K = 13 admixture analysis of Mesolithic and Neolithic Latvian and Ukrainian genomes

Below is a plot for a K = 13 admixture analysis that includes eight genomes from Mesolithic and Neolithic Latvia and Ukraine. The table above the plot gives some information for these samples.

The samples from the Mesolithic Kunda and Narva cultures are similar to the Mesolithic samples from Motala, Sweden, being made up mostly of the dark blue Western component, but also having about 25% of the medium blue Eastern component.

Latvia_HG3 and Latvia_MN1 are indistinguishable from the Western European hunter-gatherers in this analysis, being made up entirely of the dark blue component.

The hunter-gatherer sample from the Comb Ware culture is similar to the earlier hunter-gatherer samples from Karelia and Samara in Russia, being made up mostly of the medium blue Eastern component, but also having about 25% of the dark blue Western component.

The Corded Ware sample from Latvia is similar to the Pit Grave and Afanasevo samples, but with a bit less of the pine green Caucasus-related component. It has more of the medium blue component than any other sample in this analysis. It differs from all of the other Corded Ware samples in that it completely lacks the light blue early farmer component.

The Mesolithic sample from Ukraine and the sample from the Neolithic Dnieper-Donets culture of Ukraine are similar to each other, being made up mostly of the medium blue Eastern component, but also having around 35–45% of the dark blue Western component.

Sample       Period            Culture         Date BC
Latvia_HG1   Mesolithic        Kunda           6467–6249
Latvia_HG2   Mesolithic        Narva           5841–5636
Latvia_HG3   Early Neolithic   Unassigned      5302–4852
Latvia_MN1   Middle Neolithic  Unassigned      4251–3976
Latvia_MN2   Middle Neolithic  Comb Ware       4229–3800
Latvia_LN1   Late Neolithic    Corded Ware     3089–2676
Ukraine_HG1  Mesolithic        Unassigned      9193–8641
Ukraine_N1   Neolithic         Dnieper-Donets  4519–4343

all-13-17-1

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Phenotype SNPs from Mesolithic and Neolithic Latvia and Ukraine

Below are derived allele counts and total numbers of reads for SNPs that have a large effect on phenotype for genomes from Mesolithic and Neolithic Latvia and Ukraine. Nonzero derived allele counts are in bold. Note that small derived allele counts may be due to DNA damage.

ASIP, rs2424984, Veddoid brown skin

Sample       Period            Culture      Date BC    D/T
Latvia_HG2   Mesolithic        Narva        5841–5636  7/7
Latvia_MN1   Middle Neolithic  Unassigned   4251–3976  1/1
Latvia_LN1   Late Neolithic    Corded Ware  3089–2676  0/1
Ukraine_HG1  Mesolithic        Unassigned   9193–8641  0/1

ASIP, rs6058017, Veddoid brown skin

Sample      Period            Culture      Date BC    D/T
Latvia_HG1  Mesolithic        Kunda        6467–6249  2/2
Latvia_HG2  Mesolithic        Narva        5841–5636  1/1
Latvia_HG3  Early Neolithic   Unassigned   5302–4852  2/2
Latvia_MN2  Middle Neolithic  Comb Ware    4229–3800  0/0
Latvia_LN1  Late Neolithic    Corded Ware  3089–2676  0/1

EDAR, rs3827760, Mongoloid teeth, hair, etc.

Sample      Period            Culture      Date BC    D/T
Latvia_HG2  Mesolithic        Narva        5841–5636  0/4
Latvia_MN2  Middle Neolithic  Comb Ware    4229–3800  0/1
Latvia_LN1  Late Neolithic    Corded Ware  3089–2676  0/1

IRF4, rs12203592, light hair and eyes, freckling

Sample       Period            Culture     Date BC    D/T
Latvia_HG1   Mesolithic        Kunda       6467–6249  3/3
Latvia_HG2   Mesolithic        Narva       5841–5636  4/4
Latvia_HG3   Early Neolithic   Unassigned  5302–4852  1/1
Latvia_MN2   Middle Neolithic  Comb Ware   4229–3800  0/3
Ukraine_HG1  Mesolithic        Unassigned  9193–8641  1/2

