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

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发表于 2013-7-5 10:46 | 显示全部楼层 |阅读模式
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):


HERC2 haplotype recangular tree.jpg


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 totalN with ht3-18 data#1#2#3#4#5#6#7#8#9#10#11#12#13#14#15#16#17#18ND
Europe117130531%21%15%3%11%9%1%0%0%1%0%0%0%1%0%0%0%0%1%
West Asia62852720%4%20%8%13%20%7%0%0%1%0%0%0%1%0%0%0%0%5%
South Asia4052987%3%25%6%20%21%11%0%0%4%0%1%0%1%0%0%0%0%2%
Southeast Asia1721511%0%29%10%21%28%11%0%0%0%0%0%0%0%0%0%0%0%0%
Northeast Asia1971972%2%29%1%37%26%2%0%0%1%0%0%1%0%0%0%0%0%1%
Central Asia66665%6%18%7%32%23%2%0%0%2%0%0%0%1%1%0%0%0%5%
Northern Africa211775%0%24%17%6%19%10%6%0%1%1%0%0%1%0%0%0%0%1%
Subsaharan Africa1411410%1%5%8%4%13%11%19%5%7%7%1%4%0%0%1%1%0%12%
America2851866%3%23%6%22%6%3%7%1%4%1%0%1%2%1%0%0%0%11%
Denisova110%0%0%0%0%0%0%0%0%0%0%0%100%0%0%0%0%0%0%
Neanderthal*110%0%0%0%0%0%0%0%0%0%0%0%50%0%0%0%0%50%0%



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


http://kurdishdna.blogspot.com/2013/07/the-color-of-eyes-at-least-17-herc2.html
 楼主| 发表于 2013-7-5 10:55 | 显示全部楼层
N#1#2#3#4#5#6#7#8#9#10#11#12#13#14#15#16#17#18ND
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Kargopol_Russian2536%46%8%2%4%4%0%0%0%0%0%0%0%0%0%0%0%0%0%
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Argyll_Scottish317%17%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND67%
Cornish3033%17%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND50%
Kent3626%7%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND67%
Utah_USA8931%20%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND49%
Finnish9637%21%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND42%
Swedes3642%54%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND4%
Danes1952%32%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND16%
Germans9146%33%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND21%
Austrian4955%28%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND17%
Swiss1669%25%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND6%
French2731%30%19%4%6%11%0%0%0%0%0%0%0%0%0%0%0%0%0%
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Spanish_Pais_Vasco819%6%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND75%
Spanish_Andalucia40%0%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND100%
Spanish_Aragon50%0%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND100%
Spanish_Baleares86%6%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND88%
Spanish_Canarias20%0%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND100%
Spanish_Cantabria60%0%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND100%
Spanish_Castilla_La_Mancha413%13%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND75%
Spanish_Castilla_Y_Leon120%0%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND100%
Spanish_Cataluna50%0%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND100%
Spanish_Extremadura80%0%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND100%
Spanish_Galicia80%0%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND100%
Galician21530%17%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND53%
Spanish_Murcia60%0%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND100%
Spanish_Valencia1010%0%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND90%
Spanish1136%5%32%9%9%5%0%0%0%0%0%0%0%5%0%0%0%0%0%
Spanish10%0%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND100%
Sardinian2419%4%40%6%10%19%0%0%0%0%0%0%0%2%0%0%0%0%0%
Ashkenazy_Jews2138%14%12%2%12%7%2%0%0%2%0%0%0%10%0%0%0%0%0%
Sephardic_Jews1825%11%25%3%11%14%11%0%0%0%0%0%0%0%0%0%0%0%0%
 楼主| 发表于 2013-7-5 10:58 | 显示全部楼层
Cypriots1233%0%21%13%17%13%4%0%0%0%0%0%0%0%0%0%0%0%0%
Lezgins1619%3%22%6%22%25%3%0%0%0%0%0%0%0%0%0%0%0%0%
Nogay1439%0%21%4%21%11%4%0%0%0%0%0%0%0%0%0%0%0%0%
North_Ossetian1331%15%35%8%4%8%0%0%0%0%0%0%0%0%0%0%0%0%0%
Kumyk1338%12%15%0%19%12%0%0%0%0%0%0%4%0%0%0%0%0%0%
Balkar1638%6%13%9%22%9%3%0%0%0%0%0%0%0%0%0%0%0%0%
Abhkasian1817%6%22%14%17%22%3%0%0%0%0%0%0%0%0%0%0%0%0%
Adygei1726%6%12%3%18%26%0%0%0%0%0%0%0%0%0%0%0%0%0%
Chechen1831%11%14%3%19%22%0%0%0%0%0%0%0%0%0%0%0%0%0%
Georgians1446%0%7%4%18%21%4%0%0%0%0%0%0%0%0%0%0%0%0%
Iranians163%6%28%3%13%28%13%0%0%0%0%0%0%0%0%0%0%0%6%
Hazara176%0%26%3%29%26%3%0%0%0%0%0%0%0%0%0%0%0%6%
Balochi5010%4%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND86%
Balochi1510%3%10%17%23%23%7%0%0%0%0%0%0%0%0%0%0%0%7%
Kurd2619%4%19%15%21%17%4%0%0%0%0%0%0%0%0%0%0%0%0%
Turks1921%8%29%8%13%16%5%0%0%0%0%0%0%0%0%0%0%0%0%
Iranian_Jews413%0%13%0%0%63%13%0%0%0%0%0%0%0%0%0%0%0%0%
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Lebanese413%0%38%38%0%13%0%0%0%0%0%0%0%0%0%0%0%0%0%
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Armenian2724%2%19%9%2%9%4%0%0%6%0%0%0%0%0%0%0%0%26%
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Druze2025%0%8%3%8%18%3%0%0%13%0%3%0%3%0%0%0%0%20%
Syrians1533%0%13%3%23%20%3%0%0%3%0%0%0%0%0%0%0%0%0%
Palestinian5118%3%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND-21%
Palestinian3124%2%13%6%8%26%15%2%0%0%0%0%0%2%0%0%0%0%3%
Jordanians1913%8%29%5%13%21%11%0%0%0%0%0%0%0%0%0%0%0%0%
Saudis195%0%26%0%8%13%26%3%0%0%3%0%0%0%0%0%0%0%16%
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Burusho2518%12%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND-30%
Burusho2514%10%18%0%16%14%4%0%0%8%0%2%0%2%0%0%0%0%12%
Kalash2512%16%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND100%
Brahmins_TN&UP96%0%17%11%6%28%11%0%0%11%0%11%0%0%0%0%0%0%0%
Chamar96%0%33%11%11%11%17%0%0%11%0%0%0%0%0%0%0%0%0%
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Chenchus40%0%38%0%13%0%0%0%0%13%0%13%25%0%0%0%0%0%0%
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 楼主| 发表于 2013-7-5 10:59 | 显示全部楼层
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Ethiopian_Afar30%0%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND100%
Ethiopian_Amhara180%0%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND100%
Ethiopian_Anuak180%0%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND100%
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Ethiopian_Ari_cultivator150%0%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND100%
Ethiopian_Gumuz60%0%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND100%
Ethiopian_Oromo170%0%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND100%
Ethiopian_Tigray170%0%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND100%
Ethiopian_Wolayta30%0%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND100%
Somali140%0%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND100%
Sudanese170%0%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND100%
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Bantu180%0%0%0%0%0%11%28%3%3%19%0%3%0%0%0%6%0%28%
Mandenka180%0%8%3%19%0%11%25%3%3%11%0%0%0%0%6%0%0%11%
Mbuti_Pygmies130%0%0%0%0%15%12%31%0%4%15%0%15%0%0%0%0%0%8%
Biaka_Pygmies220%0%0%14%0%9%2%36%14%2%0%7%0%2%0%0%0%0%14%
San312%3%10%5%3%34%2%5%0%13%6%0%0%0%0%2%0%0%16%
Sandawe280%0%9%23%2%14%13%11%11%4%0%0%11%0%0%0%0%0%4%
African_American332%5%5%17%3%0%9%26%6%3%2%0%0%2%2%0%0%0%21%
Peruvian530%0%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND100%
Colombian308%5%13%5%17%10%3%0%0%12%0%0%0%5%3%0%2%0%17%
Ecuadorian169%3%22%6%34%6%3%0%0%3%0%0%0%0%0%0%0%0%13%
Puerto_Rican2610%6%35%6%10%8%6%8%0%0%2%0%2%0%0%2%0%0%8%
Dominican254%4%28%4%10%12%0%8%2%6%6%0%2%2%0%0%0%0%12%
Mexican468%1%NDNDNDNDNDNDNDNDNDNDNDNDNDNDNDND91%
West_Greenlanders1020%15%25%0%30%5%5%0%0%0%0%0%0%0%0%0%0%0%0%
East_Greenlanders714%7%21%0%14%14%0%0%0%14%0%7%0%7%0%0%0%0%0%
Pima100%0%25%0%75%0%0%0%0%0%0%0%0%0%0%0%0%0%0%
Surui317%0%33%0%50%0%0%0%0%0%0%0%0%0%0%0%0%0%0%
Karitiana633%0%17%0%33%0%0%0%0%0%0%0%0%0%0%0%0%0%17%
Mayan208%0%43%0%50%0%0%0%0%0%0%0%0%0%0%0%0%0%0%
Denisova10%0%0%0%0%0%0%0%0%0%0%0%100%0%0%0%0%0%0%
Neanderthal*10%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


















