DNA and Skin Color

Recent study shows association rs1426654 SNP with skin pigmentation, explaining about 27% of total phenotypic* variation.  Previous studies have showed that rs1426654 SNP accounts for lighter skin in Europeans but not in East Asians.

Basically for South Asians if rs1426654 SNP is AA then light skin, if AG then medium dark and GG dark (see graph).  My rs1426654 is AG and I am medium dark. Also see this post on my DNA and heroin addiction etc.

Excerpts

We date the coalescence of the light skin associated allele at 22–28 KYA. Both our sequence and genome-wide genotype data confirm that this gene has been a target for positive selection among Europeans.


One of the key pigmentation genes in humans is SLC24A5.  That a non-synonymous variant (ref SNP ID: rs1426654) in the third exon of this gene explains 25–38% of the skin color variation between Europeans and West Africans. The ancestral (G) allele of the SNP predominates in African and East Asian populations (93–100%), whereas the derived (A) allele is almost fixed in Europe (98.7–100%)

In India here is a general trend of rs1426654-A allele frequency being higher in the Northern (0.70±0.18) and Northwestern regions (0.87±0.13), moderate in the Southern (0.55±0.22), and very low or virtually absent in Northeastern populations of the Indian subcontinent (Figure 2, Table S6). Notably, the Onge and the Great Andamanese populations of Andaman Islands also showed absence of the derived-A allele.

Loss of pigmentation in eastern and western Eurasia seems to be a case of convergent evolution (different mutations in overlapping sets of genes), the H. sapiens sapiens ancestral condition of darker skin is well conserved from Melanesia to Africa.

More at
http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003912

Via
http://blogs.discovermagazine.com/gnxp/2013/11/big-sweeps-happen/#.UoHuzxC-X1U


*Genotype vs. Phenotype:
Very important concept. Even if the genes are identical (genotype) the outward expression / looks (phenotype) could be different. Example would be identical twin, who have the same genes will have differences and fingerprints will be different. Another example would be children of short parents (and also have the sort genes) could be taller because of better nutrition.

The opposite is also true in that just because outward appearance is similar (phenotype) the genes (genotype) do not have to be similar. Example: Africans and Papua New Guineans though superficially similar are about the furthest apart genetically.

Vijaya Kuveni: Paradigm for M mtDNA in South Asia

PCA (left) and Admixture Bar (right)  plot

All Sri Lankans know the story of Vijaya and Kuveni from the Mahavamsa and Rajavali.  The basic crux of the story is that invaders, predominantly male married local women.  The gist of what DNA research is saying is that in India (and for Sri Lanka*) our mothers ancestry (mtDNA) is the same, but our paternal lines (Y-DNA) can be different.  One paper found that 70%  of India including 26 tribal populations carried the M mtDNA haplogroup.   In the Harappa DNA project 50% of the few Sri Lankan participants (8) had M mtDNA.  Two of the four self identified Tamils and two of the four self identified Sinhalese.
(* my extrapolation)

Before I get to excerpts of the research articles a few words on the PCA (Principal Component Analysis) plot on this page.  Its one of the few plots that I have seen where PCA captures the geographic distribution without a geo position data in the PCA analysis.  What I am trying to say is the V shape of India's genetic Cline is evident in the in the PCA Plot.

 From Chandrasekar et al

Macrohaplogroup M is ubiquitous in India and covers more than 70 per cent of the Indian mtDNA lineages The lineages M2, M3, M4, M5, M6, M18 and M25 are exclusive to South Asia, with M2 reported to be the oldest lineage on the Indian sub-continent.

The deep rooted lineages of macrohaplogroup ‘M’ suggest in-situ origin of these haplogroups in India. Most of these deep rooting lineages are represented by multiple ethnic/linguist groups including tribals of India

From Discover Magazine

An interesting point though is that the mtDNA, the female lineage, does not seem to diverge from other South Asians much at all. I find it intriguing that this is the same pattern we see along the major NW-SE axis of variation. It seems that mtDNA lineages unite South Asians, while the Y lineages separate them (by caste and region). The generality has many exceptions, but it points to a peculiar sex mediated admixture process from both the northwest and northeast. Men on the move have reshaped the genetics and culture of South Asia, but the mtDNA lineages still point to an ancient Eurasian group with distant but stronger affinities to the east than the west. The mtDNA are likely the purest distillation of ASI (Ancestral South Indian). 

From  Witas et al in PLOSone

Ancient DNA methodology was applied to analyse freshly unearthed remains (teeth) of 4 individuals. Dated to the period between 2.5 Kyrs BC and 0.5 Kyrs AD the studied individuals carried mtDNA haplotypes corresponding to the M4b1, M49 and/or M61 haplogroups, which are believed to have arisen in the area of the Indian subcontinent during the Upper Paleolithic and are absent in people living today in Syria . 

