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View Full Version : The Light Skin Allele of SLC24A5 in South-Asians & Europeans Shares Identity by Desce



kenji.aryan
02-24-2017, 02:57 AM
http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003912

chenmatthew0428
02-24-2017, 04:14 AM
http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003912

Can you post your 23andme results?

MonkeyDLuffy
02-24-2017, 04:24 AM
I get AA on it.

chenmatthew0428
02-24-2017, 08:01 AM
I get AA on it.

Can you post your 23andme results?

khanabadoshi
02-24-2017, 12:40 PM
Myself:
Brother:
Sister (Hanif):
Grandmother (Balq):
Grandmother Brother:
Grandfather Sister (Sadia):
Uncle (Jam):
Aunt:
2nd Cousin:
Mohmand:
Lahori:
Multani:
Ashkenazi:

A/G
A/A
A/G
A/A
A/A
A/A
A/G
A/A
A/A
A/A
A/A
A/A
A/A

Kaido
02-24-2017, 01:16 PM
Me - AA
Mother - AA
Cousin 1 - AA
Cousin 2 - AA

MonkeyDLuffy
02-24-2017, 01:29 PM
Myself:
Brother:
Sister (Hanif):
Grandmother (Balq):
Grandmother Brother:
Grandfather Sister (Sadia):
Uncle (Jam):
Aunt:
2nd Cousin:
Mohmand:
Lahori:
Multani:
Ashkenazi:

A/G
A/A
A/G
A/A
A/A
A/A
A/G
A/A
A/A
A/A
A/A
A/A
A/A




I'm surprised, could it be because of your Uzbek side?

Reza
02-24-2017, 01:35 PM
Myself - AA
Mother - AA
Father - AA
Wife - AG

Pakistani Pahari friend - AA

redifflal
02-24-2017, 01:43 PM
Can someone explain the actual phenotype effect that this SLC24A5 is supposed to have? From what I know and see colloquially, there seems to be a difference between Europeans that can tan vs Europeans who only burn in the sun. Generally those from the Mediterranean countries can tan, while more northwesterly Europeans particularly Irish descent folks only burn. I'd imagine the Indian subcontinent light skin is the same as the Mediterranean variety. Never came across an Indian that only gets sun burn but doesn't actually darken from exposure under the sun. So shouldn't there be an actual genetic difference between the can-tan vs cannot-tan versions?

Reza
02-24-2017, 01:53 PM
There was also this paper (http://www.sciencedirect.com/science/article/pii/S0022202X16326483) which identified rs2470102 as correlating with skin colour in south Asians.

Abstract


Our understanding of the genetics of skin pigmentation has been largely skewed towards populations of European ancestry, imparting less attention to South Asian populations, who behold huge pigmentation diversity. Here, we investigate skin pigmentation variation in a cohort of 1,167 individuals in the Middle Gangetic Plain of the Indian subcontinent. Our data confirm the association of rs1426654 with skin pigmentation among South Asians, consistent with previous studies, and also show association for rs2470102 single nucleotide polymorphism. Our haplotype analyses further help us delineate the haplotype distribution across social categories and skin color. Taken together, our findings suggest that the social structure defined by the caste system in India has a profound influence on the skin pigmentation patterns of the subcontinent. In particular, social category and associated single nucleotide polymorphisms explain about 32% and 6.4%, respectively, of the total phenotypic variance. Phylogeography of the associated single nucleotide polymorphisms studied across 52 diverse populations of the Indian subcontinent shows wide presence of the derived alleles, although their frequencies vary across populations. Our results show that both polymorphisms (rs1426654 and rs2470102) play an important role in the skin pigmentation diversity of South Asians.

chenmatthew0428
02-24-2017, 02:13 PM
This thread was post under the 23andme forum. It will be better if some members post their 23andme results on here.

khanabadoshi
02-24-2017, 03:16 PM
I'm surprised, could it be because of your Uzbek side?

I don't think so, because my uncle isn't from that side. The only thing differentiating myself, my sister, and him is the Kashmiri. However, my brother falls in the same category. The Lahori guy is also half Kashmiri. I was surprised Sadia was A/A, considering her maternal side is more Southern/Eastern.

khanabadoshi
02-24-2017, 03:27 PM
This thread was post under the 23andme forum. It will be better if some members post their 23andme results on here.

Most of us have posted that in other threads. But here you go:

https://i.gyazo.com/aaa7a9d0bcdd80b3d4f3d91a921f86c5.png

Reza
02-24-2017, 03:29 PM
I'd have expected the G allele to be quite rare in your ancestry groups too?

Have a look at this (http://grch37.ensembl.org/Homo_sapiens/Variation/Population?r=15:48432994-48433994;v=rs2470102;vdb=variation;vf=1823172)

In the Gujrati GIH population, only < 5% carried a G copy.

Although in the Punjabi PJL, a G carrier was upto 19%.

khanabadoshi
02-24-2017, 03:29 PM
There was also this paper (http://www.sciencedirect.com/science/article/pii/S0022202X16326483) which identified rs2470102 as correlating with skin colour in south Asians.

