Chinchorro DNA paper published on bioRxiv

I’ve written a paper on my discovery of European admixture in a Chinchorro mummy DNA sample, and it’s now published on bioRxiv:

European admixture in Chinchorro DNA

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K = 14 admixture analysis of Neolithic Estonian genomes

Below is a plot for a K = 14 admixture analysis that includes seven genomes from Neolithic Estonia. The table above the plot gives some information for these samples.

The hunter-gatherer samples from the Comb Ware culture are similar to the Comb Ware sample from Latvia, the earlier hunter-gatherer samples from Karelia and Samara in Russia, and the earlier Mesolithic and Dnieper-Donets samples from Ukraine. All of these samples are made up mostly of the medium blue Eastern component, but also have significant amounts of the dark blue Western component. The Baltic Comb Ware samples have more of the Western component than the Russian samples, but less than the Ukrainian samples.

The Estonian Corded Ware samples are indistinguishable from the other Corded Ware samples from Germany and Poland. They differ from the Corded Ware sample from Latvia, which lacks the light blue early farmer component.

Sample       Culture      Date BC
Kudruküla 2  Comb Ware    3831–3426
Kudruküla 3  Comb Ware    3950–1850
Ardu 1       Corded Ware  2850–2050
Ardu 2       Corded Ware  2921–2555
Kunila 1     Corded Ware  2850–2050
Kunila 2     Corded Ware  2626–2390
Sope         Corded Ware  2625–2400

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Phenotype SNPs from Neolithic Estonia

Below are derived allele counts and total numbers of reads for SNPs that have a large effect on phenotype for genomes from Neolithic Estonia. 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    Culture      Date BC    D/T
Ardu 1    Corded Ware  2850–2050  0/1
Ardu 2    Corded Ware  2921–2555  1/1
Kunila 2  Corded Ware  2626–2390  8/8

ASIP, rs6058017, Veddoid brown skin

Sample    Culture      Date BC    D/T
Ardu 2    Corded Ware  2921–2555  1/1
Kunila 2  Corded Ware  2626–2390  5/5
Sope      Corded Ware  2625–2400  1/1

EDAR, rs3827760, Mongoloid teeth, hair, etc.

Sample       Culture       Date BC    D/T
Kudruküla 2  Comb Ceramic  3831–3426  0/1
Ardu 2       Corded Ware   2921–2555  0/1
Kunila 1     Corded Ware   2850–2050  0/1
Kunila 2     Corded Ware   2626–2390  0/8
Sope         Corded Ware   2625–2400  0/1

IRF4, rs12203592, light hair and eyes, freckling

Sample    Culture      Date BC    D/T
Ardu 1    Corded Ware  2850–2050  1/1
Ardu 2    Corded Ware  2921–2555  0/1
Kunila 1  Corded Ware  2850–2050  0/3
Kunila 2  Corded Ware  2626–2390  2/3

KITLG, rs12821256, blond hair

Sample    Culture      Date BC    D/T
Kunila 2  Corded Ware  2626–2390  0/2

MC1R, rs1110400, red hair

Sample    Culture      Date BC    D/T
Ardu 2    Corded Ware  2921–2555  0/4
Kunila 1  Corded Ware  2850–2050  0/2
Kunila 2  Corded Ware  2626–2390  0/16
Sope      Corded Ware  2625–2400  0/1

MC1R, rs11547464, red hair

Sample       Culture       Date BC    D/T
Kudruküla 2  Comb Ceramic  3831–3426  0/1
Ardu 1       Corded Ware   2850–2050  0/3
Ardu 2       Corded Ware   2921–2555  0/2
Kunila 1     Corded Ware   2850–2050  0/2
Kunila 2     Corded Ware   2626–2390  1/12

MC1R, rs1805005, blond hair, fair skin

Sample    Culture      Date BC    D/T
Ardu 1    Corded Ware  2850–2050  0/1
Ardu 2    Corded Ware  2921–2555  0/1
Kunila 2  Corded Ware  2626–2390  0/12
Sope      Corded Ware  2625–2400  0/2

