_Med -
West_Asian 31.04%
East_Med -
Red_Sea -
South_Asian 4.19%
East_Asian -
Siberian -
Amerindian 2.84%
Oceanian -
Northeast_African -
Sub-Saharan -
Admix Results (sorted):

# Population Percent
1 Baltic 41.63
2 North_Atlantic 25.00
3 West_Asian 24.26
4 Amerindian 4.99
5 South_Asian 4.11
I0443Yamnaya-YamnayaEBALopatino II, Sok River, Samara, Russia; SVP57-3300-2700 BCE-R1b1a2a[L51-Z2105-]

http://img705.imageshack.us/img705/4687/eurasians1.png

Coldmountains
06-21-2015, 05:48 PM
Isn't this a kind of exaggeration? I wouldn' count that Swedish R1b-U106 sample, as it apparently shows no relationship to CWC/BA (other than location in a former BA cemetery), so we just have one very doubtful case of R1b in Corded Ware (RISE1, a sample of extremely low quality with probably just one positive read for a mutation known to be positioned downstream of M343), as opposed to at least eight secure R1a samples from different locations (Germany, Poland, Sweden).
You are right it is a exaggeration I corrected that.

Jean M
06-21-2015, 06:10 PM
YFull's analysis, first "batch". Published by Vladimir Tagankin on Facebook group.

All except the puzzling RISE525 are now on http://www.ancestraljourneys.org/ancientdna.shtml with my thanks to Vladimir Tagankin.

Michał
06-21-2015, 06:14 PM
It may not be an error if the burial was dug into the Meshovskaya layer, but is much more recent, as Artmar suggested. The skeleton itself was not dated. That's why I need a Russian reader to get to the bottom of this. The alternative would be contamination, I agree.
As far as I can understand Russian, it seems indeed quite likely that there was a secondary "burial" representing a more recent culture. They don't provide any details (as only about a half of the material was thoroughly investigated so far), although it is mentioned that this "secondary material" includes something resembling "zolniks" (piles of ashes) from the Late Bronze Trans-Ural cultures. This statement is accompanied by a reference to another work about such Late Bronze West Siberian "zolniks":
Корочкова О.Н., 2009. О западносибирских зольниках эпохи поздней бронзы // Российская археология. №1.

George
06-21-2015, 06:33 PM
So you would rather draw a sharp genetic border between the yamnaya themselves? Can you please justify that? People are only drawing that line within the yamnaya because of what has been sampled. Thats not how science works. You don't just say, well, the stuff we didn't test is going to be different.



The situations are fundamentally different. We have one culture, one time period, and 2 different regions within that culture which were sampled.

Just a friendly tip (:=)). If you reread Anthony pp. 299ff. you will get a better idea of what the "Yamna horizon" really was.

nuadha
06-21-2015, 06:44 PM
Just a friendly tip (:=)). If you reread Anthony pp. 299ff. you will get a better idea of what the "Yamna horizon" really was.

Was it not highly mobile and unlikely for r1a to dominate the western yamnaya but not have a single showing in the samples found thus far? Keep in mind there has also been a considerable degree of regularity of r1b findings in sampled yamnaya and the mesolithic samara guy.

If thats not so, ill read it soon.

Jean M
06-21-2015, 07:10 PM
this "secondary material" includes something resembling "zolniks" (piles of ashes) from the Late Bronze Trans-Ural cultures. This statement is accompanied by a reference to another work about such Late Bronze West Siberian "zolniks":

Extremely helpful, thank you so much.

