Tuesday, July 2, 2013

The color of the eyes: at least 17 HERC2 variants in Human gene pool

Today, after analyzing the Kurdish gene pool for HERC2 and the Eurasian gene pool for HERC2 I want to add the third post in the HERC2 trilogy. I analyzed additional data from other parts of the world and discovered 10 more existing Human haplotypes and one extinct haplotype in Neanderthals.

All the HERC2 haplotypes of humans, Neanderthals, Denisova and many mammals can be found in the spreadsheet I generated.

Interestingly, the ancestral HERC2 haplotype is ht13, which is present in the Denisova genome and most likely in the Neanderthal gene pool. Ht13 survived at low frequencies in Kumyk from the Caucasus (4%), Chenchus from India (25%), Mongolia (5-6%),  Bantu (3%), Mbuti Pygmies (15%), Sandawe (11%), Puerto Rican (2%) and Dominican (2%).

Below is a rectangular tree of these haplotypes (ht1 and h2 give light eye colors):



The highest variability of HERC2 can be found in Subsaharan Africa and in mixed population of the New World (African American, Dominican, Colombian, Puerto Rican).




 N total N with ht3-18 data #1 #2 #3 #4 #5 #6 #7 #8 #9 #10 #11 #12 #13 #14 #15 #16 #17 #18 ND
Europe 1171 305 31% 21% 15% 3% 11% 9% 1% 0% 0% 1% 0% 0% 0% 1% 0% 0% 0% 0% 1%
West Asia 628 527 20% 4% 20% 8% 13% 20% 7% 0% 0% 1% 0% 0% 0% 1% 0% 0% 0% 0% 5%
South Asia 405 298 7% 3% 25% 6% 20% 21% 11% 0% 0% 4% 0% 1% 0% 1% 0% 0% 0% 0% 2%
Southeast Asia 172 151 1% 0% 29% 10% 21% 28% 11% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Northeast Asia 197 197 2% 2% 29% 1% 37% 26% 2% 0% 0% 1% 0% 0% 1% 0% 0% 0% 0% 0% 1%
Central Asia 66 66 5% 6% 18% 7% 32% 23% 2% 0% 0% 2% 0% 0% 0% 1% 1% 0% 0% 0% 5%
Northern Africa 211 77 5% 0% 24% 17% 6% 19% 10% 6% 0% 1% 1% 0% 0% 1% 0% 0% 0% 0% 1%
Subsaharan Africa 141 141 0% 1% 5% 8% 4% 13% 11% 19% 5% 7% 7% 1% 4% 0% 0% 1% 1% 0% 12%
America 285 186 6% 3% 23% 6% 22% 6% 3% 7% 1% 4% 1% 0% 1% 2% 1% 0% 0% 0% 11%
Denisova 1 1 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 100% 0% 0% 0% 0% 0% 0%
Neanderthal* 1 1 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 50% 0% 0% 0% 0% 50% 0%





