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

Posted in Uncategorized

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

Posted in Uncategorized

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
Posted in Uncategorized

Y-SNP calls from Neolithic central Asia Minor

In the table below are links to Y-SNP calls for Neolithic samples from central Asia Minor.

Sample  Period                 Date BC    Haplogroup
Bon004  Pre-Pottery Neolithic  > 8300     G2a2b2b-F705      calls
Bon001  Pre-Pottery Neolithic  8212–7952  G2a2b2b1a-PF3422  calls
Tep001  Pottery Neolithic      7500–5800  G, J2, or R1b     calls
Tep006  Pottery Neolithic      7500–5800  C1a2-Y10446       calls
Tep003  Pottery Neolithic      7500–5800  G2a2a-PF3159*     calls
Posted in Uncategorized

K = 11 admixture analysis of Amerindians and Eskimos

At the bottom of this post is a plot for a K = 11 admixture analysis of Old World populations. Above it is a plot of the results of projecting Amerindian, Eskimo, and some Eastern Siberian populations onto the components produced by the Old World analysis.

new-world-11-12-1

old-world-11-12-1

Posted in Uncategorized

Phenotype SNPs from the ancient Americas

Below are derived allele counts and total numbers of reads for SNPs that have a large effect on phenotype for ancient DNA samples from the Americas. 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    Tribe    Region               Years BP   D/T
939       Unknown  British Columbia     6260–5890  2/2
MARC1492  Micmac   New Brunswick        516–258    1/1
BC25      Pericú   Baja California Sur  800–300    1/1
BC30      Pericú   Baja California Sur  800–300    2/2
MA577     Selknam  Tierra del Fuego     ~200       8/8
890       Yaghan   Tierra del Fuego     ~200       4/4
894       Yaghan   Tierra del Fuego     ~200       4/4
895       Yaghan   Tierra del Fuego     ~200       6/6

ASIP, rs6058017, Veddoid brown skin

Sample    Tribe     Region             Years BP  D/T
MARC1492  Micmac    New Brunswick      516–258   1/1
AM74      Alacaluf  Chilean Patagonia  132       1/1
MA577     Selknam   Tierra del Fuego   ~200      6/6
890       Yaghan    Tierra del Fuego   ~200      13/13
895       Yaghan    Tierra del Fuego   ~200      3/3

EDAR, rs3827760, Mongoloid teeth, hair, etc.

Sample  Tribe     Region               Years BP  D/T
BC25    Pericú    Baja California Sur  800–300   1/1
BC30    Pericú    Baja California Sur  800–300   1/1
AM71    Alacaluf  Chilean Patagonia    132       1/1
MA577   Selknam   Tierra del Fuego     ~200      4/4
890     Yaghan    Tierra del Fuego     ~200      1/1
894     Yaghan    Tierra del Fuego     ~200      5/5
895     Yaghan    Tierra del Fuego     ~200      5/5

IRF4, rs12203592, light hair and eyes, freckling

Sample    Tribe     Region             Years BP   D/T
939       Unknown   British Columbia   6260–5890  0/3
MARC1492  Micmac    New Brunswick      516–258    0/1
AM74      Alacaluf  Chilean Patagonia  132        0/1
MA577     Selknam   Tierra del Fuego   ~200       0/2
894       Yaghan    Tierra del Fuego   ~200       0/1
895       Yaghan    Tierra del Fuego   ~200       0/2

KITLG, rs12821256, blond hair

Sample  Tribe     Region               Years BP  D/T
BC25    Pericú    Baja California Sur  800–300   0/1
BC29    Pericú    Baja California Sur  800–300   0/1
AM74    Alacaluf  Chilean Patagonia    132       0/1
MA577   Selknam   Tierra del Fuego     ~200      0/2

KITLG, rs642742, Veddoid brown skin

Sample  Tribe    Region            Years BP   D/T
939     Unknown  British Columbia  6260–5890  1/1
MA577   Selknam  Tierra del Fuego  ~200       1/1

