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DMXX
07-05-2013, 05:51 PM
While conducting some research for my eye colour project (http://www.anthrogenica.com/showthread.php?1057-DMXX-s-Eye-Colour-Project-(v-2)), I stumbled upon some interesting maps on light pigmentation genotypes from S. Walsh's excellent DNA Phenotyping: The prediction of human pigmentation traits from genetic data.

Several lines of inquiry into different areas of human pigmentation (hair, eye) were investigated in the compilation. As shown in the maps, the primary populations used are those from the HGDP-CEPH database (http://www.cephb.fr/en/hgdp/diversity.php/).


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The maps are shown in this thread. What immediately caught my attention was the genotype presentation in Pakistan, the Kalash in particular. On numerous anthropology boards, the Kalash (an Indo-Iranian speaking ethnic minority situated near the Karakoram mountain range) (http://en.wikipedia.org/wiki/Kalash_people) are a "hot topic" due to pictures circulated online showing fair featured individuals (Google search example (https://www.google.co.uk/search?safe=off&q=kalash&bav=on.2,or.r_cp.r_qf.&bvm=bv.48705608,d.bmk&biw=1280&bih=659&um=1&ie=UTF-8&hl=en&tbm=isch&source=og&sa=N&tab=wi&ei=RgDXUen6JMGIrQee6YAQ)).

However, as these maps demonstrate, there is an obvious pigmentation cline away from Europe which even the Kalash do not defy. Most of the charts reveal that, as one may expect if the distribution of light pigmentation is tied predominantly to geography, Near-Eastern groups such as Palestinians or the Druze tend to match or exceed the values observed in Pakistan. This leaves us with a fairly plausible conclusion; increased light pigmentation among West Eurasians correlates with increased proximity to Europe.


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It is worth acknowledging that the Kalash do pull closer towards Europe than their Pakistani compatriots, to the point they cluster with Sardinians and the Druze (Figure 6); however, the majority (approximately 80%) are predicted to have brown eyes (Figure 5).
Referring again to the genotype maps, it is certainly apparent that the Kalash generally have an increased incidence of lighter pigmentation relative to their neighbours. I suspect a combination of long-standing endogamy due to geographical and cultural isolation is responsible for the increased lighter pigmentation relative to the nearby Pathan and Burusho. The tendency for the Kalash to form their own autosomal components when included in datasets supports this.

A very similar trend can be observed in the hair colour results, although I am hesitant to comment on these owing to an embargo on those sections of Walsh's compilation.

This begs the question; if the Kalash are demonstrated to predominantly be brown-eyed, why is there such a large volume of circulated images of light-eyed ones online? It is most probable that foreign travellers in the region took exceptional and simultaneous notice to the distinct culture of the Kalash and some differences in phenotype relative to other populations in the region.

The hard data conclusively demonstrates that the Kalash are, contrary to the discussions had online, only remarkable in a relative sense when it comes to pigmentation. This is an important lesson regarding the propagation of assertions in discussions based almost entirely on data which may themselves be biased (in this case likely cherrypicked photos).

Although the bulk of this post concerns interpretations of the Kalash results, please feel free to discuss any other aspect of the maps themselves.

newtoboard
07-05-2013, 08:09 PM
I believe old school anthropologists noticed a light eyes of a frequency of 20% in Pashtuns are who are definitely darker than Pashtuns.

I'd be more interested in seeing where the Pamiris fall and to a lesser degree where the Nuristanis fall.

This map might interest you.

http://cogweb.ucla.edu/ep/images/Frost-2.jpg

DMXX
07-05-2013, 08:28 PM
I believe old school anthropologists noticed a light eyes of a frequency of 20% in Pashtuns are who are definitely darker than Pashtuns.

I'd be more interested in seeing where the Pamiris fall and to a lesser degree where the Nuristanis fall.


There's a typo in your first line, so I do not know whom you are referring to, newtoboard. Nevertheless, the Pashtuns of Pakistan are shown to have as much predicted light eyes as the Palestinians.

That would be quite interesting to see, but I'd imagine their values wouldn't stray too far from the Kalash. As explained in the post, geography predominates the picture. The Pamiris sit due north of the Kalash.

newtoboard
07-06-2013, 03:01 PM
I meant to say:

I believe old school anthropologists noticed light eyes at a frequency of 20% in Pashtuns are who are definitely darker than the Kalash ( and other Dardic speakers minus Kashmiris).