N #1 #2 #3 #4 #5 #6 #7 #8 #9 #10 #11 #12 #13 #14 #15 #16 #17 #18 ND
Lithuanians 10 35% 60% 0% 0% 0% 5% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Belorussians 7 36% 64% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Erzya 9 39% 56% 0% 0% 6% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Kargopol_Russian 25 36% 46% 8% 2% 4% 4% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Russians 5 60% 20% 0% 0% 10% 10% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Ukrainian 20 43% 38% 8% 0% 8% 5% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Moksha 5 30% 50% 10% 0% 0% 10% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Hungarians 18 17% 50% 14% 0% 14% 6% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Chuvash 16 28% 31% 19% 0% 13% 6% 3% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Dolgans 6 0% 0% 25% 0% 50% 25% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Bulgarian 13 31% 12% 12% 0% 0% 4% 0% 0% 0% 19% 0% 0% 0% 8% 0% 0% 0% 0% 15%
Romanians 14 29% 25% 21% 4% 14% 7% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Orcadian 11 27% 41% 5% 5% 18% 5% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Orcadian 19 42% 21% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 37%
Argyll_Scottish 3 17% 17% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 67%
Cornish 30 33% 17% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 50%
Kent 36 26% 7% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 67%
Utah_USA 89 31% 20% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 49%
Finnish 96 37% 21% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 42%
Swedes 36 42% 54% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 4%
Danes 19 52% 32% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 16%
Germans 91 46% 33% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 21%
Austrian 49 55% 28% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 17%
Swiss 16 69% 25% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 6%
French 27 31% 30% 19% 4% 6% 11% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
North_Italian 13 42% 27% 8% 4% 8% 8% 4% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Tuscan 80 8% 3% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 89%
Tuscan 8 25% 19% 6% 0% 19% 31% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
French_Basque 24 19% 21% 17% 6% 23% 8% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Spanish_Pais_Vasco 8 19% 6% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 75%
Spanish_Andalucia 4 0% 0% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 100%
Spanish_Aragon 5 0% 0% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 100%
Spanish_Baleares 8 6% 6% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 88%
Spanish_Canarias 2 0% 0% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 100%
Spanish_Cantabria 6 0% 0% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 100%
Spanish_Castilla_La_Mancha 4 13% 13% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 75%
Spanish_Castilla_Y_Leon 12 0% 0% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 100%
Spanish_Cataluna 5 0% 0% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 100%
Spanish_Extremadura 8 0% 0% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 100%
Spanish_Galicia 8 0% 0% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 100%
Galician 215 30% 17% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 53%
Spanish_Murcia 6 0% 0% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 100%
Spanish_Valencia 10 10% 0% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 90%
Spanish 11 36% 5% 32% 9% 9% 5% 0% 0% 0% 0% 0% 0% 0% 5% 0% 0% 0% 0% 0%
Spanish 1 0% 0% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 100%
Sardinian 24 19% 4% 40% 6% 10% 19% 0% 0% 0% 0% 0% 0% 0% 2% 0% 0% 0% 0% 0%
Ashkenazy_Jews 21 38% 14% 12% 2% 12% 7% 2% 0% 0% 2% 0% 0% 0% 10% 0% 0% 0% 0% 0%
