Catalog

With stdpopsim, you can run simulations from a number of demographic models that were implemented from published demographic histories. These models have been rigorously checked and tested by multiple people, so you can rest easy knowing that your simulations are reproducible and bug-free!

This catalog shows you all of the possible options that you can use to configure your simulation. It is organised around a number of choices that you’ll need to make about the Species you wish to simulate:

  1. Which chromosome? (ie. which Genome object?)

  2. Which genetic map? (ie. which GeneticMap object?)

  3. Which model of demographic history? (ie. which DemographicModel object)

For instance, suppose you are interested in simulating modern human samples of

  1. chromosome 22, using

  2. the HapMapII genetic map, under

  3. a 3-population Out-of-Africa model.

The following command simulates 2 samples from each of the three populations, and saves the output to a file called test.trees:

$ stdpopsim HomSap -c chr22 -o test.trees -g HapMapII_GRCh37 -d OutOfAfrica_3G09 2 2 2

(To learn more about using stdpopsim via the command-line, read our Tutorials about it.)

Are there other well-known organisms, genetic maps or models that you’d like to see in stdpopsim? Head to our Development page to learn about the process for adding new items to the catalog. Then, if you feel ready, make an issue on our GitHub page.

Arabidopsis thaliana

ID

AraTha

Name

Arabidopsis thaliana

Common name

A. thaliana

Generation time

1.0 (Donohue, 2002)

Population size

10000 (1001GenomesConsortium, 2016)

Genome

ID

Length

Recombination rate

Mutation rate

chr1

30427671

8.06452e-10

7e-09

chr2

19698289

8.06452e-10

7e-09

chr3

23459830

8.06452e-10

7e-09

chr4

18585056

8.06452e-10

7e-09

chr5

26975502

8.06452e-10

7e-09


Genetic Maps

ID

Year

Description

SalomeAveraged_TAIR7

2012

Crossover frequency map averaged over 17 populations

SalomeAveraged_TAIR7

This map is based on the study of crossover frequencies in over 7000 plants in 17 F2 populations derived from crosses between 18 A. thaliana accessions. Salomé et al provide genetic maps for each of these populations. To get a single map for each chromosome, the Haldane map function distances were converted to recombination rates (cM/Mb) for each cross and then averaged across the 17 populations using loess.

Citations


Models

ID

Description

SouthMiddleAtlas_1D17

South Middle Atlas piecewise constant size

African2Epoch_1H18

South Middle Atlas African two epoch model

African3Epoch_1H18

South Middle Atlas African three epoch model

South Middle Atlas piecewise constant size

This model comes from MSMC using two randomly sampled homozygous individuals (Khe32 and Ifr4) from the South Middle Atlas region from the Middle Atlas Mountains in Morocco. The model is estimated with 32 time periods. Because estimates from the recent and ancient past are less accurate, we set the population size in the first 7 time periods equal to the size at the 8th time period and the size during last 2 time periods equal to the size in the 30th time period.

Details

ID

SouthMiddleAtlas_1D17

Description

South Middle Atlas piecewise constant size

Num populations

1

Populations

Index

ID

Sampling time

Description

0

SouthMiddleAtlas

0

Arabidopsis Thaliana South Middle Atlas population

Citations

Demographic Model parameters

Parameter Type (units)

Value

Description

Population size

73,989

Ancestral population size

Population size

121,796

Pop. size during 1st time interval

Population size

165,210

Pop. size during 2nd time interval

Population size

198,019

Pop. size during 3rd time interval

Population size

217,752

Pop. size during 4th time interval

Population size

228,222

Pop. size during 5th time interval

Population size

238,593

Pop. size during 6th time interval

Population size

246,984

Pop. size during 7th time interval

Population size

241,400

Pop. size during 8th time interval

Population size

217,331

Pop. size during 9th time interval

Population size

181,571

Pop. size during 10th time interval

Population size

143456

Pop. size during 11th time interval

Population size

111,644

Pop. size during 12th time interval

Population size

91,813

Pop. size during 13th time interval

Population size

83,829

Pop. size during 14th time interval

Population size

83,932

Pop. size during 15th time interval

Population size

87,661

Pop. size during 16th time interval

Population size

96,283

Pop. size during 17th time interval

Population size

110,745

Pop. size during 18th time interval

Population size

111,132

Pop. size during 19th time interval

Population size

78,908

Pop. size during 20th time interval

Time (yrs.)

1,537,686

Begining of 1st time interval

Time (yrs.)

1,119,341

Begining of 2nd time interval

Time (yrs.)

954,517

Begining of 3rd time interval

Time (yrs.)

813,610

Begining of 4th time interval

Time (yrs.)

693,151

Begining of 5th time interval

Time (yrs.)

590,173

Begining of 6th time interval

Time (yrs.)

502,139

Begining of 7th time interval

Time (yrs.)

426,879

Begining of 8th time interval

Time (yrs.)

362,541

Begining of 9th time interval

Time (yrs.)

307,540

Begining of 10th time interval

Time (yrs.)

260,520

Begining of 11th time interval

Time (yrs.)

220,324

Begining of 12th time interval

Time (yrs.)

185,960

Begining of 13th time interval

Time (yrs.)

156,584

Begining of 14th time interval

Time (yrs.)

131,471

Begining of 15th time interval

Time (yrs.)