MC1R, rs1805006, red hair, fair skin

Sample       Culture       Date BC    D/T
Kudruküla 2  Comb Ceramic  3831–3426  0/1
Kudruküla 3  Comb Ceramic  3950–1850  0/1
Ardu 1       Corded Ware   2850–2050  0/1
Ardu 2       Corded Ware   2921–2555  0/1
Kunila 1     Corded Ware   2850–2050  0/2
Kunila 2     Corded Ware   2626–2390  0/11

MC1R, rs1805007, red hair, fair skin

Sample    Culture      Date BC    D/T
Ardu 2    Corded Ware  2921–2555  0/4
Kunila 1  Corded Ware  2850–2050  0/2
Kunila 2  Corded Ware  2626–2390  1/13
Sope      Corded Ware  2625–2400  0/1

MC1R, rs1805008, red hair, fair skin

Sample    Culture      Date BC    D/T
Ardu 2    Corded Ware  2921–2555  0/6
Kunila 2  Corded Ware  2626–2390  0/19

MC1R, rs1805009, red hair, fair skin

Sample    Culture      Date BC    D/T
Ardu 1    Corded Ware  2850–2050  0/1
Ardu 2    Corded Ware  2921–2555  0/2
Kunila 1  Corded Ware  2850–2050  0/2
Kunila 2  Corded Ware  2626–2390  0/2
Sope      Corded Ware  2625–2400  0/2

MCM6, rs182549, ability to digest milk

Sample    Culture      Date BC    D/T
Kunila 1  Corded Ware  2850–2050  0/1
Kunila 2  Corded Ware  2626–2390  0/7
Sope      Corded Ware  2625–2400  0/1

MCM6, rs4988235, ability to digest milk

Sample    Culture      Date BC    D/T
Ardu 1    Corded Ware  2850–2050  0/1
Ardu 2    Corded Ware  2921–2555  0/2
Kunila 1  Corded Ware  2850–2050  0/1
Kunila 2  Corded Ware  2626–2390  0/2

OCA2, rs1800407, green or hazel eyes

Sample    Culture      Date BC    D/T
Ardu 2    Corded Ware  2921–2555  0/2
Kunila 1  Corded Ware  2850–2050  0/2
Kunila 2  Corded Ware  2626–2390  0/6

OCA2, rs1800414, Mongoloid light skin

Sample    Culture      Date BC    D/T
Ardu 2    Corded Ware  2921–2555  0/2
Kunila 2  Corded Ware  2626–2390  0/1

OCA2/HERC2, rs12913832, blue eyes

Sample       Culture       Date BC    D/T
Kudruküla 3  Comb Ceramic  3950–1850  0/1
Kunila 1     Corded Ware   2850–2050  1/2
Kunila 2     Corded Ware   2626–2390  0/2
Sope         Corded Ware   2625–2400  1/2

SLC24A5, rs1426654, Caucasoid light skin

Sample       Culture       Date BC    D/T
Kudruküla 3  Comb Ceramic  3950–1850  1/2
Ardu 2       Corded Ware   2921–2555  2/2
Kunila 1     Corded Ware   2850–2050  2/2
Kunila 2     Corded Ware   2626–2390  7/7
Sope         Corded Ware   2625–2400  2/2

SLC45A2, rs16891982, Caucasoid light skin

Sample    Culture      Date BC    D/T
Ardu 1    Corded Ware  2850–2050  1/1
Ardu 2    Corded Ware  2921–2555  0/2
Kunila 1  Corded Ware  2850–2050  0/5
Kunila 2  Corded Ware  2626–2390  0/4

TYR, rs1042602, light skin, absence of freckles

Sample    Culture      Date BC    D/T
Ardu 2    Corded Ware  2921–2555  0/2
Kunila 1  Corded Ware  2850–2050  0/1
Kunila 2  Corded Ware  2626–2390  0/2

TYR, rs1393350, blond hair, blue eyes

Sample    Culture      Date BC    D/T
Ardu 2    Corded Ware  2921–2555  1/2
Kunila 2  Corded Ware  2626–2390  0/2