KITLG, rs12821256, blond hair

Sample      Period           Culture     Date BC    D/T
Latvia_HG1  Mesolithic       Kunda       6467–6249  0/4
Latvia_HG3  Early Neolithic  Unassigned  5302–4852  0/1

KITLG, rs642742, Veddoid brown skin

Sample      Period            Culture     Date BC    D/T
Latvia_HG2  Mesolithic        Narva       5841–5636  3/3
Latvia_HG3  Early Neolithic   Unassigned  5302–4852  1/2
Latvia_MN2  Middle Neolithic  Comb Ware   4229–3800  3/3

MC1R, rs1110400, red hair

Sample      Period            Culture    Date BC    D/T
Latvia_HG1  Mesolithic        Kunda      6467–6249  0/2
Latvia_HG2  Mesolithic        Narva      5841–5636  0/3
Latvia_MN2  Middle Neolithic  Comb Ware  4229–3800  0/1

MC1R, rs11547464, red hair

Sample       Period            Culture     Date BC    D/T
Latvia_HG1   Mesolithic        Kunda       6467–6249  0/4
Latvia_HG2   Mesolithic        Narva       5841–5636  0/4
Latvia_MN2   Middle Neolithic  Comb Ware   4229–3800  0/3
Ukraine_HG1  Mesolithic        Unassigned  9193–8641  0/1

MC1R, rs1805005, blond hair, fair skin

Sample      Period           Culture      Date BC    D/T
Latvia_HG1  Mesolithic       Kunda        6467–6249  0/3
Latvia_HG2  Mesolithic       Narva        5841–5636  0/5
Latvia_HG3  Early Neolithic  Unassigned   5302–4852  0/2
Latvia_LN1  Late Neolithic   Corded Ware  3089–2676  0/1

MC1R, rs1805006, red hair, fair skin

Sample       Period            Culture         Date BC    D/T
Latvia_HG1   Mesolithic        Kunda           6467–6249  0/1
Latvia_HG2   Mesolithic        Narva           5841–5636  0/5
Latvia_HG3   Early Neolithic   Unassigned      5302–4852  0/1
Latvia_MN2   Middle Neolithic  Comb Ware       4229–3800  0/1
Latvia_LN1   Late Neolithic    Corded Ware     3089–2676  0/1
Ukraine_HG1  Mesolithic        Unassigned      9193–8641  0/1
Ukraine_N1   Neolithic         Dnieper-Donets  4519–4343  0/1

MC1R, rs1805007, red hair, fair skin

Sample      Period            Culture    Date BC    D/T
Latvia_HG1  Mesolithic        Kunda      6467–6249  0/3
Latvia_HG2  Mesolithic        Narva      5841–5636  0/4
Latvia_MN2  Middle Neolithic  Comb Ware  4229–3800  0/3

MC1R, rs1805008, red hair, fair skin

Sample      Period      Culture  Date BC    D/T
Latvia_HG2  Mesolithic  Narva    5841–5636  0/6

MC1R, rs1805009, red hair, fair skin

Sample      Period           Culture     Date BC    D/T
Latvia_HG1  Mesolithic       Kunda       6467–6249  0/2
Latvia_HG2  Mesolithic       Narva       5841–5636  0/4
Latvia_HG3  Early Neolithic  Unassigned  5302–4852  0/2

MCM6, rs182549, ability to digest milk

Sample      Period            Culture     Date BC    D/T
Latvia_HG1  Mesolithic        Kunda       6467–6249  0/2
Latvia_HG2  Mesolithic        Narva       5841–5636  0/3
Latvia_HG3  Early Neolithic   Unassigned  5302–4852  0/1
Latvia_MN1  Middle Neolithic  Unassigned  4251–3976  0/1
Latvia_MN2  Middle Neolithic  Comb Ware   4229–3800  0/3