MC1R, rs1110400, red hair

Sample    Tribe     Region               Years BP   D/T
939       Unknown   British Columbia     6260–5890  0/1
Enoque65  Unknown   Northeastern Brazil  3635–3483  0/1
AM74      Alacaluf  Chilean Patagonia    132        0/2
MA577     Selknam   Tierra del Fuego     ~200       0/6
890       Yaghan    Tierra del Fuego     ~200       0/6
894       Yaghan    Tierra del Fuego     ~200       0/1
895       Yaghan    Tierra del Fuego     ~200       0/7

MC1R, rs11547464, red hair

Sample  Tribe     Region             Years BP  D/T
AM74    Alacaluf  Chilean Patagonia  132       0/1
MA572   Selknam   Tierra del Fuego   ~200      0/1
MA577   Selknam   Tierra del Fuego   ~200      0/11
890     Yaghan    Tierra del Fuego   ~200      0/8
895     Yaghan    Tierra del Fuego   ~200      0/12

MC1R, rs1805005, blond hair, fair skin

Sample  Tribe     Region             Years BP   D/T
939     Unknown   British Columbia   6260–5890  0/2
AM71    Alacaluf  Chilean Patagonia  132        0/1
AM74    Alacaluf  Chilean Patagonia  132        0/1
MA577   Selknam   Tierra del Fuego   ~200       0/6
890     Yaghan    Tierra del Fuego   ~200       0/10
894     Yaghan    Tierra del Fuego   ~200       0/1
895     Yaghan    Tierra del Fuego   ~200       0/6

MC1R, rs1805006, red hair, fair skin

Sample  Tribe     Region               Years BP  D/T
BC28    Pericú    Baja California Sur  800–300   0/1
AM71    Alacaluf  Chilean Patagonia    132       0/1
MA577   Selknam   Tierra del Fuego     ~200      0/8
890     Yaghan    Tierra del Fuego     ~200      0/11
894     Yaghan    Tierra del Fuego     ~200      0/1
895     Yaghan    Tierra del Fuego     ~200      0/7

MC1R, rs1805007, red hair, fair skin

Sample    Tribe     Region               Years BP   D/T
939       Unknown   British Columbia     6260–5890  0/1
Enoque65  Unknown   Northeastern Brazil  3635–3483  0/1
AM74      Alacaluf  Chilean Patagonia    132        0/2
MA577     Selknam   Tierra del Fuego     ~200       0/6
890       Yaghan    Tierra del Fuego     ~200       0/5
894       Yaghan    Tierra del Fuego     ~200       0/1
895       Yaghan    Tierra del Fuego     ~200       0/7

MC1R, rs1805008, red hair, fair skin

Sample    Tribe     Region               Years BP   D/T
939       Unknown   British Columbia     6260–5890  0/1
Enoque65  Unknown   Northeastern Brazil  3635–3483  0/1
AM74      Alacaluf  Chilean Patagonia    132        0/2
MA577     Selknam   Tierra del Fuego     ~200       0/8
890       Yaghan    Tierra del Fuego     ~200       0/7
894       Yaghan    Tierra del Fuego     ~200       0/0
895       Yaghan    Tierra del Fuego     ~200       0/7

MC1R, rs1805009, red hair, fair skin

Sample  Tribe     Region               Years BP  D/T
BC25    Pericú    Baja California Sur  800–300   0/3
BC30    Pericú    Baja California Sur  800–300   0/1
AM66    Alacaluf  Chilean Patagonia    132       0/1
MA577   Selknam   Tierra del Fuego     ~200      0/2
890     Yaghan    Tierra del Fuego     ~200      0/2
894     Yaghan    Tierra del Fuego     ~200      0/1
895     Yaghan    Tierra del Fuego     ~200      0/1

