The color of the eyes: 7 HERC2 variants in the Eurasian gene pool

In my previous post I briefly described the presence of 7 different HERC2 haplotypes in the Kurdish gene pool. Today, I want to show HERC2 haplotype data of populations from Eurasia. The blogger Davidski provided me with the raw data for HERC2 from the Human Genome Diversity Project (HGDP) and similar databases. I focused on Eurasian populations that had information for the following SNPs: rs12913832, rs7183877, rs11635884, rs11636232, rs8043281, rs6497284, rs8028689, rs9302376, rs16950960, rs8039195, rs16950987, and rs1667394. I added the Kurdish data that I collected.

In most Eurasian individuals I was able to explain their HERC2 genotypes by combining 2 of the 7 HERC2 haplotypes, however, in a few individuals the data set was not complete, in a few individuals other haplotypes must have been present but could not determined. Those data are labeled as "not determined".

Please take the percentages with a grain of salt because the number (N) of tested individuals per population is low, sometimes with only N=1, these data should be ignored.

Reminder: The phenotype of HERC2 haplotype#1 and #2 are light eye colors.

The annotated data can be seen here.

	N	#1	#2	#3	#4	#5	#6	#7	Not Determined
Abhkasian	18	17%	6%	22%	14%	17%	22%	3%	0%
Adygei	14	25%	4%	14%	4%	21%	32%	0%	0%
Altaians	12	0%	0%	13%	0%	13%	17%	0%	58%
Armenian	27	20%	2%	17%	9%	2%	9%	4%	37%
Ashkenazy_Jews	21	31%	14%	10%	2%	12%	5%	2%	24%
Balkar	16	38%	6%	13%	9%	22%	9%	3%	0%
Balochi	15	10%	3%	10%	17%	23%	23%	7%	7%
Bedouin	40	10%	0%	19%	14%	1%	19%	15%	23%
Belorussians	7	36%	64%	0%	0%	0%	0%	0%	0%
Bengali	1	50%	0%	50%	0%	0%	0%	0%	0%
Brahmins_TN	9	6%	0%	11%	6%	6%	17%	11%	44%
Brahui	20	3%	0%	13%	10%	20%	13%	3%	40%
Bulgarian	13	12%	4%	12%	0%	0%	4%	0%	69%
Burusho	25	10%	8%	16%	0%	12%	14%	4%	36%
Buryats	15	7%	0%	10%	0%	57%	23%	3%	0%
Cambodian	10	0%	0%	25%	10%	30%	25%	0%	10%
Chamar	9	6%	0%	33%	11%	0%	11%	17%	22%
Chechen	18	31%	11%	14%	3%	19%	22%	0%	0%
Chenchus	4	0%	0%	0%	0%	0%	0%	0%	100%
Chukchis	11	0%	0%	41%	0%	45%	9%	5%	0%
Chuvash	16	28%	31%	19%	0%	13%	6%	3%	0%
Cochin_Jews	3	0%	0%	17%	0%	17%	33%	0%	33%
Cypriots	12	33%	0%	21%	13%	17%	13%	4%	0%
Dai	10	0%	0%	35%	0%	10%	55%	0%	0%
Daur	9	0%	0%	17%	0%	56%	28%	0%	0%
Dharkars	8	0%	0%	25%	6%	31%	19%	19%	0%
Dolgans	6	0%	0%	25%	0%	50%	25%	0%	0%
Druze	20	18%	0%	3%	3%	8%	13%	3%	55%
Dusadh	6	0%	0%	25%	0%	25%	8%	8%	33%
Egyptians	11	23%	0%	18%	18%	14%	18%	9%	0%
Erzya	9	39%	56%	0%	0%	6%	0%	0%	0%
Evenkis	11	0%	0%	32%	0%	45%	23%	0%	0%
French	27	31%	30%	19%	4%	6%	11%	0%	0%
French_Basque	21	14%	24%	19%	7%	26%	10%	0%	0%
Georgians	14	46%	0%	7%	4%	18%	21%	4%	0%
Gond	2	0%	0%	25%	0%	0%	25%	0%	50%
Hakkipikki	4	0%	0%	13%	0%	13%	38%	13%	25%
Hazara	17	6%	0%	26%	3%	29%	26%	3%	6%
Hezhen	7	0%	0%	43%	0%	36%	21%	0%	0%
Hungarians	18	17%	50%	14%	0%	14%	6%	0%	0%
Iranian_Jews	4	13%	0%	13%	0%	0%	63%	13%	0%
Iranians	16	3%	6%	28%	3%	13%	28%	13%	6%
Iraqi_Jews	9	17%	0%	28%	17%	11%	28%	0%	0%
Jordanians	19	13%	8%	29%	5%	13%	21%	11%	0%
Kanjars	7	0%	0%	14%	0%	14%	64%	7%	0%
Kargopol_Russian	25	36%	46%	8%	2%	4%	4%	0%	0%
Karitiana	6	33%	0%	17%	0%	33%	0%	0%	17%
Kol	14	0%	0%	36%	4%	21%	25%	14%	0%
Koryaks	10	0%	0%	40%	0%	50%	0%	10%	0%
Kshatriya	7	0%	0%	29%	0%	29%	43%	0%	0%
Kumyk	13	35%	12%	15%	0%	19%	12%	0%	8%
Kurd	26	19%	4%	19%	15%	21%	17%	4%	0%
Kurmi	1	0%	0%	0%	0%	0%	0%	100%	0%
Kurumba	3	33%	0%	17%	0%	33%	0%	17%	0%
Lambadi	1	0%	0%	50%	0%	0%	50%	0%	0%
Lebanese	4	13%	0%	38%	38%	0%	13%	0%	0%
Lebanese_Christian	24	31%	6%	15%	10%	4%	19%	6%	8%
Lebanese_Druze	23	17%	0%	28%	11%	13%	13%	13%	4%
Lebanese_Muslim	25	14%	8%	14%	12%	12%	32%	8%	0%
Lezgins	16	19%	3%	22%	6%	22%	25%	3%	0%
Lithuanians	10	35%	60%	0%	0%	0%	5%	0%	0%
Makrani	20	10%	3%	18%	8%	33%	20%	5%	5%
Malay	87	1%	0%	22%	13%	28%	29%	5%	2%
Miaozu	10	0%	0%	25%	0%	25%	50%	0%	0%
Moksha	5	30%	50%	10%	0%	0%	10%	0%	0%
Mongola	10	0%	0%	35%	0%	25%	30%	0%	10%
Mongolians	9	0%	0%	28%	0%	50%	11%	0%	11%
Mumbai_Jews	4	13%	0%	25%	0%	0%	0%	38%	25%
Muslim_India	5	10%	0%	20%	40%	0%	20%	10%	0%
NAN_Melanesian	10	0%	0%	20%	0%	0%	15%	65%	0%
Nganassans	9	0%	0%	28%	0%	56%	11%	6%	0%
Nihali	1	0%	0%	0%	0%	50%	50%	0%	0%
Nogay	14	39%	0%	21%	4%	21%	11%	4%	0%
North_Italian	13	42%	27%	8%	4%	8%	8%	4%	0%
North_Kannadi	4	25%	0%	25%	38%	0%	13%	0%	0%
North_Ossetian	13	31%	15%	35%	8%	4%	8%	0%	0%
Orcadian	11	27%	41%	5%	5%	18%	5%	0%	0%
Oroqen	9	0%	0%	17%	0%	61%	22%	0%	0%
Palestinian	31	23%	0%	13%	6%	8%	26%	15%	10%
Pathan	21	19%	2%	14%	7%	24%	17%	17%	0%
Piramalai	8	0%	0%	31%	6%	25%	19%	19%	0%
Pulliyar	1	0%	0%	0%	0%	100%	0%	0%	0%
Romanians	14	29%	25%	21%	4%	14%	7%	0%	0%
Russians	5	60%	20%	0%	0%	10%	10%	0%	0%
Sardinian	24	19%	4%	40%	6%	10%	17%	0%	4%
Saudis	19	3%	0%	26%	0%	8%	13%	24%	26%
Selkups	9	39%	44%	11%	0%	6%	0%	0%	0%
Sephardic_Jews	18	25%	11%	25%	3%	11%	14%	11%	0%
She	9	0%	0%	33%	0%	11%	56%	0%	0%
Sindhi	14	4%	0%	29%	7%	14%	32%	7%	7%
Singapore_Indian	78	8%	2%	26%	4%	17%	26%	12%	6%
Spanish	11	32%	5%	32%	9%	9%	5%	0%	9%
Surui	3	17%	0%	33%	0%	50%	0%	0%	0%
Syrians	15	30%	0%	13%	3%	23%	20%	3%	7%
Tadjik	14	7%	11%	18%	7%	36%	18%	4%	0%
Tamil_Nadu	1	0%	0%	50%	0%	50%	0%	0%	0%
Tharus	2	25%	0%	25%	0%	0%	25%	25%	0%
Tibeto-Burman_Burmese	14	0%	0%	32%	18%	18%	21%	11%	0%
Tibeto-Burman_Garo	2	0%	0%	25%	0%	50%	25%	0%	0%
Tu	8	0%	0%	13%	0%	31%	44%	0%	13%
Tujia	10	0%	0%	5%	5%	45%	35%	10%	0%
Turks	19	21%	8%	29%	8%	13%	16%	5%	0%
Tuscan	8	25%	19%	6%	0%	19%	31%	0%	0%
Tuvinians	13	0%	0%	42%	0%	35%	23%	0%	0%
Ukrainian	20	43%	38%	8%	0%	8%	5%	0%	0%
Uttar_Pradesh	5	0%	0%	60%	0%	20%	20%	0%	0%
Uygur	10	10%	0%	20%	0%	35%	35%	0%	0%
Uzbeks	15	3%	13%	27%	23%	13%	20%	0%	0%
Velamas	7	7%	0%	21%	0%	43%	0%	29%	0%
Xibo	9	0%	0%	11%	0%	39%	39%	0%	11%
Yakut	20	0%	0%	40%	0%	43%	18%	0%	0%
Yemenese	7	7%	0%	14%	7%	7%	14%	21%	29%
Yemenite_Jews	15	7%	0%	27%	3%	0%	27%	10%	27%
Yizu	10	0%	0%	35%	0%	15%	40%	0%	10%
Yukaghirs	4	0%	13%	38%	0%	38%	13%	0%	0%

