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Thread: Lactose persistence genes spread in India

  1. #1
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    Post Lactose persistence genes spread in India

    India being very diverse origins, so their lactose persistence genes are sourced from numerous waves of population expansions from Africa, Arabia, Iran, Fareast, Siberia etc...

    The earlier papers on lactose genes on Indians didn't had enough information at the genomic level so they focused only on the LP genes found in the Europeans which is present in Brahmin populations

    eg. paper by RK Tandon describes only European genes but possess zero knowledge on Middle East, african & Far east genomes. The C/T-13910 polymorphism is an european variant found in populations exposed to Steppe migrations.

    https://www.ncbi.nlm.nih.gov/pubmed/7234720


    In mammals, lactase, the enzyme that hydrolyzes the milk sugar lactose, is normally down-regulated after weaning, but at least five human populations around the world have independently evolved mutations regulating the expression of the lactase-phlorizin-hydrolase gene. These mutations result in a dominant lactase persistence phenotype and continued lactase tolerance in adulthood. A single nucleotide polymorphism (SNP) at C/T-13910 is responsible for most lactase persistence in European populations, but when and where the T-13910 polymorphism originated and the evolutionary processes by which it rose to high frequency in Europe have been the subject of strong debate. A history of dairying is presumed to be a prerequisite, but archaeological evidence is lacking. In this study, DNA was extracted from the dentine of 36 individuals excavated at a medieval cemetery in Dalheim, Germany. Eighteen individuals were successfully genotyped for the C/T-13910 SNP by molecular cloning and sequencing, of which 13 (72%) exhibited a European lactase persistence genotype: 44% CT, 28% TT. Previous ancient DNA-based studies found that lactase persistence genotypes fall below detection levels in most regions of Neolithic Europe. Our research shows that by AD 1200, lactase persistence frequency had risen to over 70% in this community in western Central Europe. Given that lactase persistence genotype frequency in present-day Germany and Austria is estimated at 71-80%, our results suggest that genetic lactase persistence likely reached modern levels before the historic population declines associated with the Black Death, thus excluding plague-associated evolutionary forces in the rise of lactase persistence in this region.

    https://www.ncbi.nlm.nih.gov/pubmed/24465990


    https://www.sciencedirect.com/scienc...02929707000183 provides a high level look on Middle east & African varieties

    The European T−13910 and the earlier identified East African G−13907 LP allele share the same ancestral background and most likely the same history, probably related to the same cattle domestication event. In contrast, the compound Arab allele shows a different, highly divergent ancestral haplotype, suggesting that these two major global LP alleles have arisen independently, the latter perhaps in response to camel milk consumption. These results support the convergent evolution of the LP in diverse populations, most probably reflecting different histories of adaptation to milk culture.


    https://pdfs.semanticscholar.org/1ab...f768a6c9f3.pdf
    provides

    Table 3 Frequencies of other lactase persistence alleles in the MCM6 gene
    Country or population Alleles Frequency (%) Reference
    Saudi Arabia LCT-13915T.G 48.9; 59.4 25,30
    Jordan 39.1 25
    Sudan (Beni Amir) 24.4 25
    Ethiopia (Afar) 15 25
    Sudan (Jaali) 14.2 25
    Ethiopia (Amharic) 13.2 25
    Ethiopia (Somali camel herders) 5.1 28
    Tanzania LCT-14010G.C 31.9 29
    Kenya 27.6 29
    Xhosa (South Africa) 12.8 27
    Xhosa (mixed ancestry) 8.1 27
    Angola ,7 17
    Mozambique No LP allele 17
    Ethiopia (Somali camel herders) 0.5 28
    Sudan (Afro-Asiatic Beja) LCT-13907C.G 20.6 29
    Ethiopia (Afar) 20 25
    Ethiopia (Somali camel herders) 5.6 28
    Northern Russia LCT-13914G.A Rare variant 31
    Austria Two individuals 12
    China (Kazak) LCT-22018G.A/ 18 32
    China (Northern) LCT-13910CC 6.8 32
    Japanese Brazilians 5.3 33
    Tanzania (Akie) One individual 29
    Sudan (Jaali) LCT-14009T.G 6.6 28
    Ethiopia (Somali camel herders) 1.4 28


    In India there are many Lactose Persistence gene variant that are found in Africa, Far East, Latin Americas, South Europe, Finns etc... The following table shows an approximate mappings from the test populations found on Calculator sites.

    nMonte3 current
    Velamas Gujarati_D Muslim_UP Tharus Punjabi_1000genomes
    1.859005 3.210341 4.491247 4.998440 6.040323

    G25 Ancients Dist 0.99 Shahr_I_Sokhta_BA3:S8728.E1.L1 65.2 Saidu_Sharif_IA_o:S7722.E1.L1 17.8 Udegram_IA:I1985 7.8 Jordanian:S_Jordanian-1 4.4 Barikot_IA:I6545 2.2 Scotland_N:I26602 Narva_Lithuania: Donkalnis6

    mtDNA mutation 309.1C 315.1C 522.1A 522.2C G8572A G8860A T11368C T16093a T16154C C16519T
    C195T

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  3. #2
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    World Wide spread of different lactose persistence genes summed



    http://kurdishdna.blogspot.com/2012/...tolerance.html

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    The Two major SNP that I checked on FTDNA were rs4988243 & rs3213871 which are in HT74-76 group part of ht5 profile as documented by some of these sites that are catering to Kurds. As you can see in the ITU/STU/GIH/BEB/PJL groups there is like 10% of total in Ht5 & close 30% of total in ht6 consistent with Kurdish profiles which have about similar figures. The overall population figures are 1-2% in Ht5 & 5-6% in Ht6.


    rs4988243 found in the historical DA125 Kang Ju genome at http://www.open-genomes.org/genomes/...nome_DA125.txt
    It has high presence in North East Asia

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    http://kurdishdna.blogspot.com/2017/...e-mcm6-of.html

    Looks like there are Denisova branches & HT5 came out from Denisova admix

    Grey branch (Denisova/Neanderthals/previous and current ht5):
    ht5 is derived from the Denisova genome. The frequency of the ht5 suggests that the admixture Denisova and our ancestors occurred in Asia, which is in accordance with the current state of scientific knowledge.
    Denisova derived branch




    ht75 is the ancestor of the red branch and can be found in all parts of the world: 1-4% in Africans, 6-10% in Americans, 7-10% East Asians, 3-14% in Europeans (North/South gradient), and 7-9% in South Asians. Two subbranches emerged from ht75: a) ht76 and b) ht74 -40
    a) ht76 is derived from ht75 and is present especially in Native Americans 3-13% (not through European ancestry because the highest levels are found in Peruvians and Mexicans), it is also present in Europe 0-2%, and South Asians 0-3% but not in Africans and East Asians.
    b) ht74 and hg40 are derived from ht75 and are basically only present in South Asians (1-6%) with a clear North/South gradient. ht72 was a little bit more successful and made it to South Asians (1-3%), East Asians (0-3%), Europeans (1-3%), and especially in Native Americans 1-7% (not through European ancestry because the highest levels are found in Peruvians and Mexicans).

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    From @DMXX

    For the sake of clarity, that blog is run by a long-time contributor to the genealogy forums with the alias 'Palisto' (a Kurdish-American whom I've long considered a friend). He has no relation to the user Kurd. Thanks to Palisto for categorizing the branches

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