PDA

View Full Version : Pigmentation, phylogeny, history, and adaptation



Jean M
08-07-2013, 03:27 PM
Razib Khan makes a point: http://blogs.discovermagazine.com/gnxp/2013/08/pigmentation-phylogeny-history-and-adaptation/


The above figure is from Norton et al.’s Genetic Evidence for the Convergent Evolution of Light Skin in Europeans and East Asians. It shows that rs16891982 on the SLC45A2 locus exhibits strong differentiation between Europe and the rest of the world. This is in contrast to SLC24A5, where the well known allele which differentiates Africans/East Asians from Europeans is found at very high frequencies across Western Eurasia (both my parents are homozygotes for the “European” variant; in fact SLC24A5′s derived variant is found at fractions on the order of ~50% in eastern and southern India). The ancestral allele on SLC24A5 is very difficult to find in Europeans, it is so close to fixation for the derived variant. In contrast SLC45A2‘s minor allele is segregating at appreciable frequencies in places like southern Spain, and the derived allele is not fixed even in Northern Europe.

He has collated results from several studies on frequencies of SLC45A2 and notes that:


The frequency of the “European” variant in ~140 northern Ethiopians is 0%. This is peculiar for a population which may be on the order of ~50% West Eurasian. Second, the fraction of SLC45A2 derived variant in South Asians coincidentally tracks the “NE Euro” percentage in Zack Ajmal’s results.

For the latter see http://blogs.discovermagazine.com/gnxp/2013/08/what-the-harappa-ancestry-project-has-resolved/

J Man
08-07-2013, 08:46 PM
So I am assuming then that the ''European'' or light skin version of SLC45A2 rs16891982 is GG at 23andme correct?

Jean M
08-07-2013, 09:24 PM
Yes. See http://snpedia.com/index.php/Rs16891982

See also http://snpedia.com/index.php/Skin_color


SNPs in two genes are known to be involved:

in the SLC24A5 gene:
rs1426654

in the SLC45A2 gene:
rs16891982


http://snpedia.com/index.php/Rs1426654
rs1426654(A), indicates light-skinned European ancestry.

It appears as if this SNP is a relatively new one in human evolution; one estimate is that the rs1426654(A) allele, in other words, light skin pigmentation, spread through the European population around 6,000 - 12,000 years ago. Prior to that, "European ancestors" were most likely relatively brown-skinned.

This SNP is one of three from the SLC24A5 gene that can be analyzed to categorize the ancestry of a person as either European, African, or Asian, based on a 2009 study.

Jean M
08-07-2013, 09:29 PM
See also M. Soejima and Y. Koda, Population differences of two coding SNPs in pigmentation-related genes SLC24A5 and SLC45A2, Int J Legal Med, 121(1):36-9 (2007 Jan) http://www.ncbi.nlm.nih.gov/pubmed/16847698?dopt=Abstract

Abstract


The two genes SLC24A5 and SLC45A2 were recently identified as major determinants of pigmentation in humans and in other vertebrates. The allele p.A111T in the former gene and the allele p.L374F in the latter gene are both nearly fixed in light-skinned Europeans, and can therefore be considered ancestry informative marker (AIMs). AIMs are becoming useful for forensic identification of the phenotype from a DNA profile sampled, for example, from a crime scene. Here, we generate new allelic data for these two genes from samples of Chinese, Uygurs, Ghanaians, South African Xhosa, South African Europeans, and Sri Lankans (Tamils and Sinhalese). Our data confirm the earlier results and furthermore demonstrate that the SLC45A2 allele is a more specific AIM than the SLC24A5 allele because the former clearly distinguishes the Sri Lankans from the Europeans.

DMXX
08-07-2013, 10:24 PM
I'm AA @ rs1426654, GG @ rs16891982. Taken from Razib's blog since it's interesting to see:


http://blogs.discovermagazine.com/gnxp/files/2013/08/slc45a2.jpg
(SLC45A2)

http://blogs.discovermagazine.com/gnxp/files/2013/08/slc24a5.jpg
(SLC24A5)

J Man
08-08-2013, 12:07 AM
Here are my results for these two SNPs/genes.


rs16891982 SLC45A2: GG
rs1426654 SLC24A5: AA

This makes sense as I am of all European background.