TYRP1, rs2733831, light hair and eyes

Sample  Culture      Date BC    D/T
Ardu 2  Corded Ware  2921–2555  0/2
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Y-SNP calls from Neolithic Estonia

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

Sample       Culture       Date BC    Haplogroup
Kudruküla 3  Comb Ceramic  3950–1850  R1a1-YP1335      calls
Ardu 1       Corded Ware   2850–2050  R1a1a1b-Z645     calls
Ardu 2       Corded Ware   2921–2555  R1a1a1b1-Z283    calls
Kunila 1     Corded Ware   2850–2050  R1a1a1b-Z645     calls
Kunila 2     Corded Ware   2626–2390  R1a1a1b1a-Y2395  calls
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High-resolution K = 13 analysis of the European admixture in Chinchorro DNA

Below is a plot for a high-resolution K = 13 admixture analysis that includes a Chinchorro mummy sample from Chile dated to 3972–3806 BC.

Here are the admixture percentages for the Chinchorro sample:

      0.00%
      0.00%
      6.76%
      0.00%
      10.81%
      0.00%
      17.81%
      0.00%
      1.10%
      0.00%
      0.00%
      63.51%
      0.00%

Here the Chinchorro sample has significant amounts of the dark blue, light blue, and plain green components, and a small amount of the plain yellow component.

The Magdalenians are made up almost entirely of the dark blue component, which excludes them as the source of the European admixture in the Chinchorro sample.

The medium blue component is completely absent in the Chinchorro sample, and since the Eastern European and Western Siberian hunter-gatherers are made up mostly of that component, they are also excluded as sources of the admixture.

The pre-LGM Europeans are the only samples in this analysis which have significant amounts of the same non-Amerindian components present in the Chinchorro sample, which identifies the pre-LGM Aurignacians or Gravettians, or possibly the LGM Solutreans, as the source of the European admixture in that sample.

The sum of the non-Amerindian component percentages in this analysis is 36.49%, which is about the same as the 37% sum in the preceding analysis.

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High-resolution K = 9 analysis of the European admixture in Chinchorro DNA

Below is a plot for a high-resolution K = 9 admixture analysis that includes a Chinchorro mummy sample from Chile dated to 3972–3806 BC.

Here are the admixture percentages for the Chinchorro sample:

      0.00%
      10.37%
      8.12%
      0.00%
      18.52%
      0.00%
      0.00%
      63.00%
      0.00%

Here the Chinchorro sample has significant amounts of the plain blue, light blue, and plain green components.

The pre-LGM Europeans also have significant amounts of the plain blue, light blue, and plain green components.

The pine green component is completely absent in the Chinchorro sample, and, with the exception of Kostenki 14, it is also completely absent in the pre-LGM Europeans.

The plain green component is absent in post-Magdalenian Europeans, and the pine green component is present in significant amounts in Europeans from the Copper Age on, which eliminates modern contamination as a possible source of the European admixture in the Chinchorro sample.

This analysis leaves pre-LGM, LGM, and Magdalenian-era Europeans as the only remaining possible sources of the European admixture in the Chinchorro sample, and the pre-LGM Europeans are a better visual match for that admixture than the Magdalenians.

The sum of the non-Amerindian component percentages in this analysis is 37%, which is a bit more than the 34.3% sum in the preceding analysis.

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High-resolution K = 7 analysis of the European admixture in Chinchorro DNA

Below is a plot for a high-resolution K = 7 admixture analysis that includes a Chinchorro mummy sample from Chile dated to 3972–3806 BC.

Here are the admixture percentages for the Chinchorro sample:

      0.00%
      8.84%
      8.51%
      15.08%
      0.00%
      65.70%
      1.87%

Here the Chinchorro sample has significant amounts of the plain blue, light blue, and green components, and a small amount of the purple component.

The pre-LGM Europeans also have significant amounts of the plain blue, light blue, and green components, but they generally have less of the green component than either of the blue components, whereas the Chinchorro sample has more of the green component than either of the blue components.

The sum of the non-Amerindian component percentages in this analysis is 34.30%, a bit more than the sums for the preceding analyses.

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