Sephardic_Jews 18 25% 11% 25% 3% 11% 14% 11% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Cypriots 12 33% 0% 21% 13% 17% 13% 4% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Lezgins 16 19% 3% 22% 6% 22% 25% 3% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Nogay 14 39% 0% 21% 4% 21% 11% 4% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
North_Ossetian 13 31% 15% 35% 8% 4% 8% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Kumyk 13 38% 12% 15% 0% 19% 12% 0% 0% 0% 0% 0% 0% 4% 0% 0% 0% 0% 0% 0%
Balkar 16 38% 6% 13% 9% 22% 9% 3% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Abhkasian 18 17% 6% 22% 14% 17% 22% 3% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Adygei 17 26% 6% 12% 3% 18% 26% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Chechen 18 31% 11% 14% 3% 19% 22% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Georgians 14 46% 0% 7% 4% 18% 21% 4% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Iranians 16 3% 6% 28% 3% 13% 28% 13% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 6%
Hazara 17 6% 0% 26% 3% 29% 26% 3% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 6%
Balochi 50 10% 4% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 86%
Balochi 15 10% 3% 10% 17% 23% 23% 7% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 7%
Kurd 26 19% 4% 19% 15% 21% 17% 4% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Turks 19 21% 8% 29% 8% 13% 16% 5% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Iranian_Jews 4 13% 0% 13% 0% 0% 63% 13% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Iraqi_Jews 9 17% 0% 28% 17% 11% 28% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Lebanese 4 13% 0% 38% 38% 0% 13% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Lebanese_Muslim 25 14% 8% 14% 12% 12% 32% 8% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Armenian 27 24% 2% 19% 9% 2% 9% 4% 0% 0% 6% 0% 0% 0% 0% 0% 0% 0% 0% 26%
Lebanese_Christian 24 33% 6% 15% 10% 6% 19% 6% 0% 2% 0% 0% 0% 0% 2% 0% 0% 0% 0% 0%
Lebanese_Druze 24 17% 2% 31% 10% 13% 13% 13% 2% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Druze 20 25% 0% 8% 3% 8% 18% 3% 0% 0% 13% 0% 3% 0% 3% 0% 0% 0% 0% 20%
Syrians 15 33% 0% 13% 3% 23% 20% 3% 0% 0% 3% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Palestinian 51 18% 3% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND -21%
Palestinian 31 24% 2% 13% 6% 8% 26% 15% 2% 0% 0% 0% 0% 0% 2% 0% 0% 0% 0% 3%
Jordanians 19 13% 8% 29% 5% 13% 21% 11% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Saudis 19 5% 0% 26% 0% 8% 13% 26% 3% 0% 0% 3% 0% 0% 0% 0% 0% 0% 0% 16%
Yemenese 7 7% 0% 14% 7% 7% 14% 21% 14% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 14%
Yemenite_Jews 15 7% 0% 30% 3% 0% 30% 10% 0% 0% 0% 0% 0% 0% 7% 0% 0% 0% 0% 13%
Bedouin 40 11% 0% 20% 15% 1% 20% 16% 0% 0% 4% 0% 1% 0% 1% 0% 0% 0% 0% 10%
Brahui 20 3% 0% 23% 10% 25% 13% 5% 0% 0% 10% 0% 0% 0% 8% 0% 0% 0% 0% 5%
Brahui 25 2% 2% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 100%
Burusho 25 18% 12% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND -30%
Burusho 25 14% 10% 18% 0% 16% 14% 4% 0% 0% 8% 0% 2% 0% 2% 0% 0% 0% 0% 12%
Kalash 25 12% 16% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 100%
Brahmins_TN&UP 9 6% 0% 17% 11% 6% 28% 11% 0% 0% 11% 0% 11% 0% 0% 0% 0% 0% 0% 0%
Chamar 9 6% 0% 33% 11% 11% 11% 17% 0% 0% 11% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Hakkipikki 4 0% 0% 25% 0% 13% 38% 13% 0% 0% 0% 0% 13% 0% 0% 0% 0% 0% 0% 0%
Chenchus 4 0% 0% 38% 0% 13% 0% 0% 0% 0% 13% 0% 13% 25% 0% 0% 0% 0% 0% 0%
Gond 2 0% 0% 50% 0% 0% 25% 0% 0% 0% 25% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Dharkars 9 0% 0% 22% 11% 28% 17% 17% 0% 0% 6% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Dusadh 6 0% 0% 33% 0% 25% 8% 8% 0% 0% 8% 0% 0% 0% 0% 0% 0% 0% 0% 17%