Studied remains were excavated at two archaeological sites in the middle Euphrates valley and dated between the Early Bronze Age and the Late Roman period. The obtained data enrich the as yet modest database of Mesopotamian ancient DNA and suggest a possible genetic link of the region with the Indian subcontinent in the past leaving no traces in the modern population.

Update
This means the genes of prehistoric people are still prevalent among modern Sri Lankans

We report here the first complete mitochondrial sequences for Mesolithic hunter-gatherers from two cave sites. The mitochondrial haplogroups of pre-historic individuals were M18a and M35a. Pre-historic mitochondrial lineage M18a was found at a low prevalence among Sinhalese, Sri Lankan Tamils, and Sri Lankan Indian Tamil in the Sri Lankan population, whereas M35a lineage was observed across all Sri Lankan populations with a comparatively higher frequency among the Sinhalese.

First AASI mtDNA genomes from Sri Lanka (2500 and 5500 BC)
Please Read comments as well, knowledgeable
https://www.brownpundits.com/2022/11/30/first-aasi-mtdna-genomes-from-sri-lanka-2500-and-5500-bc/

Also see:

Sinhalese and Tamil DNA Admixture Analyis
My DNA 01: Heroin Addiction, Smoking etc
Sri Lankan Population DNA Genetics 01
Basic Primer on Population DNA Genetics
List of reference and excerpts

Sinhalese and Tamil DNA Admixture Analyis

Updated analysis of DNA admixture of Sri Lankan participants at HarappaDNA. There are 7 Sri Lankans (3 Sinhalese, 4 Tamils). I have not included the part Sri Lankans whose immediate parents are not from Sri Lanka.

For comparison of Sri Lankan DNA with neighboring populations I have included seven other populations, TN Tamil(7), TN Tamil Brahmins(14), Kerala(10), Bengali(7), Punjabi(18) and Iranian(8). (TN=Tamil Nadu, (#) = the number of individuals). So before the results,
  *please consider getting a DNA test. Its USD 99 at 23andMe.
  *All Charts are Interactive. Clicking on them will sort the chart or table and info on data point.

Average Component Admixture for Populations

Components are based on reference population peaks. Please see National Geographic Reference Populations Overview and Regions overview for lucid description of similar analysis. Do also have a look at the complete Harappa World Admixture. This analysis is a subset of Harappa World Admixture.

South Indian Component
1) Decreases from TN Tamil (60%) > SL Tamil (58%) > Sinhalese (55.5%)
2) Bengali's, Kerala and TN Tamil Brahmins have approx the same (48%)
3) As expected Iranias have the least (3%). Europeans (not in this data) have 0%.

Baloch Component
Ranges from 40% (Punjabi's) to 29.1% (TN Tamil) for South Asian populations. Sinhalese and SL Tamils are in the mid range with approx 31%.

Caucasian Component
Iranians have 41% of this component. The Punjabis have 9.8%. Southern and East South Asians have less that 5%, with Sinhalese 3.3% and Tamil 2.1%

South East (SE) Asian Component
Bengali's have the highest percentage (4.7%) of this component reflecting proximity of borders with SE Asian populations. Sinhalese have 1.6% of SE component while, TN-Tamils and SL-Tamils both have 1.3% of SE Asian component.

Chart of Component Admixture for each Individual

The South Indian component is close to 60% for both Sinhalese and Tamils except for individual HRP0122 (49%) and HRP0232 (53%). HRP0232 is I, this blog author. The low f53% (for Sri Lankan) South Indian component is probably because of a maternal great grandmother who was probable European. Thats is reflected in the elevated NE European component of 4.7% compared other Sri Lankans with less than 2%. HRP0122 too has elevated NE European component of 4%. Maybe HRP0122  may care to comment on the elevated NE European component. HRP0122 and I we have corresponded by email and know of our identities.

Table of HarappaID's etc

Table has the Sri Lankan (Sinhalese and Tamil) and few subset individuals with their Harappa ID, Self ID'd Ethnicity and Assigned Group Population for this Analysis.

Resources:
a) Excel Spreadsheet of Data used in this analysis.
b) The complete World Admixture results at HarappaDNA.

Also See:
1) My DNA 01: Heroin Addiction, Smoking etc
2) Sri Lankan Population DNA Genetics 01
3) Basic Primer on Population DNA Genetics

My DNA 01: Heroin Addiction, Smoking etc

Got my DNA results from 23andMe, very quick in almost 3 weeks.
First off,  the 23andMe autosomal, Y-DNA, mtDNA and mitochondrial data can be downloaded here.

