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Extended Data Table 1
Allele sharing between early modern humans and other humans
We compute D(Non-African1, Non-African2; Early Modern Human, African) to test whether an early modern human (Oase 1, Ust’-Ishim, or Kostenki 14) shares more alleles with Non-African1 (in which case the statistic is positive) or Non-African2 (negative). We use a pool of six sub-Saharan African genomes (2 Mbuti, 2 Yoruba, 2 Dinka) as an outgroup; a pool of four genomes (2 French, 2 Sardinians) to represent Europeans; a pool of four genomes (2 Han, 2 Dai) to represent East Asians; and a pool of three genomes (2 Karitiana, 1 Mixe) to represent Native Americans. Results are based on 242,122 transition and transversion SNPs covered by at least one deaminated fragment in Oase 1, and covered in all other samples with the possible exception of MA1 (for MA1, 176,569 SNPs are used).
Non-African1 Non-African2 Oase 1 Ust’-Ishim Kostenki 14
D Z D Z D Z
Oase 1 Ust’-Ishim −0.0033 −3.8
Oase 1 Kostenki 14 −0.0037 −4.1
Oase 1 MA1 −0.0032 −3.5 −0.0092 −9.8
Oase 1 Loschbour −0.0032 −3.9 −0.0101 −12.2
Oase 1 East Asian −0.0027 −3.8 −0.0011 −1.6
Oase 1 Native American −0.0030 −4.1 −0.0039 −5.5
Ust’-Ishim Kostenki 14 −0.0005 −0.6
Ust’-Ishim MA1 −0.0007 −0.8 −0.0059 −6.4
Ust’-Ishim Loschbour 0.0002 0.3 −0.0068 −8.5
Ust’-Ishim East Asian 0.0000 −0.1 0.0022 3.3
Ust’-Ishim Native American −0.0007 −1.0 −0.0006 −0.8
Kostenki 14 MA1 −0.0004 −0.6 0.0003 0.4
Kostenki 14 Loschbour 0.0007 1.0 0.0006 0.8
Kostenki 14 East Asian 0.0004 0.6 0.0011 1.6
Kostenki 14 Native American −0.0002 −0.3 0.0008 1.1
MA1 Loschbour 0.0012 1.7 0.0005 0.7 −0.0012 −1.5
MA1 East Asian 0.0008 1.2 0.0007 1.1 0.0079 10.6
MA1 Native American 0.0001 0.1 0.0004 0.6 0.0051 7.0
Loschbour East Asian −0.0002 −0.4 0.0005 0.9 0.0090 13.7
Loschbour Native American −0.0009 −1.5 0.0002 0.3 0.0062 9.0
East Asian Native American −0.0006 −1.6 −0.0003 −0.8 −0.0028 −6.6
European Oase 1 0.0004 0.6 0.0049 7.3
European Ust’-Ishim −0.0023 −3.5 0.0016 2.4
European Kostenki 14 −0.0028 −4.7 −0.0033 −5.1
European MA1 −0.0033 −5.4 −0.0031 −5.1 −0.0041 −6.0
European Loschbour −0.0021 −4.5 −0.0027 −5.7 −0.0052 −9.1
European East Asian −0.0024 −5.2 −0.0022 −5.3 0.0039 9.2
European Native American −0.0030 −6.4 −0.0025 −5.9 0.0010 2.2
European Stuttgart −0.0007 −1.5 −0.0001 −0.2 −0.0002 −0.3
Stuttgart Oase 1 0.0005 0.6 0.0051 6.7
Stuttgart Ust’-Ishim −0.0017 −2.3 0.0018 2.3
Stuttgart Kostenki 14 −0.0021 −3.2 −0.0032 −4.6
Stuttgart MA1 −0.0027 −3.9 −0.0029 −4.2 −0.0041 −5.0
Stuttgart Loschbour −0.0015 −2.4 −0.0027 −4.6 −0.0050 −7.5
Stuttgart East Asian −0.0017 −2.9 −0.0022 −3.8 0.0040 6.8
Stuttgart Native American −0.0024 −3.9 −0.0025 −4.4 0.0012 1.9
Extended Data Table 2
Allele sharing between early modern humans and other humans (transversions only)
We compute D(Non-African1, Non-African2; Early Modern Human, African), to test whether an early modern human (Oase 1, Ust’-Ishim, or Kostenki 14) shares more alleles with Non-African1 (in which case the statistic is positive) or Non-African2 (negative). We use a pool of six sub-Saharan African genomes (2 Mbuti, 2 Yoruba, 2 Dinka) as an outgroup; a pool of four genomes (2 French, 2 Sardinians) to represent Europeans; a pool of four genomes (2 Han, 2 Dai) to represent East Asians; and a pool of three genomes (2 Karitiana, 1 Mixe) to represent Native Americans. Statistics are as in Extended Data Table 1 but are based on 106,004 transversion SNPs covered by at least one deaminated fragment in Oase 1 and that also have coverage for all other samples although not necessarily MA1. For analyses involving MA1, a subset of 76,715 transversion SNPs is analyzed.
