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4. Tests of admixture with populations not of East Asian ancestry using f4-analyses
We examined a series of f4-statistics addressing the relationship of several more distantly
related populations to East Asians, Tibetans, and Siberians to determine asymmetric
relationships that suggest admixture.
(1) Native Americans: It has previously been observed that some South Americans (69)
(e.g. Surui) share excess ancestry with present-day Papuan and Onge (70), as well as a
40,000-year-old Tianyuan individual, unlike other Native Americans (e.g. Mixe). We used
f4(Mbuti, North/South; Surui, Mixe) to test for this connection in the North and South
groups (Fig. S3A, S3D).
(2) Ancient West Eurasians: A 35,000-year-old individual from Belgium (69) was shown
to share connections to the 40,000-year-old Tianyuan individual (20), and some 8,000-
year-old West European hunter-gatherers (Loschbour) showed connections to present-day
East Asians (20, 69). We tested for these West Eurasian connections in the North and South
groups, using f4(Mbuti, North/South; Vestonice16, GoyetQ116-1/Loschbour) (Fig. S3B-3C,
S3E-3F), where Vestonice16 is a 35,000-year-old European (69).
(3) Paleosiberian: A 9,800-year-old individual with a close relationship to Native
Americans (Kolyma) was also sequenced from Siberia (9). We performed a symmetry test,
using f4(Mbuti, Kolyma; X, Y), where X and Y are all Neolithic East Asians, Siberians, and
Tibetans of East Asian ancestry (Table S4).
(4) Southeast Asia: ‘Early Asian’ ancestry found in Hòabìnhians (G1) that exist in partial
amounts in ancient Southeast Asians (7) make it difficult to use f-statistics to explore the
relationship of Southeast Asians to East Asians. Different types of East Asian ancestry
have had an influence on ancient Southeast Asians (6, 7), so we developed a symmetry test
to determine the types of East Asian ancestry that played a role in migration to Southeast
Asia (Table S7).
(5) Jōmon: A connection between the Jōmon (Ikawazu) and Hòabìnhians (G1) has been
previously proposed. Here, we test the connection to Hòabìnhians, as well as East Asians.
We performed the outgroup f3-test, f3(Mbuti; Hòabìnhian, X), where X are ancient and
present-day East Eurasians, and the f4-test, f4(Mbuti, G1; Ikawazu, North/South), to
determine if the Jōmon share higher genetic similarity with G1 than East Asians (Table
S8a). S8a). We also used a symmetry test for Ikawazu, of the form f4(Mbuti, Ikawazu;
North/South, North/South), with results in Table S9.
Fig. S3. Results for f4(Mbuti, P2 – North/South; X, Y), where X and Y are populations
without East Asian ancestry.
5. Inferring a maximum likelihood phylogeny with migration events
In the Treemix analysis, we included the following populations.
1. Mbuti: present-day population from Central Africa that we designated as outgroup
(68)
2. UstIshim: 45,000-year-old individual from a population basal to both Europeans
and Asians (71)
3. Yana: two 37,000-year-old individuals from Siberia with early European
affiliations (9)
4. Tianyuan: 40,000-year-old ‘early Asian’ from China from a population that
separated early from East Asians (20)
5. Ikawazu: 2,700-year-old ‘early Asian’ from the Japanese archipelago belonging to
the Jōmon culture (7)
6. Shamanka_EN: 7,900-year-old individuals from the Lake Baikal region with a
close relationship to East Asians belonging to the steppe Siberia_EN group (72)
7. DevilsCave_EN: 7,700-year-old individuals from the Primorye region with a close
relationship to East Asians (72), in the coastal Siberia_EN group
8. Chokhopani: 3,150-year-old individual from the Himalayan region of the Tibetan
Plateau with a close relationship to East Asians (68), in the Tibet_LN group
9. Vanuatu: 2,900-year-old individuals from Vanuatu island in the southwest Pacific
related to the Lapita culture with a close relationship to Austronesians (73), in the
Austronesian_LN/B group
10. Yumin: 8,500-year-old newly sampled individual from Inner Mongolia belonging
to the inland nEastAsia_EN group
11. Coastal nEastAsia_EN: 9,500-7,500-year-old newly sampled individuals from the
lower reaches of the Yellow River
12. sEastAsia_EN: 9,000-7,500-year-old newly sampled individuals from southern
mainland China and Liang Island in the Taiwan strait
13. sEastAsia_LN: 5,000-4,000-year-old newly sampled individuals from southern
mainland China and Penghu Island in the Taiwan strait
The coastal nEastAsia_EN and sEastAsia_EN/LN groups merged individuals from Table
S1 belonging to that group. For instance, Xitoucun, Suogang, and Tanshishan individuals
were all included in coastal sEastAsia_LN.
