Analyses of the Kostenki 14 genome

At the bottom of this post are the results of analyses of the Kostenki 14 genome. The Kostenki 14 sample is from a human skeleton that was buried at an Early Upper Paleolithic site on the west bank of the Middle Don River in Russia. The skeleton has been dated to 38,684–36,262 BP.
The mt-SNP calls for Kostenki 14 show that he belonged to mitochondrial haplogroup U2*.
The Y-SNP calls for Kostenki 14 show that he belonged to Y haplogroup C1b1-K281*. C1b1-K281 is today found primarily in South Asia, but also in Southeast Asia, the Middle East, Central Asia, and northern China.
The largest autosomal components for Kostenki 14 tended to be the North European components, which is typical for the hunter-gatherers of Upper Paleolithic and Mesolithic Europe. The second and third largest components tended to be the Veddoid South Asian or Indian components and the Caucasoid Mediterranean components, in varying order.
In this post on the Tianyuan sample I said that if we ever got 40,000-year-old DNA from Europe I expected it to show as much of the Veddoid components as Tianyuan. Kostenki 14 is pretty close to being 40,000 years old, but he had around half as much of the Veddoid components as Tianyuan. Tianyuan had 35.39% of the globe13 South Asian component, while Kostenki 14 had 16.03%. Tianyuan had 24.62% of the MDLP World-22 Indian component, while Kostenki 14 had 14.46%. This shows that Kostenki 14 was further up the path of Caucasoid evolution from Veddoids than Tianyuan was up the path of Mongoloid evolution from Veddoids.
Below are the genotypes for Kostenki 14 for SNPs that have a large effect on phenotype, with derived alleles shown in bold. Several of these results are unexpected. They show Kostenki 14 as only having one of the three Veddoid depigmentation mutations in the genes ASIP and KITLG. If the genotypes for these SNPs are correct, they suggest that there was some complexity in the distribution of these mutations in the Veddoid population before that population expanded throughout Eurasia. The results also show Kostenki 14 as having derived alleles associated with red hair, milk digestion, Mongoloid light skin, and blond hair and blue eyes.
Some caution must be exercised in interpreting these results, because the Kostenki 14 genome is not nearly as high-coverage as some of the other prehistoric genomes. But the results also can’t simply be dismissed, because it’s not impossible that Kostenki 14 did have the derived alleles shown below.

Gene        SNP         Genotype  Phenotype
ASIP        rs2424984   TC        Veddoid brown skin
ASIP        rs6058017   GG        Veddoid brown skin
ASIP        rs6119471   CC
EDAR        rs3827760   AA        Mongoloid teeth, hair, etc.
IRF4        rs12203592  CC        light hair and eyes, freckling
KITLG       rs12821256  TT        blond hair
KITLG       rs642742    TT        Veddoid brown skin
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   TC        red hair, fair skin
MC1R        rs1805008   CC        red hair, fair skin
MC1R        rs1805009   GG        red hair, fair skin
MC1R        rs2228479   GG
MC1R        rs885479    GG
MCM6        rs182549    CT        ability to digest milk
MCM6        rs4988235   GG        ability to digest milk
OCA2/HERC2  rs12913832  AA        blue eyes
OCA2        rs1545397   AA
OCA2        rs1800407   CC        green or hazel eyes
OCA2        rs1800414   CC        Mongoloid light skin
PIGU/ASIP   rs2378249   GG
SLC24A4     rs12896399  TT
SLC24A4     rs2402130   AG
SLC24A5     rs1426654   GG        Caucasoid light skin
SLC45A2     rs16891982  CC        Caucasoid light skin
SLC45A2     rs28777     CC
TYRP1       rs2733831   AA        light hair and eyes
TYRP1       rs683       CC
TYR         rs1042602   CC        light skin, absence of freckles
TYR         rs1393350   GA        blond hair, blue eyes

globe4

• 65.22% European
• 16.86% Asian
• 9.45% African
• 8.47% Amerindian

globe10

• 42.19% Atlantic_Baltic
• 17.10% South_Asian
• 9.86% Southern
• 6.94% West_Asian
• 6.31% Neo_African
• 4.95% Australasian
• 4.36% Amerindian
• 3.89% East_Asian
• 2.61% Siberian
• 1.79% Palaeo_African

globe13

• 31.53% North_European
• 16.10% Mediterranean
• 16.03% South_Asian
• 6.32% Southwest_Asian
• 5.80% West_Asian
• 4.91% Australasian
• 4.06% East_Asian
• 3.96% East_African
• 3.83% Amerindian
• 3.31% West_African
• 1.59% Palaeo_African
• 1.31% Arctic
• 1.25% Siberian

