Phenotype SNPs from early Holocene Alaska

Below are derived allele counts and total numbers of reads for SNPs that have a large effect on phenotype for two genomes dating to the early Holocene from the Upward Sun River site in central Alaska. Nonzero derived allele counts are highlighted. Note that small derived allele counts may be due to DNA damage.

ASIP, rs2424984, Veddoid brown skin

Sample Location Culture Date BP D/T
USR1 Alaska Denali 11,600–11,230 21/21

ASIP, rs6058017, Veddoid brown skin

Sample Location Culture Date BP D/T
USR1 Alaska Denali 11,600–11,230 18/18

EDAR, rs3827760, Mongoloid teeth, hair, etc.

Sample Location Culture Date BP D/T
USR1 Alaska Denali 11,600–11,230 6/13

IRF4, rs12203592, light hair and eyes, freckling

Sample Location Culture Date BP D/T
USR1 Alaska Denali 11,600–11,230 0/37

KITLG, rs12821256, blond hair

Sample Location Culture Date BP D/T
USR1 Alaska Denali 11,600–11,230 0/16
USR2 Alaska Denali 11,600–11,230 0/1

KITLG, rs642742, Veddoid brown skin

Sample Location Culture Date BP D/T
USR1 Alaska Denali 11,600–11,230 16/16
USR2 Alaska Denali 11,600–11,230 1/1

MC1R, rs1110400, red hair

Sample Location Culture Date BP D/T
USR1 Alaska Denali 11,600–11,230 0/15

MC1R, rs11547464, red hair

Sample Location Culture Date BP D/T
USR1 Alaska Denali 11,600–11,230 0/18

MC1R, rs1805005, blond hair, fair skin

Sample Location Culture Date BP D/T
USR1 Alaska Denali 11,600–11,230 0/20

MC1R, rs1805006, red hair, fair skin

Sample Location Culture Date BP D/T
USR1 Alaska Denali 11,600–11,230 0/25

MC1R, rs1805007, red hair, fair skin

Sample Location Culture Date BP D/T
USR1 Alaska Denali 11,600–11,230 0/22

MC1R, rs1805008, red hair, fair skin

Sample Location Culture Date BP D/T
USR1 Alaska Denali 11,600–11,230 0/19

MC1R, rs1805009, red hair, fair skin

Sample Location Culture Date BP D/T
USR1 Alaska Denali 11,600–11,230 0/17

MCM6, rs182549, ability to digest milk

Sample Location Culture Date BP D/T
USR1 Alaska Denali 11,600–11,230 0/16

MCM6, rs4988235, ability to digest milk

Sample Location Culture Date BP D/T
USR1 Alaska Denali 11,600–11,230 0/22

OCA2, rs1800407, green or hazel eyes

Sample Location Culture Date BP D/T
USR1 Alaska Denali 11,600–11,230 0/21

OCA2, rs1800414, Mongoloid light skin

Sample Location Culture Date BP D/T
USR1 Alaska Denali 11,600–11,230 0/25

OCA2/HERC2, rs12913832, blue eyes

Sample Location Culture Date BP D/T
USR1 Alaska Denali 11,600–11,230 0/26

SLC24A5, rs1426654, Caucasoid light skin

Sample Location Culture Date BP D/T
USR1 Alaska Denali 11,600–11,230 0/21

SLC45A2, rs16891982, Caucasoid light skin

Sample Location Culture Date BP D/T
USR1 Alaska Denali 11,600–11,230 0/23

TYR, rs1042602, light skin, absence of freckles

Sample Location Culture Date BP D/T
USR1 Alaska Denali 11,600–11,230 0/22

TYR, rs1393350, blond hair, blue eyes

Sample Location Culture Date BP D/T
USR1 Alaska Denali 11,600–11,230 0/35
USR2 Alaska Denali 11,600–11,230 0/1

TYRP1, rs2733831, light hair and eyes

Sample Location Culture Date BP D/T
USR1 Alaska Denali 11,600–11,230 0/14
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2 comments on “Phenotype SNPs from early Holocene Alaska
  1. AJ says:

    Is this a diploid genome? Would the 6/13 reads (as close to 1/2 as possible given the odd number of reads) be consistent with possessing 1 derived allele and one ancestral? If so what would the implications of this be, seeing as from your data here…
    https://genetiker.wordpress.com/2013/07/25/mongoloid-edar-snp-rs3827760-allele-frequencies/
    Modern day Native Americans appear essentially fixed for the derived allele

    • Genetiker says:

      Yes, it means that USR1 was heterozygous for the EDAR mutation. Anzick 1 was also heterozygous for it. I don’t draw any greater implications from those two findings.

      And yes, all pure modern Amerindian populations are fixed or close to being fixed for the mutation.

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