Limited information in Polish: https://pl.wikipedia.org/wiki/Zolnik
English abstract of S. A. Pletneva, On the Meaning of Zolniks on Settlements of Khazar Time in the Basin of the Don, Stratum plus. 2001-2002. №5, Pages: 264-269: http://www.e-anthropology.com/English/Catalog/History/STM_DWL_DTts_2MD0wYSMMxzP.aspx



The article is dedicated to such a scarcely studied category of archaeological objects as zolniks or ‘ash spots’. I.P. Rusanova distinguished 6 features; taken together, they enable a characterisation of zolniks as objects of cult. Similar sites are met in the Bronze age, in the Scythian time and during the early Middle Ages. While zolniks of the Bronze Age were studied by S.S. Berezanskaya, the Scythian ones – by I.P Rusanova, for the Medieval period there has been no systematic examination of this group of sites. The settlements with zolniks are found in the basin of the Don as forest-steppe and steppe versions of the Saltov-Mayatskaya culture. Judging by the most typical sites with zolniks, the author draws a conclusion that zolniks were typical for large permanent settlements and are never met on small ones or on what remains of nomads’ camps. The main mass of ash in the mounds comes from regularly cleaned hearths, which played a critical role in religion of all peoples in the world. The ancient cults of fire and hearth have been dominating in the spiritual life of man since the early antiquity. The ash-pits on settlements, most likely, played the role of independent shrines and had no link to other kinds of shrines.

I'm not sure how best to deal with this. It doesn't look like the ash pile is enough to date the secondary burial. On the other hand, we don't know if RISE525 was the secondary burial.

George
06-21-2015, 07:16 PM
Was it not highly mobile and unlikely for r1a to dominate the western yamnaya but not have a single showing in the samples found thus far? Keep in mind there has also been a considerable degree of regularity of r1b findings in sampled yamnaya and the mesolithic samara guy.

If thats not so, ill read it soon.

What I meant was not to come to any firm conclusions until we actually get some samples from the area west of the Don (Yamna and others).

Silesian
06-21-2015, 07:23 PM
Was it not highly mobile and unlikely for r1a to dominate the western yamnaya but not have a single showing in the samples found thus far? Keep in mind there has also been a considerable degree of regularity of r1b findings in sampled yamnaya and the mesolithic samara guy.
If thats not so, ill read it soon.

Like the red and green dots in this picture spanning 2000 years +/-? From from 7650B.P. to 5000B.P +/-?
5016
R1b
5650-5555 BC R1b1* M343+, L278+, M478- , M269-
5013
R1b
3300-2700 BC R1b1a2a* L49+, L23+, PF6399+, L150+, L1353+, PF6509+, M269+, CTS12478+, L51-, Z2105-
5014
R1b
2910-2875 BC R1b1a2a2* CTS1078+, Z2105+, L23+, PF6399+, L265+, PF6434+, L150.1+, PF6482+, M269+, L584-
5015

http://www.ancestraljourneys.org/ancientdna.shtml

Sein
06-21-2015, 08:42 PM
Belarusians have more ANE/Teal/WHG and nuch less EEF than Norwegians so I really doubt that Norwegians have more Yamnaya ancestry than them. Haaks figures don't look accurate in my opinion and Yamnaya-like ancestry in Eastern Europe is slightly higher than in Scandinavia. Volga Finns/Baltic Finns are closest to Yamnaya by far and after them Lithuanians/Russians/Belarusians/Poles/ Ukrainians. But of course Scandinavians and NW Europeans have much Yamnaya-like ancestry (40% - 50%)

Untill now all ancient samples from Hungary/Carpathian basin showed quite low Yamnaya-admixture results much lower than among modern North Europeans so it seems more and more unlikely that Bell Beakers and NW Europeans got their Yamnaya ancestry from Hungarian Yamnaya. Maybe they overlooked something but much if not most of R1b in Northern Europe could originate from Corded Ware. Western Yamnaya R1b tribes had maybe only a direct impact in the Balkan and were quickly assimilated by local farmers without leaving such much genetic traces

M. Myllylä has also used qpAdm, and the estimates he has obtained for Yamnaya ancestry in Europeans seem more reasonable than Haak et al., since he has included EHG and SHG in the models.