So until I get Zacks analysis of ancestral groups, here are a very few of the large amount of health and trait indicators I got with my DNA results analysis.  Please Note most of this type of research has been done on people with European ancestry, and applicability to South Asians is yet to be determined.

rsid       chromosome position  genotype       Trait rs1799971     6       154402490    AG       Heroin Addiction rs17822931   16        46815699    TT       Ear Wax Type rs762551     15        72828970    AA       Caffeine Metabolism rs1051730    15        76681394    AG       Smoking Behavior

Heroin Addiction: rs1799971  AG: Substantially higher odds
This study of 139 heroin addicts (primarily Swedes) and 170 non-addicts found that people with at least one G at rs1799971 have almost 2.9 times the odds of being a heroin addict. .
I was dead scared of the horse because of all the stuff I had read about teeth falling out etc. Good thing I am no longer a young adult and that I read all the warnings when i was a young adult.

• Zhang H et al. (2006) . “Association between two mu-opioid receptor gene (OPRM1) haplotype blocks and drug or alcohol dependence.” Hum Mol Genet 15(6):807-19.
• Bart G et al. (2004) . “Substantial attributable risk related to a functional mu-opioid receptor gene polymorphism in association with heroin addiction in central Sweden.” Mol Psychiatry 9(6):547-9.

Ear Wax: rs17822931  TT: Dry Ear wax
Earwax type is highly heritable. This means that this trait is controlled almost entirely by your genes-environmental factors play little or no role. Because of this, simply knowing your genotype is enough to know your earwax type.
I have dry earwax and body sweat does not smell all that much (according to others) even though I sweat profusely (overweight). The sweat does tend to smell when I eat steak over two three days (this happens only during Christmas/Year end) and when I eat Ethiopian/Indian food. I think this because of larger amounts of Fenugreek (sinhala uluhal) in Berbere and Indian curry powder.  I guess that is Environment overshadowing Genes.

• for more info see Ear Wax and Armpit Odor 

Caffeine Metabolism: rs762551  AA: Substantially higher odds
The form of the SNP rs762551 a person has determines how fast CYP1A2 metabolizes caffeine. In this study, people with the slower version of the CYP1A2 enzyme who also drank at least two to three cups of coffee per day had a significantly increased risk of a non-fatal heart attack. The study found that fast metabolizers, on the other hand, may have actually reduced their heart attack risk by drinking coffee.
I drink more than 6 cups of black coffee at work (US), specially because its free. Drink the stuff even before I go to sleep. 

• Cornelis MC et al. (2006) . “Coffee, CYP1A2 genotype, and risk of myocardial infarction.” JAMA 295(10):1135-41. 

Smoking Behavior: rs1051730  AG: More on Average if Smoker
Genes vs. Environment: Not all smokers are created equal—some light up just a few times a day, while others go through multiple packs. There are many social and environmental factors that affect whether people start smoking, but once they do, research based on Dutch Twins has shown that genetic factors play a large part in how dependent on nicotine they'll become and how much they'll smoke.
I used to smoke almost 3 packs (20 packs) as a teenager and young adult. Then stopped for about 13 years, started again and was smoking about 30 cigarettes. The only reason it was not more was cost and restrictions in ability to smoke in many locations. Stopped again and its been more than 6 years with the main motivation for stopping being cost and that I am a little too old to be bumming cigarettes.

• Lerman C., Berrettini W. Elucidating the role of genetic factors in smoking behavior and nicotine dependence. Am. J. Med. Genet. B Neuropsychiatr. Genet. 2003;118B:48-54.

Also see
Sinhalese and Tamil DNA Admixture Analyis

Vijaya Kuveni: Paradigm for M mtDNA in South Asia

Wet or Dry Ear wax and Armpit Odor

Excerpt from a Nature Genetics Article.

They write that earwax type and armpit odor are correlated, since populations with dry earwax, such as those of East Asia, tend to sweat less and have little or no body odor, whereas the wet earwax populations of Africa and Europe sweat more and so may have greater body odor.

They show that a SNP, 538G A (rs17822931), in the ABCC11 gene is responsible for determination of earwax type. The AA genotype corresponds to dry earwax, and GA and GG to wet type. A 27-bp deletion in ABCC11 exon 29 was also found in a few individuals of Asian ancestry.

I think the excerpt of article is self explanatory. When I have my autosomal DNA, I too will check for rsID rs17822931 and see the genotype. I already know my ear wax type. (Please see here on reading rsID from a typical autosomal file).

According to the ALFRED database, This SNP is the first example of DNA polymorphism determining a visible genetic trait.


From:  Gene Expression: Wet or Dry Ear Wax 
Original article:  Nature Genetics 38, 324 - 330 (2006) A SNP in the ABCC11 gene is the determinant of human earwax type Koh-ichiro Yoshiura et al
Other related articles:  The impact of natural selection on an ABCC11 SNP determining earwax type Ohashi J et al 2011  (A blog post discussing article)