110,001

Begining of 16th time interval

Time (yrs.)

91,648

Begining of 17th time interval

Time (yrs.)

75,958

Begining of 18th time interval

Time (yrs.)

62,544

Begining of 19th time interval

Time (yrs.)

51,077

Begining of 20th time interval


South Middle Atlas African two epoch model

Model estimated from site frequency spectrum of synonymous SNPs from African South Middle Atlas samples using Williamson et al. 2005 methodology. Values come from supplementary table 1 of Huber et al 2018. Sizes change from N_A -> N_0 and t_1 is time of the second epoch.

Details

ID

African2Epoch_1H18

Description

South Middle Atlas African two epoch model

Num populations

1

Populations

Index

ID

Sampling time

Description

0

SouthMiddleAtlas

0

Arabidopsis Thaliana South Middle Atlas population

Citations

Demographic Model parameters

Parameter Type (units)

Value

Description

Population size

746,148

Ancestral pop. size

Population size

100,218

Pop. size during second epoch

Epoch Time (gen.)

568,344

Time of second epoch


South Middle Atlas African three epoch model

Model estimated from site frequency spectrum of synonymous SNPs from African (South Middle Atlas) samples using Williamson et al. 2005 methodology. Values come from supplementary table 1 of Huber et al 2018. Sizes change from N_A -> N_2 -> N_3 and t_2 is the time of the second epoch and t_3 is the time of the 3rd epoch.

Details

ID

African3Epoch_1H18

Description

South Middle Atlas African three epoch model

Num populations

1

Populations

Index

ID

Sampling time

Description

0

SouthMiddleAtlas

0

Arabidopsis Thaliana South Middle Atlas population

Citations

Demographic Model parameters

Parameter Type (units)

Value

Description

Population size

161,744

Ancestral pop. size

Population size

24,076

Pop. size during second epoch

Population size

203,077

Pop. size during Third epoch

Epoch Time (gen.)

7,420

Time of second epoch

Epoch Time (gen.)

14,534

Time of third epoch

Canis familiaris

ID

CanFam

Name

Canis familiaris

Common name

Dog

Generation time

3

Population size

13000 (Lindblad-Toh et al., 2005)

Genome

ID

Length

Recombination rate

Mutation rate

chr1

122678785

7.636e-09

4e-09

chr2

85426708

8.79852e-09

4e-09

chr3

91889043

8.00087e-09

4e-09

chr4

88276631

8.0523e-09

4e-09

chr5

88915250

9.34433e-09

4e-09

chr6

77573801

8.19219e-09

4e-09

chr7

80974532

7.29347e-09

4e-09

chr8

74330416

8.29131e-09

4e-09

chr9

61074082

9.28772e-09

4e-09

chr10

69331447

9.10715e-09

4e-09

chr11

74389097

7.63945e-09

4e-09

chr12

72498081

7.76106e-09

4e-09

chr13

63241923

8.41302e-09

4e-09

chr14

60966679

9.02812e-09

4e-09

chr15

64190966

7.85675e-09

4e-09

chr16

59632846

8.61406e-09

4e-09

chr17

64289059

9.71883e-09

4e-09

chr18

55844845

1.02993e-08

4e-09

chr19

53741614

1.04251e-08

4e-09

chr20

58134056

9.99097e-09

4e-09

chr21

50858623

1.0339e-08

4e-09

chr22

61439934

8.61505e-09

4e-09

chr23

52294480

9.12664e-09

4e-09

chr24

47698779

1.1146e-08

4e-09

chr25

51628933

1.15437e-08

4e-09

chr26

38964690

1.20846e-08

4e-09

chr27

45876710

1.12603e-08

4e-09

chr28

41182112

1.24636e-08

4e-09

chr29

41845238

1.10136e-08

4e-09

chr30

40214260

1.16876e-08

4e-09

chr31

39895921

1.13977e-08

4e-09

chr32

38810281

1.15559e-08

4e-09

chr33

31377067

1.33394e-08

4e-09

chr34

42124431

1.04838e-08

4e-09

chr35

26524999

1.42991e-08

4e-09

chr36

30810995

1.18752e-08

4e-09

chr37

30902991

1.38346e-08

4e-09

chr38

23914537

1.43637e-08

4e-09

chrX

123869142

9.50648e-09

4e-09


Genetic Maps

ID

Year

Description

Campbell2016_CanFam3_1

2016

Pedigree-based crossover map from 237 individuals

Campbell2016_CanFam3_1

Sex-averaged crossover frequency map based on 163,400 autosomal SNPs genotyped in a pedigree of 237 Labrador Retriever x Greyhound crosses. Genotypes were phased without respect to the pedigree, using SHAPEIT2, recombinations were called using duoHMM, and genetic distances were obtained using Haldane’s map function.