J Man
08-08-2013, 12:13 AM
Yes as we can see rs16891982 SLC45A2 GG is much more restricted in it's geographic distribution being really common only among Europeans. On the other hand rs1426654 SLC24A5 AA has a much broader pan West Eurasian distribution. rs1426654 SLC24A5 is thought to have a fairly recent origin but I wonder how old the rs16891982 SLC45A2 GG mutation may be? Mesolithic, Neolithic or post-Neolithic?

DMXX
08-08-2013, 12:22 AM
rs16891982 SLC45A2: GG
rs1426654 SLC24A5: AA


Not surprised at all; it appears most Europeans have the rs16891982=GG - rs1426654=AA combination.

G @ rs16891982 (SLC45A2) seems to be more European-oriented whereas A @ rs1426654 (SLC24A5) has a West Eurasian distribution. This alone supports the assertion of A @ rs1426654 originating before G @ rs16891982 does given the wider distribution of populations with >90%.

As they're clearly using the HGDP-CEPH samples as references we have sampling black holes (as usual) in the Horn of Africa and West Asia proper (Anatolia, Caucasus, Iranian plateau). I'd speculate most West Asians will be AA @ rs1426654 and a larger proportion will be heterozygous (CG) @ rs16891982, but if we presume a cline exists between the east Mediterranean coast and Pakistan, more will be "non-European" (CC) than "European" (GG).

soulblighter
08-08-2013, 02:46 AM
My results
SLC45A2 : CC
SLC24A5 : AA

MikeWhalen
08-08-2013, 11:30 AM
No suprise I have the 'European values, as I am Irish ,Scot-Irish ,Scot and Devonshire English in 15 of 16 Great Great Grandparents...the one 'black sheep' or last of the 16 was from Holland...:)


SLC45A2 33951693 rs16891982 C or G GG

SLC24A5 48426484 rs1426654 A or G AA

Mike

J Man
08-08-2013, 01:27 PM
Not surprised at all; it appears most Europeans have the rs16891982=GG - rs1426654=AA combination.

G @ rs16891982 (SLC45A2) seems to be more European-oriented whereas A @ rs1426654 (SLC24A5) has a West Eurasian distribution. This alone supports the assertion of A @ rs1426654 originating before G @ rs16891982 does given the wider distribution of populations with >90%.

As they're clearly using the HGDP-CEPH samples as references we have sampling black holes (as usual) in the Horn of Africa and West Asia proper (Anatolia, Caucasus, Iranian plateau). I'd speculate most West Asians will be AA @ rs1426654 and a larger proportion will be heterozygous (CG) @ rs16891982, but if we presume a cline exists between the east Mediterranean coast and Pakistan, more will be "non-European" (CC) than "European" (GG).

Well the rs16891982 SLC45A2 GG result was found in 0% of a large number of Ethiopians as Razib states in his write up but I do not know if they count as Horners or not? Also I think you are probably right in that the rs16891982 SLC45A2 GG mutation is younger than the rs1426654 SLC24A5 AA one as it has a much more limited distribution. Would you say then that a Neolithic or post-Neolithic origin of rs16891982 SLC45A2 GG is quite likely?

DMXX
08-08-2013, 01:41 PM
Well the rs16891982 SLC45A2 GG result was found in 0% of a large number of Ethiopians as Razib states in his write up but I do not know if they count as Horners or not? Also I think you are probably right in that the rs16891982 SLC45A2 GG mutation is younger than the rs1426654 SLC24A5 AA one as it has a much more limited distribution. Would you say then that a Neolithic or post-Neolithic origin of rs16891982 SLC45A2 GG is quite likely?

Ah yes, completely overlooked the part about Ethiopians. Yes, they're certainly located on the African Horn.

A neolithic spread of rs16891982=G is pretty likely in my opinion given its' specification in parts of Eurasia associated with West Eurasian-originating neolithic movements. Notice it is present on the steppes and South-Central Asia alongside Europe and West Asia.

J Man
08-08-2013, 02:20 PM
Ah yes, completely overlooked the part about Ethiopians. Yes, they're certainly located on the African Horn.

A neolithic spread of rs16891982=G is pretty likely in my opinion given its' specification in parts of Eurasia associated with West Eurasian-originating neolithic movements. Notice it is present on the steppes and South-Central Asia alongside Europe and West Asia.

Yes I did notice that rs16891982=G is present on both the steppes and South-Central Asia as well. It even has a small presence in Mongolia from the looks of it. Would you say it probably originated in Europe itself? Or would West Asia be a better candidate do you think?

