Results 1 to 10 of 10

Thread: Which snps are responsible for the extremely dark skin tones found in Nilo-Saharans?

  1. #1
    Gold Class Member
    Posts
    1,736
    Sex
    Omitted
    Location
    Arabsiyo,Somaliland
    Nationality
    Canadian
    Y-DNA (P)
    E-V32>E-FT385910
    mtDNA (M)
    L0a1d1*
    Y-DNA (M)
    T-FGC92488

    Somaliland Adal Sultanate Yemen African Union Canada

    Which snps are responsible for the extremely dark skin tones found in Nilo-Saharans?

    Nilo-Saharans are a very special case in Africa, as even they stand out as extremely dark in comparison to non-Eurasian admixed Sub-Saharan Africans. Is their dark almost blue-like skin the original tone of early humans or was it artificially selected?

  2. The Following 8 Users Say Thank You to drobbah For This Useful Post:

     Aben Aboo (07-16-2021),  Angoliga (07-18-2021),  Hurricane (07-15-2021),  J-Live (07-15-2021),  Lupriac (07-15-2021),  Luso (07-15-2021),  pmokeefe (07-15-2021),  Tsakhur (08-02-2021)

  3. #2
    Gold Class Member
    Posts
    951
    Sex
    Location
    San Diego, CA
    Ethnicity
    Polish/British Isles
    Nationality
    U.S.
    Y-DNA (P)
    R-A9185
    mtDNA (M)
    H1
    mtDNA (P)
    J1c2

    Poland England Ireland Munster
    Quote Originally Posted by drobbah View Post
    Nilo-Saharans are a very special case in Africa, as even they stand out as extremely dark in comparison to non-Eurasian admixed Sub-Saharan Africans. Is their dark almost blue-like skin the original tone of early humans or was it artificially selected?
    Evolutionary genetics of skin pigmentation in African populations
    Recent genomic studies show that the ancestral alleles of many predicted functional pigmentation variants in Africa are associated with lighter skin, suggesting our human ancestors may have had light or moderately pigmented skin (23). Combined with the fact that our closest evolutionary relatives, chimpanzees, have light skin (24), these results suggest that dark skin may be a derived trait in the Homo genus, and that both light and dark skin have continued to evolve over hominid history (23,25)
    ...
    Nilo-Saharan-speaking populations from East Africa have some of the darkest pigmented skin on Earth
    ...
    They found that the derived allele of rs4932620 (T) is significantly associated with dark skin pigmentation and at highest frequency in Ethiopian Nilo-Saharan populations
    ...
    The derived allele of rs7948623 (T), associated with dark pigmentation, is at highest global frequency in East African populations with Nilo-Saharan ancestry, who inhabit high UVR environments and have darkly pigmented skin.
    ...
    Specifically, the derived alleles at the synonymous variant rs56203814 (T) and the intronic variant rs10424065 (T) significantly associate with dark pigmentation and are at highest frequency in East Africans with Nilo-Saharan ancestry



    Here's a few recent papers:
    Loci associated with skin pigmentation identified in African populations
    Abstract
    Despite the wide range of skin pigmentation in humans, little is known about its genetic basis in global populations. Examining ethnically diverse African genomes, we identify variants in or near SLC24A5, MFSD12, DDB1, TMEM138, OCA2 and HERC2 that are significantly associated with skin pigmentation. Genetic evidence indicates that the light pigmentation variant at SLC24A5 was introduced into East Africa by gene flow from non-Africans. At all other loci, variants associated with dark pigmentation in Africans are identical by descent in southern Asian and Australo-Melanesian populations. Functional analyses indicate that MFSD12 encodes a lysosomal protein that affects melanogenesis in zebrafish and mice, and that mutations in melanocyte-specific regulatory regions near DDB1/TMEM138 correlate with expression of UV response genes under selection in Eurasians.

    Evolutionary genetics of skin pigmentation in African populations
    Abstract
    Skin color is a highly heritable human trait, and global variation in skin pigmentation has been shaped by natural selection, migration and admixture. Ethnically diverse African populations harbor extremely high levels of genetic and phenotypic diversity, and skin pigmentation varies widely across Africa. Recent genome-wide genetic studies of skin pigmentation in African populations have advanced our understanding of pigmentation biology and human evolutionary history. For example, novel roles in skin pigmentation for loci near MFSD12 and DDB1 have recently been identified in African populations. However, due to an underrepresentation of Africans in human genetic studies, there is still much to learn about the evolutionary genetics of skin pigmentation. Here, we summarize recent progress in skin pigmentation genetics in Africans and discuss the importance of including more ethnically diverse African populations in future genetic studies. In addition, we discuss methods for functional validation of adaptive variants related to skin pigmentation.