Geography does fit the Kalash but the Pamiri Tajiks are likely off the South Asian cline that the Kalash sit on imo. While we are on the topic of Pamiris do you think the ancient Sakas represent SE Iranian speakers? So much for their Scythian origin in that case.

What are the Central S Asian populations closest to the Kalash and the ME population near them?

DMXX
07-06-2013, 04:30 PM
Geography does fit the Kalash but the Pamiri Tajiks are likely off the South Asian cline that the Kalash sit on imo. While we are on the topic of Pamiris do you think the ancient Sakas represent SE Iranian speakers? So much for their Scythian origin in that case.

What are the Central S Asian populations closest to the Kalash and the ME population near them?

The data actually shows Tajiks are also a part of the South Asian cline (https://docs.google.com/spreadsheet/ccc?key=0ArJDEoCgzRKedEY4Y3lTUVBaaFp0bC1zZlBDcTZEY lE#gid=0) (technically Iranians sit on that cline as well going by their S. Asian component values relative to Armenians and Turks, refer to the same link). It is unfortunate that the Geno 2.0 components do not separate South Asia from (South)West Asia, otherwise we'd have a good idea concerning how the Pamiris stack up against generic Tajiks.

I had a document which dissected the linguistic basis of the Iranic family classifications, will post more about that if I find it.

As you know, the Kalash are notorious for forming their own component in autosomal DNA runs such as ADMIXTURE. Dienekes did manage to calculate the closest populations to the modal (most common) component among them (http://dodecad.blogspot.com/2011/10/origin-of-kalash-inferred-with.html) and it was thoroughly West Asian (note the very large genetic distance):



[186,] "Kurd_D" "50.2"
[187,] "Kurds_Y" "50.7"
[188,] "Armenian_D" "50.9"
[189,] "Armenians_Y" "51.2"
[190,] "Adygei" "51.5"
[191,] "Chechens_Y" "53"
[192,] "North_Ossetians_Y" "53.2"
[193,] "Lezgins" "54.4"
[194,] "Georgians" "59.8"
[195,] "Georgian_D" "60.1"
[196,] "Abhkasians_Y" "60.5"
[197,] "Kalash" "63.2"


Zack at the Harappa Project carried out an investigation into the ChromoPainter chunk counts of various populations (http://www.harappadna.org/2012/08/eurasian-chromopainter-chunk-counts/), one of which included the Kalash. The top donors listed were neighbouring populations. The top non-South Asian donors were Tajiks.

So, when the Kalash do not form their own component and their genetic peculiarities are manually unpacked, they match best with their immediate neighbours (Pathan, Burusho), then the Tajiks, and finally show distant connections with West Asians next.

DMXX
07-06-2013, 09:35 PM
The results make geographical sense but I get the impression the Genographic Project has just arbitrarily sampled "Indians" from the four corners of the country without taking into account their caste or religious affiliation, which has been shown in genetics to play a very significant factor in the results.

Fire Haired
10-19-2013, 01:42 AM
The origin of light pigmentation in Kalash is they are Indo Iranian speakers like Scythians who were described by Greek historian as having bright red hair and blue eyes. You can look at pigmentation genes from Bronze and Iron age suspected Indo Iranian cultures in Siberia and central asia they have mainly blonde-light brown hair and blue or green eyes and all have fair to medium skin(Indo Iranian and Tocherian DNA (http://www.anthrogenica.com/showthread.php?1431-INdo-Iranian-and-Tocherian-DNA)). They had high amount so mtDNA haplogroups typical of Russian Mesolithic European hunter gathers U5a, U2e, and U4 and high amount of mtDNA more typical of samples from Neolithic European farmers H, T(almost all T1 then T1a), K, I, and W, with a few very J's. Their Y DNA 16 out of 17 R1a1 which is very popular in modern Indo Iranian speakers including Kalash specifically subclade R1a1a1b2 Z93. I have also seen in austomal DNA spreadsheets from Dodecade "North Euro"(from pre farming Europe) admixture in Indo Iranian speakers like Kurds that does not exist in their non Indo Iranian neighbors Assyrians, Samaritans, Palestine's, etc. It is the same story for Gedorsian in western Europe which shows almost identical distribution to Germanic Italo Celtic R1b1a2a1a L11 which makes sense since its ancestor subclades originated in the Near east. I think that also means not all "west Asian" in Europe is Neolithic some may have come in copper and bronze ages. There is no doubt there is a small amount of European admixture Indo Iranian speakers have that other Near easterns and south Asians do not which can explain why some ethnic groups like Kalash are known for fair features.