Jean M
08-08-2013, 02:56 PM
G @ rs16891982 (SLC45A2) seems to be more European-oriented whereas A @ rs1426654 (SLC24A5) has a West Eurasian distribution. This alone supports the assertion of A @ rs1426654 originating before G @ rs16891982 does given the wider distribution of populations with >90%.

Makes sense to me.

parasar
01-04-2014, 07:58 PM
SLC45A2 : CG
SLC24A5 : AA

Dr_McNinja
01-05-2014, 04:45 PM
SLC45A2: CC
SLC24A5: AA

Same for me and my mom. There must be some other genes involved though because my mom is quite light skinned compared to me even though I've been raised in New York and she in Pakistan (so it isn't due to tanning).

I checked for an Afghan Pashtun (HRP0370) whose 23andMe profile I manage and they had AA @ SLC24A5 and GG at SLC45A2.

Darko
11-08-2015, 12:52 AM
SLC45A2 : CC
SLC24A5 : AA

Mestace
11-08-2015, 07:44 AM
http://s29.postimg.org/oy9rghdcn/bapsn1.jpg

The magic of DNA confirming on a random sunday morning, after all these years of doubts, that you are basically white.

Darko
11-08-2015, 11:44 AM
I have checked carefully my promethease report at the skin color topic (2 alllele ) and my result is ( for my family finder raw data):

rs1426654(A;A): SLC24A5

but at SLC45A2 i have only rs26722(C;C) alllele .

and i dont know if rs26722(C;C) is equivalent to Rs16891982 or not?

Kurd
11-08-2015, 12:43 PM
SLC 45A2 - CG
SLC 24A5- AA

Kurd
11-08-2015, 01:30 PM
There are many other genes that affect pigmentation and sun sensitivity. For example, rs4911414, which affects sun sensitivity. I tend to think that G is the ancestral allele. From SNPedia:



(G;G) (http://www.snpedia.com/index.php/Rs4911414%28G;G%29)
0
normal


(G;T) (http://www.snpedia.com/index.php/Rs4911414%28G;T%29)
2
2-4x higher risk of sun sensitivity if part of risk haplotype


(T;T) (http://www.snpedia.com/index.php/Rs4911414%28T;T%29)
2
2-4x higher risk of sun sensitivity if part of risk haplotype




Mine is GG, but I have a family member who is GT.

I have also noticed a cline in rs28777 in Eurasians, where Europeans seem to be fixed for the A allele. Mine is AC. There are many more that are associated with pigmentation.

DMXX
11-08-2015, 01:43 PM
I'm AA for rs28777 and GT for rs4911414. My other results were posted in this thread some years back.

As far as my own phenotype goes, I'm fair skinned (exposed areas are now permanently tanned to various degrees, unexposed is pink-white, but a touch more beige than untanned NW Euro's). I tan then burn in exposed areas, burn immediately in unexposed (as I learned the hard way last year after shaving my head... In the British winter sun).

Skin pigmentation is polygenic and not all of the implicated genes are tied to melanocyte function. Also, for Dr_McNinja, epigenetics no doubt has a role to play in the discrepancy between you and your mother's results, even if your genotypes happened to be identical by luck.

icebreaker
11-08-2015, 01:48 PM
My results

rs1426654 AA
rs16891982 GG

Coldmountains
11-08-2015, 01:56 PM
rs28777 AA
rs4911414 GG

rs16891982 GG
rs1426654 AA


My phenotype is quite light: fair skin, blue green eyes and light brown hair with some blonder areas. Untill I was 11/12 years old I had dirty blonde hair. I tann very slowly if at all and get quickly a burn.

SwampThing27
11-08-2015, 03:47 PM
There are many other genes that affect pigmentation and sun sensitivity. For example, rs4911414, which affects sun sensitivity. I tend to think that G is the ancestral allele. From SNPedia:



(G;G) (http://www.snpedia.com/index.php/Rs4911414%28G;G%29)
0
normal


(G;T) (http://www.snpedia.com/index.php/Rs4911414%28G;T%29)
2
2-4x higher risk of sun sensitivity if part of risk haplotype


(T;T) (http://www.snpedia.com/index.php/Rs4911414%28T;T%29)
2
2-4x higher risk of sun sensitivity if part of risk haplotype




Mine is GG, but I have a family member who is GT.

I have also noticed a cline in rs28777 in Eurasians, where Europeans seem to be fixed for the A allele. Mine is AC. There are many more that are associated with pigmentation.