Unfortunately, this data set does not include many Germanic speaker populations (Austrians, Germans, Swiss). In the previous HERC2 analysis these populations showed peak frequencies for haplotype#1.

Haplotype#1 is ancestral towards haplotype#2. Peak frequencies of haplotype#2 can be found in Belorussians, Lithuanians, some Uralic language speakers from Russia (Moksha, Selkups). Interestingly, these populations show no or very little haplotype#3, the ancestral haplotype of #1 and #2.

Haplotype#3 peaks in populations of East-Siberia (Hezhen, Tuvinians, Chukchis, Koryaks, Yakut, Yukaghirs), West-Asia (Lebanese, North Ossetians, Turks, Jordanians, Lebanese Druze, Iranians, Iraqi Jews). Interestingly, in East-Siberia haplotype#3 correlates with the presence of haplotype#5 and #6. Highest frequencies of haplotype#3 in Europe can be found in Sardinia and Spain.

Edit: July 02, 2013:

I got some questions why some populations have let's say 20% Branch/haplotype #1 and #2 but not 20% of the population has light eye colors. The reasons is because haplotype 1 and 2 are recessive.
Thus, in order to get light eye colors not one but 2 copies/alleles are needed, one inherited from the father, one from the mother.
How to calculate frequency of light eyes in a population based on my presented tables (based on the Hardy-Weinberg principle):
Frequency of light eyes in a population = (%ht1 +%ht2)²

Example1: Germans have 46% ht1 and 33% ht2.
(46%+33%)²
= (0.46 + 0.33)²
= 0.79²
= 0.62
= 62%
62% of the Germans have light eye color based on the HERC2 genotype.