Makrani 20 10% 3% 18% 8% 33% 23% 5% 0% 0% 3% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Pathan 21 19% 2% 14% 7% 24% 17% 17% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Lambadi 1 0% 0% 50% 0% 0% 50% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Meena 1 0% 0% 50% 0% 50% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Nihali 1 0% 0% 0% 0% 50% 50% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Tharus 2 25% 0% 25% 0% 0% 25% 25% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Uttar_Pradesh 5 0% 0% 60% 0% 20% 20% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Gujarati 32 0% 0% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 100%
Sindhi 14 4% 0% 29% 7% 14% 32% 11% 0% 0% 0% 0% 0% 0% 4% 0% 0% 0% 0% 0%
Bengali 1 50% 0% 50% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Kurmi 1 0% 0% 0% 0% 0% 0% 100% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Kurumba 3 33% 0% 17% 0% 33% 0% 17% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
North_Kannadi 4 25% 0% 25% 38% 0% 13% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Muslim_India 5 10% 0% 20% 40% 0% 20% 10% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Meghawal 1 0% 0% 0% 50% 50% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Kol 14 0% 0% 36% 4% 21% 25% 14% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Kanjars 7 0% 0% 14% 0% 14% 64% 7% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Cochin_Jews 3 0% 0% 17% 0% 17% 33% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 33%
Mumbai_Jews 4 13% 0% 25% 0% 0% 0% 38% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 25%
Kshatriya 7 0% 0% 29% 0% 29% 43% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Velamas 7 7% 0% 21% 0% 43% 0% 29% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Pulliyar 1 0% 0% 0% 0% 100% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Tamil_Nadu 1 0% 0% 50% 0% 50% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Piramalai 8 0% 0% 31% 6% 25% 19% 19% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Singapore_Indian 78 8% 2% 27% 4% 18% 26% 12% 0% 0% 3% 0% 0% 0% 1% 0% 0% 0% 0% 0%
Austroasiatic 11 5% 0% 32% 5% 5% 36% 18% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Tibeto-Burman_Burmese 14 0% 0% 32% 18% 18% 21% 11% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Tibeto-Burman_Garo 2 0% 0% 25% 0% 50% 25% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Cambodian 10 0% 0% 25% 10% 30% 25% 5% 0% 0% 0% 0% 0% 0% 5% 0% 0% 0% 0% 0%
Vietnamese 21 0% 0% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 100%
Malay 87 1% 0% 22% 13% 28% 30% 6% 1% 0% 0% 0% 1% 0% 0% 0% 0% 0% 0% 0%
NAN_Melanesian 10 0% 0% 20% 0% 0% 15% 65% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Papuan 17 0% 0% 68% 0% 0% 26% 6% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Miaozu 10 0% 0% 25% 0% 25% 50% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Oroqen 9 0% 0% 17% 0% 61% 22% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
She 9 0% 0% 33% 0% 11% 56% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Daur 9 0% 0% 17% 0% 56% 28% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Mongola 10 0% 0% 35% 5% 25% 30% 0% 0% 0% 0% 0% 0% 5% 0% 0% 0% 0% 0% 0%
Mongolians 9 0% 0% 28% 0% 50% 11% 6% 0% 0% 0% 0% 0% 6% 0% 0% 0% 0% 0% 0%
Tuvinians 13 0% 0% 42% 0% 35% 23% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Nganassans 9 0% 0% 28% 0% 56% 11% 6% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Koryaks 10 0% 0% 40% 0% 50% 0% 10% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Chukchis 11 0% 0% 41% 0% 45% 9% 5% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Dai 10 0% 0% 35% 0% 10% 55% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Evenkis 11 0% 0% 32% 0% 45% 23% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Yakut 20 0% 0% 40% 0% 43% 18% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Hezhen 7 0% 0% 43% 0% 36% 21% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Xibo 9 0% 0% 11% 0% 44% 39% 0% 0% 0% 6% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Tu 8 0% 0% 13% 0% 31% 50% 0% 0% 0% 6% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Tujia 10 0% 0% 5% 5% 45% 35% 10% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Yizu 10 0% 0% 35% 0% 15% 40% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 10%