Citations


Models

ID

Description

Drosophila melanogaster

ID

DroMel

Name

Drosophila melanogaster

Common name

D. melanogaster

Generation time

0.1 (Li et al., 2006)

Population size

1720600 (Li et al., 2006)

Genome

ID

Length

Recombination rate

Mutation rate

chrX

23542271

8.4e-09

5.49e-09

chr2L

23513712

8.4e-09

5.49e-09

chr2R

25286936

8.4e-09

5.49e-09

chr3L

28110227

8.4e-09

5.49e-09

chr3R

32079331

8.4e-09

5.49e-09

chr4

1348131

8.4e-09

5.49e-09

chrY

3667352

8.4e-09

5.49e-09


Genetic Maps

ID

Year

Description

ComeronCrossover_dm6

2012

Crossover map from meioses products of 8 lab crosses

ComeronCrossover_dm6

The crossover map from a study of 8 crosses of 12 highly inbred lines of D. melanogaster. This is based on the products of 5,860 female meioses from whole genome sequencing data. Recombination rates were calculated from the density of individual recombination events that were detected in crosses. This map was subsequently lifted over to the dm6 assembly.

Citations


Models

ID

Description

African3Epoch_1S16

Three epoch African population

OutOfAfrica_2L06

Three epoch model for African and European populations

Three epoch African population

The three epoch (modern, bottleneck, ancestral) model estimated for a single African Drosophila Melanogaster population from Sheehan and Song (2016). Population sizes are estimated by a deep learning model trained on simulation data. NOTE: Due to differences in coalescence units between PSMC (2N) and msms (4N) the number of generations were doubled from PSMC estimates when simulating data from msms in the original publication. We have faithfully represented the published model here.

Details

ID

African3Epoch_1S16

Description

Three epoch African population

Num populations

1

Populations

Index

ID

Sampling time

Description

0

AFR

0

African D. melanogaster population

Citations

Demographic Model parameters

Parameter Type (units)

Value

Description

Population size

100,000

Reference population size

Population size

652,700

Ancestral pop. Size

Population size

145,300

Bottleneck pop. size

Population size

544,200

Recent pop. size

Epoch Time (gen.)

2,200,000

Onset of bottleneck

Epoch Time (gen.)

200,000

Population expansion

Generation time (yrs.)

0.1

Generation time


Three epoch model for African and European populations

The three epoch (modern, bottleneck, ancestral) model estimated for two Drosophila Melanogaster populations: African (ancestral) and European (derived) from Li and Stephan (2006).

Details

ID

OutOfAfrica_2L06

Description

Three epoch model for African and European populations

Num populations

2

Populations

Index

ID

Sampling time

Description

0

AFR

0

African D. melanogaster population

1

EUR

0

European D. melanogaster population

Citations

Demographic Model parameters

Parameter Type (units)

Value

Description

Population size

1,720,600

Ancestral pop. Size

Population size

8,603,000

Post-expansion African pop. Size

Population size

2,200

European bottleneck pop. size

Population size

1,075,000

Modern European pop. size

Epoch Time (gen.)

600,000

Expansion of population in Africa

Epoch Time (gen.)

158,000

African-European divergence

Epoch Time (gen.)

154,600

European pop. Expansion

Generation time (yrs.)

0.1

Generation time

Escherichia coli

ID

EscCol

Name

Escherichia coli

Common name

E. coli

Generation time

3.805175e-05 (Sezonov et al., 2007)

Population size

180000000.0 (Lapierre et al., 2016)

Genome

ID

Length

Recombination rate

Mutation rate

None

4641652

0

0.00021


Genetic Maps

ID

Year

Description


Models

ID

Description

Homo sapiens

ID

HomSap

Name

Homo sapiens

Common name

Human

Generation time

30 (Tremblay and Vezina, 2000)

Population size

10000 (Takahata, 1993)

Genome

ID

Length

Recombination rate

Mutation rate

chr1

249250621

1.14856e-08

1.29e-08

chr2

243199373

1.10543e-08

1.29e-08

chr3

198022430

1.12796e-08

1.29e-08

chr4

191154276

1.12312e-08

1.29e-08

chr5

180915260

1.12809e-08

1.29e-08

chr6

171115067

1.12229e-08

1.29e-08

chr7

159138663

1.17646e-08

1.29e-08

chr8

146364022

1.14785e-08

1.29e-08

chr9

141213431

1.17807e-08

1.29e-08

chr10

135534747

1.33651e-08

1.29e-08

chr11

135006516

1.17193e-08

1.29e-08

chr12

133851895

1.30502e-08

1.29e-08

chr13

115169878

1.09149e-08

1.29e-08

chr14

107349540

1.11973e-08

1.29e-08

chr15

102531392

1.38358e-08

1.29e-08

chr16

90354753

1.48346e-08

1.29e-08

chr17

81195210

1.58249e-08

1.29e-08

chr18

78077248

1.5076e-08

1.29e-08

chr19

59128983

1.82201e-08

1.29e-08

chr20

63025520

1.71783e-08

1.29e-08

chr21

48129895

1.30452e-08

1.29e-08

chr22

51304566

1.4445e-08

1.29e-08

chrX

155270560

1.16466e-08

1.29e-08

chrY

59373566

0

1.29e-08


Genetic Maps

ID

Year

Description

HapMapII_GRCh37

2007

HapMap Phase II lifted over to GRCh37

DeCodeSexAveraged_GRCh36

2010

Sex averaged map from deCode family study

HapMapII_GRCh37

This genetic map is from the Phase II Hapmap project and based on 3.1 million genotyped SNPs from 270 individuals across four populations (YRI, CEU, CHB and JPT). Genome wide recombination rates were estimated using LDHat. This version of the HapMap genetic map was lifted over to GRCh37 (and adjusted in regions where the genome assembly had rearranged) for use in the 1000 Genomes project. Please see the README file on the 1000 Genomes download site for details of these adjustments.