Related:
The color of the eyes: 7 HERC2 variants in the Kurdish gene pool 
The color of the eyes: 7 HERC2 variants in the Eurasian gene pool 
The color of the eyes: at least 17 HERC2 variants in Human gene pool

The color of the eyes: 7 HERC2 variants in the Kurdish gene pool

Today, I want to present some genetic data focusing on different eye colors of Kurds and their genetic origin. The color of the eye is mostly determined by only one SNP in the human genome, rs12913832 in the HERC2 gene.
GG at rs12913832 in the HERC2 gene results in light eyes (blue/green) eyes; AG and AA results in brown eyes.

My goal is not only look at the rs12913832 SNP itself but to determine the number of DNA segments that carry the SNP rs12913832; the goal is to determine the number of HERC2 variants (=number of different HERC2 segments) in the Kurdish gene pool. 23andme (and other companies) have a chip-based analysis approach, thus, the genetic read-out only contains data about the single SNPs but not in relation to other neighboring SNPs. The only way to determine DNA segments is to have genetic data of multiple close relatives.

Example with very short DNA segment consisting of two SNPs only:
Person A:  rs12913832=AG; neighboring SNP rs7183877=AC.
With this amount of information it is impossible to determine the two DNA segments that were inherited from father and mother of person A. Is rs12913832=A and rs7183877=A on the same DNA segment and inherited from the same parent? With this amount of data we cannot know. "Phased DNA", a new tool at gedmatch can somewhat address this question but not in all cases.
Let's say father and mother of person A have rs12913832=AG and rs7183877=AC as well. We still cannot say if rs12913832=A and rs7183877=A are on the same DNA segment.
Let's say we also know the SNP results of as sibling of person A" rs12913832=AA; neighboring SNP rs7183877=AA. Now, we can determine the DNA segments
DNA segment1: rs12913832=A and rs7183877=A
DNA segment2: rs12913832=G and rs7183877=C
Person A and both parents of person A have one copy of segment1 and one of segment2, while the sibling of personA has two copies of segment1.

This example was only based on two SNPs but it is more interesting to cover a larger DNA segment consisting of all tested SNPs of the HERC2 gene (at least all the SNPs tested by 23andme).

Having genetic data of multiple relatives I was able to determine a total 7 DNA segments of the HERC2 gene variants: two HERC2 variants correlate with light eye colors, the five other HERC2 variants of the HERC2 correlate with dark eyes.

 The SNP data of the HERC2 variants are presented in the spreadsheet.

Some observations/results:
1.
Kurdish DNA segments for light eye colors are
rs12913832=A
rs1129038=T
rs916977=C
rs1667394=T

2. Kurdish DNA segments for dark eye colors are
rs12913832=G
rs1129038=C
rs916977=C,T*
rs1667394=C,T*

*From other Kurdish SNP data we know that this correlation is always true for Kurdish DNA segments for light eye colors, always true for rs1129038, but not always for rs916977 and rs1667394 (Branch#3 for dark eye colors is also rs916977=C, rs1667394=T).

HERC2 SNP results of all tested Kurds can be described by combining 2 of the 7 HERC2 variants.

Example:
HERC2 SNPs of KD014 are a mix of Branch#1 and Branch#6.

Next, I generated a phylogenetic tree of the 7 HERC2 variants. Branch#7 is the most ancestral branch. The two branches that result in light eye colors (Branch#1 and Branch#2) are closely related and descendent from Branch#3.

The difference of Branch#1 and Branch#2 is the SNP rs11636232; the difference between these two branches and the other five branches is SNP rs12913832. With the help of ALFRED I could determine the frequency of Branch#1 and Branch#2 in several populations (assuming that there is no other HERC2 variant for light eye color):

Sorted by Branch#1:

	Branch#1	Branch#2
Brahui	2%	2%
Balochi	8%	2%
Balochi	12%	6%
Kalash	12%	16%
Sardinian	16%	4%
Palestinian	18%	3%
Burusho	18%	12%
Basque	19%	21%
Italians	25%	19%
Adygei	26%	6%
Orcadian	28%	41%
Galician	30%	17%
French	32%	30%
Russians	36%	46%
Italians	42%	27%
Swedes	42%	54%
Germans	46%	33%
Danes	52%	32%
Austrian	55%	28%
Swiss	69%	25%

 Sorted by Branch#2:

	Branch#1	Branch#2
Brahui	2%	2%
Balochi	8%	2%
Palestinian	18%	3%
Sardinian	16%	4%
Balochi	12%	6%
Adygei	26%	6%
Burusho	18%	12%
Kalash	12%	16%
Galician	30%	17%
Italians	25%	19%
Basque	19%	21%
Swiss	69%	25%
Italians	42%	27%
Austrian	55%	28%
French	32%	30%
Danes	52%	32%
Germans	46%	33%
Orcadian	28%	41%
Russians	36%	46%
Swedes	42%	54%

Edit 06/10/2013:
Maju asked for the "percentage of Kurds in each branch". With the limited number of 23andme tested Kurds (N=20) the percentages can be off.

Percentage of Kurds in each HERC2 branch

Branch#1	22.5%
Branch#2	5.0%
Branch#3	20.0%
Branch#4	10.0%
Branch#5	17.5%
Branch#6	20.0%
Branch#7	5.0%

From the few East-Europeans 23andme results of HERC2 I have seen so far I can say that East-Europeans have Branch#1, #2, #5 and #6, but not Branch#3, Branch#4 and Branch#7 (Note: Branch#3 and Branch#4 are the ancestral haplotypes of the two light eye color branches #1 and#2).
Besides Kurds, I found Branch#3 in one person from the Philippines (Branch#3 and #5), one Maltese (Branch#3 and #5), one Turk (Branch#3 and #1), and one multi-ethnic Canadian (Branch#3 and #2).
Besides Kurds, I found Branch#4 in one multi-ethnic US American (Branch#4 and #6), one Assyrian (Branch#4 and #1), and one British (Branch#4 and #2). I found one Ethiopian 23andme result that cannot be described with the 7 branches, so there might be more branches for brown eye color in Africa.