Non-African1 Non-African2 Oase 1 Ust’-Ishim Kostenki 14
D Z D Z D Z
Oase 1 Ust’-Ishim −0.0019 −2.1
Oase 1 Kostenki 14 −0.0031 −3.3
Oase 1 MA1 −0.0026 −2.9 −0.0071 −6.5
Oase 1 Loschbour −0.0023 −2.6 −0.0081 −8.8
Oase 1 East Asian −0.0013 −1.9 0.0007 1.0
Oase 1 Native American −0.0019 −2.7 −0.0018 −2.3
Ust’-Ishim Kostenki 14 −0.0012 −1.4
Ust’-Ishim MA1 −0.0006 −0.7 −0.0050 −5.1
Ust’-Ishim Loschbour 0.0003 0.4 −0.0062 −7.1
Ust’-Ishim East Asian 0.0005 0.7 0.0026 3.8
Ust’-Ishim Native American −0.0003 −0.4 0.0001 0.1
Kostenki 14 MA1 0.0001 0.1 0.0002 0.3
Kostenki 14 Loschbour 0.0015 2.0 0.0008 1.1
Kostenki 14 East Asian 0.0017 2.3 0.0017 2.5
Kostenki 14 Native American 0.0009 1.2 0.0012 1.6
MA1 Loschbour 0.0019 2.2 0.0010 1.3 −0.0013 −1.3
MA1 East Asian 0.0011 1.4 0.0013 1.9 0.0075 8.5
MA1 Native American 0.0006 0.7 0.0007 1.1 0.0051 6.0
Loschbour East Asian 0.0001 0.2 0.0009 1.5 0.0088 12.3
Loschbour Native American −0.0006 −0.9 0.0004 0.6 0.0063 8.4
East Asian Native American −0.0008 −1.7 −0.0006 −1.3 −0.0025 −5.3
European Oase 1 −0.0005 −0.7 0.0029 3.9
European Ust’-Ishim −0.0023 −3.3 0.0010 1.4
European Kostenki 14 −0.0035 −5.1 −0.0035 −5.2
European MA1 −0.0033 −4.5 −0.0033 −5.2 −0.0038 −4.8
European Loschbour −0.0020 −3.6 −0.0027 −5.1 −0.0052 −8.4
European East Asian −0.0018 −3.6 −0.0018 −4.0 0.0036 7.8
European Native American −0.0026 −4.8 −0.0023 −5.2 0.0011 2.1
European Stuttgart −0.0009 −1.7 −0.0010 −2.2 −0.0012 −2.3
Stuttgart Oase 1 0.0005 0.7 0.0041 4.7
Stuttgart Ust’-Ishim −0.0014 −1.8 0.0022 2.6
Stuttgart Kostenki 14 −0.0026 −3.3 −0.0025 −3.5
Stuttgart MA1 −0.0026 −3.1 −0.0023 −3.2 −0.0031 −3.4
Stuttgart Loschbour −0.0011 −1.6 −0.0017 −2.8 −0.0040 −5.2
Stuttgart East Asian −0.0010 −1.4 −0.0008 −1.3 0.0048 7.2
Stuttgart Native American −0.0017 −2.4 −0.0013 −2.2 0.0023 3.4
Allele sharing between early modern humans and other humans
We compute D(Non-African1, Non-African2; Early Modern Human, African) to test whether an early modern human (Oase 1, Ust’-Ishim, or Kostenki 14) shares more alleles with Non-African1 (in which case the statistic is positive) or Non-African2 (negative). We use a pool of six sub-Saharan African genomes (2 Mbuti, 2 Yoruba, 2 Dinka) as an outgroup; a pool of four genomes (2 French, 2 Sardinians) to represent Europeans; a pool of four genomes (2 Han, 2 Dai) to represent East Asians; and a pool of three genomes (2 Karitiana, 1 Mixe) to represent Native Americans. Results are based on 242,122 transition and transversion SNPs covered by at least one deaminated fragment in Oase 1, and covered in all other samples with the possible exception of MA1 (for MA1, 176,569 SNPs are used).