Citations

DeCodeSexAveraged_GRCh36

This genetic map is from the deCode study of recombination events in 15,257 parent-offspring pairs from Iceland. 289,658 phased autosomal SNPs were used to call recombinations within these families, and recombination rates computed from the density of these events. This is the combined male and female (sex averaged) map. See https://www.decode.com/addendum/ for more details.

Citations


Models

ID

Description

OutOfAfrica_3G09

Three population out-of-Africa

OutOfAfrica_2T12

Two population out-of-Africa

Africa_1T12

African population

AmericanAdmixture_4B11

American admixture

OutOfAfricaArchaicAdmixture_5R19

Three population out-of-Africa with archaic admixture

Zigzag_1S14

Periodic growth and decline.

AncientEurasia_9K19

Multi-population model of ancient Eurasia

PapuansOutOfAfrica_10J19

Out-of-Africa with archaic admixture into Papuans

AshkSub_7G19

Ashkenazi Jewish with substructure and European admixture

Three population out-of-Africa

The three population Out-of-Africa model from Gutenkunst et al. 2009. It describes the ancestral human population in Africa, the out of Africa event, and the subsequent European-Asian population split. Model parameters are the maximum likelihood values of the various parameters given in Table 1 of Gutenkunst et al.

Details

ID

OutOfAfrica_3G09

Description

Three population out-of-Africa

Num populations

3

Populations

Index

ID

Sampling time

Description

0

YRI

0

1000 Genomes YRI (Yorubans)

1

CEU

0

1000 Genomes CEU (Utah Residents (CEPH) with Northern and Western European Ancestry

2

CHB

0

1000 Genomes CHB (Han Chinese in Beijing, China)

Citations

Demographic Model parameters

Parameter Type (units)

Value

Description

Population size

7,300

Ancestral pop. size

Population size

12,300

YRI pop. size

Population size

2,100

OOA pop. size

Population size

1,000

CEU pop. size after EU/AS divergence

Population size

510

CHB pop. size after EU/AS divergence

Growth rate (per gen.)

0.4

CEU pop. growth rate (per gen.)

Growth rate (per gen.)

0.55

CHB pop. growth rate (per gen.)

Migration rate (x10^-5)

25

YRI-OOA migration rate (per gen.)

Migration rate (x10^-5)

3

YRI-CEU migration rate (per gen.)

Migration rate (x10^-5)

1.9

YRI-CHB migration rate (per gen.)

Migration rate (x10^-5)

9.6

CEU-CHB migration rate (per gen.)

Epoch Time (gen.)

8,800

Expansion time of ancestral pop.

Epoch Time (gen.)

5,600

Time of OOA event

Epoch Time (gen.)

848

Time of CEU-CHB split

Generation time (yrs.)

25

Generation time


Two population out-of-Africa

The model is derived from the Tennesen et al. analysis of the jSFS from European Americans and African Americans. It describes the ancestral human population in Africa, the out of Africa event, and two distinct periods of subsequent European population growth over the past 23kya. Model parameters are taken from Fig. S5 in Fu et al.

Details

ID

OutOfAfrica_2T12

Description

Two population out-of-Africa

Num populations

2

Populations

Index

ID

Sampling time

Description

0

AFR

0

African Americans

1

EUR

0

European Americans

Citations

Demographic Model parameters

Parameter Type (units)

Value

Description

Population size

7,310

Ancestral pop. size

Population size

14,474

AFR pop. size

Population size

1,861

OOA pop. size

Population size

1,032

EU pop. size after EU/AS divergence

Population size

9,279

EU pop. size after 1st expansion

Population size

501,436

EU pop. size after 2nd expansion

Population size

432,125

AFR pop. size after 1st expansion

Growth rate (per gen.)

0.00307

EU pop. growth rate 1st expansion

Growth rate (per gen.)

0.0195

EU pop. growth rate 2st expansion

Growth rate (per gen.)

0.0166

AFR pop. growth rate 1st expansion

Migration rate (x10^-5 per gen.)

15

AFR-OOA migration rate

Migration rate (x10^-5 per gen.)

2.5

AFR-EU migration rate (both expansions)

Epoch Time (gen.)

5,920

Expansion time of ancestral pop.

Epoch Time (gen.)

2,040

Time of OOA event

Epoch Time (gen.)

920

Beginning of 1st EU growth period

Epoch Time (gen.)

204.6

Beginning of 2nd EU/1st AFR growth period

Generation time (yrs.)

25

Generation time


African population

The model is a simplification of the two population Tennesen et al. model with the European-American population removed so that we are modeling the African population in isolation.

Details

ID

Africa_1T12

Description

African population

Num populations

1

Populations

Index

ID

Sampling time

Description

0

AFR

0

African

Citations

Demographic Model parameters

Parameter Type (units)

Value

Description

Population size

7,310

Ancestral pop. size

Population size

14,474

AFR pop. size

Population size

432,125

AFR pop. size after 1st expansion

Growth rate (per gen.)

0.0166

AFR pop. growth rate 1st expansion

Epoch Time (gen.)

5,920

Expansion time of ancestral pop.

Epoch Time (gen.)

204.6

Beginning of AFR growth period

Generation time (yrs.)