In the spreadsheet I now added all potential combinations of the 7 variants in a separate sheet.

Edit: July 02, 2013:

I got some questions why some populations have let's say 20% Branch/haplotype #1 and #2 but not 20% of the population has light eye colors. The reasons is because haplotype 1 and 2 are recessive.
Thus, in order to get light eye colors not one but 2 copies/alleles are needed, one inherited from the father, one from the mother.
How to calculate frequency of light eyes in a population based on my presented tables (based on the Hardy-Weinberg principle):
Frequency of light eyes in a population = (%ht1 +%ht2)²

Example1: Germans have 46% ht1 and 33% ht2.
(46%+33%)²
= (0.46 + 0.33)²
= 0.79²
= 0.62
= 62%
62% of the Germans have light eye color based on the HERC2 genotype.


Related:
The color of the eyes: 7 HERC2 variants in the Kurdish gene pool 
The color of the eyes: 7 HERC2 variants in the Eurasian gene pool 
The color of the eyes: at least 17 HERC2 variants in Human gene pool

R1a tree

Today, I want to update the STR111 tree of R1a1a that I have presented earlier here and here and here. For the first time I tried to implement some SNP information into the tree as well, which made the R1a1a branching much clearer but it is still not perfect. Assuming an initial branching of R1a 8000BP I also calculated the age of each node of the tree (see table below). Last but not least, I increased the number of individuals in this tree (N=547).

Rectangular tree of R1a (as pdf):

Polar tree of R1a (as pdf):

SNP	Age in years based on tree	Age in years based on STR111 variability
M420	8000	8000
SRY10831.2	7798	7907
L664	4965	4375
Z645/Z647	6117	7294
Z283	5938	6751
M458	4625	3931
L260	3598	2411
CTS11962	4013	3069
L1029	4341	3078
Z280	5614	6050
Z92	4597	3996
CTS1211	5322	5381
P278	3719	2473
CTS3402	5046	4937
L366	3079	1038
L365	4095	2041
L1280	3281	2169
Z284	5063	4688
L448	4069	2857
CTS4179	3740	2212
L176	2956	1128
Z287/Z288	4908	4499
Z93	5989	6979
Z94	5795	6900
Z2121/Z2124	5322	5319
Z2122	4124	2457
Z2123	4781	3998
L657	4729	4131
Y7	3885	2197

Due to the size of the tree I split the tree into pieces.

 

Edit May 25th 2013:

I did not use a molecular clock, I just defined the total age of the whole tree at 8000 years BP.

Example Z94:
1. First I calculated the standard deviation (STDEV) for each STR within Z94+ individuals (Note: For STDEV I only used individuals with STR111 data).
2. I calculated the sum of all STR111 standard deviations (STDEV DYS393 + STDEV DYS390 + STDEV DYS19+ STDEV DYS391 + STDEV DYS385a + STDEV DYS385b + STDEV DYS426 + STDEV DYS388 + STDEV DYS439 + STDEV DYS389i + STDEV DYS392 + STDEV DYS389ii + etc.). For Z94+ individuals sum of all STR111 standard deviations is 51.307. The sum of all STR111 standard deviations within R1a (all individuals of tree N=547) is 53.823.
3. I figured out a correlation between the sum of all STR111 standard deviations within Z94+ individuals and the relative age of the SNP (see formula below).
4. Arbitrarily, I defined the total age of the whole tree at 8000 years BP. It might be better to see the age estimates as relative age estimates, not as absolute age estimates.

Age of SNP Z94=8000/(2.8863*e^(0.0588*(sum of all STR111 standard deviations within all 547 R1a individuals)))*(2.8863*e^(0.0588*(sum of all STR111 standard deviations within Z94+ individuals)))

Age of SNP Z94=8000*(2.8863*e^(0.0588*51.307))/(2.8863*e^(0.0588*53.823))
=8000*(2.8863*2.71828^(0.0588*51.307))/(2.8863*2.71828^(0.0588*53.823))
=8000*59.0/68.4
=6900

Update 06/18/2013:

I generated a Z282+* STR67 tree.

Radial tree:

Rectangular tree:

Kurdish mtDNA data IX

Just an update (N=97):