MCM6, rs4988235, ability to digest milk

Sample      Period            Culture     Date BC    D/T
Latvia_HG2  Mesolithic        Narva       5841–5636  0/1
Latvia_HG3  Early Neolithic   Unassigned  5302–4852  0/1
Latvia_MN2  Middle Neolithic  Comb Ware   4229–3800  0/3

OCA2, rs1800407, green or hazel eyes

Sample      Period            Culture    Date BC    D/T
Latvia_HG2  Mesolithic        Narva      5841–5636  1/4
Latvia_MN2  Middle Neolithic  Comb Ware  4229–3800  0/2

OCA2, rs1800414, Mongoloid light skin

Sample      Period            Culture     Date BC    D/T
Latvia_HG1  Mesolithic        Kunda       6467–6249  0/1
Latvia_HG2  Mesolithic        Narva       5841–5636  0/4
Latvia_HG3  Early Neolithic   Unassigned  5302–4852  0/1
Latvia_MN2  Middle Neolithic  Comb Ware   4229–3800  0/1

OCA2/HERC2, rs12913832, blue eyes

Sample      Period            Culture     Date BC    D/T
Latvia_HG1  Mesolithic        Kunda       6467–6249  0/1
Latvia_HG2  Mesolithic        Narva       5841–5636  4/4
Latvia_MN1  Middle Neolithic  Unassigned  4251–3976  1/1
Latvia_MN2  Middle Neolithic  Comb Ware   4229–3800  0/1

SLC24A5, rs1426654, Caucasoid light skin

Sample      Period            Culture     Date BC    D/T
Latvia_HG1  Mesolithic        Kunda       6467–6249  0/1
Latvia_HG2  Mesolithic        Narva       5841–5636  0/5
Latvia_HG3  Early Neolithic   Unassigned  5302–4852  1/1
Latvia_MN2  Middle Neolithic  Comb Ware   4229–3800  1/1

SLC45A2, rs16891982, Caucasoid light skin

Sample      Period            Culture         Date BC    D/T
Latvia_HG1  Mesolithic        Kunda           6467–6249  0/1
Latvia_HG2  Mesolithic        Narva           5841–5636  0/3
Latvia_HG3  Early Neolithic   Unassigned      5302–4852  0/1
Latvia_MN2  Middle Neolithic  Comb Ware       4229–3800  1/1
Ukraine_N1  Neolithic         Dnieper-Donets  4519–4343  1/1

TYR, rs1042602, light skin, absence of freckles

Sample       Period            Culture      Date BC    D/T
Latvia_HG1   Mesolithic        Kunda        6467–6249  0/2
Latvia_HG2   Mesolithic        Narva        5841–5636  0/2
Latvia_HG3   Early Neolithic   Unassigned   5302–4852  0/1
Latvia_MN2   Middle Neolithic  Comb Ware    4229–3800  0/2
Latvia_LN1   Late Neolithic    Corded Ware  3089–2676  0/1
Ukraine_HG1  Mesolithic        Unassigned   9193–8641  0/2

TYR, rs1393350, blond hair, blue eyes

Sample       Period            Culture         Date BC    D/T
Latvia_HG2   Mesolithic        Narva           5841–5636  0/1
Latvia_HG3   Early Neolithic   Unassigned      5302–4852  0/2
Latvia_MN2   Middle Neolithic  Comb Ware       4229–3800  0/1
Latvia_LN1   Late Neolithic    Corded Ware     3089–2676  0/1
Ukraine_HG1  Mesolithic        Unassigned      9193–8641  0/2
Ukraine_N1   Neolithic         Dnieper-Donets  4519–4343  0/2

TYRP1, rs2733831, light hair and eyes

Sample      Period            Culture    Date BC    D/T
Latvia_HG1  Mesolithic        Kunda      6467–6249  1/3
Latvia_HG2  Mesolithic        Narva      5841–5636  2/5
Latvia_MN2  Middle Neolithic  Comb Ware  4229–3800  2/2
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Y-SNP calls from Mesolithic and Neolithic Latvia and Ukraine

In the table below are links to Y-SNP calls for samples from Mesolithic and Neolithic Latvia and Ukraine.

