Analyses of the Oase 1 genome

At the bottom of this post are the results of analyses of the Oase 1 genome. The Oase 1 sample is from a human mandible found in a cave in the Carpathian Mountains of southwestern Romania. The mandible is dated to 37,800–42,000 years BP.

The mt-SNP calls for Oase 1 show that he belonged to mitochondrial haplogroup N*.

The Y-SNP calls for Oase 1 show that he belonged to Y haplogroup K. He had positive calls for the IJK-defining SNPs PF3497 and PF3500, and for the K-defining SNP PF5495. Like Ust’-Ishim, Oase 1 had a positive call for the SNP Z4842 and a negative call for the SNP F650. These are two of the SNPs that define haplogroup X, which was created when the Y chromosome of an Indian Telugu was found to share seven mutations with haplogroup NO Y chromosomes. Like Ust’-Ishim, Oase 1 had only negative calls for NO-defining SNPs.

Like the 45,000-year-old Ust’-Ishim sample from Siberia, and the 40,000-year-old Tianyuan sample from China, the largest autosomal components for Oase 1 were the Veddoid South Asian or Indian components. This once again confirms the account of extra-African human evolution that I introduced two and a half years ago, in which Negritoids in India evolved into Veddoids, and Veddoids then evolved into Caucasoids and Mongoloids.

Kostenki 14 lived a few thousand years after Oase 1 in Russia, and his smaller amounts of the Veddoid components and larger amounts of the Caucasoid components showed that he had partially ascended the evolutionary path from Veddoids to Caucasoids.

Oase 1 had more of the Negroid components than Tianyuan, Ust’-Ishim, and Kostenki 14, and he had more of the MDLP K23b archaic human component than Ust’-Ishim and Kostenki 14. This is due to the 6–9% Neanderthal admixture that Oase 1 had received at some time in the past four to six generations.

Below are all of the available genotypes for Oase 1 for SNPs that have a large effect on phenotype. Oase 1 had only ancestral alleles for these SNPs.

Gene     SNP         Genotype  Phenotype
EDAR     rs3827760   AA        Mongoloid teeth, hair, etc.
MC1R     rs1110400   TT        red hair
MC1R     rs11547464  GG        red hair
MC1R     rs1805005   GG        blond hair, fair skin
MC1R     rs1805006   CC        red hair, fair skin
MC1R     rs1805007   CC        red hair, fair skin
MC1R     rs1805008   CC        red hair, fair skin
MC1R     rs1805009   GA        red hair, fair skin
MC1R     rs885479    GG
MCM6     rs4988235   GG        ability to digest milk
SLC45A2  rs16891982  CC        Caucasoid light skin
TYR      rs1042602   CC        light skin, absence of freckles
TYR      rs1393350   GG        blond hair, blue eyes

globe4

  • 39.07% European
  • 37.09% Asian
  • 20.75% African
  • 3.09% Amerindian

globe10

  • 25.40% South_Asian
  • 14.55% East_Asian
  • 13.92% Atlantic_Baltic
  • 12.12% Neo_African
  • 9.99% Australasian
  • 8.44% West_Asian
  • 6.10% Palaeo_African
  • 4.94% Southern
  • 2.39% Siberian
  • 2.15% Amerindian

globe13

  • 24.46% South_Asian
  • 14.60% East_Asian
  • 12.10% North_European
  • 9.93% Australasian
  • 8.36% West_African
  • 7.60% West_Asian
  • 5.85% Palaeo_African
  • 4.80% East_African
  • 4.52% Southwest_Asian
  • 3.49% Mediterranean
  • 2.13% Arctic
  • 1.36% Amerindian
  • 0.80% Siberian

K7b

  • 30.20% South_Asian
  • 19.12% African
  • 18.86% East_Asian
  • 12.65% Atlantic_Baltic
  • 10.63% West_Asian
  • 5.12% Southern
  • 3.42% Siberian

K10a

  • 29.22% South_Asian
  • 14.16% Southeast_Asian
  • 13.26% Atlantic_Baltic
  • 11.66% Sub_Saharan
  • 7.98% West_Asian
  • 6.66% Palaeoafrican
  • 5.95% Red_Sea
  • 4.94% East_Asian
  • 3.52% Siberian
  • 2.66% Mediterranean

K12b

  • 27.69% South_Asian
  • 13.77% Southeast_Asian
  • 11.42% Sub_Saharan
  • 11.29% North_European
  • 10.04% East_African
  • 9.93% Gedrosia
  • 6.25% East_Asian
  • 3.25% Southwest_Asian
  • 2.48% Atlantic_Med
  • 2.00% Siberian
  • 1.85% Caucasus
  • 0.03% Northwest_African

dv3

  • 27.24% South_Asian
  • 20.51% Southeast_Asian
  • 10.35% West_European
  • 8.40% Palaeo_African
  • 8.21% East_African
  • 7.47% East_European
  • 6.31% Neo_African
  • 4.86% Northeast_Asian
  • 3.12% Southwest_Asian
  • 3.07% Mediterranean
  • 0.39% Northwest_African
  • 0.07% West_Asian