Non-African1 Non-African2 Oase 1 Ust’-Ishim Kostenki 14
D Z D Z D Z
Oase 1 Ust’-Ishim −0.0033 −3.8
Oase 1 Kostenki 14 −0.0037 −4.1
Oase 1 MA1 −0.0032 −3.5 −0.0092 −9.8
Oase 1 Loschbour −0.0032 −3.9 −0.0101 −12.2
Oase 1 East Asian −0.0027 −3.8 −0.0011 −1.6
Oase 1 Native American −0.0030 −4.1 −0.0039 −5.5
Ust’-Ishim Kostenki 14 −0.0005 −0.6
Ust’-Ishim MA1 −0.0007 −0.8 −0.0059 −6.4
Ust’-Ishim Loschbour 0.0002 0.3 −0.0068 −8.5
Ust’-Ishim East Asian 0.0000 −0.1 0.0022 3.3
Ust’-Ishim Native American −0.0007 −1.0 −0.0006 −0.8
Kostenki 14 MA1 −0.0004 −0.6 0.0003 0.4
Kostenki 14 Loschbour 0.0007 1.0 0.0006 0.8
Kostenki 14 East Asian 0.0004 0.6 0.0011 1.6
Kostenki 14 Native American −0.0002 −0.3 0.0008 1.1
MA1 Loschbour 0.0012 1.7 0.0005 0.7 −0.0012 −1.5
MA1 East Asian 0.0008 1.2 0.0007 1.1 0.0079 10.6
MA1 Native American 0.0001 0.1 0.0004 0.6 0.0051 7.0
Loschbour East Asian −0.0002 −0.4 0.0005 0.9 0.0090 13.7
Loschbour Native American −0.0009 −1.5 0.0002 0.3 0.0062 9.0
East Asian Native American −0.0006 −1.6 −0.0003 −0.8 −0.0028 −6.6
European Oase 1 0.0004 0.6 0.0049 7.3
European Ust’-Ishim −0.0023 −3.5 0.0016 2.4
European Kostenki 14 −0.0028 −4.7 −0.0033 −5.1
European MA1 −0.0033 −5.4 −0.0031 −5.1 −0.0041 −6.0
European Loschbour −0.0021 −4.5 −0.0027 −5.7 −0.0052 −9.1
European East Asian −0.0024 −5.2 −0.0022 −5.3 0.0039 9.2
European Native American −0.0030 −6.4 −0.0025 −5.9 0.0010 2.2
European Stuttgart −0.0007 −1.5 −0.0001 −0.2 −0.0002 −0.3
Stuttgart Oase 1 0.0005 0.6 0.0051 6.7
Stuttgart Ust’-Ishim −0.0017 −2.3 0.0018 2.3
Stuttgart Kostenki 14 −0.0021 −3.2 −0.0032 −4.6
Stuttgart MA1 −0.0027 −3.9 −0.0029 −4.2 −0.0041 −5.0
Stuttgart Loschbour −0.0015 −2.4 −0.0027 −4.6 −0.0050 −7.5
Stuttgart East Asian −0.0017 −2.9 −0.0022 −3.8 0.0040 6.8
Stuttgart Native American −0.0024 −3.9 −0.0025 −4.4 0.0012 1.9
Extended Data Table 2
Allele sharing between early modern humans and other humans (transversions only)
We compute D(Non-African1, Non-African2; Early Modern Human, African), to test whether an early modern human (Oase 1, Ust’-Ishim, or Kostenki 14) shares more alleles with Non-African1 (in which case the statistic is positive) or Non-African2 (negative). We use a pool of six sub-Saharan African genomes (2 Mbuti, 2 Yoruba, 2 Dinka) as an outgroup; a pool of four genomes (2 French, 2 Sardinians) to represent Europeans; a pool of four genomes (2 Han, 2 Dai) to represent East Asians; and a pool of three genomes (2 Karitiana, 1 Mixe) to represent Native Americans. Statistics are as in Extended Data Table 1 but are based on 106,004 transversion SNPs covered by at least one deaminated fragment in Oase 1 and that also have coverage for all other samples although not necessarily MA1. For analyses involving MA1, a subset of 76,715 transversion SNPs is analyzed.