Sample       Culture           Date BC    Haplogroup
Latvia_HG2   Narva             5841–5636  pre-R1b1a1a1-M73  calls
Latvia_HG3   Early Neolithic   5302–4852  pre-R1b1a1a1-M73  calls
Latvia_MN1   Middle Neolithic  4251–3976  R1b1a1a-P297      calls
Ukraine_HG1  Mesolithic        9193–8641  I2a2a-M223        calls
Ukraine_N1   Dnieper-Donets    4519–4343  R1a1-M459*        calls
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K = 14 admixture analysis of Lapita genomes

Below is a plot for a K = 14 admixture analysis that includes four genomes from the Lapita culture on the islands of Vanuatu and Tonga in the South Pacific. The table above the plot gives some information for these samples.

The plot shows that the people of the Lapita culture were genetically similar to Taiwanese aborigines like the Ami and Atayal, and the indigenous Igorot people of the Philippines. It also shows that they had no Melanesian admixture.

Sample  Location  Date BP
I1368   Vanuatu   2990–2740
I1369   Vanuatu   3000–2750
I1370   Vanuatu   3110–2780
CP30    Tonga     2680–2340

all-14-15-1

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Phenotype SNPs from the Lapita culture

Below are derived allele counts and total numbers of reads for SNPs that have a large effect on phenotype for genomes from the Lapita culture on the islands of Vanuatu and Tonga in the South Pacific. Nonzero derived allele counts are in bold. Note that the nonzero counts for red hair alleles below are due to DNA damage.

ASIP, rs6058017, Veddoid brown skin

Sample  Location  Date BP    D/T
CP30    Tonga     2680–2340  1/1

EDAR, rs3827760, Mongoloid teeth, hair, etc.

Sample  Location  Date BP    D/T
I1369   Vanuatu   3000–2750  2/2
CP30    Tonga     2680–2340  0/3

IRF4, rs12203592, light hair and eyes, freckling

Sample  Location  Date BP    D/T
I1368   Vanuatu   2990–2740  0/1

MC1R, rs1110400, red hair

Sample  Location  Date BP    D/T
I1368   Vanuatu   2990–2740  0/3
I1369   Vanuatu   3000–2750  0/2
I1370   Vanuatu   3110–2780  0/3
CP30    Tonga     2680–2340  0/2

MC1R, rs11547464, red hair

Sample  Location  Date BP    D/T
I1368   Vanuatu   2990–2740  0/1
CP30    Tonga     2680–2340  1/2

MC1R, rs1805005, blond hair, fair skin

Sample  Location  Date BP    D/T
I1368   Vanuatu   2990–2740  0/1
I1369   Vanuatu   3000–2750  0/1
CP30    Tonga     2680–2340  0/2

MC1R, rs1805006, red hair, fair skin

Sample  Location  Date BP    D/T
I1368   Vanuatu   2990–2740  0/3
I1369   Vanuatu   3000–2750  0/2
I1370   Vanuatu   3110–2780  0/1
CP30    Tonga     2680–2340  0/1

MC1R, rs1805007, red hair, fair skin

Sample  Location  Date BP    D/T
I1368   Vanuatu   2990–2740  0/1
I1370   Vanuatu   3110–2780  1/2
CP30    Tonga     2680–2340  0/3

MC1R, rs1805008, red hair, fair skin

Sample  Location  Date BP    D/T
I1368   Vanuatu   2990–2740  0/3
I1369   Vanuatu   3000–2750  0/4
I1370   Vanuatu   3110–2780  0/2
CP30    Tonga     2680–2340  0/2

MC1R, rs1805009, red hair, fair skin

Sample  Location  Date BP    D/T
I1368   Vanuatu   2990–2740  0/2
I1370   Vanuatu   3110–2780  0/1
CP30    Tonga     2680–2340  0/2