发表于 2013-7-5 13:09 | 显示全部楼层
  ...
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.
198401 发表于 2013-7-5 10:46

可能也不尽然,比如混血的费翔一支眼睛就是铁灰色的,而按照楼主提供的数据东亚民族(不包括蒙古族)的ht1和ht2基本上是0.

关于欧洲和西亚的数据与我平时的观察接近,比如南欧人普遍ht2偏低,还有,西亚与高加索的黎巴嫩车臣穆斯林ht2高于格鲁吉亚人(格鲁吉亚人平时的确很少看到蓝睛,相反,车臣人倒是经常可以看到),也符合平时的观察。
不过对伊朗人的ht2低于黎巴嫩人感到有一点意外,可能也为印欧语以及雅利安人的起源提供了一些有益的线索~
 楼主| 发表于 2013-7-5 14:13 | 显示全部楼层
5# imvivi001
主要是样本量太少。
ht1,ht2是隐性基因,发生率应该是ht1+ht2之后的平方(原文中2是上标
)。
发表于 2013-7-5 19:09 | 显示全部楼层
6# 198401

可能是样本比较少,不过结果大致上与常人的观察相符。

如果是二者之和的²,那计算出来的比例会更低,这样来看,即便是日耳曼人,浅色眼瞳的比例也不过是50%左右~
 楼主| 发表于 2013-7-5 19:19 | 显示全部楼层
7# imvivi001

是的,符合常规。
德国也不是金发碧眼最高发的。
Example1: Germans have 46% ht1 and 33% ht2.
(46%+33%)^2
= (0.46 + 0.33)^2
= 0.79^2
= 0.62
= 62%
62% of the Germans have light eye color based on the HERC2 genotype.
发表于 2013-7-5 19:28 | 显示全部楼层
8# 198401

我是简单地来一个四舍五入目测0.4+0.3之后的^2,大致上是50%左右,因此误差较大~
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