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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K = 13 admixture analysis of ancient Iranian genomes

Below is a plot for a K = 13 admixture analysis that includes five new ancient genomes from the Zagros Mountains of Iran. The following table gives some information for these samples.

Sample  Period           Date BC
AH1     Early Neolithic  Unknown
AH2     Early Neolithic  8205–7756
AH4     Early Neolithic  8204–7755
WC1     Early Neolithic  7455–7082
F38     Early Iron Age   971–832

all-13-12-1

Posted in Uncategorized

Phenotype SNPs from ancient Iran

Below are derived allele counts and total numbers of reads for SNPs that have a large effect on phenotype for five new ancient genomes from the Zagros Mountains of Iran. 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
AH1     Early Neolithic  Unknown    3/3
AH2     Early Neolithic  8205–7756  1/1
AH4     Early Neolithic  8204–7755  0/2
WC1     Early Neolithic  7455–7082  16/16

ASIP, rs6058017, Veddoid brown skin

Sample  Period           Date BC    D/T
AH1     Early Neolithic  Unknown    2/2
WC1     Early Neolithic  7455–7082  15/15
F38     Early Iron Age   971–832    0/2

EDAR, rs3827760, Mongoloid teeth, hair, etc.

Sample  Period           Date BC    D/T
AH1     Early Neolithic  Unknown    0/1
AH2     Early Neolithic  8205–7756  0/1
AH4     Early Neolithic  8204–7755  0/2
WC1     Early Neolithic  7455–7082  0/14
F38     Early Iron Age   971–832    0/5

IRF4, rs12203592, light hair and eyes, freckling

Sample  Period           Date BC    D/T
AH1     Early Neolithic  Unknown    0/1
AH2     Early Neolithic  8205–7756  0/1
AH4     Early Neolithic  8204–7755  0/3
WC1     Early Neolithic  7455–7082  0/22
F38     Early Iron Age   971–832    0/4

KITLG, rs12821256, blond hair

Sample  Period           Date BC    D/T
AH2     Early Neolithic  8205–7756  0/2
AH4     Early Neolithic  8204–7755  0/1
WC1     Early Neolithic  7455–7082  0/12
F38     Early Iron Age   971–832    0/2

KITLG, rs642742, Veddoid brown skin

Sample  Period           Date BC    D/T
AH1     Early Neolithic  Unknown    1/1
AH2     Early Neolithic  8205–7756  1/1
AH4     Early Neolithic  8204–7755  1/2
WC1     Early Neolithic  7455–7082  16/16
F38     Early Iron Age   971–832    2/2

MC1R, rs1110400, red hair

Sample  Period           Date BC    D/T
AH1     Early Neolithic  Unknown    0/2
AH2     Early Neolithic  8205–7756  0/1
AH4     Early Neolithic  8204–7755  0/3
WC1     Early Neolithic  7455–7082  0/10

MC1R, rs11547464, red hair

Sample  Period           Date BC    D/T
AH1     Early Neolithic  Unknown    0/3
AH2     Early Neolithic  8205–7756  0/2
AH4     Early Neolithic  8204–7755  1/2
WC1     Early Neolithic  7455–7082  0/15
F38     Early Iron Age   971–832    0/1

MC1R, rs1805005, blond hair, fair skin

Sample  Period           Date BC    D/T
AH1     Early Neolithic  Unknown    0/2
AH2     Early Neolithic  8205–7756  0/1
AH4     Early Neolithic  8204–7755  0/1
WC1     Early Neolithic  7455–7082  0/12
F38     Early Iron Age   971–832    0/5

MC1R, rs1805006, red hair, fair skin

Sample  Period           Date BC    D/T
AH1     Early Neolithic  Unknown    0/1
AH2     Early Neolithic  8205–7756  0/1
AH4     Early Neolithic  8204–7755  0/3
WC1     Early Neolithic  7455–7082  0/14
F38     Early Iron Age   971–832    0/2

MC1R, rs1805007, red hair, fair skin

Sample  Period           Date BC    D/T
AH1     Early Neolithic  Unknown    0/3
AH2     Early Neolithic  8205–7756  0/1
AH4     Early Neolithic  8204–7755  0/3
WC1     Early Neolithic  7455–7082  0/14
F38     Early Iron Age   971–832    0/1

MC1R, rs1805008, red hair, fair skin

Sample  Period           Date BC    D/T
AH1     Early Neolithic  Unknown    0/2
AH2     Early Neolithic  8205–7756  0/2
AH4     Early Neolithic  8204–7755  0/2
WC1     Early Neolithic  7455–7082  0/8
F38     Early Iron Age   971–832    0/1

MC1R, rs1805009, red hair, fair skin

Sample  Period           Date BC    D/T
AH1     Early Neolithic  Unknown    0/1
AH2     Early Neolithic  8205–7756  0/1
AH4     Early Neolithic  8204–7755  0/2
WC1     Early Neolithic  7455–7082  1/15
F38     Early Iron Age   971–832    0/1

MCM6, rs182549, ability to digest milk

Sample  Period           Date BC    D/T
AH1     Early Neolithic  Unknown    1/3
AH2     Early Neolithic  8205–7756  0/1
AH4     Early Neolithic  8204–7755  2/5
WC1     Early Neolithic  7455–7082  1/19
F38     Early Iron Age   971–832    0/2

