R1a1a STR111 tree

Today, I want to update the STR111 tree of R1a1a that I have presented earlier here and here. I have now collected a much larger number of samples, which makes the tree more complex. Since a lot of individuals in this tree are in the R1a1a and subclades project, I added the group name of all these individuals. Of course, this tree is based on STR data only, so the initial branching of the different SNPs can be off, e.g. Z93+ is split into multiple clusters. However, some clusters are fairly robust in terms of structure and subbranching.

Rectangular tree of R1a1a STR111 (as pdf):

Polar tree of R1a1a STR111 (as pdf):

Due to the size of the tree I split the tree into pieces. Let's look into the details:
As mentioned the initial branching in the STR111 tree is pretty messy with no clear clustering but overlapping of various SNPs. At least N86494 from Belarus with M417- ended up in the pole position. Besides very small clusters from Ireland and England and a mix of Z93+ individuals (L657+ and L657-) from Central Asia and Middle East, the first clear cluster in this tree is "4. A2. Z283+ M458+ L260+ Central European branch, West Slavic subclade", most individuals are from Poland.

Next, the narrow "9. E1. Z93+ Z94+ Z2122+ "Ashkenazi-Levite" cluster" emerges. The closest isolate individual to this R1a1a Ashkenazi-Levite cluster is the Iraqi Kurdish individual H1483. I described this close genetic proximity in some earlier posts (here and here) when STR data were still very limited, but now we have STR111 data of H1483 confirming the predicted proximity.
Other close matches to the Ashkenazi-Levite cluster are 116213 from Palestine and two Scots (162927 and 221184).

On the next two parts, we have the Z280+ individuals forming a lot of clusters, one of them is the cluster "6. J1. Z280+ CTS1211+ (CTS3402+) Southern Baltic type". Within this large mega-cluster a few Z93+ isolated individuals and isolated clusters sneaked in, e.g. the "9. C7. Z93+ Z94+ L657- Z2122-, Arabic II" cluster, and the "9. C5. Z93+ Z94+ L657-(?), Bashkirs" cluster.

Next, we have no real clustering but a mess...

Next, the nice "Z280+ CT1211+ (CTS3402-) Carpathian cluster" comes up with a clear cut between P278+ and P278- individuals.

Next, the second group of M458+ individuals appears (L260- only) forming a nice cluster. This "Z283+ M458+ L1029+ L260-" is a Central European branch.

Next, we have a mix of individuals from both major branches (Z93 and Z283) followed by CTS3402+ individuals from Eastern Europe.

Next, we have a mix, no real clustering.

Next, we have Z284+ individuals forming a cluster:

Next, we have the L664+ individuals forming a large nice cluster. Based on the current R1a SNP tree, L664+ was a very early split.  Most of these individuals are from the UK and Ireland.

Next, the Z92+ cluster emerges with people mostly from Eastern Europe.

Next, we have the Z284+ individuals forming two clusters, the Z288+/Z287+ cluster and a cluster of Z287- individuals.

Finally, the last cluster in this this tree: Z284+, L448+.

If you are getting confused by all these abbreviations, then this is okay. For clarification, I can recommend this schematic tree made by Michal.
http://eng.molgen.org/download/file.php?id=237&mode=view

Haplogroup J1 (L222.2-) tree STR111

Today, I want to present the haplogroup J1 tree with STR111 data. Most of the tested individuals are from the Arabian peninsula, form a narrow cluster and have the haplogroup J1b2b1 (aka J1c3d2) L222.2+, which could be seen in my previous J1 tree. I excluded those L222.2+ from the new tree, and Roberto Raciti helped me collecting all J1 L222.2- individuals with STR111 data (N=179).

Here are the results.

I highlighted Anatolian cluster in cyan to turquoise.
I highlighted Jewish clusters in orange to brownish.
I highlighted Arab clusters in pink to purple.