K7b

• 41.82% Atlantic_Baltic
• 19.06% South_Asian
• 10.45% Southern
• 9.76% West_Asian
• 8.61% African
• 6.66% East_Asian
• 3.66% Siberian

K10a

• 36.39% Atlantic_Baltic
• 18.19% South_Asian
• 14.45% Mediterranean
• 7.03% West_Asian
• 6.32% Southeast_Asian
• 5.61% Red_Sea
• 5.10% Sub_Saharan
• 4.44% Siberian
• 2.44% Palaeoafrican
• 0.03% East_Asian

K12b

• 26.45% North_European
• 19.54% Atlantic_Med
• 15.98% South_Asian
• 11.83% Gedrosia
• 6.59% Southeast_Asian
• 4.92% East_African
• 4.58% Southwest_Asian
• 4.39% Sub_Saharan
• 3.28% Siberian
• 2.00% Northwest_African
• 0.45% East_Asian
• 0.00% Caucasus

dv3

• 28.14% West_European
• 17.38% South_Asian
• 13.45% Mediterranean
• 11.28% East_European
• 7.68% Southeast_Asian
• 4.50% Southwest_Asian
• 4.29% Northeast_Asian
• 3.87% Palaeo_African
• 3.18% Neo_African
• 3.17% East_African
• 1.88% Northwest_African
• 1.17% West_Asian

MDLP K=5

• 25.52% East-Eurasian
• 25.20% West-Eurasian
• 20.41% Paleo-mediterranean
• 17.15% Caucasian
• 11.71% South-Asian

MDLP K=6

• 23.26% East-Euroasian
• 22.96% West-Eurasian
• 17.89% Paleo-Mediterranean
• 16.47% Caucasian
• 11.24% South-Asian
• 8.18% North-West-Eurasian

MDLP K=7

• 22.90% West-Eurasian
• 22.56% Altaic-Turkic
• 17.66% Paleo-Mediterranean
• 15.56% Caucasian
• 11.16% South-Central-Asian
• 6.87% Volga-Uralic
• 3.28% Paleo-Scandinavian

MDLP K=8

• 22.54% Altaic-Turkic
• 17.59% East-European
• 15.23% West-European
• 13.46% Caucasian
• 11.72% Paleo-Mediterranean
• 11.10% South-Central-Asian
• 6.33% Volga-Finnic
• 2.02% Paleo-Scandinavian

MDLP K=9

• 22.46% Altaic-Turkic
• 17.32% East-European
• 14.82% West-European
• 13.27% Caucasian
• 12.36% Paleo-Mediterranean
• 11.07% South-Central-Asian
• 6.36% Volga-Finnic
• 2.03% Paleo-Scandinavian
• 0.30% Paleo-Balkanic

MDLP K=10

• 22.35% Altaic-Turkic
• 15.31% British
• 12.87% East-European
• 11.74% Paleo-Mediterranean
• 11.23% Caucasian
• 11.03% South-Central-Asian
• 7.07% Iberian
• 6.17% Volga-Finnic
• 1.93% Paleo-North-European
• 0.30% Paleo-Balkanic

MDLP K=11

• 21.82% Altaic-Turkic
• 15.07% Celto-Germanic
• 12.44% East-European
• 11.69% Mediterranean
• 11.08% Caucasian
• 10.97% South-Central-Asian
• 6.73% Iberian
• 4.15% Uralic-Permic
• 3.96% Volga-Uralic
• 1.80% Paleo-North-European
• 0.28% Paleo-Balkanic

MDLP K=12

• 21.76% Alatic-Turkic
• 14.44% Celto-Germanic
• 11.38% Paleo-Mediterranean
• 10.92% South-Central Asian
• 10.71% Caucasian
• 10.69% East-European
• 6.45% Iberian
• 4.54% Balto-Finnic
• 4.02% Uralic-Permic
• 3.82% Volga-Uralic
• 1.00% Paleo-North-European
• 0.27% Paleo-Balkanic