(his blog, http://terheninenmaa.blogspot.fi/)

Norwegian
56.7% EEF + 27% Yamnaya + 22.3% SHG/WHG + 15.1% EHG + 3.2% ENA

chisq=0.710

tail probability=0.701024

Belarussian
39.9% EEF + 29.9% Yamnaya + 27% SHG/WHG + 3.2% ENA

chisq=0.399

tail probability=0.940481

Agamemnon
06-21-2015, 11:29 PM
If true, this would mean that the current YFull TMRCA estimates are likely underestimates (by at least 10-20%), which is actually what I have suspected from the very beginning.

That's exactly what I thought when I looked at YFull's TMRCA estimates for J1-YSC234 and its main branches.

parasar
06-22-2015, 02:31 AM
If true, this would mean that the current YFull TMRCA estimates are likely underestimates (by at least 10-20%), which is actually what I have suspected from the very beginning.


...

So M417 is perhaps 10200 years old?

Michał
06-22-2015, 06:56 AM
So M417 is perhaps 10200 years old?
I cannot access the YFull tree at the moment (are they correcting their estimates?), and don't remember exactly what their TMRCA estimate for M417 was, but most likely something around 5400 ybp. According to my "guessimates" (as they were called on this forum), it should be rather in the 6.0-7.0 range, with the separation from the YP1051 lineage taking place about 8-10 kya.

smal
06-22-2015, 11:18 AM
Smal's results now added to http://www.ancestraljourneys.org/ancientdna.shtml


Re-assignment of R1b samples from Haak et al. 2015 and Allentoft et al. 2015

I0410, Els Trocs [Troc3] 5178-5066 BC
Haak ei al. 2015: M415+, M343+, M478-, PF6399-, L265-, L150-, M269-, V35-, V69-

Re-assignment: (M343eq: M343/PF6242+, M415/PF6251+) > (L754eq: L774/PF6245/YSC277+, PF1144+) > (V88eq: PF6376+) > (V88 subclades: V35-, V69-) (P297eq: FGC57/L1067/M12189/PF6424/SK2079/Z8148-, PF6106-) (M269eq: PF6399/S10-, PF6426/YSC72-, L265/PF6431-, L150.1/PF6274.1/S351.1-, PF6448-, CTS1738/FGC55/PF6449-, L753/PF6486/YSC18-, M269/PF6517-) (M478eq: M478-, Y13199-, Y13871-, Y13872-, Y13886-)
There is also Y416/Z8156+ which can be positioned in the P297 level. However, Y416/Z8156 is highly recurrent marker. So, I think it cannot be a reliable marker for the P297 level.

I0124, Lebyazhinka IV on the Sok River [SVP44], 5640-5555 BC ‘Samara hunter-gatherer’
Haak ei al. 2015: M343+, L278+ M269-, M478-

Re-assignment: (M343eq: M343/PF6242+, PF6248+, L278+, L1349/PF6268/YSC231+) > (L754eq: n/a) > (P297eq: PF6513+) > (M478eq: Y13872+, M478-, Y13866-) (M269eq: L150.1/PF6274.1/S351.1-, M269/PF6517-)
Modern samples have at least 49 phylogenetically equivalent markers in the M478 level. The presence of positive and negative markers in the M478 node can reflect an intermediate stage of its formation.

R.Rocca
06-22-2015, 11:40 AM
Re-assignment of R1b samples from Haak et al. 2015 and Allentoft et al. 2015

I0410, Els Trocs [Troc3] 5178-5066 BC
Haak ei al. 2015: M415+, M343+, M478-, PF6399-, L265-, L150-, M269-, V35-, V69-

Re-assignment: (M343eq: M343/PF6242+, M415/PF6251+) > (L754eq: L774/PF6245/YSC277+, PF1144+) > (V88eq: PF6376+) > (V88 subclades: V35-, V69-) (P297eq: FGC57/L1067/M12189/PF6424/SK2079/Z8148-, PF6106-) (M269eq: PF6399/S10-, PF6426/YSC72-, L265/PF6431-, L150.1/PF6274.1/S351.1-, PF6448-, CTS1738/FGC55/PF6449-, L753/PF6486/YSC18-, M269/PF6517-) (M478eq: M478-, Y13199-, Y13871-, Y13872-, Y13886-)
There is also Y416/Z8156+ which can be positioned in the P297 level. However, Y416/Z8156 is highly recurrent marker. So, I think it cannot be a reliable marker for the P297 level.