Rectangular tree of J1 L222.2- STR111 (as pdf):

Polar tree of J1 L222.2- STR111 (as pdf):

Edit 02/26/13:
I added six more individuals (N=185).
Rectangular tree of J1 L222.2- STR111 (as pdf):

Polar tree of J1 L222.2- STR111 (as pdf):

 

Edit 03/27/13:
I added sixteen more individuals (N=201).
Rectangular tree of J1 L222.2- STR111 (as pdf):

Polar tree of J1 L222.2- STR111 (as pdf):

Haplogroup T STR111 tree

Today, I want to present the STR111 tree of haplogroup T, and I used the same method as before.

The number of individuals that tested all 111 STR values is fairly small (N=66). Still, I think that some clades are clearly visible, even without using any SNP information.

The nomenclature at FTDNA is based on ISOGG 2011, however, not exactly, e.g. L453, L454 are not labeled as T1 only, not as T1a:

T   L206, L445, L452, L455, M184/Page34/USP9Y+3178, M193, M272, Page129
•     T*   -
•     T1   M70/Page46, Page78
•    •     T1*   -
•    •     T1a   L162/Page21, L299, L453, L454
•    •     •     T1a*   -
•    •     •     T1a1   L208/Page2
•    •     •    •     T1a1*   -
•    •     •    •     T1a1a   M320
•    •     •    •     T1a1b   P77
•    •     •    •     T1a1c   P330
•    •     •    •     T1a1d   P321
•    •     •    •     •     T1a1d*   -
•    •     •    •     •     T1a1d1   P317
•    •     T1b   L131
•    •     •     T1b*   -
•    •     •     T1b1   P322, P328
•    •     •    •     T1b1*   -
•    •     •    •     T1b1a   P327

Rectangular STR111 tree of haplogroup T (pdf version):

Polar STR111 tree of haplogroup T (pdf version):
 

Roots of Haplogroup R1b: STR111 tree

Today, I want to present the STR111 tree of haplogroup R1b, and I used the same method as before.
Due to the large number of individuals having haplogroup R1b I decided to focus only on the roots of this haplogroup. This is the biggest tree I created so far with a total of 1141 individuals.

Most of these individuals are from the UK and Ireland.

Rectangular tree of haplogroup R1b root (pdf version)
Polar tree of haplogroup R1b root (pdf version)

Next, I decided to exclude all samples with US or unknown ancestry, I ended up with 738 individuals, still a huge tree. Because of the size I still cannot use FITCH for a "fine-scale" tree but "only" NJ tree at SplitsTree.
 
Rectangular tree of haplogroup R1b root excluding samples with US or unknown ancestry (pdf version)
Polar tree of haplogroup R1b root excluding samples with US or unknown ancestry (pdf version)


Finally,  I decided to exclude all samples with US, UK, Irish or unknown ancestry, the vast majority of samples. I ended up with 103 individuals. Here, FITCH was used and showed a much better tree.

Rectangular tree of haplogroup R1b root excluding samples with US, UK, Irish or unknown ancestry (pdf version):

Polar tree of haplogroup R1b root excluding samples with US, UK, Irish or unknown ancestry (pdf version):

Haplogroup J2 STR111 tree

Today, I want to present the STR111 tree of haplogroup J2, and I used the same method as before.

 In a previous attempt I analyzed 95 J2 individuals with STR111 data. The new trees are based on 223 individuals.
The nomenclature is based on ISOGG 2010:

   J2   M172, L228
•      •       J2*   -
•      •       J2a   M410, L152, L212
•      •       •       J2a*   -
•      •       •       J2a1   (not currently in use by ISOGG)
•      •       •       J2a2   M340
•      •       •       J2a3   P279
•      •       •       J2a4   DYS413≤18, L26/S57, L27
•      •       •      •       J2a4*   -
•      •       •      •       J2a4a   M47, M322
•      •       •      •       J2a4b   M67/S51
•      •       •      •       •       J2a4b*   -
•      •       •      •       •       J2a4b1   M92, M260
•      •       •      •       •      •       J2a4b1*   -
•      •       •      •       •      •       J2a4b1a   M327
•      •       •      •       •       J2a4b2   M163, M166
•      •       •      •       •       J2a4b3   L210, L218, L227
•      •       •      •       J2a4c   M68
•      •       •      •       J2a4d   M319
•      •       •      •       J2a4e   M339
•      •       •      •       J2a4f   M419
•      •       •      •       J2a4g   P81   
•      •       •      •       J2a4h   L24, L207.1
•      •       •      •       •       J2a4h*   -
•      •       •      •       •       J2a4h1    L25
•      •       •      •       •      •       J2a4h1*   -
•      •       •      •       •      •       J2a4h1a    DYS445≤7
•      •       •      •       •      •       •       J2a4h1a*   -
•      •       •      •       •      •       •       J2a4h1a1   L70
•      •       •      •       •      •       •      •       J2a4h1a1   -
•      •       •      •       •      •       •      •       J2a4h1a1a   M137
•      •       •      •       •      •       •      •       J2a4h1a1b   M289   (location under DYS445≤7 uncertain)
•      •       •      •       •      •       •      •       J2a4h1a1c   M318
•      •       •      •       •      •       J2a4h1b    L192.2
•      •       •      •       •      •       •       J2a4h1b*   --
•      •       •      •       •      •       •       J2a4h1b1   L271
•      •       •      •       •      •       J2a4h1c   L243
•      •       •      •       •      •       J2a4h1d   L254
•      •       •      •       •       J2a4h2   M158   (location under L24 uncertain)
•      •       •      •       J2a4i   L88.2, L198
•      •       J2b   M12, M102, M221, M314
•      •       •       J2b*   -
•      •       •       J2b1   M205
•      •       •       J2b2   M241
•      •       •      •       J2b2*   -
•      •       •      •       J2b2a   M99
•      •       •      •       J2b2b   M280
•      •       •      •       J2b2c   M321
•      •       •      •       J2b2d   P84
•      •       •      •       J2b2e   DYS455≤9


Rectangular STR111 tree of haplogroup J2 (pdf version):

Polar STR111 tree of haplogroup J2 (pdf version):

The light green cluster is Jewish. Based on the ISOGG 2010 nomenclature these individuals have the haplogroup J2a4b1 (M92, M260); in the latest ISOGG 2012 nomenclature M92, M260 is named as J2a1b1. 

Edit:
Here is a smaller image file of the polar tree:

 

Haplogroup G STR111 tree

Today, I want to present the STR111 tree of haplogroup G, and I used the same method as before.

Haplogroup G is quiet common in the Caucasus region and neighboring region, however, it also reached Europe in ancient times. The most famous European individual with haplogroup G is Ötzi the Iceman who lived 3,300 BCE in South Tyrol.
Different subbranches can be found in presented trees below:
- G1 (blue) is dominating in the Middle East
- G2c (purple) is a very narrow branch with very little STR variability. Haplogroup G2c is mostly found in Eastern Europe (Poland, Lithuania, Belorussia)
- G2a1a (dark yellow) is dominated by individuals from North Ossetia and Georgia (probably South Ossetia). Joseph Stalin has this haplogroup.
- G2a3b1 (orange) is the most commonly tested subbranch of haplogroup G. G is found from Caucasus to Ireland and from Caucasus to the Arabian Peninsula.

Rectangular STR111 tree of haplogroup G (pdf version):

Polar STR111 tree of haplogroup G (pdf version):

Radial STR111 tree of haplogroup G (pdf version):

Contrary to others, conclusions based on haplotype trees, even at STR111 level, are mostly erroneous and heavily influences by subjective believes. Sometimes, these trees do not fit perfectly with haplogroups, sometimes they do. I don't want to participate in such guesstimates, I let the trees speak for themselves, and most of my comments are primarily descriptive.

Haplogroup I STR111 tree

Today, I want to present the STR111 tree of haplogroup I, and I used the same method as before. Again, most of the individuals are European but there also some individuals from Turkey (Tur-), Iran (Irn-), Iraq (Irq-), Armenia (Arm-). A total of 862 individuals are included in the trees presented below.

Due to the size of the tree details can be only seen in the actual pdf files.