MDLP K=13

• 21.83% Altaic
• 16.74% Paleo-Mediterranean
• 14.10% Celto-Germanic
• 11.80% Mediterrean
• 7.94% East-Mediterranean
• 6.73% East-European
• 6.35% South-Central-Asian
• 3.92% Iberian
• 3.19% Volga-Uralic
• 3.08% Baltic-Finnic
• 2.33% Uralic-Permic
• 1.39% Paleo-North-European
• 0.60% Caucasian

MDLP K=14

• 21.60% Altaic
• 12.82% Celto-Germanic
• 10.45% South-Central-Asian
• 9.82% Balto-Slavic
• 7.87% East-Mediterranean
• 7.35% Mediterranean
• 7.17% Caucasian
• 5.34% Paleo-Mediterranean
• 5.00% Iberian
• 4.11% Balto-Finnic
• 3.85% Uralic-Permic
• 3.56% Volga-Finnic
• 0.90% Paleo-Scandinavian
• 0.15% Paleo-Balkanic

MDLP K=15

• 18.69% West-Altaic
• 12.97% Celto-Germanic
• 10.27% South-Central-Asian
• 9.93% Balto-Slavic
• 7.64% East-Mediterranean
• 7.23% Balkanic-1
• 7.13% Caucasian
• 5.15% West-Mediterranean
• 4.87% Iberian
• 4.08% Balto-Finnic
• 3.83% Uralic-Permic
• 3.73% East-Altaic
• 3.48% Volga-Uralic
• 0.85% Paleo-North-European
• 0.14% Balkanic-2

MDLP World-22

• 27.67% North-East-European
• 14.46% Indian
• 14.30% Atlantic_Mediterranean_Neolithic
• 6.81% Near_East
• 6.50% West-Asian
• 6.29% Sub-Saharian
• 4.02% East-South-Asian
• 3.27% Indo-Iranian
• 3.11% Austronesian
• 2.41% North-European-Mesolithic
• 2.31% North-Amerind
• 1.93% Paleo-Siberian
• 1.43% Indo-Tibetan
• 1.22% Samoedic
• 1.18% Melanesian
• 1.11% South-African
• 1.03% Mesoamerican
• 0.84% Pygmy
• 0.06% South-America_Amerind
• 0.05% Arctic-Amerind
• 0.00% East-Siberean
• 0.00% North-Siberean

MDLP Ancient Roots K17

• 21.63% Ancestral_East_European_ANE
• 14.90% Ancestral_South_Indian
• 12.58% West_European_HG
• 9.94% African_Sub_Saharian
• 9.13% Ancestral_North_Indian
• 8.40% Ancestral_Mediterranean_EEF
• 4.08% South_East_Asian
• 3.96% Melano-Austronesian
• 3.73% Amerindian
• 2.93% Caucasian-Basal
• 2.78% Ancestral_West_Siberian
• 2.43% Uralic
• 1.44% Ancestral_East_Siberian
• 1.41% Ancestral_Sami-Finnic
• 0.36% Circumpolar
• 0.15% Archaic_African
• 0.15% Near-East-Basal

MDLP Ancient Roots K18

• 17.00% East_European
• 16.09% North_West_European
• 12.72% South_Indian
• 10.18% South_Central_Asian
• 7.39% Afroasiatic
• 6.22% East_African
• 5.46% Mediterranean
• 5.04% Melano-Austronesian
• 4.61% South_East_Asian
• 4.44% Amerindian
• 3.34% West_Siberian
• 2.99% Volga-Uralic
• 2.97% Archaic_African
• 1.44% Sami-Finnic
• 0.06% East_Siberian
• 0.05% Arctic
• 0.01% Roma
• 0.00% Caucasian

MDLP K23b

• 19.43% European_Hunters_Gatherers
• 14.12% European_Early_Farmers
• 13.12% Ancestral-South-Indian
• 7.78% Ancestral-North-Indian
• 7.02% Near-East
• 6.45% Ancestral-North-Eurasian
• 5.05% Caucasian
• 3.48% Archaic-African
• 3.20% Austroloid
• 3.15% North-African
• 2.99% East-African
• 2.72% Amerindian
• 2.58% Melano-Polinesian
• 1.89% Austronesian
• 1.44% South-East-Asian
• 1.31% Altaiс
• 1.29% East-Siberian
• 0.95% Subsaharian
• 0.83% Arctic
• 0.42% Archaic-Human
• 0.36% Khoisan
• 0.32% African-Pygmy
• 0.09% Paleo-Siberian
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