I0124, Lebyazhinka IV on the Sok River [SVP44], 5640-5555 BC ‘Samara hunter-gatherer’
Haak ei al. 2015: M343+, L278+ M269-, M478-

Re-assignment: (M343eq: M343/PF6242+, PF6248+, L278+, L1349/PF6268/YSC231+) > (L754eq: n/a) > (P297eq: PF6513+) > (M478eq: Y13872+, M478-, Y13866-) (M269eq: L150.1/PF6274.1/S351.1-, M269/PF6517-)
Modern samples have at least 49 phylogenetically equivalent markers in the M478 level. The presence of positive and negative markers in the M478 node can reflect an intermediate stage of its formation.

Thanks smal. On the re-assignment, I just want to make sure I am reading your list correctly...are you saying that El Trocs is PF6376+ which is a V88 equivalent?

Jean M
06-22-2015, 12:09 PM
Re-assignment of R1b samples from Haak et al. 2015 and Allentoft et al. 2015

I0410, Els Trocs [Troc3] 5178-5066 BC
Haak ei al. 2015: M415+, M343+, M478-, PF6399-, L265-, L150-, M269-, V35-, V69-

Re-assignment: (M343eq: M343/PF6242+, M415/PF6251+) > (L754eq: L774/PF6245/YSC277+, PF1144+) > (V88eq: PF6376+) > (V88 subclades: V35-, V69-) (P297eq: FGC57/L1067/M12189/PF6424/SK2079/Z8148-, PF6106-) (M269eq: PF6399/S10-, PF6426/YSC72-, L265/PF6431-, L150.1/PF6274.1/S351.1-, PF6448-, CTS1738/FGC55/PF6449-, L753/PF6486/YSC18-, M269/PF6517-) (M478eq: M478-, Y13199-, Y13871-, Y13872-, Y13886-)


Els Trocs [Troc3] reassignment to R1b1c now up at http://www.ancestraljourneys.org/europeanneolithicdna.shtml with grateful thanks. Sorts out that issue!

smal
06-22-2015, 12:11 PM
Thanks smal. On the re-assignment, I just want to make sure I am reading your list correctly...are you saying that El Trocs is PF6376+ which is a V88 equivalent?
Yes, PF6376 is a V88 equivalent and it is positive in I0410.

R.Rocca
06-22-2015, 12:14 PM
Yes, PF6376 is a V88 equivalent and it is positive in I0410.

Thanks. Have these samples been re-sequenced, or a more extensive call list been made available?

Jean M
06-22-2015, 12:28 PM
I0124, Lebyazhinka IV on the Sok River [SVP44], 5640-5555 BC ‘Samara hunter-gatherer’
Haak ei al. 2015: M343+, L278+ M269-, M478-

Re-assignment: (M343eq: M343/PF6242+, PF6248+, L278+, L1349/PF6268/YSC231+) > (L754eq: n/a) > (P297eq: PF6513+) > (M478eq: Y13872+, M478-, Y13866-) (M269eq: L150.1/PF6274.1/S351.1-, M269/PF6517-)
Modern samples have at least 49 phylogenetically equivalent markers in the M478 level. The presence of positive and negative markers in the M478 node can reflect an intermediate stage of its formation.

Re-assignment of Sok River, Samara [SVP44] to R1b1a now at http://www.ancestraljourneys.org/mesolithicdna.shtml with grateful thanks. Very interesting. So it could be an ancestor of R1b1a1 (M73). Makes sense.

smal
06-22-2015, 12:29 PM
Thanks. Have these samples been re-sequenced, or a more extensive call list been made available?
Haak et al. have analysed the data against ISOGG version 8.22 as of April 22, 2013. But we have now many NGS data for V88 (1 from 1KGP, 4 BigY and 2 articles of Francalacci). The current SNP list is much better.

parasar
06-22-2015, 12:40 PM
Re-assignment of Sok River, Samara [SVP44] to R1b1a now at http://www.ancestraljourneys.org/mesolithicdna.shtml with grateful thanks. Very interesting. So it could be an ancestor of R1b1a1 (M73). Makes sense.