Rectangular STR111 tree of haplogroup I (pdf version):

Polar STR111 tree of haplogroup I (pdf version):

Radial STR111 tree of haplogroup I (pdf version)

Haplogroup N STR111 tree

Today, I want to present the STR111 tree of haplogroup N, and I used the same method as before. Again, most of the individuals are European (mostly haplogroup N1c1). A total of 124 individuals are included in the trees presented below.

Rectangular STR111 tree of haplogroup N (pdf version):

Polar STR111 tree of haplogroup N (pdf version):

Radial STR111 tree of haplogroup N (pdf version):

Haplogroup Q STR111 tree

Today, I want to present the haplogroup Q STR111 tree. To do so I used the same method as before. The number of individuals is fairly small (N=47) and the ethnic background of these tested individuals is mostly European, so the whole diversity of haplogroup Q is not covered. However, some observation can be still made.
The clearest split within haplogroup Q can be seen between haplogroup Q1a and Q1b, and this split is visible with using STR111 data only.

Most of the Q1b individuals from Europe have paternal Ashkenazi ancestry, and they form a cluster (red). The Huff/Hoff family from the Netherlands (purple) are represented with multiple individuals (Unk-191247, Unk-159126, Net-166843, Net-133381, Unk-127754, Net-169897, Ger--81111, Net-189374, Unk-165855, Unk-156072). From the Huff individual Unk-156072 we know that they have haplogroup Q1b1a. In this tree the Huff/Hoff family from the Netherlands is forming the second cluster within Q1b.
Contrary, haplogroup Q1a2-M25 does not show a clear clustering, which highlights its age. 

Haplogroup Q1a3a1 (cyan-blue) is "Native American". All Q1a3a1 individuals in the presented trees below are from Northern America.

Rectangular STR111 tree of haplogroup Q (pdf version):

Polar STR111 tree of haplogroup Q (pdf version):

Radial STR111 tree of haplogroup Q (pdf version):

Haplogroup Tree J1 STR67

Today, I want to present haplogroup J1 tree with STR67 data. I used the same method as before. The goal was to get a tree for the oldest branches of the J1 haplogroup.
To do so I only used individuals that are labeled as J1 (not J1c, J1b, etc.) at FTDNA. In a lot of cases SNPs downstream of J1 were not tested, so I had to help myself: I excluded all individuals that show high similarity with known J1c and J1b individuals. Then, I generated the first tree with 200 individuals.

Polar tree of haplogroup J1 (excluding known J1b and J1c individuals):

J1 is split into two parts: the Arabian Peninsula (highlighted in magenta) and the rest. My assumption is that all these individuals from the Arabian Peninsula have the haplogroup J1c3d2 L222.2+ or at least J1c but they were just not tested for it.

Next, I excluded those individuals, I repeated the analysis with the remaining individuals.

1. Rectangular tree of haplogroup J1:

 


2. Polar tree of haplogroup J1:

Note:
The individuals from Iran (Irn-187962), Iraq (Irq--92829) and Turkey (Tur-191398,  Aintab, Turkey) are Assyrians. All other individuals from Iran and most individuals from Turkey (Tur-...) are actually Armenians. Unfortunately, no known Kurd is included in this analysis but based on the names there is one individual from Turkey (Tur-221845, Ahmed) that is Muslim and thus, not an Armenian or Assyrian, so he could be a Kurd.

Resume:
The oldest branches of haplogroup J1 can be found in Northern Mesopotamia and Eastern Anatolia. 

Haplogroup J1 tree STR111

Edit 09/12/2012:
I updated this post to make it shorter/easier for readers.

Today, I want to present the haplogroup J1 tree with STR111 data. I used the same method as before. Most of the individuals in this tree are from the Arabian peninsula and have the haplogroup J1b2b1 (aka J1c3d2) L222.2+. Some of them did not test for L222.2 but I am pretty confident about this. Based on the tree I predicted the haplogroups of some others.

Unfortunately, there is no Kurdish data included in this tree but we can assume that most Kurds with J1 belong to the same subclade as their closest neighbors, i.e. J1* M267. Of course, this has to be confirmed.