I was surprised to find that I am TT for rs4911414 since I tan pretty well, don't burn too bad and don't freckle. Interestingly, I don't have the risk haplotype though because I am also TT or AA on Rs1015362.

Jean M
11-08-2015, 05:34 PM
I'm AA for rs28777 and GT for rs4911414.

Snap (on 23andMe).

DMXX
11-08-2015, 05:38 PM
Snap (on 23andMe).

I'm a bit confused (though it's probably the stress of seeing the Arsenal-Tottenham score). What does this mean?

Jean M
11-08-2015, 06:10 PM
I'm a bit confused ... What does this mean?

It means that I am also AA for rs28777 and GT for rs4911414 (as shown on 23andMe).

"Snap" is a children's card game. I have forgotten exactly how it is played, but if you have a card in your hand with the same picture as the one face up on the table (or whatever), you say "snap" (= a match), as you put it down. Sorry! I sometimes forget to use plain English.

DMXX
11-08-2015, 06:20 PM
"Snap" is a children's card game. I have forgotten exactly how it is played, but if you have a card in your hand with the same picture as the one face up on the table (or whatever), you say "snap" (= a match), as you put it down. Sorry! I sometimes forget to use plain English.

Ah yes, I used to play that as a child. I thought you either meant "snp" (as in, "where are these SNPs on 23andMe?") or another verb-based meaning of the word (n.11 here (http://dictionary.reference.com/browse/snap)).

MikeWhalen
11-08-2015, 07:25 PM
lol-where I come from, 'snap' is the very polite equivalent to %$#%

:)

Mike


It means that I am also AA for rs28777 and GT for rs4911414 (as shown on 23andMe).

"Snap" is a children's card game. I have forgotten exactly how it is played, but if you have a card in your hand with the same picture as the one face up on the table (or whatever), you say "snap" (= a match), as you put it down. Sorry! I sometimes forget to use plain English.

Mestace
11-08-2015, 07:53 PM
Sun sensitivity

intergenic 32729444 rs4911414 G or T GT


I can tan well, after a few days of red skin :amen:

What's the "risk haplotype"?

Jean M
11-08-2015, 08:05 PM
lol-where I come from, 'snap' is the very polite equivalent to %$#%

Oh dear. Yet another reason for plain English. :biggrin1:

surbakhunWeesste
11-08-2015, 10:35 PM
Sun sensitivity

intergenic 32729444 rs4911414 G or T GT


I can tan well, after a few days of red skin :amen:

What's the "risk haplotype"?

its T

Krefter
11-08-2015, 10:36 PM
My results.

rs1426654 AA
rs16891982 CG

bored
11-08-2015, 10:39 PM
Mine

rs1426654 - AA
rs16891982- CG

Sun sensitivity

rs4911414 - GG
rs28777- AA

Reza
11-08-2015, 10:41 PM
rs1426654 AA
rs16891982 CC

rs28777 AC
rs4911414 GG

Pretty average skin colour for a Bengali!

Varun R
11-08-2015, 11:50 PM
rs1426654 AG
rs16891982 CC

rs28777 CC
rs4911414 GG

AnnieD
11-09-2015, 12:49 AM
I am CG on rs16891982 which seems a little curious given my (assumed) mostly British descent. However, most of my kin are also Colonial American, so the admixture possibilities in the gene pool may be endless. ;)

Very few of my classmates and friends growing up, who were of mostly British and German descent, had any tanning ability. In fact, my maternal Scottish GGGF was nicknamed "Red" not only for his hair but also for his skin color. Both parents were blue-eyed, and 3 out of 4 GP were also blue-eyed, with maternal side also being of fair skin and hair. On my paternal side, it is curious that my GM was the lone brown-eyed family member with dark hair but pale skin. My father has lightish hair in his early childhood photo that turned quite dark by adolescence, and he and his father GF both had skin that could tan quite well. As the CG mixed allele must come from this line, it is curious that it is conjoined with light eyes. La Brana lives on in Colonial USA, or possible NA or other ancestry? ;)

MitchellSince1893
11-09-2015, 04:50 AM
Results for me and both parents (they are all the same on each SNP except for last one)

rs1426654 AA
rs16891982 GG

rs28777 AA
rs4911414 GG (mother and me) GT for father

My father and I are fair complected, my mother can tan well

jeanL
11-09-2015, 03:57 PM
My results:

rs1426654 AA
rs16891982 GG

rs28777 AA
rs4911414 GG

I tan mostly in the upper(that is the part that has hair opposite to palm of my hand) part of my arms if I have continue low sun exposure. Otherwise my neck gets really red and if and when I go to the beach I will still get badly sunburnt. The most ridiculous case was last time I went I forgot to put sunscreen on the top part of my feet and I got sunburnt there.