25

Generation time


American admixture

Demographic model for American admixture, taken from Browning et al. 2011. This model extends the Gravel et al. (2011) model of African/European/Asian demographic history to simulate an admixed population with admixture occurring 12 generations ago. The admixed population had an initial size of 30,000 and grew at a rate of 5% per generation, with 1/6 of the population of African ancestry, 1/3 European, and 1/2 Asian.

Details

ID

AmericanAdmixture_4B11

Description

American admixture

Num populations

4

Populations

Index

ID

Sampling time

Description

0

AFR

0

Contemporary African population

1

EUR

0

Contemporary European population

2

ASIA

0

Contemporary Asian population

3

ADMIX

0

Modern admixed population

Citations

Demographic Model parameters

Parameter Type (units)

Value

Description

Population size

7,310

Ancestral pop. size

Population size

14,474

AFR pop. size

Population size

1,861

OOA pop. size

Population size

1,032

EU pop. size after EU/AS divergence

Population size

554

ASN pop. size after EU/AS divergence

Population size

30,000

Initial ADMIX pop. size

Growth rate (per gen.)

0.0038

EU pop. growth rate (per gen.)

Growth rate (per gen.)

0.0048

ASN pop. growth rate (per gen.)

Growth rate (per gen.)

0.05

ADMIX pop. growth rate (per gen.)

Migration rate (x10^-5)

15

AFR-OOA migration rate (per gen.)

Migration rate (x10^-5)

2.5

AFR-EU migration rate (per gen.)

Migration rate (x10^-5)

0.78

AFR-ASN migration rate (per gen.)

Migration rate (x10^-5)

3.11

EU-ASN migration rate (per gen.)

Epoch Time (gen.)

5,920

Expansion time of ancestral pop.

Epoch Time (gen.)

2,040

Time of OOA event

Epoch Time (gen.)

920

Time of EU-ASN split

Epoch Time (gen.)

12

Time of ADMIX population emergence

ADMIX percentage

1/6

Amount African admixture

ADMIX percentage

1/3

Amount European admixture

ADMIX percentage

1/2

Amount Asian admixture

Generation time (yrs.)

25

Generation time


Three population out-of-Africa with archaic admixture

The three population out-of-African model popularized by Gutenkunst et al. (2009) and augmented by archaic contributions to both Eurasian and African populations. Two archaic populations split early in human history, before the African expansion, and contribute to Eurasian populations (putative Neanderthal branch) and to the African branch (a deep diverging branch within Africa). Admixture is modeled as symmetric migration between the archaic and modern human branches, with contribution ending at a given time in the past.

Details

ID

OutOfAfricaArchaicAdmixture_5R19

Description

Three population out-of-Africa with archaic admixture

Num populations

5

Populations

Index

ID

Sampling time

Description

0

YRI

0

1000 Genomes YRI (Yorubans)

1

CEU

0

1000 Genomes CEU (Utah Residents (CEPH) with Northern and Western European Ancestry

2

CHB

0

1000 Genomes CHB (Han Chinese in Beijing, China)

3

Neanderthal

None

Putative Neanderthals

4

ArchaicAFR

None

Putative Archaic Africans

Citations

Demographic Model parameters

Parameter Type (units)

Value

Description

Population size

3,600

Ancestral pop. size

Population size

13,900

YRI pop. size

Population size

880

OOA pop. size

Population size

2,300

CEU pop. size after EU/AS divergence

Population size

650

CHB pop. size after EU/AS divergence

Growth rate (per gen.)

0.00125

CEU pop. growth rate (per gen.)

Growth rate (per gen.)

0.00372

CHB pop. growth rate (per gen.)

Migration rate (x10^-5)

52.2

YRI-OOA migration rate (per gen.)

Migration rate (x10^-5)

2.48

YRI-CEU migration rate (per gen.)

Migration rate (x10^-5)

0

YRI-CHB migration rate (per gen.)

Migration rate (x10^-5)

11.3

CEU-CHB migration rate (per gen.)

Time (kya)

300

Expansion time of ancestral pop.

Time (kya)

61

Time of OOA event

Time (kya)

36

Time of CEU-CHB split

Time (kya)

499

Archaic African split time

Time (kya)

125

Archaic African migration begins

Migration rate (x10^-5)

1.95

Arch Afr-Nean migration rate (per gen.)

Time (kya)

559

Neanderthal split time

Migration rate (x10^-5)

0.825

OOA pops-Nean migration rate (per gen.)

Time (kya)

18.7

Archaic migrations end

Generation time (yrs.)

29

Generation time


Periodic growth and decline.

A validation model used by Schiffels and Durbin (2014) and Terhorst and Terhorst, Kamm, and Song (2017) with periods of exponential growth and decline in a single population.

Details

ID

Zigzag_1S14

Description

Periodic growth and decline.

Num populations

1

Populations

Index

ID

Sampling time

Description

0

generic

0

Generic expanding and contracting population

Citations

Demographic Model parameters

Parameter Type (units)

Value

Description

Population size

1,431

Ancient pop. size

Population size

14,312

Recent pop. size

Growth rate (per gen.)

8.99448 x 10^(-5)

Growth rate for 1st growth

Growth rate (per gen.)

-0.00035977

Growth rate for 1st decline

Growth rate (per gen.)

0.0014391

Growth rate for 2nd growth

Growth rate (per gen.)

-0.005756

Growth rate for 2rd decline

Growth rate (per gen.)

