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 E STR111 tree

Today, I want to present the haplogroup E tree with STR111 data. I used the same method as before. Most individuals belong the subbranch E1b1. Two individuals from Poland seem to be outliers. They show clear differences in their STR values (e.g. DYS532=9) to other E1b1 individuals.
STR values are mostly in agreement with the SNP status making the presented STR trees a nice tool to get an overview over the variety of haplogroup E1b1. However, some STR values of neighboring SNPs are so close to each other that no clear STR clustering is visible (e.g. E1b1a, E1b1a7a and E1b1a8a).

So far as I know no Kurd is included in this tree but there is one Alevi Kurmanji Kurd from Dersim (KD002) with haplogroup E1b1b1c1a-M84 (dark blue).
Cinnioglu et al, 2004 described two types of haplogroup E in Eastern Anatolia: E1b1b1c1-M34 (light blue) and E1b1b1a1-M78 (pink); underlying SNPs were not analyzed.


Rectangular STR111 tree of haplogroup E (pdf version):

Polar STR111 tree of haplogroup E (pdf version):

Radial STR111 tree of haplogroup E (pdf version):

mtDNA Haplogroup H5

The interesting thing about the Kurdish individual with the H5a1 haplogroup is that the mtDNA contains SNPs that are characteristic for H5a iand H5b. I discovered it by using the mtDNA haplogroup predictor and GenBank data summarized by Ian Logan:

H2a2a1(rCRS) ⇨ 263G ⇨ H2a2a ⇨ 8860G 15326G ⇨ H2a2 ⇨ 750G ⇨ H2a ⇨ 4769G ⇨ H2 ⇨ 1438G ⇨ H ⇨ 456T ⇨ H5'36 ⇨ 16304C ⇨ H5 ⇨ 4336C ⇨ H5a ⇨ 15833T ⇨ H5a1 ⇨ 3397G 5471A

The definition of mtDNA haplogroup H5b is having a mutation from G to A at postion 5471, a.k.a. G5471A (or short 5471A). Other mtDNA haplogroups with this G5471A mutation are HV7 and N1b. To summarize, this mutation occurred multiple times during human evolution.

Another thing that effects the the midpoint and thus the outcome of the analysis are repeating mtDNA samples in the tree, so I am excluding them, too.

In the H5 branch I am excluding these because they are exactly like [HM625680 Kloss]:
GQ983083(Italy) Santoro
GQ983085(Italy) Santoro
GQ983086(Italy) Santoro
GQ983094(Italy) Santoro

In the H36 branch I am excluding these because they are exactly like [FJ348166 Irene]:
FJ348167 Irene
FJ348168 Irene
FJ348169 Irene

In the H36 branch I am also excluding these because they are exactly like [FJ348151 Irene]:
FJ348152 Irene

 In Figtree, I generated rectangular tree of H5:

Same data of H5 as polar tree:

From the first look at the data, it seems like that the root European H5a originated in the Middle East (bright yellow), which is in agreement with ancient DNA data.

From Wikipedia:

H5 has been dated to around 11,500 BP (9500 BC).[5] It appears to be most frequent and diverse in the Western Caucasus, so an origin there has been suggested, while its subclade H5a appears European.[6] However samples of mtDNA with T16304C in the HVR1 region have been found in four individuals of around 6800 BC from the Pre-Pottery Neolithic B site of Tell Halula, Syria,[7] suggesting that H5 may have arrived in the Caucasus with farmers from the Near East.

   This blunt conclusion needs more thoughts. I will update it.

mtDNA Haplogroup H5a1

Today, I want show some data about mtDNA haplogroup H5a1 because there is a Kurdish individual with H5a1 in this Kurdish DNA project.

I analyzed the phylogeny of this haplogroup by using fully sequenced and published mtDNA data from GenBank.

To do so I first downloaded the data from GenBank, then I used CLUSTALW, (mode: slow accurate pairwise alignment) to align the sequences and create a rooted phylogenetic tree with branch length (UPGMA). The data were pasted into CLUSTALW in the Fasta format.

I realized that all the data of Herrnstadt et al. 2002 are lacking the first 577 nucleotides, which is messing up the position of Herrnstadt samples in the trees/network and is messing up the position of the rest. The same effect can be seen with the two samples of Kivisild et al.; they are lacking 236 nucleotides. Thus, I excluded these samples.