MCM6, rs182549, ability to digest milk

Sample  Location  Date BP    D/T
I1370   Vanuatu   3110–2780  0/1

MCM6, rs4988235, ability to digest milk

Sample  Location  Date BP    D/T
CP30    Tonga     2680–2340  0/2

OCA2, rs1800407, green or hazel eyes

Sample  Location  Date BP    D/T
I1368   Vanuatu   2990–2740  1/1

OCA2, rs1800414, Mongoloid light skin

Sample  Location  Date BP    D/T
I1369   Vanuatu   3000–2750  0/1

SLC24A5, rs1426654, Caucasoid light skin

Sample  Location  Date BP    D/T
I1370   Vanuatu   3110–2780  0/1

SLC45A2, rs16891982, Caucasoid light skin

Sample  Location  Date BP    D/T
I1368   Vanuatu   2990–2740  0/1
I1369   Vanuatu   3000–2750  0/1
I1370   Vanuatu   3110–2780  0/2

TYR, rs1042602, light skin, absence of freckles

Sample  Location  Date BP    D/T
I1368   Vanuatu   2990–2740  0/2
I1369   Vanuatu   3000–2750  0/1

TYR, rs1393350, blond hair, blue eyes

Sample  Location  Date BP    D/T
I1368   Vanuatu   2990–2740  0/1
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K = 13 admixture analysis of genomes from Neolithic central Asia Minor

Below is a plot for a K = 13 admixture analysis that includes nine Neolithic genomes from central Asia Minor. The table above the plot gives some information for these samples.

The Pre-Pottery Neolithic samples are similar to the early Neolithic samples from northwestern Asia Minor, while the later Pottery Neolithic samples show more admixture from people like the early inhabitants of Iran and the Caucasus region.

Sample  Period                 Date BC
Bon004  Pre-Pottery Neolithic  > 8300
Bon005  Pre-Pottery Neolithic  8300–8240
Bon002  Pre-Pottery Neolithic  8279–7977
Bon001  Pre-Pottery Neolithic  8212–7952
Tep001  Pottery Neolithic      7500–5800
Tep002  Pottery Neolithic      7500–5800
Tep003  Pottery Neolithic      7500–5800
Tep004  Pottery Neolithic      7500–5800
Tep006  Pottery Neolithic      7500–5800

all-13-14-1

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Phenotype SNPs from Neolithic central Asia Minor

Below are derived allele counts and total numbers of reads for SNPs that have a large effect on phenotype for Neolithic genomes from central Asia Minor. Nonzero derived allele counts are in bold. Note that small derived allele counts may be due to DNA damage.

ASIP, rs2424984, Veddoid brown skin

Sample  Period                 Date BC    D/T
Bon004  Pre-Pottery Neolithic  > 8300     1/1
Bon002  Pre-Pottery Neolithic  8279–7977  5/5

ASIP, rs6058017, Veddoid brown skin

Sample  Period                 Date BC    D/T
Bon002  Pre-Pottery Neolithic  8279–7977  4/4

EDAR, rs3827760, Mongoloid teeth, hair, etc.

Sample  Period                 Date BC    D/T
Bon002  Pre-Pottery Neolithic  8279–7977  0/2
Tep002  Pottery Neolithic      7500–5800  0/1
Tep003  Pottery Neolithic      7500–5800  0/2
Tep004  Pottery Neolithic      7500–5800  0/1
Tep006  Pottery Neolithic      7500–5800  0/1

IRF4, rs12203592, light hair and eyes, freckling

Sample  Period                 Date BC    D/T
Bon002  Pre-Pottery Neolithic  8279–7977  0/1

KITLG, rs12821256, blond hair

Sample  Period                 Date BC    D/T
Bon002  Pre-Pottery Neolithic  8279–7977  0/1
Tep003  Pottery Neolithic      7500–5800  0/1
Tep004  Pottery Neolithic      7500–5800  0/1

KITLG, rs642742, Veddoid brown skin

Sample  Period                 Date BC    D/T
Bon002  Pre-Pottery Neolithic  8279–7977  10/11
Tep004  Pottery Neolithic      7500–5800  1/1
Tep006  Pottery Neolithic      7500–5800  1/1