MCM6, rs4988235, ability to digest milk

Sample  Period           Date BC    D/T
AH1     Early Neolithic  Unknown    0/1
AH2     Early Neolithic  8205–7756  0/1
AH4     Early Neolithic  8204–7755  0/3
WC1     Early Neolithic  7455–7082  2/11
F38     Early Iron Age   971–832    0/2

OCA2, rs1800407, green or hazel eyes

Sample  Period           Date BC    D/T
AH1     Early Neolithic  Unknown    0/1
AH4     Early Neolithic  8204–7755  0/1
WC1     Early Neolithic  7455–7082  1/19
F38     Early Iron Age   971–832    0/2

OCA2, rs1800414, Mongoloid light skin

Sample  Period           Date BC    D/T
AH1     Early Neolithic  Unknown    0/2
AH4     Early Neolithic  8204–7755  0/1
WC1     Early Neolithic  7455–7082  0/15
F38     Early Iron Age   971–832    0/3

OCA2/HERC2, rs12913832, blue eyes

Sample  Period           Date BC    D/T
AH1     Early Neolithic  Unknown    0/1
AH2     Early Neolithic  8205–7756  0/3
WC1     Early Neolithic  7455–7082  7/20

SLC24A5, rs1426654, Caucasoid light skin

Sample  Period           Date BC    D/T
AH1     Early Neolithic  Unknown    2/4
AH2     Early Neolithic  8205–7756  0/4
AH4     Early Neolithic  8204–7755  2/2
WC1     Early Neolithic  7455–7082  5/13
F38     Early Iron Age   971–832    4/4

SLC45A2, rs16891982, Caucasoid light skin

Sample  Period           Date BC    D/T
AH1     Early Neolithic  Unknown    0/1
AH2     Early Neolithic  8205–7756  0/1
AH4     Early Neolithic  8204–7755  0/1
WC1     Early Neolithic  7455–7082  0/13

TYR, rs1042602, light skin, absence of freckles

Sample  Period           Date BC    D/T
AH1     Early Neolithic  Unknown    0/2
AH2     Early Neolithic  8205–7756  0/1
AH4     Early Neolithic  8204–7755  0/1
WC1     Early Neolithic  7455–7082  0/19
F38     Early Iron Age   971–832    0/3

TYR, rs1393350, blond hair, blue eyes

Sample  Period           Date BC    D/T
AH1     Early Neolithic  Unknown    0/1
AH2     Early Neolithic  8205–7756  0/1
WC1     Early Neolithic  7455–7082  0/16
F38     Early Iron Age   971–832    0/5

TYRP1, rs2733831, light hair and eyes

Sample  Period           Date BC    D/T
AH1     Early Neolithic  Unknown    0/1
WC1     Early Neolithic  7455–7082  0/7
F38     Early Iron Age   971–832    0/2
Posted in Uncategorized

Y-SNP calls from ancient Iran

In the table below are links to Y-SNP calls for ancient DNA samples from the Zagros Mountains of Iran.

Sample  Period           Date BC    Haplogroup
AH2     Early Neolithic  8205–7756  J2b-M12*                calls
WC1     Early Neolithic  7455–7082  G2b2a-Z8022             calls
F38     Early Iron Age   971–832    R1b1a1a2a2a-Y:24376846  calls
Posted in Uncategorized

K = 13 admixture analysis of ancient Near Eastern genomes

Below is a plot for a K = 13 admixture analysis that includes 45 ancient Near Eastern genomes.

This analysis produced five Caucasoid components. Three of them are similar to components in the preceding K = 12 analysis, while a fourth represents Western European hunter-gatherer DNA, and a fifth represents DNA from the hunter-gatherers of Eastern Europe and Western Siberia, and the later Copper and Bronze Age populations of Eastern Europe.

Over the past week I began to suspect that the Caucasus-related pine green component appearing in large amounts in European samples in my recent K = 13 analyses, which I thought was linked with the spread of R1b-L51 people, was somehow spurious. This analysis, along with others I’ve done over the past few days, confirms my suspicion. The plot below shows most European populations as having only small amounts of the Caucasus-related pine green component.

all-13-8-1

Posted in Uncategorized

K = 12 admixture analysis of ancient Near Eastern genomes

Below is a plot for a K = 12 admixture analysis that includes 45 ancient Near Eastern genomes.

This analysis produced four Caucasoid components, one peaking in European hunter-gatherers, one in the early Neolithic farmers of Asia Minor and Europe, one in the hunter-gatherers of the Caucasus region, and one in the hunter-gatherers of the Epipaleolithic Natufian culture of the Levant.

The plot shows the Mesolithic R1b, R1a, and J1 hunter-gatherers of Samara and Karelia in Russia as being very similar to the other Mesolithic European hunter-gatherers, but also as having some of the Caucasus-related component. The amount of this component increases in the people of the middle Copper Age Khvalynsk culture, and then increases further in the people of the late Copper Age and early Bronze Age Pit Grave culture.

all-12-8-1

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