Mellifluous
11-10-2015, 08:36 AM
skin tone

SLC24A5 rs1426654 AA
SLC45A2 rs16891982 CG

sun sensitivity

SLC45A2 rs28777 AC
rs4911414 GG

I also have a recessive ginger gene and blonde gene
rs35264875 AT
rs1805007 CT

I don't tan well unless I try to tan slowly. Usually, I turn red and then I burn. I have some freckles, but not on my face.

Mellifluous
11-10-2015, 09:39 AM
Found two genes that are related to freckling: rs2153271 and rs4778138

I have rs2153271 TT and rs4778138 AA, so I have more freckles than usual.

http://www.mrbill.net/dna/results/23andMe/Traits/Freckling%20Report/Freckling%20Report%20-%2023andMe.html

Dorkymon
11-10-2015, 07:53 PM
rs1426654 AA
rs16891982 CG

rs28777 AC
rs4911414 GG

rs2153271 CC
rs4778138 AA


I tan quite well, although I may burn during the first days, and my head hair usually discolours to a blondish brown from overexposure to sun rays. Most of the year though, I am pale to such a degree that people might be concerned about my health. There are few freckles below my eyes, but a decent amount of moles on the rest of my body. Lately, the number of reds has been increasing.

Darko
11-10-2015, 11:28 PM
I checked my family finder raw data via promethease tool and i got this result (with yoruba African ethnicity reference ):
skin color (2):
rs1426654(A;A): (frequency 0%)
rs26722(C;C): (frequency 88.4%)

Hair color(2):
rs1805008(C;C): (frequency 95.9%)
rs1805005(G;G): (frequency 99.3%)

So finally FTDNA don't test rs16891982 and the other allele only 23andme which test those allele.

MonkeyDLuffy
11-11-2015, 12:59 AM
SLC45A2 = CC
SLC24A5 = AA

I'm light brown with reddish tint. Light for SA standards.

ashwinb
11-11-2015, 04:20 AM
SLC24A5 rs1426654 AG
SLC45A2 rs16891982 CC
I'm totally brown.

kenji.aryan
11-15-2015, 12:58 PM
I do have risk type (T) under sun sensitivity .

parasar
11-16-2015, 05:49 PM
SLC45A2 : CG
SLC24A5 : AA

SLC24A5 rs1426654
GG (Bichon, Upper Paleolithic Switzerland)
AA (Kotias Upper Paleolithic Georgia)
AA (Satsurblia Mesolithic Georgia)

SLC45A2 rs16891982, respectively
CC
CC
CC

MonkeyDLuffy
11-16-2015, 09:07 PM
I do have risk type (T) under sun sensitivity .

Rs1015362 = CT

what does that mean?

MonkeyDLuffy
11-16-2015, 09:09 PM
There are many other genes that affect pigmentation and sun sensitivity. For example, rs4911414, which affects sun sensitivity. I tend to think that G is the ancestral allele. From SNPedia:



(G;G) (http://www.snpedia.com/index.php/Rs4911414%28G;G%29)
0
normal


(G;T) (http://www.snpedia.com/index.php/Rs4911414%28G;T%29)
2
2-4x higher risk of sun sensitivity if part of risk haplotype


(T;T) (http://www.snpedia.com/index.php/Rs4911414%28T;T%29)
2
2-4x higher risk of sun sensitivity if part of risk haplotype




Mine is GG, but I have a family member who is GT.

I have also noticed a cline in rs28777 in Eurasians, where Europeans seem to be fixed for the A allele. Mine is AC. There are many more that are associated with pigmentation.

I'm GT, does that mean my skin burn's quickly?

SwampThing27
11-17-2015, 03:32 AM
I'm GT, does that mean my skin burn's quickly?

Based on studies, people who are heterozygous for both Rs1015362 and rs4911414 are more sensitive to the sun. Those two snps form a haplotype so you have to look at both to see the effect. http://snpedia.com/index.php/Rs1015362

Basically if you have a G in Rs1015362 and a T in rs4911414.