Yukaghirs 4 0% 13% 38% 0% 38% 13% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Selkups 9 39% 44% 11% 0% 6% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Altaians 12 0% 4% 17% 0% 17% 21% 0% 0% 0% 8% 0% 0% 0% 4% 4% 0% 0% 0% 25%
Tadjik 14 7% 11% 18% 7% 36% 18% 4% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Uzbeks 15 3% 13% 27% 23% 13% 20% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Uygur 10 10% 0% 20% 0% 35% 35% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Buryats 15 7% 0% 10% 0% 57% 23% 3% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Egyptians 11 23% 0% 18% 18% 14% 18% 9% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Moroccan_Jews 12 33% 8% 17% 8% 8% 25% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Moroccans 7 0% 0% 29% 7% 7% 21% 29% 7% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Mozabite_Berber 18 6% 0% 44% 25% 0% 14% 6% 0% 0% 0% 3% 0% 0% 3% 0% 0% 0% 0% 0%
Ethiopian_Jews 10 5% 0% 15% 20% 0% 15% 15% 15% 0% 5% 0% 0% 0% 0% 0% 0% 0% 0% 10%
Ethiopians 19 8% 0% 16% 16% 11% 24% 11% 16% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Ethiopian_Afar 3 0% 0% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 100%
Ethiopian_Amhara 18 0% 0% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 100%
Ethiopian_Anuak 18 0% 0% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 100%
Ethiopian_Ari_blacksmith 6 0% 0% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 100%
Ethiopian_Ari_cultivator 15 0% 0% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 100%
Ethiopian_Gumuz 6 0% 0% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 100%
Ethiopian_Oromo 17 0% 0% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 100%
Ethiopian_Tigray 17 0% 0% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 100%
Ethiopian_Wolayta 3 0% 0% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 100%
Somali 14 0% 0% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 100%
Sudanese 17 0% 0% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 100%
Hadza 11 0% 0% 0% 0% 5% 0% 45% 9% 5% 32% 5% 0% 0% 0% 0% 0% 0% 0% 0%
Bantu 18 0% 0% 0% 0% 0% 0% 11% 28% 3% 3% 19% 0% 3% 0% 0% 0% 6% 0% 28%
Mandenka 18 0% 0% 8% 3% 19% 0% 11% 25% 3% 3% 11% 0% 0% 0% 0% 6% 0% 0% 11%
Mbuti_Pygmies 13 0% 0% 0% 0% 0% 15% 12% 31% 0% 4% 15% 0% 15% 0% 0% 0% 0% 0% 8%
Biaka_Pygmies 22 0% 0% 0% 14% 0% 9% 2% 36% 14% 2% 0% 7% 0% 2% 0% 0% 0% 0% 14%
San 31 2% 3% 10% 5% 3% 34% 2% 5% 0% 13% 6% 0% 0% 0% 0% 2% 0% 0% 16%
Sandawe 28 0% 0% 9% 23% 2% 14% 13% 11% 11% 4% 0% 0% 11% 0% 0% 0% 0% 0% 4%
African_American 33 2% 5% 5% 17% 3% 0% 9% 26% 6% 3% 2% 0% 0% 2% 2% 0% 0% 0% 21%
Peruvian 53 0% 0% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 100%
Colombian 30 8% 5% 13% 5% 17% 10% 3% 0% 0% 12% 0% 0% 0% 5% 3% 0% 2% 0% 17%
Ecuadorian 16 9% 3% 22% 6% 34% 6% 3% 0% 0% 3% 0% 0% 0% 0% 0% 0% 0% 0% 13%
Puerto_Rican 26 10% 6% 35% 6% 10% 8% 6% 8% 0% 0% 2% 0% 2% 0% 0% 2% 0% 0% 8%
Dominican 25 4% 4% 28% 4% 10% 12% 0% 8% 2% 6% 6% 0% 2% 2% 0% 0% 0% 0% 12%
Mexican 46 8% 1% ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND ND 91%
West_Greenlanders 10 20% 15% 25% 0% 30% 5% 5% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
East_Greenlanders 7 14% 7% 21% 0% 14% 14% 0% 0% 0% 14% 0% 7% 0% 7% 0% 0% 0% 0% 0%
Pima 10 0% 0% 25% 0% 75% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Surui 3 17% 0% 33% 0% 50% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Karitiana 6 33% 0% 17% 0% 33% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 17%
Mayan 20 8% 0% 43% 0% 50% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0%
Denisova 1 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 100% 0% 0% 0% 0% 0% 0%
Neanderthal* 1 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 50% 0% 0% 0% 0% 50% 0%
*rs11635884=C and rs6497284=C predicted