0.023025

Growth rate for 3st growth

Time (gen.)

34,133.31

Beginning of 1st growth

Time (gen.)

8,533.33

Beginning of 1st decline

Time (gen.)

2,133.33

Beginning of 2nd growth

Time (gen.)

533.33

Beginning of 2nd decline

Time (gen.)

133.33

Beginning of 3rd growth

Time (gen.)

33.333

End of 3rd growth

Generation time

30

Generation time in years


Multi-population model of ancient Eurasia

This is the best-fitting model of a history of multiple ancient and present-day human populations sampled across Eurasia over the past 120,000 years. The fitting was performed using momi2 (Kamm et al. 2019), which uses the multi-population site-frequency spectrum as input data. The model includes a ghost admixture event (from unsampled basal Eurasians into early European farmers), and two admixture events where the source is approximately well-known (from Neanderthals into Non-Africans and from Western European hunter-gatherers into modern Sardinians. There are three present-day populations: Sardinians, Han Chinese and African Mbuti. Additionally, there are several ancient samples obtained from fossils dated at different times in the past: the Altai Neanderthal (Prufer et al. 2014), a Mesolithic hunter-gatherer (Lazaridis et al. 2014), a Neolithic early European sample (Lazaridis et al. 2014), and two Palaeolithic modern humans from Siberia - MA1 (Raghavan et al. 2014) and Ust’Ishim (Fu et al. 2014). All the ancient samples are represented by a single diploid genome.

Details

ID

AncientEurasia_9K19

Description

Multi-population model of ancient Eurasia

Num populations

9

Populations

Index

ID

Sampling time

Description

0

Mbuti

0

Present-day African Mbuti

1

LBK

320

Early European farmer (EEF)

2

Sardinian

0

Present-day Sardinian

3

Loschbour

300

Western hunter-gatherer (WHG)

4

MA1

960

Upper Palaeolithic MAl’ta culture

5

Han

0

Present-day Han Chinese

6

UstIshim

1800

early Palaeolithic Ust’-Ishim

7

Neanderthal

2000

Altai Neanderthal from Siberia

8

BasalEurasian

None

Basal Eurasians

Citations

Demographic Model parameters

Parameter Type (units)

Value

Description

Population size

17,300

Mbuti pop. size

Population size

75.7

EEF pop. size

Population size

15,000

Sardinian pop. size

Population size

1,920

Size of WHG, Bazal, Mal’ta and Ust’-Ishim populations

Population size

6,300

Han Chinese pop. size

Population size

86.9

Neanderthal pop. size after exp. decline

Population size

2,340

(WHG + Han chinese) pop. size before divergence

Population size

29,100

(WHG + Mbuti) pop. size before divergence

Population size

18,200

Ancestral pop. size and Nean. size before exp. decline

Population size

12,000

(Sardinian + EEF) pop. size before divergence

Time (yrs.)

696,000

Time of WHG and Neanderthal split

Time (yrs.)

95,800

Time of WHG and Mbuti split, start of Nean. decline

Time (yrs.)

79,800

Time of WHG and Bazal split

Time (yrs.)

51,500

Time of WHG and Ust’Ishim split

Time (yrs.)

50,400

Time of WHG and Han Chinese split

Time (yrs.)

44,900

Time of WHG and Mal’ta split

Time (yrs.)

37,700

Time of WHG and EEF split

Time (yrs.)

7,690

Time of EEF and Sardinian split

Time (yrs.)

56,800

Time of Neanderthal to Eurasian (WHG) admixture

Time (yrs.)

33,700

Time of Bazal to EEF admixture

Time (yrs.)

1,230

Time of WHG to Sardinian admixture

ADMIX percentage

2.96

Amount of Neanderthal admixture in Eurasian pop.

ADMIX percentage

9.36

Amount of Bazal admixture in EEF pop.

ADMIX percentage

3.17

Amount of WHG admixture in Sardinian pop.

Time (yrs.)

8,000

Time of EEF samples

Time (yrs.)

7,500

Time of WHG samples

Time (yrs.)

24,000

Time of MAl’ta samples

Time (yrs.)

45,000

Time of Ust’-Ishim samples

Time (yrs.)

50,000

Time of Neanderthal samples

Generation time (yrs.)

25

Generation time


Out-of-Africa with archaic admixture into Papuans

A ten population model of out-of-Africa, including two pulses of Denisovan admixture into Papuans, and several pulses of Neandertal admixture into non-Africans. Most parameters are from Jacobs et al. (2019), Table S5 and Figure S5. This model is an extension of one from Malaspinas et al. (2016), thus some parameters are inherited from there.

Details

ID

PapuansOutOfAfrica_10J19

Description

Out-of-Africa with archaic admixture into Papuans

Num populations

10

Populations

Index

ID

Sampling time

Description

0

YRI

0

1000 Genomes YRI (Yorubans)

1

CEU

0

1000 Genomes CEU (Utah Residents (CEPH) with Northern and Western European Ancestry

2

CHB

0

1000 Genomes CHB (Han Chinese in Beijing, China)

3

Papuan

0

Papuans from Indonesian and New Guinea

4

DenA

2058

Altai Denisovan (sampling) lineage

5

NeaA

2612

Altai Neandertal (sampling) lineage

6

Den1

None

Denisovan D1 (introgressing) lineage

7

Den2

None

Denisovan D2 (introgressing) lineage

8

Nea1

None

Neandertal N1 (introgressing) lineage

9

Ghost

None

Out-of-Africa lineage

Citations

Demographic Model parameters

Parameter Type (units)

Value

Description

Generation time (yrs.)