1x B4b1a (Kurd from Turkey) 
1x C4b (=C4b+A248G, A14566G, T16519C, A249A (not deleted)) (Alevi Kurmanji)
1x G2a (=G2a+T16172C) (Sorani)
1x H CRS (Kurds from Iran; Quintana-Murci et al., 2004)
6x H (Kurds from Georgia; Comas et al., 2000)
2x H with T16311C  (Kurds from Georgia; Comas et al., 2000)
1x H with C16218T (=H1ag1a or H1aq1 or H20) (Kurds from Georgia; Comas et al., 2000)
1x H with C16192R, C16261T (similar to: JN415470(Italy-LHON) Achilli Haplogroup H 19-AUG-2012 (Kurds from Georgia; Comas et al., 2000)
1x H5'36 (Kurd from Turkey)
1x H5  16051G, 16255A, 16304C, 16319A, 16327T, 263G, 315.1C, 456T (Kurds from Iraq; Al-Zahery et al., 2012)   
1x H5a1 (H5a1+T16304G, A3397G, G5471A) (G5471A usually in H5b) (Sorani)
1x H13a2b2 (Alevi Kurmanji from Dersim)
1x H14b T3197C (=H14b+C4086T, A16265T) (Yezidi)
1x H14a with T16311C, C16256T, T16352C (=H14a +T16311C ) (Kurds from Georgia; Comas et al., 2000)
1x H15a1 (=H15a1+309.1C, 309.2C, 315.1C, A15316G) (Sorani; mtDNA fully sequenced here and here)
1x H15b (Sorani)
1x H15b T16086C (close to EU600353(Druze) Shlush)(Kurds from Iran; Quintana-Murci et al., 2004)
1x HV* CRS (Kurds from Iran; Quintana-Murci et al., 2004)
1x HV* 16174 (Kurds from Iran; Quintana-Murci et al., 2004)
1x HV1a1 C16067T, C16355T (=HV1a1) (Kurds from Iran; Quintana-Murci et al., 2004)
1x HV2 C16168T, T16189C, T16217C, C16287T (Kurds from Iran; Quintana-Murci et al., 2004)
1x HV14 T16311C, G4655A, T15115C (Sorani)
1x HV A73G, T391C, G16153A (Kurmanji from Zakho)
1x HV (Kurmanji from Diyarbakir (Amed)/Turkey)
1x I1a G16129A, C16168T, T16172C, 16173, C16223T (Kurds from Iran; Quintana-Murci et al., 2004)
1x I with G16129A, C16223T (Kurds from Georgia; Comas et al., 2000)
1x I1a1d with G16129A, C16223T, T16172C, T16189C, C16083T, C16355T (=I1a1d+C16083T, C16355T) (Kurds from Georgia; Comas et al., 2000)
1x I5a pre-I5a3  because G5231A, A15052G = I5a3 but still C150C, T6278T = I5a; additional   C16301T (Zaza from Dersim)
1x I5a (Zaza from Baltas/Varto, Turkey)
1x J1b C16069T, T16126C, G16145A, C16222T, A16235G, C16261T, T16311C (Kurds from Iran; Quintana-Murci et al., 2004)
1x J1b3 T1822C, A8460G, T16311C  (=J1b3+T1822C+T16311C) (Sorani)
2x J1b1b1 C16069T, T16126C, G16145A, C16261T, 16519C, A73G, A263G, C295T, 309.1C    315.1C, C462T, T489C, 523DEL, 524DEL   (very close to JF939049(Armenian)) (Kurds from Iraq; Al-Zahery et al., 2012)
1x J1b3b A73G, A263G, C295T, T489C, A750G, A1438G, A2706G, G3010A, T4216C, A4769G, C7028T, G8269A, A8460G, A8860G, A10398G, A11251G, G11719A, A12612G, G13708A, C14766T, A15326G, C15452A, T15530C, C16069T, T16126C, G16145A, C16222T, A16235G, C16261T (1/2 Alevi Kurmanji paternally, 1/2 Sunni Kurmanji maternally from Bingol, Kighi, Turkey)
1x J1b4 C16069T, T16126C, G16145A, C16222T, C16261T,  C16278T, C16287T (Kurds from Iran; Quintana-Murci et al., 2004)
1x J1c (=J1c+G185T, 4812A, C16290T, T16519C) (Alevi Kurmanji from Dersim)
1x J1c2m (old J1c2a)  C16069T, T16126C, 16148T, A73G, 185A, 228A, A263G, C295T, 315.1C, C462T, T489C, 523DEL, 524DEL  (close to JQ797801 from Romania and  JQ797802 from West-Siberia (Khanty))(Kurds from Iraq; Al-Zahery et al., 2012)  
1x J1d (=J1d+A15218G, T16519C) (Feyli, originally from Iran)
1x J1d (Kurd from Iraq)
1x J2a1a1 (=J2a1a1+A10044G, G11914A, C16264T)  (Kurd from Turkey)
1x J2b1 (Kurd from Iraq/Iran)
1x JT with T16126C, C16067T, T16311C (=JT) (Kurds from Georgia; Comas et al., 2000)
1x K1a T16093C, T16224C, T16311C (Kurds from Iran; Quintana-Murci et al., 2004)
1x K 16129, T16224C, T16311C (= K1a11 or K2b2) (Kurds from Iran; Quintana-Murci et al., 2004)
1x K with T16224C, T16311C (Kurds from Georgia; Comas et al., 2000)
2x K with T16224C, T16311C, T16093C, C16260T (=K1a1+C16260T, or K1a17a+T16093C)(Kurds from Georgia; Comas et al., 2000)
1x K with T16224C, T16311C, A16240G (=K+A16240G) (Kurds from Georgia; Comas et al., 2000)
1x K with T16224C, T16311C, A16272G (=K+A16272G) (Kurds from Georgia; Comas et al., 2000)
1x L3e5 16037G, A16041G, C16223T, A73G, C150T, A263G, 315.1C, T398C, 523DEL, 524DEL
(Kurds from Iraq; Al-Zahery et al., 2012)
1x M1a1 G16129A, 16182C, 16183C, T16189C, C16223T, T16249C, T16311C, T16359C, C16360T, T16519C, A73G, T195C, A263G, 309.1C, 309.2C, 315.1C, T489C (Kurds from Iraq; Al-Zahery et al., 2012)