Actually, one individual in this figure is definitely from Iraqi Kurdistan: Irq---92829 is an Assyrian of Erbil :-)

I know of one Kurd of Sharif descent that is J1b2b. Unfortunately, he has only STR67 analyzed, so I cannot include him in the STR111 trees presented below. However, he is grouped with 100329 (unknown origin) and M4284 (from UAE) in the FTDNA J Haplogroup Project, so he would be close to these in the tree, and both 100329 and M4284 are at the root of the very large J1b2b branch (The previous name of J1b2b was J1c3d; at 23andme it is called J1e; details about the name changes can be found at ISOGG).

Color code:
J1 M267 Z1834-, Z1842- grey ("oldest" branch)
J1 M267 Z1842+ light blue
J1a M365.1 red (only one individual: Antonio Gomes 1635, Milhazes, Barcelos, Portugal [Por---73612]) 
J1b* L136  light green
J1b2* P58 dark green (clover)
J1b2b* L147.1 blue
J1b2b* Jewish Cohanim Cluster orange
J1b2b*  L859+ yellow
J1b2b1 L222.2+ purple    


Here are the results.
Rectangular tree of J1 (as jpg and as pdf):

Polar tree of J1 (as jpg and as pdf):

Based on this STR111-based tree the history of J1 is much clearer. 

1. The ancestral region of J1 is Caucasus, Northern Mesopotamia or Eastern Anatolia.
2. There is an early split of J1 into two branches.


Edit 09/24/12:
Rob1 (eng.molgen.org user) helped me collecting more J1 STR111 data. The new tree has a total of 313 users (see below). Three Jewish clusters emerged in the STR tree, all three clusters are highlighted in light orange, orange, and dark orange. Arab clusters within the blue J1b2b* L147.1 area are highlighted in light brown, brown, dark brown, and asparagus green. The greenish Arab cluster is at the root of the J1b2b1 L222.2+ purple cluster. The most obvious cluster within the J1b2b1 L222.2+ purple cluster is Bany Zaid cluster (highlighted in red).

Edit 09/30/12:
Iyyovi (eng.molgen.org user) asked me to upload pdf versions of the latest J1 rectangular and polar tree.
pdf polar tree
pdf rectangular tree

Haplogroup J2 tree STR111

Today, I want to present the haplogroup J2 tree with STR111 data. I used the same method as before (The annotation is not ready...)

Here are the results.

1. Rectangular tree of haplogroup J2:

2. Polar tree of haplogroup J2:

Edit:
A better J2 tree.

Whole Genome Analysis of Kurds (930K SNPs) Part 1

Today, I want to present my first approach to analyze the whole genome of 16 Kurdish participants and their genetic relationships based on 930K SNPs. Others analyzed Kurds, too, but they focused on the SNPs that could be compared to raw data of scientific data. I used all available SNPs from chromosome 1-22. Additionally, measured the distance of two individuals by counting the SNPs that are completely different for both alleles, e.g. AA vs CC or AA vs TT but not AC vs AA. About 6.1% (5.7%-7.3%) of the SNPs between Kurds are completely different.
I visualized these results by using a rooted ReticulateNetwork (EqualAngle180) from SplitsTree.

It is clearly visible that KD011/KD012 and KD10/KD014 are closely related. Interestingly, people from the Dersim region (Alevi Kurmanji and Zaza) are the closest to the root of the network of the Kurds.
As you can see the other differences aren't that great this is why I zoomed into the center (see below).

 Most of the cross-connections show how these individuals are distantly related to each other.

Dodecad K12b visualization:

I used the same visualization method (ReticulateNetwork (EqualAngle180) from SplitsTree) for the adjusted distances of Dodecad K12b ADMIXTURE results. The goal is to compare the approach presented above with ADMIXTURE Euclidean distances.

ADMIXTURE is "annotating" and grouping the SNPs into a defined number of components and then it compares the components, not the SNPs themselves. Thus, ADMIXTURE cannot "see" shared DNA segments==> ADMIXTURE does not pick up that KD011 and KD012 are closely related; it also does not pick up that KD010 and KD014 are closely related.
However, ADMIXTURE can "see" overall similarities in the genome and can group based on that. Again, people Alevi Kurmanji and Zazas are the closest to the root of the network of the Kurds.