Rooted phylogenetic tree with branth length (UPGMA) of H5a1:

The nice thing about CLUSTALW is that it also generates a "dnd file" and an "aln file" of the alignment.

The dnd file can be opened with the Figtree software. In Figtree, I generated another tree of H5a1:

The aln file can be opened with the Splitstree software. In Splitstree4, I generated a network (Convex Hull) of H5a1:

H5a1a (T721C mutation): three individuals in these trees have this mutation [AF346975(Dutch) Ingman; Q983087(Italy) Santoro; HQ659693(Polish) FTDNA]


H5a1b (G11719A mutation): two individuals in these trees have this mutation [AY495167(European) Coble; AY495176(European) Coble]

H5a1c1a (C4095T  G13194A G9055A A2851G mutations): only one individual in these trees has these mutations [HQ663878(Danish) FTDNA]

H5a1d (A8803D mutation): only one individual in these trees has this mutation [AY495171(European) Coble]

H5a1e (A16166G mutation): two individuals from Finland belong to the H5a1e branch [AY339431(Finland) Moilanen; AY339432(Finland) Moilanen].

H5a1f (T961C mutation): one individual in these trees has this mutation [ JN646689(Polish) FTDNA]

H5a1g1 (T16172C, A444G, G9804A, T16311C mutations): two individuals in these trees have these mutations [EU294323 FTDNA; HQ645111(English) FTDNA]. Since HQ645111 has the additional  T1284C and A7517G mutations it belongs to H5a1g1a.

Note: In the Finland DNA project I found one individual (N48161 Mary Anne Bodle, b.1791, Plumstead, Kent) that originated in England and has the same mutations of H5a1g1 HV regions, i.e.  A444G, T16172C, T16311C.

H5a1k (T12864C): two individuals have this mutation [AY495170(European) Coble, GQ983064(Italy) Santoro]


H5a1p (T16093C): three individuals have this mutation [FJ966912 FTDNA, GQ983075(Italy) Santoro, GQ983084(Italy) Santoro]

Cultural Distance Calculator Part2

This is a follow-up for the Cultural Distance Calculator:

Since there are some cultural data available I decided to use phylogeny software to present the results. This helps to detects groups of population that have similar cultural values and behavior.  In order to visualize the data of the first 4 dimensions.First, I calculated a distance matrix for all populations of the "Old World" (N=69). Then, I had to adjust the IDs to 10 digits to prevent malfunction of the Fitch software. In Fitch, I used 10 randomized runs to improve the results.

The tree of "Old world" cultures:
Europe: red
Middle East and North Africa: green
Asia: green asparagus
New World "Latin America": brown
New World "English-speaking": grey 
Pacific: pink
Africa: black

Some of the surprising and interesting observations:

1. Scandinavians form one cultural cluster.
2. Australia, USA, Canada, New Zealand and South Africa are in the British/Irish cultural cluster.
3. The closest to British/Irish cultural cluster are Central Europeans and Israelis.
4. The "Catholic Cluster" is formed by Argentina, Spain, France, Belgium, Poland, and Malta.
5. The "Arab World Cluster" (Iraq, Saudi-Arabia, UAE, Kuwait) shows cultural similarities to some Latin-Americans (Guatemala, Panama, Surinam, Mexico, Brazil) and some East Europeans, mostly Orthodox Christians (Russia, Serbia, Romania)
6. Culturally, Turkey is more similar to Balkan people (Bulgaria, Croatia) than to the Middle East.
7. Culturally, Albania is more similar to Ecuador, Colombia and Venezuela than to the Balkan
8. Some European countries (Portugal, Greece, Slovenia) form a cultural cluster with Latin Americans (Uruguay, Chile, Costa Rica, El Salvador, Peru) and South Korea. Egypt is not far away from that cluster.
9. Singapore, Hong Kong, China, and Vietnam on one side, and Philippines, Malaysia, and Bhutan on the other side form two closely related clusters.
10. Dominican Republic forms a cultural cluster Ethiopia and Kenya.
11. Culturally, Nepal is more similar to some African countries (Malawi, Zambia, Namibia, Tanzania, Sierra Leone, Senegal)
12. Honduras, Indonesia and the Fiji Islands form a cultural cluster.
  

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.