1x N1b1 (=N1b1+C16176C, C1703A, C3921A, G7337A, T16519C) (Alevi Kurmanji from Dersim)
1x N1b1 with C16223T, G16145A, C16176G (=N1b1) (Kurds from Georgia; Comas et al., 2000)
1x N2a with C16223T, T16086C, G16153A, G16319A (=N2a+T16086C) (Kurds from Georgia; Comas et al., 2000)
1x R0 16519C, 16524C, A263G, 315.1C (Kurds from Iraq; Al-Zahery et al., 2012)
1x R0 16368C, 16519C, A263G, 309.1C, 315.1C (Kurds from Iraq; Al-Zahery et al., 2012)   
1x R2 with C16071T, G16145A, C16234 (=R2 +G16145A+C16234) (Kurds from Georgia; Comas et al., 2000)
1x T1 (=T1a2b+C12633T, G5460A, G11914A, T16311C, (T16519C))(Feyli)
1x T1a7 T16126C, A16163G, C16186T, T16189C, G16274A, C16294T, T16519C, A73G, A263G, 309.1C, 315.1C, A512G  (close to EU935435(Egypt) Kujanova and JQ798027 (Israel))(Kurds from Iraq; Al-Zahery et al., 2012)
1x T1b T16126C, A16163G, T16189C, T16243C, A16247G, C16294T, T16519C, A73G, 152C, A263G, 309.1C, 315.1C, 524.1A, 524.2C (Kurds from Iraq; Al-Zahery et al., 2012)
1x T2a1b2b with T16126C, C16294T, C16296T, C16256T, A16317G (=T2a1b2b +A16317G) (Kurds from Georgia; Comas et al., 2000)
1x T2b (Kurd from Turkey)
1x U1a1 A14070A, T16163C (Zaza)
1x U1a1a (Sorani) with A11467G,  A12308G,  G12372A, C285T,  T12879C,  A13104G, A14070G, G15148A, A15954C, T16249C, C2218T, G14364A, T16189C, G4991A, G6026A, T7581C, A385G, 3158.1T, G3591A, A13422G, G9575A, C2836T, G4659A, 573.1C, 573.2C, A10283G, (309.1C), (315.1C), (523-), (524-), (16182C), (16183C), (16519C) (=U1a1a; shares C2836T, G4659A mutation with Indian samples HM156682(India) Govindaraj) (fully sequenced here and here)
1x U1a1 with A16182C, A16183C, T16189C, T16249C (=U1a1) (Kurds from Georgia; Comas et al., 2000)
1x U1b C16111T, 16214A, T16249C, G16319A, C16327T, T16519C, A73G, T146C, T152C, A263G, C285T, 315.1C, 572T (Kurds from Iraq; Al-Zahery et al., 2012)
1x U2 (Alevi with Zaza ancestry)
1x U2e1a with A16051G, T152C, A508G, A3720G, A5390G, T5426C, C6045T, T6152C, A10876, T13020C, T13734C, A15907G, G16129C, T16362C, C340T, C11197T, T11732C, G7337A, A15218G, T16311C, T16519C (Sorani from Sulaymaniyah/Iraq)
1x U3 with A16343G (=U3) (Kurds from Georgia; Comas et al., 2000)
1x U3a with C150T, A14139G,  T15454C, A2294G,  T4703C,  G9266A, T6518A (flip!),  A10506G,  C13934T,  G16390A,  C2766A, 10790C, G16129A, 16257T, T16519C (Sorani from Sulaymaniyah/Iraq); (similar to HM852895(Georgian45) Schoenberg also with C2766A)
1x U3c with A16343G, C16193T, T16249C (=U3c) (Kurds from Georgia; Comas et al., 2000)
1x U3c C16193T, T16249C, A16343G, G16526A, A73G, C150T, A263G, 315.1C  (close to HM852797(Azeri34) and HM852803(Azeri42) Schoenberg)(Kurds from Iraq; Al-Zahery et al., 2012)   
1x U4 T16356C, T16519C, A73G, T195C, A263G, 309.1C, 315.1C, G499A, 524.1A, 524.2C
(Kurds from Iraq; Al-Zahery et al., 2012)
1x U5 T16093C, T16189C, C16270T (Kurds from Iran; Quintana-Murci et al., 2004)
1x U5a1 (Kurmanji from Dohuk)
1x U7 (Zaza from Turkey)
1x U7 C16069T, A16227G, C16278T, A16318C, T16359C (very close to HM852853(Turk 187) Schoenberg) (Kurds from Iran; Quintana-Murci et al., 2004)
1x U7 C16192T, A16309G, A16318T (Kurds from Iran; Quintana-Murci et al., 2004)
1x U7 T16243C, A16309G, A16318T (Kurds from Iran; Quintana-Murci et al., 2004)
1x U7 A16309G, A16318T (Kurds from Iran; Quintana-Murci et al., 2004)
1x U7 A16309G, A16318T (Kurds from Georgia; Comas et al., 2000)
1x U7a A16309G, A16318T, T16519C, A73G, C151T, T152C, A263G, 309.1C, 315.1C, 523DEL, 524DEL (Kurds from Iraq; Al-Zahery et al., 2012)
1x U8b1a1 A16066G, G16129A, C16169T, A16183C, T16189C, C16234T, T16311C (Kurds from Iran; Quintana-Murci et al., 2004)
1x U8b C16111T, T16172C, A16183C, T16189C, T16311C (Kurds from Iran; Quintana-Murci et al., 2004)
1x U8b (Feyli)
1x U8b (Zaza from Sivas, originally from Dersim) 
1x W C16223T, C16292T (Kurds from Iran; Quintana-Murci et al., 2004)
1x W3 G16153A, C16223T, C16292T, C16294T, T16519C, A73G, T152C, A189G, C194T, T195C, T199C, T204C, G207A, A263G, 309.1C, 315.1C (Kurds from Iraq; Al-Zahery et al., 2012)
1x W4a C16223T, C16292T, C16286T (Kurds from Iran; Quintana-Murci et al., 2004)
1x W6 with C16292T, C16192T, C16223T,  T16324C (=W6) (Kurds from Georgia; Comas et al., 2000)
1x X with T16189C, C16278T, C16186T (=X+C16186T) (Kurds from Georgia; Comas et al., 2000)