29

Generation time

Population size

48,433

African pop. size

Population size

6,962

European pop. size

Population size

9,025

East Asian pop. size

Population size

8,834

Papuan pop. size

Population size

5,083

Altai Denisovan pop. size

Population size

826

Altai Neandertal pop. size

Population size

13,249

Introgressing Denisovan D1 pop. size

Population size

13,249

Introgressing Denisovan D2 pop. size

Population size

13,249

Introgressing Neandertal pop. size

Population size

8,516

Ghost (out-of-Africa lineage) pop. size

Population size

12,971

(European + East Asian) pop. size before divergence

Population size

41,563

(Ghost + African) pop. size before divergence

Population size

13,249

(Denisovan + Neandertal) pop. size before divergence

Population size

32,671

(Human + Archaic) pop. size before divergence

Population size

100

(Altai Denisovan + Introgressing Denisovan D1) pop. size before divergence

Population size

100

(Altai Denisovan + Introgressing Denisovan D2) pop. size before divergence

Population size

13,249

(Altai Neandertal + Introgressing Neandertal) pop. size before divergence

Time (yrs.)

37,497

Time of European and East Asian split

Time (yrs.)

50,982

Time of Ghost and (European + East Asian) split

Time (yrs.)

51,736

Time of Ghost and Papuan split

Time (yrs.)

64,322

Time of Ghost and African split

Time (yrs.)

97,875

Time of Altai Neandertal and Introgressing Neandertal split

Time (yrs.)

282,750

Time of Altai Denisovan and Introgressing Denisovan D1 split

Time (yrs.)

362,500

Time of Altai Denisovan and Introgressing Denisovan D2 split

Time (yrs.)

437,610

Time of Denisovan and Neandertal split

Time (yrs.)

586,525

Time of Human and Archaic split

Population size

2,231

(European + East Asian) bottleneck pop. size

Population size

243

Papuan bottleneck pop. size

Population size

1,394

Ghost (out-of-Africa) bottleneck pop. size

Time (yrs.)

48,111

Time of the (European + East Asian) bottleneck

Time (yrs.)

48,865

Time of the Papuan bottleneck

Time (yrs.)

61,451

Time of the Ghost (out-of-Africa) bottleneck

ADMIX percentage

2.2

Amount of Denisovan D1 admixture in Papaun pop.

ADMIX percentage

1.8

Amount of Denisovan D2 admixture in Papaun pop.

ADMIX percentage

2.4

Amount of Neandertal admixture in Ghost pop.

ADMIX percentage

1.1

Amount of Neandertal admixture in (European + East Asian) pop.

ADMIX percentage

0.2

Amount of Neandertal admixture in Papuan pop.

ADMIX percentage

0.2

Amount of Neandertal admixture in East Asian pop.

Time (yrs.)

29,800

Time of Denisovan D1 to Papuan admixture

Time (yrs.)

45,700

Time of Denisovan D2 to Papuan admixture

Time (yrs.)

53,737

Time of Neandertal to Ghost admixture

Time (yrs.)

45,414

Time of Neandertal to (European + East Asian) admixture

Time (yrs.)

40,948

Time of Neandertal to Papuan admixture

Time (yrs.)

25,607

Time of Neandertal to East Asian admixture

Migration rate (x10^-4)

1.79

Ghost–African migration rate

Migration rate (x10^-4)

4.42

Ghost–European migration rate

Migration rate (x10^-4)

31.4

European–East Asian migration rate

Migration rate (x10^-4)

57.2

East Asian–Papuan migration rate

Migration rate (x10^-4)

5.72

(European + East Asian)–Papuan migration rate

Migration rate (x10^-4)

4.42

(European + East Asian)–Ghost migration rate

Time (yrs.)

37,497

(European + East Asian)–Papuan migration begins

Time (yrs.)

37,497

(European + East Asian)–Ghost migration begins


Ashkenazi Jewish with substructure and European admixture

This was the best fit model of Ashkenazi Jewish demographic history from Gladstein and Hammer 2019, shown in Figure 1, labeled “Substructure Model”. Model choice and parameter estimation were performed with Approximate Bayesian Computation. Parameter values are based on the mode from ABC found in Table S3 of Gladstein and Hammer 2019. In this model, the ancestors of Europeans and Middle Eastern populations diverge. Non-Ashkenazi Jewish populations then diverge from the Middle Eastern population. The Ashkenazi Jews then diverge from the other Jewish populations and experience a substantial reduction in population size and a single pulse of gene flow from Europeans (corresponding to their arrival in Europe). After the gene flow from Europeans to the Ashkenazi Jews, the Ashkenazi Jews split into two groups, the Western and Eastern. Finally, the Western Ashkenazi Jews experience moderate instantaneous population size increase, and the Eastern experience a massive population size increase. In addition to the demographic model Gladstein and Hammer 2019 also incorporated an SNP array ascertainment scheme into the simulation. This demographic model does not include the SNP array ascertainment scheme. It should be noted that Gladstein and Hammer 2019 simulated with a mutation rate of 2.5e-8.