Abstract


Our understanding of the genetics of skin pigmentation has been largely skewed towards populations of European ancestry, imparting less attention to South Asian populations, who behold huge pigmentation diversity. Here, we investigate skin pigmentation variation in a cohort of 1,167 individuals in the Middle Gangetic Plain of the Indian subcontinent. Our data confirm the association of rs1426654 with skin pigmentation among South Asians, consistent with previous studies, and also show association for rs2470102 single nucleotide polymorphism. Our haplotype analyses further help us delineate the haplotype distribution across social categories and skin color. Taken together, our findings suggest that the social structure defined by the caste system in India has a profound influence on the skin pigmentation patterns of the subcontinent. In particular, social category and associated single nucleotide polymorphisms explain about 32% and 6.4%, respectively, of the total phenotypic variance. Phylogeography of the associated single nucleotide polymorphisms studied across 52 diverse populations of the Indian subcontinent shows wide presence of the derived alleles, although their frequencies vary across populations. Our results show that both polymorphisms (rs1426654 and rs2470102) play an important role in the skin pigmentation diversity of South Asians.

It's not genotyped for me on 23andme. Too bad.

EDIT: I checked my FTDNA raw data, it's genotyped.



rs2470102

AG





So I am A/G in both rs1426654 and rs2470102.

From the website Reza linked to:

https://i.gyazo.com/db30fb543ff7ea383dadb753c2faad7a.png


https://i.gyazo.com/5895dd7b1fde5213a07ebcd533afcb30.png


It's too bad they don't have frequency data for other populations. I was very curious to see what Baloch or Makrani would get or Pashtun/Pathan.

chenmatthew0428
02-24-2017, 04:03 PM
Most of us have posted that in other threads. But here you go:

https://i.gyazo.com/aaa7a9d0bcdd80b3d4f3d91a921f86c5.png

What is your ethnicity?

drobbah
02-24-2017, 05:20 PM
Interesting study although I'm not surprised that Afro-Asiatic Ethiopians have the A variant but I was shocked that the San and Mandenka also have it.I wonder where they got it from?

rs1426654-AG
rs2470102-Not genotyped on 23andme

VelvetNono
02-25-2017, 05:10 AM
I get AA as well.

khanabadoshi
02-25-2017, 05:45 AM
I'd have expected the G allele to be quite rare in your ancestry groups too?

Have a look at this (http://grch37.ensembl.org/Homo_sapiens/Variation/Population?r=15:48432994-48433994;v=rs2470102;vdb=variation;vf=1823172)

In the Gujrati GIH population, only < 5% carried a G copy.

Although in the Punjabi PJL, a G carrier was upto 19%.

I don't think so, I mean South Punjab and many of Balochistan and Sindh are noticeably darker-skinned than many of northern Punjab, KPK, Northern India, or upper-caste Gujarat. I would guess that A/G or G/G has a significant frequency in these areas. I am surprised that most everyone who has posted, and most everyone else in my family is A/A.

Maybe, many are A/G or G/G in rs2470102? Since most of you don't have FTDNA results to check, I guess we can't know.

Reza
02-25-2017, 09:51 AM
I don't think so, I mean South Punjab and many of Balochistan and Sindh are noticeably darker-skinned than many of northern Punjab, KPK, Northern India, or upper-caste Gujarat. I would guess that A/G or G/G has a significant frequency in these areas. I am surprised that most everyone who has posted, and most everyone else in my family is A/A.

Maybe, many are A/G or G/G in rs2470102? Since most of you don't have FTDNA results to check, I guess we can't know.

Interesting khana!

I certainly think that we'd likely be at least AG in rs2470102, shame it's not tested with 23andme.

Looking at the snapshot you posted, the prevalence seems to be roughly the same of both rs2470102 and rs1426654 across the south Asian populations.

What are your alleles for rs16891982 (SLC45A2)? I ask as we're all CC ancestral but my Pakistani Pahari friend is CG

MonkeyDLuffy
02-25-2017, 02:32 PM
Also keep in mind Punjabi PJL is usually a very high SI group probably because of lower caste background.

That'd explain high AG among them.

khanabadoshi
02-26-2017, 12:58 AM
Interesting khana!

I certainly think that we'd likely be at least AG in rs2470102, shame it's not tested with 23andme.

Looking at the snapshot you posted, the prevalence seems to be roughly the same of both rs2470102 and rs1426654 across the south Asian populations.

What are your alleles for rs16891982 (SLC45A2)? I ask as we're all CC ancestral but my Pakistani Pahari friend is CG

Here ya go:



Myself:
C/C


Brother:
C/C



Sister (Hanif):
C/C


Grandmother (Balq):
C/C


Grandmother Brother:
C/C


Grandfather Sister (Sadia):

C/G


Uncle (Jam):

C/G


Aunt:
C/C


2nd Cousin:

C/G


Mohmand:
C/G


Lahori:
C/C


Multani:
C/C


Ashkenazi:

G/G

Varun R
02-26-2017, 01:50 AM
rs1426654: AG
rs16891982: CC
rs2470102: AG

So same as Khana. Not surprising for my ancestral geography.

Deftextra
02-26-2017, 02:00 AM
Myself-
rs1426654: AA
rs16891982: Not genotyped by ancestry
rs2470102: AA