MC1R, rs1110400, red hair

Sample  Period                 Date BC    D/T
Bon002  Pre-Pottery Neolithic  8279–7977  0/3
Tep003  Pottery Neolithic      7500–5800  0/2

MC1R, rs11547464, red hair

Sample  Period                 Date BC    D/T
Bon002  Pre-Pottery Neolithic  8279–7977  0/6
Tep004  Pottery Neolithic      7500–5800  0/1

MC1R, rs1805005, blond hair, fair skin

Sample  Period                 Date BC    D/T
Bon002  Pre-Pottery Neolithic  8279–7977  0/7

MC1R, rs1805006, red hair, fair skin

Sample  Period                 Date BC    D/T
Bon002  Pre-Pottery Neolithic  8279–7977  0/4
Tep003  Pottery Neolithic      7500–5800  0/2

MC1R, rs1805007, red hair, fair skin

Sample  Period                 Date BC    D/T
Bon002  Pre-Pottery Neolithic  8279–7977  0/2
Tep003  Pottery Neolithic      7500–5800  0/1
Tep004  Pottery Neolithic      7500–5800  0/1

MC1R, rs1805008, red hair, fair skin

Sample  Period                 Date BC    D/T
Bon002  Pre-Pottery Neolithic  8279–7977  0/5
Tep003  Pottery Neolithic      7500–5800  0/1

MC1R, rs1805009, red hair, fair skin

Sample  Period                 Date BC    D/T
Bon002  Pre-Pottery Neolithic  8279–7977  0/6
Tep003  Pottery Neolithic      7500–5800  0/2

MCM6, rs182549, ability to digest milk

Sample  Period                 Date BC    D/T
Bon002  Pre-Pottery Neolithic  8279–7977  0/26
Tep003  Pottery Neolithic      7500–5800  0/3

MCM6, rs4988235, ability to digest milk

Sample  Period             Date BC    D/T
Tep002  Pottery Neolithic  7500–5800  0/1
Tep003  Pottery Neolithic  7500–5800  1/4

OCA2, rs1800407, green or hazel eyes

Sample  Period                 Date BC    D/T
Bon002  Pre-Pottery Neolithic  8279–7977  1/8
Tep003  Pottery Neolithic      7500–5800  0/1

OCA2, rs1800414, Mongoloid light skin

Sample  Period                 Date BC    D/T
Bon004  Pre-Pottery Neolithic  > 8300     0/1
Bon002  Pre-Pottery Neolithic  8279–7977  0/12
Tep002  Pottery Neolithic      7500–5800  0/1

OCA2/HERC2, rs12913832, blue eyes

Sample  Period                 Date BC    D/T
Bon004  Pre-Pottery Neolithic  > 8300     0/1
Bon002  Pre-Pottery Neolithic  8279–7977  1/6
Tep002  Pottery Neolithic      7500–5800  0/1
Tep003  Pottery Neolithic      7500–5800  0/1

SLC24A5, rs1426654, Caucasoid light skin

Sample  Period                 Date BC    D/T
Bon002  Pre-Pottery Neolithic  8279–7977  2/3

SLC45A2, rs16891982, Caucasoid light skin

Sample  Period             Date BC    D/T
Tep006  Pottery Neolithic  7500–5800  1/1

TYR, rs1042602, light skin, absence of freckles

Sample  Period                 Date BC    D/T
Bon002  Pre-Pottery Neolithic  8279–7977  0/3
Tep003  Pottery Neolithic      7500–5800  0/2
Tep004  Pottery Neolithic      7500–5800  0/1

TYR, rs1393350, blond hair, blue eyes

Sample  Period                 Date BC    D/T
Bon002  Pre-Pottery Neolithic  8279–7977  0/10

TYRP1, rs2733831, light hair and eyes

Sample  Period                 Date BC    D/T
Bon005  Pre-Pottery Neolithic  8300–8240  0/1
Bon002  Pre-Pottery Neolithic  8279–7977  2/3
Tep002  Pottery Neolithic      7500–5800  1/2
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