Details

ID

AshkSub_7G19

Description

Ashkenazi Jewish with substructure and European admixture

Num populations

7

Populations

Index

ID

Sampling time

Description

0

YRI

0

1000 Genomes YRI (Yorubans)

1

CHB

0

1000 Genomes CHB (Han Chinese in Beijing, China)

2

CEU

0

1000 Genomes CEU (Utah Residents (CEPH) with Northern and Western European Ancestry

3

ME

0

Middle Eastern

4

J

0

non-Ashkenazi Jewish

5

WAJ

0

Western Ashkenazi Jewish

6

EAJ

0

Eastern Ashkenazi Jewish

Citations

Demographic Model parameters

Parameter Type (units)

Value

Description

Population size

7,300

Ancestral African pop. size

Population size

18,197

YRI pop. size

Population size

4,073

CHB pop. size

Population size

33,113

CEU pop. size

Population size

436,515

Middle Eastern pop. size

Population size

354,813

non-AJ Jewish pop. size

Population size

6,606

Western AJ pop. size

Population size

1,949,844

Eastern AJ founder pop. size

Epoch Time (gen.)

8,800

Expansion time of YRI ancestral pop.

Epoch Time (gen.)

2,105

Time of OOA event

Epoch Time (gen.)

850

Time of CEU-CHB split

Epoch Time (gen.)

481

Time of Middle Eastern-CEU split

Epoch Time (gen.)

211

Time of Jewish-Middle Eastern split

Epoch Time (gen.)

29

Time of AJ-Jewish split

Epoch Time (gen.)

28

Time of geneflow (not inferred)

Epoch Time (gen.)

14

Time of Eastern-Western AJ split

Epoch Time (gen.)

13

Time of AJ growth (not inferred)

ADMIX percentage

0.17

European to AJ gene flow

Generation time (yrs.)

25

Generation time

Pongo abelii

ID

PonAbe

Name

Pongo abelii

Common name

Sumatran orangutan

Generation time

20 (Locke et al., 2011)

Population size

17900.0 (Locke et al., 2011)

Genome

ID

Length

Recombination rate

Mutation rate

chr1

229942017

5.19e-09

1.5e-08

chr2a

113028656

5.43e-09

1.5e-08

chr2b

135000294

5.38e-09

1.5e-08

chr3

202140232

5.36e-09

1.5e-08

chr4

198332218

5.43e-09

1.5e-08

chr5

183952662

5.2e-09

1.5e-08

chr6

174210431

5.22e-09

1.5e-08

chr7

157549271

5.73e-09

1.5e-08

chr8

153482349

5.67e-09

1.5e-08

chr9

135191526

5.34e-09

1.5e-08

chr10

133410057

5.91e-09

1.5e-08

chr11

132107971

5.29e-09

1.5e-08

chr12

136387465

5.44e-09

1.5e-08

chr13

117095149

4.91e-09

1.5e-08

chr14

108868599

4.7e-09

1.5e-08

chr15

99152023

4.82e-09

1.5e-08

chr16

77800216

6.12e-09

1.5e-08

chr17

73212453

7.26e-09

1.5e-08

chr18

94050890

4.57e-09

1.5e-08

chr19

60714840

7.56e-09

1.5e-08

chr20

62736349

5.83e-09

1.5e-08

chr21

48394510

4.98e-09

1.5e-08

chr22

46535552

6.03e-09

1.5e-08

chrX

156195299

9.5e-09

1.5e-08


Genetic Maps

ID

Year

Description

NaterPA_PonAbe2

2017

From Nater et al. (2017) for Pongo abelii

NaterPP_PonAbe2

2017

From Nater et al. (2017) for Pongo pygmaeus

NaterPA_PonAbe2

This genetic map is from the Nater et al. (2017) study, inferred using LDhat from n=15 whole-genome sequenced Sumatran orangutan individuals. See https://doi.org/10.1016/j.cub.2017.09.047 for more details.

Citations

NaterPP_PonAbe2

This genetic map is from the Nater et al. (2017) study, inferred using LDhat from n=20 whole-genome sequenced Bornean orangutan individuals. See https://doi.org/10.1016/j.cub.2017.09.047 for more details.

Citations


Models

ID

Description

TwoSpecies_2L11

Two population orangutan model

Two population orangutan model

The two orang-utan species, Sumatran (Pongo abelii) and Bornean (Pongo pygmaeus) inferred from the joint-site frequency spectrum with ten individuals from each population. This model is an isolation-with- migration model, with exponential growth or decay in each population after the split. The Sumatran population grows in size, while the Bornean population slightly declines.

Details

ID

TwoSpecies_2L11

Description

Two population orangutan model

Num populations

2

Populations

Index

ID

Sampling time

Description

0

Bornean

0

Pongo pygmaeus (Bornean) population

1

Sumatran

0

Pongo abelii (Sumatran) population

Citations

Demographic Model parameters

Parameter Type (units)

Value

Description

Population size

17,934

Ancestral pop. size

Population size

10,617

Pongo pygmaeus pop. size at split

Population size

7,317

Pongo abelii pop. size at split

Population size

8,805

Modern Pongo pygmaeus pop. size

Population size

37,661

Modern Pongo abelii pop. size

Epoch Time (gen.)

20,157

Species divergence time

Generation time (yrs.)

20

Generation time