And so not ancestor of the Yamnaya M269.

Jean M
06-22-2015, 12:50 PM
And so not ancestor of the Yamnaya M269.

Exactly. It's a brother (or cousin - whatever) - or at least it could be.

Tomenable
06-22-2015, 01:41 PM
Jean M, I just want to note that there seems to be one mistake in the "Mesolithic" section of your site.

Zhizhitskaya culture were agriculturalists, at least this is what I have found about them in the internet.

Can you investigate this? If they were such, then they shoud perhaps be moved to the "Neolithic" section.

Here is my source on this (he is a knowledgeable Belarusian guy):

http://www.theapricity.com/forum/showthread.php?172936-Baltic-Finnic-N1c-arrival-in-the-Baltic-Sea-region&p=3622337&viewfull=1#post3622337


N1c1 was found in Zhizhitskaya culture in Smolensk Russia on the eastern border of Belarus dated to 4,500 years.

The Zhizhitskaya archaeological culture was surrounded by Corded-Ware culture. The differences between the Zhizhitskaya and Corded-Ware is the material culture of the former being built on tombs in the lake near water. Furthermore, people of Zhizhitskaya had agricultural practices similar to those of central Europe. Make a mental note N1c1 in Zhizhitskaya is 4,500 years old.

The Comb Ceramic culture which included the Narva culture encompassed territories of north-eastern Europe. There is some debate about the language of inhabitants of the Narva culture. Some scholars suggest that inhabitants were paleo-European speakers based on evidence of toponyms and hydronyms. The Comb Ceramic culture was replaced by Corded-ware horizon associated with IE family of languages by scholars. Proto-Finnic speakers migrated to Baltic shore around 3,000 from Volga-Ural direction as per Finnish scholars.

Who could spread N1c1 in the Baltic region in the light of this information? All three - paleo-Europeans, Indo-Europeans and proto-Finnic could be responsible for spreading N1c1 into the Baltic region. It was certainly not proto-Finnic speakers in western Russia, Smolensk 4,500 years ago given linguistic evidence. From Smolensk Russia, N1c1 could travel along Daugava/western Dvina River into northern Belarus, Latvia and Lithuania.

R.Rocca
06-22-2015, 01:52 PM
Haak et al. have analysed the data against ISOGG version 8.22 as of April 22, 2013. But we have now many NGS data for V88 (1 from 1KGP, 4 BigY and 2 articles of Francalacci). The current SNP list is much better.

Understood, but are these SNPs in Haak's original paper?

smal
06-22-2015, 02:19 PM
Understood, but are these SNPs in Haak's original paper?

They are available in their bam files, not in text of the article.

smal
06-22-2015, 02:56 PM
Re-assignment of R1b samples from Haak et al. 2015 and Allentoft et al. 2015


I0231, Ekaterinovka [SVP3], 2910-2875 BC
Haak ei al. 2015: PF6399+, L265+, PF6434+, L150.1+, PF6482+, M269+, L23+, CTS1078+, Z2105+, L584-