ND: not determined




















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

at

18 comments:

  1. Onur DincerJuly 2, 2013 at 5:28 PM

    This comment has been removed by the author.

    ReplyDelete
  2. Onur DincerJuly 2, 2013 at 5:34 PM

    The one Yukaghir individual with the light eye haplotype is almost certainly one of the two Rasmussen et al. Yukaghir individuals with recent Russian ancestry. If I were you, I would use neither of those two Yukaghir individuals with recent Russian ancestry in genetic analyses.

    The Austroasiatic individual with the light eye haplotype is most probably a Munda speaker from South Asia.

    What surprised me the most is the presence of the light eye haplotype in one Malay individual (immigrant from South Asia?). The ones in the San are very probably from recent European admixture.

    By the way, you put Dolgans in the wrong list. They are a Siberian population rather than European.

    ReplyDelete
  3. PalistoJuly 2, 2013 at 6:00 PM

    Thanks for the information. Where can see the IDs of the ones with Russian ancestry? Yukagir4 has one allele with ht2 (light eyes).

    The Austroasiatic individual with ht1 is Austroasiatic_Ho HO438.

    The Malay with ht1 is Malay SGVP00316.

    ReplyDelete
  4. PalistoJuly 2, 2013 at 7:15 PM

    I found some admixture analysis from Dienekes for Yukagirs:
    "ADMIXTURE Yukagir_12.png" in
    https://docs.google.com/file/d/0B7JDEoCgzRKeMzgzOWVhNjUtZWIxYy00MjI0LTlkYTMtNGNkZjhmMmI3NjQz/edit?pli=1
    GSM558790 and GSM558793 have "Russian" admixture. The IDs that I got from Davidski do not fit the IDs that are in the png file. Hopefully, Davidski can let us know what is what.

    FYI, I excluded "Yukagir6" because it did not data for all HERC2 SNPs but it must be have ht1 or ht2 as well. So, there are two Yukagirs with ht1/2.

    ReplyDelete
  5. MajuJuly 2, 2013 at 8:40 PM

    Wow! Really admirable work, Palisto.

    I've been taking some notes on the distribution of the various lineages on your tree and I would say the following:

    1. What I call 'haplogroup C' (hts 11, 16 &17) did not participate in the OoA, as it has only 3% of presence in Saudi Arabia.

    2. What I call 'haplogroup D' (all others but ht13 and ht8) did but did so already diversified, because all hts except ht1 and ht2 are common in Africa. Ht 9 was the only subclade that did not take part in the Eurasian adventure (only minor presence in Lebanon, surely recent).

    3. ht 13 ('haplogroup A') and ht 8 ('haplogroup B') probably also took part in the OoA but it is at least debatable if they were instead introgressed (only in Eurasians) from Neanderthals.

    4. ht 1 and 2 are found among the San totaling 5%. I find hard to believe this is because of recent European admixture (not 100% impossible however), this may mean that they also took part in the OoA as we know them or that they co-evolved in both populations from ht3 separately (which are the odds?) This one of the most interesting findings because it may well be argued that "blue eyes come from Africa", even if for whatever reason the allele is not really expressed there.

    5. ht15 and ht14 seem to have some particular Native American affinity, both via Altai.

    My thoughts so far. Thanks for this fantastic data.

    ReplyDelete
    Replies
    1. MajuJuly 2, 2013 at 8:59 PM

      PS- Actually ht15 might well have been the only haplotype to evolve in Eurasia, as it has 0% detected presence in Africa. Said that, my best guess is that it's likely to be found with wider African samples.

      Delete
    2. PalistoJuly 2, 2013 at 10:20 PM

      "4. ht 1 and 2 are found among the San totaling 5%. I find hard to believe this is because of recent European admixture (not 100% impossible however), ..."

      Take a look of the (Khoe)-San from Southafrica:
      They have a little bit of R1a1 and R1b Y-haplogroups, this is clearly recent European admixture.
      http://2.bp.blogspot.com/_Ish7688voT0/TO-pMuAmfNI/AAAAAAAAC6w/U3hRZNYQtnY/s1600/southafrica.png

      Delete
    3. MajuJuly 3, 2013 at 10:21 PM

      You may be right. Still, assuming it is the same sample, all three European lineages barely amount to 3.3%, and this is by paternal line, surely maternal lines are effectively 100% native San, so we could be talking of European admixture levels under 1.7% (probably a lot less) for the autosomal genome, say ~1%.

      Instead the European HERC2 variants are found at levels of (5+X)%, because in Europe there are also other variants which are common in Africa, like ht3. Assuming frequencies between Orcadians and French, the total European admixture inferred from HERC2 haplotypes, according to your interpretation, would be of c. 8% but the total real admixture based on Y-DNA is almost nil (est. ~1%).

      So something doesn't add up: unless this sample of yours has an unusually high level of admixture: c. 8% at overall autosomal level, what means maybe 20% at Y-DNA levels (as the original mestizos carrying those European lineages must have reintegrated to the San community, marrying local women and this continued for several generations).