    An Unexpectedly Complex Architecture for Skin Pigmentation in Africans
    Abstract
    Approximately 15 genes have been directly associated with skin pigmentation variation in humans, leading to its characterization as a relatively simple trait. However, by assembling a global survey of quantitative skin pigmentation phenotypes, we demonstrate that pigmentation is more complex than previously assumed, with genetic architecture varying by latitude. We investigate polygenicity in the KhoeSan populations indigenous to southern Africa who have considerably lighter skin than equatorial Africans. We demonstrate that skin pigmentation is highly heritable, but known pigmentation loci explain only a small fraction of the variance. Rather, baseline skin pigmentation is a complex, polygenic trait in the KhoeSan. Despite this, we identify canonical and non-canonical skin pigmentation loci, including near SLC24A5, TYRP1, SMARCA2/VLDLR, and SNX13, using a genome-wide association approach complemented by targeted resequencing. By considering diverse, under-studied African populations, we show how the architecture of skin pigmentation can vary across humans subject to different local evolutionary pressures.

    Rapid evolution of a skin-lightening allele in southern African KhoeSan

    Focus on African diversity confirms complexity of skin pigmentation genetics
    Last edited by pmokeefe; 07-15-2021 at 05:58 PM.
    YFull: YF14620 (Dante Labs 2018)

  4. The Following 10 Users Say Thank You to pmokeefe For This Useful Post:

     Aben Aboo (07-16-2021),  Angoliga (07-18-2021),  beyoku (07-20-2021),  drobbah (07-15-2021),  Hurricane (07-15-2021),  Lupriac (07-15-2021),  Mnemonics (07-16-2021),  okarinaofsteiner (08-02-2021),  Piquerobi (07-15-2021),  Riverman (07-16-2021)

  5. #3
    Registered Users
    Posts
    470
    Location
    USA
    Y-DNA (P)
    H-Z4417
    mtDNA (M)
    M3d

    Are Nilo-Saharans darker than Andamanese? How do they compare to people from Bougainville Island - read somewhere they also have one of the darkest skin tone.

  6. #4
    Gold Class Member
    Posts
    1,736
    Sex
    Omitted
    Location
    Arabsiyo,Somaliland
    Nationality
    Canadian
    Y-DNA (P)
    E-V32>E-FT385910
    mtDNA (M)
    L0a1d1*
    Y-DNA (M)
    T-FGC92488

    Somaliland Adal Sultanate Yemen African Union Canada
    Quote Originally Posted by thejkhan View Post
    Are Nilo-Saharans darker than Andamanese? How do they compare to people from Bougainville Island - read somewhere they also have one of the darkest skin tone.
    There's many Sahelians that seem darker imo then the darkest Asians

    Quote Originally Posted by pmokeefe View Post

     
    Evolutionary genetics of skin pigmentation in African populations
    Recent genomic studies show that the ancestral alleles of many predicted functional pigmentation variants in Africa are associated with lighter skin, suggesting our human ancestors may have had light or moderately pigmented skin (23). Combined with the fact that our closest evolutionary relatives, chimpanzees, have light skin (24), these results suggest that dark skin may be a derived trait in the Homo genus, and that both light and dark skin have continued to evolve over hominid history (23,25)
    ...
    Nilo-Saharan-speaking populations from East Africa have some of the darkest pigmented skin on Earth
    ...
    They found that the derived allele of rs4932620 (T) is significantly associated with dark skin pigmentation and at highest frequency in Ethiopian Nilo-Saharan populations
    ...
    he derived allele of rs7948623 (T), associated with dark pigmentation, is at highest global frequency in East African populations with Nilo-Saharan ancestry, who inhabit high UVR environments and have darkly pigmented skin.