Re-assignment: (M343eq: CTS46+ M343/PF6242+ CTS3625/S4228+ Y413+) > (L754eq: CTS3794/PF6256/S4229+ L1068/PF6264/YSC223+ L754/PF6269/YSC22+ L761/PF6258/YSC266+ L774/PF6245/YSC277+ FGC41/M2190/SK2062/V1501/Z8135/Y108+) > (P297eq: FGC57/L1067/M12189/PF6424/SK2079/Z8148+ CTS3876/PF6458+ L502/PF6487+ PF6501+ PF6513+ Y416/Z8156+ FGC69/L320/PF6092/Z8143+ L464_3+) > (M269eq: PF6399/S10+ L479/PF6408+ L265/PF6431+ PF6434+ L150.1/PF6274.1/S351.1+ L749/PF6476/YSC290+ PF6482/YSC203+ L753/PF6486/YSC18+ CTS10349/FGC42/PF6492+ PF6504/S4969+ L928/PF6515+ M269/PF6517+ PF6518+ L1351/PF6528/YSC240+) > (L23eq: L23/PF6534/S141+)> (Z2103eq: CTS1078/Z2103+, M12149/Y4371/Z8128+, M12145/Y12537/Z8129+, Z2105+) > (Z2106eq: n/a) > (Z2109eq: n/a)> (KMS75eq: KMS75+ M4170-, KMS66-, KMS73-, KMS80-, KMS85-, KMS92-, KMS91-)
Z2103>L277eq and subclades: L277- 22850103- 16433964- M12164- M12171- M12147- M12162-
Z2103>L584eq and subclades: L584- FGC14606-
Z2103>Z29823eq: Z29823- Z29829- Z29835-
Z2103*-Avar private SNPs: 15080170- 17585008- 21320569- 23170480- 23381853- 28690665-
Z2106>CTS7763 and subclades: PH4902- 8025025-
Z2106*-Tabasaran private SNPs: 7243325- 8782634- 14516869- 18131766- 19032084- 21342148- 22726374- 28502101-
Z2109>Y14414eq and subclades: Y14423- 22478069- Y14514-
Z2109> SK2087eq and NA20866 private: 4726127-, 4729883-, 15066559-, 17130284-
Z2109>CTS7822 and subclades: FGC9480/Y5590-, 22461390-, 6952026-, SK2097-, 18760244-, PH510-, PH925-
L51eq: L51/M412/PF6536/S167-
P310eq: L52/PF6541- L151/PF6542- L11/PF6539/S127- P310/PF6546/S129- P311/PF6545/S128-
M478eq: M478-

I0439, Lopatino I [SVP52], 3305-2925 BC
Haak ei al. 2015: M173+, M306+, P297+, L51-

Re-assignment: (M343eq: CTS910/FGC66/PF6244+ CTS944/FGC58/PF6096+) > (L754eq: n/a) > (P297eq: P297/PF6398+ FGC57/L1067/M12189/PF6424/SK2079/Z8148+ PF6513+) > (M269eq: CTS12478/PF6529+ CTS12713/PF1331+) > (L23eq: n/a)> (Z2103eq: n/a) > (Z2106eq: n/a) > (Z2109eq: n/a)> (KMS75eq and private: 14168106(A/G)+, KMS80-, KMS92-, KMS94-)
Z2103>L277eq and subclades: Y4370- M12147-
Z2103>L584eq and subclades: L584-
Z2103>Z29823eq: n/a
Z2103*-Avar private SNPs: 17585008-
Z2106>CTS7763 and subclades: n/a
Z2106*-Tabasaran private SNPs: 14305646- 18131766-
Z2109>Y14414eq and subclades: n/a
Z2109> SK2087eq and NA20866 private: 2999695-
Z2109>CTS7822 and subclades: 22461390-
L51eq: PF6535- L51/M412/PF6536/S167-
P310eq: L151/PF6542- L11/PF6539/S127-

There are 2 BigY tested samples from Burzyan Bashkir people, FTDNA-181183 (YFull-YF03134) and FTDNA-329335. They have 45 common SNPs under Z2103>Z2106>Z2109. And they are negative for all SNPs of the CTS7822, SK2087, and Y14414 subclades under Z2109. One of these Burzyan specific SNPs, KMS75, is positive for I0231. The second marker, 14168106 (A/G), is positive in FTDNA-181183 (YFull-YF03134) and I0439. Unfortunately, FTDNA-329335 does not have “reads” in this position.

