Table 1 Open in new tab Parameters Used...

	N_e during Bottleneck	Admixture Proportion (%)a	Gene Flow (Effective Donors per Generation)b	Duration of Gene Flow (Generation)
Model 1	N	N	N	—	—	—	—	—
Model 1a	N	N	N	—	—	—	—	—
Model 1b	500–1,000	N	N	—	—	—	—	—
Model 1c	N	100–300	100–300	—	—	—	—	—
Model 1d	500–1,000	100–300	100–300	—	—	—	—	—
Model 2	N	N	N	—	—	2	1–2	2,000
Model 2a	N	N	N	—	—	2	1–2	2,000
Model 2b	500–1,000	N	N	—	—	2	1–2	2,000
Model 2c	N	100–300	100–300	—	—	2	1–2	2,000
Model 2d	500–1,000	100–300	100–300	—	—	2	1–2	2,000
Model 3	N	N	N	50–60	50–40	—	—	—
Model 3a	N	N	N	50–60	50–40	—	—	—
Model 3b	500–1,000	N	N	50–60	50–40	—	—	—
Model 3c	N	100–300	100–300	50–60	50–40	—	—	—
Model 3d	500–1,000	100–300	100–300	50–60	50–40	—	—	—
Model 4	N	N	N	50–60	50–40	46–35	26–35	100
Model 4a	N	N	N	50–60	50–40	46–35	26–35	100
Model 4b	500–1,000	N	N	50–60	50–40	46–35	26–35	100
Model 4c	N	100–300	100–300	50–60	50–40	46–35	26–35	100
Model 4d	500–1,000	100–300	100–300	50–60	50–40	46–35	26–35	100

N_e during Bottleneck

Admixture Proportion (%)a

Gene Flow (Effective Donors per Generation)b

Duration of Gene Flow (Generation)

Models

EUR & EASc

EURd

EASe

EUR

EAS

EUR

EAS

Model 1

—

Model 1a

—

Model 1b

500–1,000

—

Model 1c

100–300

—

Model 1d

500–1,000

100–300

—

Model 2

—

1–2

2,000

Model 2a

—

1–2

2,000

Model 2b

500–1,000

—

1–2

2,000

Model 2c

100–300

—

1–2

2,000

Model 2d

500–1,000

100–300

—

1–2

2,000

Model 3

50–60

50–40

—

Model 3a

50–60

50–40

—

Model 3b

500–1,000

50–60

50–40

—

Model 3c

100–300

50–60

50–40

—

Model 3d

500–1,000

100–300

50–60

50–40

—

Model 4

50–60

50–40

46–35

26–35

100

Model 4a

50–60

50–40

46–35

26–35

100

Model 4b

500–1,000

50–60

50–40

46–35

26–35

100

Model 4c

100–300

50–60

50–40

46–35

26–35

100

Model 4d

500–1,000

100–300

50–60

50–40

46–35

26–35

100

	N_e during Bottleneck	Admixture Proportion (%)a	Gene Flow (Effective Donors per Generation)b	Duration of Gene Flow (Generation)
Model 1	N	N	N	—	—	—	—	—
Model 1a	N	N	N	—	—	—	—	—
Model 1b	500–1,000	N	N	—	—	—	—	—
Model 1c	N	100–300	100–300	—	—	—	—	—
Model 1d	500–1,000	100–300	100–300	—	—	—	—	—
Model 2	N	N	N	—	—	2	1–2	2,000
Model 2a	N	N	N	—	—	2	1–2	2,000
Model 2b	500–1,000	N	N	—	—	2	1–2	2,000
Model 2c	N	100–300	100–300	—	—	2	1–2	2,000
Model 2d	500–1,000	100–300	100–300	—	—	2	1–2	2,000
Model 3	N	N	N	50–60	50–40	—	—	—
Model 3a	N	N	N	50–60	50–40	—	—	—
Model 3b	500–1,000	N	N	50–60	50–40	—	—	—
Model 3c	N	100–300	100–300	50–60	50–40	—	—	—
Model 3d	500–1,000	100–300	100–300	50–60	50–40	—	—	—
Model 4	N	N	N	50–60	50–40	46–35	26–35	100
Model 4a	N	N	N	50–60	50–40	46–35	26–35	100
Model 4b	500–1,000	N	N	50–60	50–40	46–35	26–35	100
Model 4c	N	100–300	100–300	50–60	50–40	46–35	26–35	100
Model 4d	500–1,000	100–300	100–300	50–60	50–40	46–35	26–35	100