    Here's a few recent papers:
    Loci associated with skin pigmentation identified in African populations
    Abstract
    Despite the wide range of skin pigmentation in humans, little is known about its genetic basis in global populations. Examining ethnically diverse African genomes, we identify variants in or near SLC24A5, MFSD12, DDB1, TMEM138, OCA2 and HERC2 that are significantly associated with skin pigmentation. Genetic evidence indicates that the light pigmentation variant at SLC24A5 was introduced into East Africa by gene flow from non-Africans. At all other loci, variants associated with dark pigmentation in Africans are identical by descent in southern Asian and Australo-Melanesian populations. Functional analyses indicate that MFSD12 encodes a lysosomal protein that affects melanogenesis in zebrafish and mice, and that mutations in melanocyte-specific regulatory regions near DDB1/TMEM138 correlate with expression of UV response genes under selection in Eurasians.

    Evolutionary genetics of skin pigmentation in African populations
    Abstract
    Skin color is a highly heritable human trait, and global variation in skin pigmentation has been shaped by natural selection, migration and admixture. Ethnically diverse African populations harbor extremely high levels of genetic and phenotypic diversity, and skin pigmentation varies widely across Africa. Recent genome-wide genetic studies of skin pigmentation in African populations have advanced our understanding of pigmentation biology and human evolutionary history. For example, novel roles in skin pigmentation for loci near MFSD12 and DDB1 have recently been identified in African populations. However, due to an underrepresentation of Africans in human genetic studies, there is still much to learn about the evolutionary genetics of skin pigmentation. Here, we summarize recent progress in skin pigmentation genetics in Africans and discuss the importance of including more ethnically diverse African populations in future genetic studies. In addition, we discuss methods for functional validation of adaptive variants related to skin pigmentation.


    An Unexpectedly Complex Architecture for Skin Pigmentation in Africans
    Abstract
    Approximately 15 genes have been directly associated with skin pigmentation variation in humans, leading to its characterization as a relatively simple trait. However, by assembling a global survey of quantitative skin pigmentation phenotypes, we demonstrate that pigmentation is more complex than previously assumed, with genetic architecture varying by latitude. We investigate polygenicity in the KhoeSan populations indigenous to southern Africa who have considerably lighter skin than equatorial Africans. We demonstrate that skin pigmentation is highly heritable, but known pigmentation loci explain only a small fraction of the variance. Rather, baseline skin pigmentation is a complex, polygenic trait in the KhoeSan. Despite this, we identify canonical and non-canonical skin pigmentation loci, including near SLC24A5, TYRP1, SMARCA2/VLDLR, and SNX13, using a genome-wide association approach complemented by targeted resequencing. By considering diverse, under-studied African populations, we show how the architecture of skin pigmentation can vary across humans subject to different local evolutionary pressures.

    Rapid evolution of a skin-lightening allele in southern African KhoeSan

    Focus on African diversity confirms complexity of skin pigmentation genetics
    Just found another study as well High Levels of Genetic Diversity within Nilo-Saharan Populations: Implications for Human Adaptation

    Nilo-Saharans have some of the darkest skin tones in the world82 and the Lugbara generally have a darker skin compared to the Basoga.83 Skin reflectance is correlated with UV radiation84 and the dark skin tones of the Nilo-Saharans could be an adaptation to the open savannah conditions of the Sahel where there is limited tree and cloud cover and which is predicted by models to be one of the regions of the world with darkest skin pigmentation.84 UVRAG may be an important contributor to the exceptionally dark skin tones of the Nilo-Saharans in conjunction with SNX13 and TYROBP in particular and possibly also IRF4, TYRP1, HERC2, SLC24A5, and OPRM1.

  7. The Following 7 Users Say Thank You to drobbah For This Useful Post:

     Angoliga (07-18-2021),  J-Live (07-15-2021),  Keneki20 (07-16-2021),  Lupriac (07-15-2021),  pmokeefe (07-15-2021),  Riverman (07-16-2021),  thejkhan (07-15-2021)

  8. #5
    Registered Users
    Posts
    255
    Sex
    Location
    Canada
    Ethnicity
    Somali
    Y-DNA (P)
    T-L208
    mtDNA (M)
    N1b2

    Canada Somaliland
    rs4932620 (T) and rs7948623 (T) seem to present in both Africans and South Asians which is interesting. I wonder if it's a result of a retention of the mutation within the OOA population that settled South Asia or a result of an independent mutation that was selected for separately. The MFSD12 variants on the other hand seem exclusively African and relatively rare even in African populations.

  9. The Following 4 Users Say Thank You to Mnemonics For This Useful Post:

     Angoliga (07-18-2021),  drobbah (07-16-2021),  J-Live (07-16-2021),  pmokeefe (07-16-2021)

  10. #6
    I believe it is to do with the UV zone resulting in said adaptation probably resulting in a unique genetic profiile. Is it not the Sudan or Bahr el Ghazal that has the highest UV penetration/coverage in the world?