lgmayka
06-22-2015, 03:01 PM
I cannot access the YFull tree at the moment (are they correcting their estimates?), and don't remember exactly what their TMRCA estimate for M417 was, but most likely something around 5400 ybp. According to my "guessimates" (as they were called on this forum), it should be rather in the 6.0-7.0 range, with the separation from the YP1051 lineage taking place about 8-10 kya.
YFull lists R-M417 (http://yfull.com/tree/R-M417/) as:
Formed 8500 ybp
TMRCA 5500 ybp

alan
06-22-2015, 03:19 PM
Re-assignment of Sok River, Samara [SVP44] to R1b1a now at http://www.ancestraljourneys.org/mesolithicdna.shtml with grateful thanks. Very interesting. So it could be an ancestor of R1b1a1 (M73). Makes sense.

I have been wondering about M73 and how it fits in but with the common ancestor with M269 back in the early Mesolithic the options are pretty huge. It makes most sense if it was a lineage at the far eastern end of the Euro steppes or even Kazakhstan. It seemed unlike M269 to have long been positioned somewhere hard for it to get into both Old Europe or SW Asia (even the M73 in the northern fringes of SW Asia seems Turkic linked today and probably brought late). Its original linguistic associations before absorbtion by Turks seem to be completely lost. They seem to have been able to dodge the Iranic steppe waves but not the Turkic ones although I think I recall that M73 is not present in the Turkic homelands so they seem to have absorbed it somewhere to the west on their travels.

R.Rocca
06-22-2015, 03:41 PM
They are available in their bam files, not in text of the article.

Thanks again smal...can you share the link to the BAM files then?

smal
06-22-2015, 03:58 PM
Thanks again smal...can you share the link to the BAM files then?
http://www.ebi.ac.uk/ena/data/view/PRJEB8448

Jean M
06-22-2015, 04:35 PM
Jean M, I just want to note that there seems to be one mistake in the "Mesolithic" section of your site.

So you said in your personal message to me, to which I just responded. I will repeat my reply here, so everyone knows the outcome:


Thank you so much for notifying me. I have checked. There is indeed something to that effect in another paper in the same volume as the DNA results. It says (pp. 67-68):


A new cultural tradition was formed on the boundary of 4–3 mill. cal. BC, which was named zhizhitskaya culture of pile dwellings. It was formed on the basis of usviatskaya middle Neolithic culture, which can explain finds of vessels attributed to these both cultures in one horizon. It was also on the boundary of 4–3 mill. cal. BC when bearers of Balkan agricultural traditions appeared in Sennitsky and Zhizhitsky archaeological microregions. A particular cultural complex was formed here under their influence.

Russian archaeologists traditionally label as Neolithic all cultures with pottery (including hunter-gatherers with pottery), so it was not clear to me before that Zhizhitskaya people were actually practising agriculture. I thought they were lake fishermen.

Many thanks. The entries have been moved.

Jean M
06-22-2015, 04:49 PM
I have been wondering about M73 ... . It seemed unlike M269 to have long been positioned somewhere hard for it to get into both Old Europe or SW Asia ... They seem to have been able to dodge the Iranic steppe waves but not the Turkic ones although I think I recall that M73 is not present in the Turkic homelands so they seem to have absorbed it somewhere to the west on their travels.

You may remember that Michal M suggested that M73 went into Afanasievo. That would be a brilliant solution, except for the R1a in the earliest Tarim mummies. But maybe this is one of those puzzles that it will take more time (and data) to sort out.

parasar
06-22-2015, 04:55 PM
YFull's analysis, first "batch". Published by Vladimir Tagankin on Facebook group.

RISE494. Karasuk. Z93>Z94>Z2124>Z2125>Z2123>Y934>YP520+
...

YP520:
R-Y934*
R-YP520YP523 * YP524 * YP525... 4 SNPs
.....R-YP520* id:HG03743STU
.....R-YP526YP530 * YP527 * YP528... 2 SNPs id:HG03750STU
http://yfull.com/tree/R-Y934/