We examined a series of f4-statistics addressing the relationship of several more distantly
related populations to East Asians, Tibetans, and Siberians to determine asymmetric
relationships that suggest admixture.
(1) Native Americans: It has previously been observed that some South Americans (69)
(e.g. Surui) share excess ancestry with present-day Papuan and Onge (70), as well as a
40,000-year-old Tianyuan individual, unlike other Native Americans (e.g. Mixe). We used
f4(Mbuti, North/South; Surui, Mixe) to test for this connection in the North and South
groups (Fig. S3A, S3D).
(2) Ancient West Eurasians: A 35,000-year-old individual from Belgium (69) was shown
to share connections to the 40,000-year-old Tianyuan individual (20), and some 8,000-
year-old West European hunter-gatherers (Loschbour) showed connections to present-day
East Asians (20, 69). We tested for these West Eurasian connections in the North and South
groups, using f4(Mbuti, North/South; Vestonice16, GoyetQ116-1/Loschbour) (Fig. S3B-3C,
S3E-3F), where Vestonice16 is a 35,000-year-old European (69).
(3) Paleosiberian: A 9,800-year-old individual with a close relationship to Native
Americans (Kolyma) was also sequenced from Siberia (9). We performed a symmetry test,
using f4(Mbuti, Kolyma; X, Y), where X and Y are all Neolithic East Asians, Siberians, and
Tibetans of East Asian ancestry (Table S4).
(4) Southeast Asia: ‘Early Asian’ ancestry found in Hòabìnhians (G1) that exist in partial
amounts in ancient Southeast Asians (7) make it difficult to use f-statistics to explore the
relationship of Southeast Asians to East Asians. Different types of East Asian ancestry
have had an influence on ancient Southeast Asians (6, 7), so we developed a symmetry test
to determine the types of East Asian ancestry that played a role in migration to Southeast
Asia (Table S7).
(5) Jōmon: A connection between the Jōmon (Ikawazu) and Hòabìnhians (G1) has been
previously proposed. Here, we test the connection to Hòabìnhians, as well as East Asians.
We performed the outgroup f3-test, f3(Mbuti; Hòabìnhian, X), where X are ancient and
present-day East Eurasians, and the f4-test, f4(Mbuti, G1; Ikawazu, North/South), to
determine if the Jōmon share higher genetic similarity with G1 than East Asians (Table
S8a). S8a). We also used a symmetry test for Ikawazu, of the form f4(Mbuti, Ikawazu;
North/South, North/South), with results in Table S9.
Fig. S3. Results for f4(Mbuti, P2 – North/South; X, Y), where X and Y are populations
without East Asian ancestry.
5. Inferring a maximum likelihood phylogeny with migration events
In the Treemix analysis, we included the following populations.
1. Mbuti: present-day population from Central Africa that we designated as outgroup
(68)
2. UstIshim: 45,000-year-old individual from a population basal to both Europeans
and Asians (71)
3. Yana: two 37,000-year-old individuals from Siberia with early European
affiliations (9)
4. Tianyuan: 40,000-year-old ‘early Asian’ from China from a population that
separated early from East Asians (20)
5. Ikawazu: 2,700-year-old ‘early Asian’ from the Japanese archipelago belonging to
the Jōmon culture (7)
6. Shamanka_EN: 7,900-year-old individuals from the Lake Baikal region with a
close relationship to East Asians belonging to the steppe Siberia_EN group (72)
7. DevilsCave_EN: 7,700-year-old individuals from the Primorye region with a close
relationship to East Asians (72), in the coastal Siberia_EN group
8. Chokhopani: 3,150-year-old individual from the Himalayan region of the Tibetan
Plateau with a close relationship to East Asians (68), in the Tibet_LN group
9. Vanuatu: 2,900-year-old individuals from Vanuatu island in the southwest Pacific
related to the Lapita culture with a close relationship to Austronesians (73), in the
Austronesian_LN/B group
10. Yumin: 8,500-year-old newly sampled individual from Inner Mongolia belonging
to the inland nEastAsia_EN group
11. Coastal nEastAsia_EN: 9,500-7,500-year-old newly sampled individuals from the
lower reaches of the Yellow River
12. sEastAsia_EN: 9,000-7,500-year-old newly sampled individuals from southern
mainland China and Liang Island in the Taiwan strait
13. sEastAsia_LN: 5,000-4,000-year-old newly sampled individuals from southern
mainland China and Penghu Island in the Taiwan strait
The coastal nEastAsia_EN and sEastAsia_EN/LN groups merged individuals from Table
S1 belonging to that group. For instance, Xitoucun, Suogang, and Tanshishan individuals
were all included in coastal sEastAsia_LN.