  11. The Following 2 Users Say Thank You to J-Live For This Useful Post:

     beyoku (07-20-2021),  okarinaofsteiner (08-02-2021)

  12. #7
    Registered Users
    Posts
    8
    Sex

    Quote Originally Posted by Mnemonics View Post
    rs4932620 (T) and rs7948623 (T) seem to present in both Africans and South Asians which is interesting. I wonder if it's a result of a retention of the mutation within the OOA population that settled South Asia or a result of an independent mutation that was selected for separately. The MFSD12 variants on the other hand seem exclusively African and relatively rare even in African populations.
    I remember reading a few years ago that the alleles associated with dark pigment, rs6510760 (A) and rs112332856 (C), were common in all African poplations (besides Khoi and San groups) and in South Asian/Austro-Melanesians populations. They also suggested that these alleles were "identical by descent" between Africans and South Asian/Austro-Melaneian populations, likely inherited from an ancestral African population. So maybe its similar case with the alleles you mentioned

    https://science.sciencemag.org/conte...m=article_link

    Individuals from South Asia and Australo-Melanesia share variants associated with dark pigmentation at MFSD12, DDB1/TMEM138, OCA2, and HERC2 that are identical by descent from Africans. This raises the possibility that other phenotypes shared between Africans and some South Asian and Australo-Melanesian populations may also be due to genetic variants identical by descent from African populations rather than convergent evolution
    Last edited by Dehlisandwich; 07-16-2021 at 08:09 PM.

  13. The Following 4 Users Say Thank You to Dehlisandwich For This Useful Post:

     Brandon S. Pilcher (07-17-2021),  Mnemonics (07-16-2021),  okarinaofsteiner (08-02-2021),  Tsakhur (08-02-2021)

  14. #8
    Registered Users
    Posts
    8
    Sex

    Quote Originally Posted by drobbah View Post
    There's many Sahelians that seem darker imo then the darkest Asians


    Just found another study as well High Levels of Genetic Diversity within Nilo-Saharan Populations: Implications for Human Adaptation
    Oh I see its already been posted it
    Last edited by Dehlisandwich; 07-16-2021 at 08:14 PM.

  15. #9
    Registered Users
    Posts
    640
    Sex
    Omitted

    Quote Originally Posted by drobbah View Post
    Nilo-Saharans are a very special case in Africa, as even they stand out as extremely dark in comparison to non-Eurasian admixed Sub-Saharan Africans. Is their dark almost blue-like skin the original tone of early humans or was it artificially selected?
    Hmm Nilo-Saharans have minor Eurasian admixture?

  16. #10
    Registered Users
    Posts
    270
    Sex
    Omitted
    Ethnicity
    Mostly Chinese
    Nationality
    USA

    United States of America China
    Quote Originally Posted by Mnemonics View Post
    rs4932620 (T) and rs7948623 (T) seem to present in both Africans and South Asians which is interesting. I wonder if it's a result of a retention of the mutation within the OOA population that settled South Asia or a result of an independent mutation that was selected for separately. The MFSD12 variants on the other hand seem exclusively African and relatively rare even in African populations.
    The usage of the word “derived” strongly implies that it isn’t found/wasn’t selected for among all Sub-Saharan Africans; only the ancestors of today’s Nilo-Saharans and possibly the original OOA population too.

Similar Threads

  1. SNPs responsible for the quantity and type of moles
    By Dorkymon in forum Medical Genetics
    Replies: 1
    Last Post: 03-18-2020, 03:00 AM
  2. Where exactly did nilo saharans originate from?
    By afbarwaaqo in forum Eastern
    Replies: 7
    Last Post: 06-22-2018, 03:47 PM
  3. Lost Dark Ages Fort Found in Scotland
    By Amerijoe in forum History (Medieval)
    Replies: 0
    Last Post: 01-24-2017, 12:56 AM
  4. Replies: 2
    Last Post: 01-10-2016, 02:06 PM
  5. Ancient DNA skin pigmentation SNPs that are on 23andme.
    By jeanL in forum Autosomal (auDNA)
    Replies: 20
    Last Post: 12-30-2014, 07:46 PM

Posting Permissions

  • You may not post new threads
  • You may not post replies
  • You may not post attachments
  • You may not edit your posts
  •