Related post:
mtDNA of Kurds Part I
mtDNA of Kurds Part II
mtDNA of Kurds Part III
mtDNA of Kurds Part IV
mtDNA of Kurds V
Kurdish mtDNA data VI 
Kurdish mtDNA data VII
Kurdish mtDNA data VIII

Kurdish Y-DNA Part IX

Just an update of Kurdish Y haplogroups (N=500):

Used publications:
Nebel et al., 2001
Wells et al., 2001
Stenersen et al., 2004
Nasidze et al., 2005
Gokcumen et al., 2011
Grugni et al., 2012
Malyarchuk et al., 2013

Haplogroup C
1x C-RPS4Y (Iranian Kurds in Malyarchuk et al., 2013)
1x C-RPS4Y (Zaza from Turkey in Nasidze et al., 2005)
1x C-RPS4Y (Kurmanji from Turkey in Nasidze et al., 2005)


Haplogroup E
7x E a.k.a. hg21 (Iraqi Kurds in Nebel et al., 2001)
3x E-YAP (Zaza from Turkey in Nasidze et al., 2005)
10x E-YAP (Kurmanji from Turkey in Nasidze et al., 2005) 
3x E-SRY4064 (Iranian Kurds in Malyarchuk et al., 2013)
5x E1b (Kurdish village Dogukoy*/Central Anatolia in Gokcumen et al., 2011)
12x E1b1 (Iraqi Kurds in Stenersen et al., 2004; based on Athey's Haplogroup predictor)
1x E1b1b1a1b-M78 (Iranian Kurds in Grugni et al., 2012)
1x E1b1b1c1a-M84 (Alevi Kurmanji from Dersim/Turkey)
1x E1b1b1c1a-M84 (Kurmanji from paternally Agri, Erzurum, Kars/Turkey)
1x E1b1b1c1a-M84 (1/2 Alevi Kurmanji paternally, 1/2 Sunni Kurmanji maternally from Bingol, Kighi, Turkey)
1x E1b1b1c1a-M84 (Sorani from Sulaymaniyah/Iraq)
8x E1b1b1a1-M34 (Iranian Kurds in Grugni et al., 2012)
3x E1b1b1c-V13 (Iranian Kurds in Grugni et al., 2012)

Haplogroup F
2x F-M89 (Zaza from Turkey in Nasidze et al., 2005)
10x F-M89 (Kurmanji from Turkey in Nasidze et al., 2005)
3x F-M89 (Kurmanji from Georgia in Nasidze et al., 2005)
6x F-M89 (Kurds from Turkmenistan in Nasidze et al., 2005; originally used in Wells et al., 2001)

Haplogroup G
2x G1-M285 (Iranian Kurds in Grugni et al., 2012)
1x G-M201 (Zaza from Turkey in Nasidze et al., 2005)
2x G-M201 (Kurmanji from Turkey in Nasidze et al., 2005)
8x G-M201 (Iraqi Kurds in Stenersen et al., 2004; based on Athey's Haplogroup predictor)
2x G-M201 (Iranian Kurds in Malyarchuk et al., 2013)
2x G2* (Iranian Kurds in Grugni et al., 2012)
3x G2a* (Iranian Kurds in Grugni et al., 2012)
1x G2a (Alevi Kurmanji from Turkey)
1x G2a (Kurd from Turkey)

16x G+I a.k.a. hg2 (Iraqi Kurds in Nebel et al., 2001)

Haplogroup H
1x H-M52  (Kurds from Turkmenistan in Nasidze et al., 2005; originally used in Wells et al., 2001) 
1x H-M52  (Iraqi Kurds in Stenersen et al., 2004; based on Athey's Haplogroup predictor)

Haplogroup I
4x I-M170 (Iraqi Kurds in Stenersen et al., 2004; based on Athey's Haplogroup predictor)
9x I-M170 (Zaza from Turkey in Nasidze et al., 2005)
14x I-M170 (Kurmanji from Turkey in Nasidze et al., 2005)
1x I-M170 (Iranian Kurds in Malyarchuk et al., 2013)
1x I2-M438 (Iranian Kurds in Grugni et al., 2012)
1x I2a2a-M223 (Kurdish village Dogukoy*/Central Anatolia in Gokcumen et al., 2011)
1x I2a2a* (old I2b1*; Z161+, L1228-, L1229-, L1230-, L1226-, L699-, L701-, L702-, L703-, L704-, M379-)(Sorani from Sulaymaniyah/Iraq)
1x I2a2b-L38 (Kurdish village Dogukoy*/Central Anatolia in Gokcumen et al., 2011)

Haplogroup J (J1+J2)
15x J-12f2 (Iranian Kurds in Malyarchuk et al., 2013)

Haplogroup J1
1x J1 a.k.a. hg9 (Eu10) (Iraqi Kurds in Nebel et al., 2001)
1x J1 (Kurdish village Dogukoy*/Central Anatolia in Gokcumen et al., 2011)
19x J1-M267 (Iraqi Kurds in Stenersen et al., 2004; based on Athey's Haplogroup predictor)
1x J1-M267 (Iranian Kurds in Grugni et al., 2012)
5x J1 (Feyli, originally from Iran)
1x J1 (Z2223+)  (Alevi with Zaza ancestry from Dersim; E11334 (Suleyman Efendi 19th century Askale Erzurum, Turkey))
1x J1 (probably L817+; Kurd from Turkey; N91920 (Kurdish Serzer, 1805 - 1846, Turkey))
1x J1b2-P58 (old J1c3; Kurd from Turkey)  
1x J1b2-P58 (old J1c3; Sorani from Iran)
1x J1b2-P58 (old J1c3; Kurd from Iraq) 
2x J1b2-P58 (old J1c3; Iranian Kurds in Grugni et al., 2012)
1x J1b2b (L147.1+, L222.2-, L92-, L93-, M267+; N88767 (Sulaymania, Iraq (Kurdistan) of sharif descent)