Table 1

Open in new tab

Parameters Used in Forward-Time Simulations

	N_e during Bottleneck			Admixture Proportion (%)a		Gene Flow (Effective Donors per Generation)b		Duration of Gene Flow (Generation)
Models	EUR & EASc	EURd	EASe	EUR	EAS	EUR	EAS	Duration of Gene Flow (Generation)
Model 1	N	N	N	—	—	—	—	—
Model 1a	N	N	N	—	—	—	—	—
Model 1b	500–1,000	N	N	—	—	—	—	—
Model 1c	N	100–300	100–300	—	—	—	—	—
Model 1d	500–1,000	100–300	100–300	—	—	—	—	—
Model 2	N	N	N	—	—	2	1–2	2,000
Model 2a	N	N	N	—	—	2	1–2	2,000
Model 2b	500–1,000	N	N	—	—	2	1–2	2,000
Model 2c	N	100–300	100–300	—	—	2	1–2	2,000
Model 2d	500–1,000	100–300	100–300	—	—	2	1–2	2,000
Model 3	N	N	N	50–60	50–40	—	—	—
Model 3a	N	N	N	50–60	50–40	—	—	—
Model 3b	500–1,000	N	N	50–60	50–40	—	—	—
Model 3c	N	100–300	100–300	50–60	50–40	—	—	—
Model 3d	500–1,000	100–300	100–300	50–60	50–40	—	—	—
Model 4	N	N	N	50–60	50–40	46–35	26–35	100
Model 4a	N	N	N	50–60	50–40	46–35	26–35	100
Model 4b	500–1,000	N	N	50–60	50–40	46–35	26–35	100
Model 4c	N	100–300	100–300	50–60	50–40	46–35	26–35	100
Model 4d	500–1,000	100–300	100–300	50–60	50–40	46–35	26–35	100

	N_e during Bottleneck			Admixture Proportion (%)a		Gene Flow (Effective Donors per Generation)b		Duration of Gene Flow (Generation)
Models	EUR & EASc	EURd	EASe	EUR	EAS	EUR	EAS	Duration of Gene Flow (Generation)
Model 1	N	N	N	—	—	—	—	—
Model 1a	N	N	N	—	—	—	—	—
Model 1b	500–1,000	N	N	—	—	—	—	—
Model 1c	N	100–300	100–300	—	—	—	—	—
Model 1d	500–1,000	100–300	100–300	—	—	—	—	—
Model 2	N	N	N	—	—	2	1–2	2,000
Model 2a	N	N	N	—	—	2	1–2	2,000
Model 2b	500–1,000	N	N	—	—	2	1–2	2,000
Model 2c	N	100–300	100–300	—	—	2	1–2	2,000
Model 2d	500–1,000	100–300	100–300	—	—	2	1–2	2,000
Model 3	N	N	N	50–60	50–40	—	—	—
Model 3a	N	N	N	50–60	50–40	—	—	—
Model 3b	500–1,000	N	N	50–60	50–40	—	—	—
Model 3c	N	100–300	100–300	50–60	50–40	—	—	—
Model 3d	500–1,000	100–300	100–300	50–60	50–40	—	—	—
Model 4	N	N	N	50–60	50–40	46–35	26–35	100
Model 4a	N	N	N	50–60	50–40	46–35	26–35	100
Model 4b	500–1,000	N	N	50–60	50–40	46–35	26–35	100
Model 4c	N	100–300	100–300	50–60	50–40	46–35	26–35	100
Model 4d	500–1,000	100–300	100–300	50–60	50–40	46–35	26–35	100

Ancestry contribution of EUR ranges from 50% to 60%, whereas that of EAS ranges from 50% to 40% so that in each single simulation the admixture proportions summed to 100% (see Materials and Methods for details).

Gene flow was simulated under the CGF model (see Materials and Methods for details).

Bottleneck shared by EUR and EAS before they diverged; N_e of 500, 600, … 1,000 were simulated; N denotes no bottleneck was simulated.

Bottleneck occurred in EUR after the divergence of EUR and EAS, N_e of 100, 200, and 300 were simulated; N denotes no bottleneck was simulated.

Bottleneck occurred in EAS after the divergence of EUR and EAS, N_e of 100, 200, and 300 were simulated; N denotes no bottleneck was simulated.

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