MCM6, rs182549, ability to digest milk

Sample  Tribe     Region             Years BP  D/T
AM71    Alacaluf  Chilean Patagonia  132       0/1
AM74    Alacaluf  Chilean Patagonia  132       0/2
MA577   Selknam   Tierra del Fuego   ~200      0/5
890     Yaghan    Tierra del Fuego   ~200      0/2
894     Yaghan    Tierra del Fuego   ~200      0/5
895     Yaghan    Tierra del Fuego   ~200      0/5

MCM6, rs4988235, ability to digest milk

Sample  Tribe     Region             Years BP   D/T
939     Unknown   British Columbia   6260–5890  0/2
AM74    Alacaluf  Chilean Patagonia  132        1/1
894     Yaghan    Tierra del Fuego   ~200       0/3
895     Yaghan    Tierra del Fuego   ~200       0/3

OCA2, rs1800407, green or hazel eyes

Sample    Tribe     Region               Years BP  D/T
MARC1492  Micmac    New Brunswick        516–258   0/1
MOM6      Unknown   Northwestern Mexico  >500      0/1
AM71      Alacaluf  Chilean Patagonia    132       0/1
AM74      Alacaluf  Chilean Patagonia    132       0/1
MA577     Selknam   Tierra del Fuego     ~200      0/5
890       Yaghan    Tierra del Fuego     ~200      0/2
894       Yaghan    Tierra del Fuego     ~200      0/5
895       Yaghan    Tierra del Fuego     ~200      0/7

OCA2, rs1800414, Mongoloid light skin

Sample    Tribe    Region               Years BP  D/T
MARC1492  Micmac   New Brunswick        516–258   0/1
BC25      Pericú   Baja California Sur  800–300   0/1
MA577     Selknam  Tierra del Fuego     ~200      0/3
894       Yaghan   Tierra del Fuego     ~200      0/4
895       Yaghan   Tierra del Fuego     ~200      0/1

OCA2/HERC2, rs12913832, blue eyes

Sample  Tribe    Region               Years BP  D/T
BC25    Pericú   Baja California Sur  800–300   0/1
MA577   Selknam  Tierra del Fuego     ~200      0/2
890     Yaghan   Tierra del Fuego     ~200      1/1
895     Yaghan   Tierra del Fuego     ~200      0/2

SLC24A5, rs1426654, Caucasoid light skin

Sample    Tribe     Region               Years BP  D/T
MARC1492  Micmac    New Brunswick        516–258   0/3
BC29      Pericú    Baja California Sur  800–300   0/1
AM71      Alacaluf  Chilean Patagonia    132       0/1
AM74      Alacaluf  Chilean Patagonia    132       0/1
MA577     Selknam   Tierra del Fuego     ~200      0/5
890       Yaghan    Tierra del Fuego     ~200      0/3
894       Yaghan    Tierra del Fuego     ~200      0/2
895       Yaghan    Tierra del Fuego     ~200      0/2

SLC45A2, rs16891982, Caucasoid light skin

Sample  Tribe     Region             Years BP   D/T
939     Unknown   British Columbia   6260–5890  0/1
AM74    Alacaluf  Chilean Patagonia  132        1/3
MA577   Selknam   Tierra del Fuego   ~200       0/4
894     Yaghan    Tierra del Fuego   ~200       0/5
895     Yaghan    Tierra del Fuego   ~200       0/1

TYR, rs1042602, light skin, absence of freckles

Sample  Tribe     Region             Years BP  D/T
AM74    Alacaluf  Chilean Patagonia  132       0/2
MA577   Selknam   Tierra del Fuego   ~200      0/2
895     Yaghan    Tierra del Fuego   ~200      0/4

TYR, rs1393350, blond hair, blue eyes

Sample  Tribe    Region            Years BP  D/T
MA577   Selknam  Tierra del Fuego  ~200      0/2
890     Yaghan   Tierra del Fuego  ~200      0/1
894     Yaghan   Tierra del Fuego  ~200      0/1
895     Yaghan   Tierra del Fuego  ~200      0/3

TYRP1, rs2733831, light hair and eyes

Sample  Tribe    Region            Years BP  D/T
MA577   Selknam  Tierra del Fuego  ~200      0/3
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