MDLP World-22

  • 16.70% East-South-Asian
  • 16.21% Indian
  • 13.87% Sub-Saharian
  • 10.98% North-East-European
  • 8.77% West-Asian
  • 6.60% Austronesian
  • 5.90% Atlantic_Mediterranean_Neolithic
  • 4.86% Paleo-Siberian
  • 3.70% Near_East
  • 2.89% Pygmy
  • 2.84% Samoedic
  • 2.02% Indo-Tibetan
  • 1.84% Melanesian
  • 1.34% South-America_Amerind
  • 1.33% South-African
  • 0.17% Indo-Iranian
  • 0.00% Arctic-Amerind
  • 0.00% East-Siberean
  • 0.00% Mesoamerican
  • 0.00% North-Amerind
  • 0.00% North-European-Mesolithic
  • 0.00% North-Siberean

MDLP Ancient Roots K17

  • 26.25% Ancestral_South_Indian
  • 20.99% African_Sub_Saharian
  • 13.65% South_East_Asian
  • 6.34% Melano-Austronesian
  • 5.67% Ancestral_North_Indian
  • 5.60% Uralic
  • 4.40% Ancestral_East_European_ANE
  • 3.45% West_European_HG
  • 3.07% Caucasian-Basal
  • 2.39% Ancestral_East_Siberian
  • 2.34% Ancestral_West_Siberian
  • 1.97% Amerindian
  • 1.49% Ancestral_Mediterranean_EEF
  • 1.43% Ancestral_Sami-Finnic
  • 0.51% Circumpolar
  • 0.22% Archaic_African
  • 0.22% Near-East-Basal

MDLP Ancient Roots K18

  • 24.01% South_Indian
  • 13.47% South_East_Asian
  • 11.38% East_African
  • 10.46% East_European
  • 8.53% Archaic_African
  • 8.52% Melano-Austronesian
  • 7.91% South_Central_Asian
  • 5.01% Volga-Uralic
  • 3.95% North_West_European
  • 2.03% East_Siberian
  • 1.57% Afroasiatic
  • 1.54% Amerindian
  • 0.69% Arctic
  • 0.47% Sami-Finnic
  • 0.18% Mediterranean
  • 0.15% West_Siberian
  • 0.14% Caucasian
  • 0.00% Roma

MDLP K23b

  • 24.49% Ancestral-South-Indian
  • 8.41% South-East-Asian
  • 7.68% Austroloid
  • 7.16% European_Hunters_Gatherers
  • 6.79% Ancestral-North-Indian
  • 5.98% Archaic-African
  • 5.35% Austronesian
  • 5.04% Archaic-Human
  • 4.69% Subsaharian
  • 4.64% Caucasian
  • 3.60% Altaiс
  • 3.40% East-African
  • 2.63% Melano-Polinesian
  • 1.75% Amerindian
  • 1.70% North-African
  • 1.58% East-Siberian
  • 1.38% Khoisan
  • 1.19% Paleo-Siberian
  • 0.89% Near-East
  • 0.81% European_Early_Farmers
  • 0.56% Ancestral-North-Eurasian
  • 0.19% African-Pygmy
  • 0.08% Arctic
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11 comments on “Analyses of the Oase 1 genome
  1. Vincenzo says:

    Thanks for this. Could you please run Oase 1 in the Eurogenes K15 calculator?

    • genetiker says:

      As far as I know, Wesolowski doesn’t make his calculator files publicly available.

      I dislike his calculators anyway, because they’re not based on unsupervised ADMIXTURE analyses. Such calculators just end up reflecting the preconceptions of whoever created them.

      • Vincenzo says:

        Ok. From what I see, there’s a significant increase in African and West Asian components in Oase 1, compared to Kostenki 14 and Ust’-Ishim. In your opinion, can this be explained by the presence of Basal Eurasians (Y-DNA E) in West Asia at that time? Maybe the ancestors of Oase 1 entered in contact with them on their way to Europe.

  2. genetiker says:

    As I explained in the post, the larger amounts of the Negroid components are due to the significant Neanderthal admixture that Oase 1 had. Archaic admixture ends up being identified as Negroid by calculators which lack an archaic component.

    I don’t see much of a difference between Oase 1, Kostenki 14, and Ust’-Ishim in their amounts of the West Asian components. For example, Oase 1 had 7.60% of the globe13 West Asian component, Kostenki 14 had 5.80%, and Ust’-Ishim had 4.50%. Those aren’t significantly different.

    • Vincenzo says:

      “As I explained in the post, the larger amounts of the Negroid components are due to the significant Neanderthal admixture that Oase 1 had.”

      Ust’-Ishim has a lot of African admixture too, but he wasn’t much more Neanderthal – admixed than modern humans. Also, Oase 1 has higher SSA/West Asian admixture even in calculators with an archaic component. There’s a cline of SSA/West Asian admixture in ~40 kyo genomes (i.e. excluding K14 because he is later in age than Ust’-Ishim, Kostenki 14 and Tianyuan): Oase 1 has the most of them, Ust’-Ishim is intermediate and Tianyuan has the least of them. All the three are from around the same period.

  3. Pete says:

    Hi Genetiker
    Is there any chance you can look at the Pinhasi samples (esp the ones relevant to west Eurasia- Turkmen, Jordan, Turkey, Servia, Hungary).

  4. This is a message from @Genetiker.

    I have asked Andrii to post it on my behalf.

    I have been locked out of my genetiker WordPress account for two weeks because of a bug in the way that WordPress processes passwords.

    I will be posting updates on the status of my blog and my efforts to regain access to it here:

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  5. […] those who missed Andrii’s comment, I have been locked out of my Genetiker WordPress account for the past month, because of a bug in […]

  6. Capra Internetensis says:

    New Poznick et al paper confirms your Y haplogroup assignment for Oase-1.

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