Since there is almost no "North Euro" in non Indo Iranian near easterns it probably means there has been very little inter marriage with Europeans in the Near east. But North Euro in North Africans mainly with pretty good amounts of Euro mtDNA V and U51b1b which probably came before Neolithic is for North Africa and can maybe explain fair features in some Berber ethnic groups like Kablye. And since there is "west Asian" and "southwest Asian" in almost all of Europe I definitely think that's mainly Neolithic there was west Asian in Otzie copper age farmer in Italy but non in all hunter gather samples from Neolithic and Mesolithic. I think that areas of Europe with over 50% combined Meditreaen, west Asian, and southwest Asian all mainly spreading in Neolithic with farming and partly in copper and bronze age in west Europe could explain darker features in mainly southern Europe compared to eastern, central, and northern Europe. It might even explain the phenomenon of brown skinned British Celts which was even mentioned by Roman writers, medieval English, and modern people and I witness it in my own family.

Jean M
11-08-2013, 05:28 PM
Chandana Basu Mallick et al., The Light Skin Allele of SLC24A5 in South Asians and Europeans Shares Identity by Descent
http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003912


Skin pigmentation is one of the most variable phenotypic traits in humans. A non-synonymous substitution (rs1426654) in the third exon of SLC24A5 accounts for lighter skin in Europeans but not in East Asians. A previous genome-wide association study carried out in a heterogeneous sample of UK immigrants of South Asian descent suggested that this gene also contributes significantly to skin pigmentation variation among South Asians. In the present study, we have quantitatively assessed skin pigmentation for a largely homogeneous cohort of 1228 individuals from the Southern region of the Indian subcontinent. Our data confirm significant association of rs1426654 SNP with skin pigmentation, explaining about 27% of total phenotypic variation in the cohort studied. Our extensive survey of the polymorphism in 1573 individuals from 54 ethnic populations across the Indian subcontinent reveals wide presence of the derived-A allele, although the frequencies vary substantially among populations. We also show that the geospatial pattern of this allele is complex, but most importantly, reflects strong influence of language, geography and demographic history of the populations. Sequencing 11.74 kb of SLC24A5 in 95 individuals worldwide reveals that the rs1426654-A alleles in South Asian and West Eurasian populations are monophyletic and occur on the background of a common haplotype that is characterized by low genetic diversity. We date the coalescence of the light skin associated allele at 2228 KYA. Both our sequence and genome-wide genotype data confirm that this gene has been a target for positive selection among Europeans. However, the latter also shows additional evidence of selection in populations of the Middle East, Central Asia, Pakistan and North India but not in South India.


Isofrequency map illustrating the geospatial distribution of SNP rs1426654-A allele across the world.
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Razib Khan comments: http://blogs.discovermagazine.com/gnxp/2013/11/big-sweeps-happen/

Mehrdad
01-15-2014, 08:30 PM
I'm rs1426654 - GG. I know Europe is usually AA and AG, I am interested in South Asia, if there's more GG since this could be a West Asian?

parasar
01-15-2014, 09:40 PM
I'm rs1426654 - GG. I know Europe is usually AA and AG, I am interested in South Asia, if there's more GG since this could be a West Asian?

West Asia, Europe and northern South Asia have all undergone a G-A sweep. So perhaps your dad is AG and mom GG.
There is no evidence of a selective sweep in southern South Asia.

toast
01-16-2014, 01:32 AM
I'm rs1426654 - AA, can anyone tell me what this means in terms of pigmentation genotype? thnx

parasar
01-16-2014, 01:26 PM
I'm rs1426654 - AA, can anyone tell me what this means in terms of pigmentation genotype? thnx
http://blogs.discovermagazine.com/gnxp/2013/08/pigmentation-phylogeny-history-and-adaptation/

tamilgangster
06-27-2014, 10:56 AM
THe North India one was probably taken from Uttarkhand or HP, the east india one was either an adivasi or a assamese. The SE asian in the south and west indian, are similar ratio to the onge component in harappa DNA. The SE asian component is a hybrid of mongoloid and australoid im estimating that it is (70% australoid 30% mongoloid)