Haplogroup J2
20x J2 (Kurdish village Dogukoy*/Central Anatolia in Gokcumen et al., 2011)
27x J2 a.k.a. hg9 (Eu9) (Iraqi Kurds in Nebel et al., 2001)
12x J2-M172 (Kurmanji from Turkey in Nasidze et al., 2005)
8x J2-M172 (Kurmanji from Georgia in Nasidze et al., 2005)
3x J2-M172 (Kurds from Turkmenistan in Nasidze et al., 2005; originally used in Wells et al., 2001)     
29x J2-M172 (Iraqi Kurds in Stenersen et al., 2004; based on Athey's Haplogroup predictor)
1x J2 (Zaza from Dersim/Turkey)
1x J2 (Zaza from Baltas/Varto, Turkey)  
1x J2 (Kurmanji from Dohuk)
1x J2 (Kurmanji from Turkey)
1x J2a*-M410 (Iranian Kurds in Grugni et al., 2012)
3x J2a1*-Page55 (Iranian Kurds in Grugni et al., 2012)
1x J2a1a-M47 (Iranian Kurds in Grugni et al., 2012)
1x J2a1a (J2a4a at ISOGG 2009; he is M47+, M322+)(Yezidi from Iraq)
4x J2a1b*-M67 (Iranian Kurds in Grugni et al., 2012)
1x J2a1b*-M67 (Zaza from Turkey)
1x J2a1b1-M92 (Iranian Kurds in Grugni et al., 2012)
4x J2a1h-M530 (Iranian Kurds in Grugni et al., 2012)

Haplogroup L
1x L a.k.a. hg28 (Iraqi Kurds in Nebel et al., 2001)
5x L-M20 (Iraqi Kurds in Stenersen et al., 2004; based on Athey's Haplogroup predictor)
2x L-M20 (Iranian Kurds in Malyarchuk et al., 2013)
1x L1-M76  (Iranian Kurds in Grugni et al., 2012)

Haplogroup P
1x P-M45 (Zaza from Turkey in Nasidze et al., 2005)
5x P-M45 (Kurmanji from Turkey in Nasidze et al., 2005)
1x P-M45 (Kurmanji from Georgia in Nasidze et al., 2005)

Haplogroup Q
1x Q  (Iraqi Kurds in Stenersen et al., 2004; based on Athey's Haplogroup predictor)

Haplogroup R1
1x R1*-M173 (Iranian Kurds in Grugni et al., 2012)

Haplogroup R1a
1x R1a (Kurdish village Dogukoy*/Central Anatolia in Gokcumen et al., 2011)
11x R1a a.k.a. hg3(Eu19) (Iraqi Kurds in Nebel et al., 2001)
7x R1a1a-M17 (Zaza from Turkey in Nasidze et al., 2005)
11x R1a1a-M17 (Kurmanji from Turkey in Nasidze et al., 2005)
2x R1a1a-M17 (Kurds from Turkmenistan in Nasidze et al., 2005; originally used in Wells et al., 2001)
12x R1a1a-M17 (Iranian Kurds in Grugni et al., 2012)
11x R1a1a-M17 (Iraqi Kurds in Stenersen et al., 2004; based on Athey's Haplogroup predictor) 
1x R1a1a (Z93+, L342+, L657-, Z2122-)(Sorani from Sulaymaniyah/Iraq)
1x R1a1a (Z283+, Z282+, Z284-, M458-, Z280-, subclade 3  only his paternal great-grandfather is Kurdish from Turkey)
1x R1a1a (Alevi Zaza from Dersim/Turkey)
1x R1a1a (Alevi Kurmanji from Dersim/Turkey)
1x R1a1a (Kurmanji from Adıyaman and Gaziantep (now in Konya area)
1x R1a1a (Kurd from Turkey)
1x R1a1a (Sorani from Sulaymaniyah/Iraq)

Haplogroup R1b?
3x R1 -M173 (Zaza from Turkey in Nasidze et al., 2005)
4x R1 -M173 (Kurmanji from Turkey in Nasidze et al., 2005)
5x R1 -M173 (Kurds from Turkmenistan in Nasidze et al., 2005; originally used in Wells et al., 2001)

Haplogroup R1b
2x R1b-M343 (Kurdish village Dogukoy*/Central Anatolia in Gokcumen et al., 2011)
1x R1b-M343 (Iranian Kurds in Grugni et al., 2012)
13x R1b-M343 (Iraqi Kurds in Stenersen et al., 2004; based on Athey's Haplogroup predictor)
1x R1b1a2*-M269 (Kurmanji from Zakho/Iraq)
2x R1b1b2a-L23/L49 (Zaza from Turkey)
1x R1b1b2a1a-L52,P311,L11,P310 (Zaza from Sivas, originally from Dersim)
1x R1b1 (P25+)(Kurmanji from Maras/Elbistan/Turkey)

16x R1+R1b+R2 a.k.a. hg1 (Iraqi Kurds in Nebel et al., 2001)


Haplogroup R2
1x R2 (Iraqi Kurds in Stenersen et al., 2004; based on Athey's Haplogroup predictor)
7x R2a-M124 (Kurmanji from Turkey in Nasidze et al., 2005)
11x R2a-M124 (Kurmanji from Georgia in Nasidze et al., 2005)
2x R2a-M124 (Iranian Kurds in Grugni et al., 2012)
1x R2a-M124 (Iranian Kurds in Malyarchuk et al., 2013)
1x R2a (Sorani from Sulaymaniyah/Iraq)

Haplogroup T
11x K-M9 (probably T) (Kurmanji from Turkey in Nasidze et al., 2005)
2x K-M9 (probably T) (Kurmanji from Georgia in Nasidze et al., 2005)
4x T a.k.a. hg26 (Iraqi Kurds in Nebel et al., 2001)
3x T-M70 (Iraqi Kurds in Stenersen et al., 2004; based on Athey's Haplogroup predictor)
1x T (Sorani from Koysinjaq/Iraq)
5x T-M70 (Iranian Kurds in Grugni et al., 2012)

More data can be found here:
Kurdish Y-DNA Part I
Kurdish Y-DNA Part II
Kurdish Y-DNA Part III
Kurdish Y-DNA Part IV
Kurdish Y-DNA Part V
Kurdish Y-DNA Part VI
Kurdish Y-DNA Part VII
Kurdish Y-DNA Part IX