      We are talking of very different levels of admixture here: differences of about 1:7 or 1:8.

      Delete
    4. PalistoJuly 3, 2013 at 11:52 PM

      I looked at the latest K16 Harappa admixture run with two data sets for San people, one is N=6 from Henn et al., 2011, the other one is the one I used (N=31) from HGDP.

      https://docs.google.com/spreadsheet/ccc?key=0AuW3R0Ys-P4HdDhib1M5OE1wWENNb2haUFFWZzNBMEE#gid=0

      The San from Henn et al., have 100% of the San component.
      The San from HGDP are clearly mixed with "only" 79% of the San component (2% S Indian, 1% Baloch, 0% Caucasian, 3% NE Euro, 1% SE Asian, 0% Siberian, 0% NE Asian, 0% Papuan, 0% American, 0% Beringian, 2% Mediterranean, 2% SW Asian, 79% San, 2% E African, 0% Pygmy, 7% W African)

      Delete
    5. MajuJuly 4, 2013 at 1:43 PM

      Thanks, that clarifies everything.

      I just posted a commentary of your work, FYI.

      As I did so I noticed that the column labeled "N with ht3-18 data" does not seem to correspond with the actual percentages for ht3-18 in the various regions. Can you explain it?

      Delete
    6. PalistoJuly 6, 2013 at 2:28 AM

      "As I did so I noticed that the column labeled "N with ht3-18 data" does not seem to correspond with the actual percentages for ht3-18 in the various regions. Can you explain it?"

      In the summary table I merged two data sets, the first data set is just focusing on ht1 and ht2 and is directly extracted from http://alfred.med.yale.edu/; the second data set is the one that I fully analyzed (based on HERC2 HGDP data Davidski provided).
      This is why I gave two N's, "N total" and "N with ht3-18 data". Frequency of Ht1 and ht2 were calculated using "N total" (N of both data sets), for all other haplotypes I had to use the number of the second data set alone.
      The table is basically a merged version of two tables.

      Delete
    7. MajuJuly 6, 2013 at 4:24 AM

      Now I understand it, thanks.

      Delete
  6. Onur DincerJuly 3, 2013 at 1:56 AM

    FYI, I excluded "Yukagir6" because it did not data for all HERC2 SNPs but it must be have ht1 or ht2 as well. So, there are two Yukagirs with ht1/2.

    This is congruent with the fact that there are two Yukaghirs in Rasmussen et al.'s database who have recent Russian admixture. One of them has even much more Russian ancestry than Yukaghir ancestry.

    ReplyDelete
  7. DavidskiJuly 10, 2013 at 1:04 AM

    Europeans don't necessarily need two copies of ht1 and/or ht2 to have light eyes.

    Sometimes only one ht1 or ht2 is needed to produce green or even blue eyes.

    But this probably depends on what the other hapltype is, and like I say, it seems to be relevant only for Europeans.

    ReplyDelete
  8. RyanSeptember 10, 2013 at 1:20 PM

    Hi Palisto,

    According to your spreadsheet titled HERC2 segment in Kurds (under All variant combinations based on V3 23andMe data)I fall under category #1_#2.

    Does this mean that I belong to ht1 or ht2?

    Thank you very much for your time and consideration. Keep up the excellent work.

    Sincerely,
    Ryan

    ReplyDelete
  9. PalistoSeptember 12, 2013 at 10:57 AM

    @ Ryan
    If your V3 23andme data is identical to "#1_#2" in the mentioned table then you belong to ht1 and ht2. You got ht1 from one parent and ht2 from your other parent.

    ReplyDelete
  10. KrefterDecember 23, 2015 at 3:44 AM

    10/10 Mesolithic Europeans have haplotype #2. All were homogeneous for rs11636232 except for one which had TC. #2 was very rare in Neolithic Europeans/Anatolians, while many had #1.

    ReplyDelete
    Replies
    1. PalistoDecember 24, 2015 at 3:03 PM

      @Krefter
      Thanks for checking ancient DNA. This makes sense

      Delete