Non-African1 Non-African2 Oase 1 Ust’-Ishim Kostenki 14
D Z D Z D Z
Oase 1 Ust’-Ishim −0.0019 −2.1
Oase 1 Kostenki 14 −0.0031 −3.3
Oase 1 MA1 −0.0026 −2.9 −0.0071 −6.5
Oase 1 Loschbour −0.0023 −2.6 −0.0081 −8.8
Oase 1 East Asian −0.0013 −1.9 0.0007 1.0
Oase 1 Native American −0.0019 −2.7 −0.0018 −2.3
Ust’-Ishim Kostenki 14 −0.0012 −1.4
Ust’-Ishim MA1 −0.0006 −0.7 −0.0050 −5.1
Ust’-Ishim Loschbour 0.0003 0.4 −0.0062 −7.1
Ust’-Ishim East Asian 0.0005 0.7 0.0026 3.8
Ust’-Ishim Native American −0.0003 −0.4 0.0001 0.1
Kostenki 14 MA1 0.0001 0.1 0.0002 0.3
Kostenki 14 Loschbour 0.0015 2.0 0.0008 1.1
Kostenki 14 East Asian 0.0017 2.3 0.0017 2.5
Kostenki 14 Native American 0.0009 1.2 0.0012 1.6
MA1 Loschbour 0.0019 2.2 0.0010 1.3 −0.0013 −1.3
MA1 East Asian 0.0011 1.4 0.0013 1.9 0.0075 8.5
MA1 Native American 0.0006 0.7 0.0007 1.1 0.0051 6.0
Loschbour East Asian 0.0001 0.2 0.0009 1.5 0.0088 12.3
Loschbour Native American −0.0006 −0.9 0.0004 0.6 0.0063 8.4
East Asian Native American −0.0008 −1.7 −0.0006 −1.3 −0.0025 −5.3
European Oase 1 −0.0005 −0.7 0.0029 3.9
European Ust’-Ishim −0.0023 −3.3 0.0010 1.4
European Kostenki 14 −0.0035 −5.1 −0.0035 −5.2
European MA1 −0.0033 −4.5 −0.0033 −5.2 −0.0038 −4.8
European Loschbour −0.0020 −3.6 −0.0027 −5.1 −0.0052 −8.4
European East Asian −0.0018 −3.6 −0.0018 −4.0 0.0036 7.8
European Native American −0.0026 −4.8 −0.0023 −5.2 0.0011 2.1
European Stuttgart −0.0009 −1.7 −0.0010 −2.2 −0.0012 −2.3
Stuttgart Oase 1 0.0005 0.7 0.0041 4.7
Stuttgart Ust’-Ishim −0.0014 −1.8 0.0022 2.6
Stuttgart Kostenki 14 −0.0026 −3.3 −0.0025 −3.5
Stuttgart MA1 −0.0026 −3.1 −0.0023 −3.2 −0.0031 −3.4
Stuttgart Loschbour −0.0011 −1.6 −0.0017 −2.8 −0.0040 −5.2
Stuttgart East Asian −0.0010 −1.4 −0.0008 −1.3 0.0048 7.2
Stuttgart Native American −0.0017 −2.4 −0.0013 −2.2 0.0023 3.4