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)

  4. Which distribution of fitness effects (ie. which DFE object) within

  5. which annotation track? (ie. which Annotation 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, with

  4. background selection acting within

  5. exons from the Ensembl Havana 104 annotations.

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

$ stdpopsim -e slim HomSap -c chr22 -o test.trees -g HapMapII_GRCh38 \
$    --dfe Gamma_K17 --dfe-annotation ensembl_havana_104_exons \
$    -d OutOfAfrica_3G09 YRI:2 CEU:2 CHB:2

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

Aedes aegypti

ID

AedAeg

Name

Aedes aegypti

Common name

Yellow fever mosquito

Generation time

0.06666666666666667 (Crawford et al., 2017)

Population size

1000000.0 (Crawford et al., 2017)

Genome

ID

Length

Recombination rate

Mutation rate

1

310827022

3.06e-09

3.5e-09

2

474425716

2.49e-09

3.5e-09

3

409777670

2.91e-09

3.5e-09

MT

16790

0

3.5e-09

Mutation and recombination rates are in units of per bp and per generation.


Anas platyrhynchos

ID

AnaPla

Name

Anas platyrhynchos

Common name

Mallard

Generation time

4 (Lavretsky et al., 2020)

Population size

156000 (Guo et al., 2021)

Genome

ID

Length

Recombination rate

Mutation rate

1

208326429

1.52e-08

4.83e-09

2

162939446

1.39e-08

4.83e-09

3

119723720

9.38e-09

4.83e-09

4

77626585

1.2e-08

4.83e-09

5

64988622

1.21e-08

4.83e-09

6

39543408

3.04e-08

4.83e-09

7

37812880

2.59e-08

4.83e-09

8

33348632

1.28e-08

4.83e-09

9

26742597

1.34e-08

4.83e-09

10

22933227

2.5e-08

4.83e-09

11

22193879

1.5e-08

4.83e-09

12

22338721

3.15e-08

4.83e-09

13

21714986

1.41e-08

4.83e-09

14

20320564

8.61e-09

4.83e-09

15

18227546

3.79e-09

4.83e-09

16

16053328

3.86e-09

4.83e-09

17

15319648

3.13e-09

4.83e-09

18

13333155

1.58e-09

4.83e-09

19

12198306

1.43e-08

4.83e-09

20

12091001

1.43e-08

4.83e-09

21

8553409

1.43e-08

4.83e-09

22

16160689

1.43e-08

4.83e-09

23

7977799

1.43e-08

4.83e-09

24

7737077

1.43e-08

4.83e-09

25

7574731

1.43e-08

4.83e-09

26

6918023

1.43e-08

4.83e-09

27

6270716

1.43e-08

4.83e-09

28

5960150

1.43e-08

4.83e-09

29

1456683

1.43e-08

4.83e-09

30

1872559

1.43e-08

4.83e-09

Z

81233375

1.43e-08

4.83e-09

31

2637124

1.43e-08

4.83e-09

32

3473573

1.43e-08

4.83e-09

33

2151773

1.43e-08

4.83e-09

34

7214884

1.43e-08

4.83e-09

35

5548691

1.43e-08

4.83e-09

36

3997205

1.43e-08

4.83e-09

37

3148754

1.43e-08

4.83e-09

38

2836164

1.43e-08

4.83e-09

39

2018729

1.43e-08

4.83e-09

40

1354177

1.43e-08

4.83e-09

Mutation and recombination rates are in units of per bp and per generation.


Demographic Models

ID

Description

MallardBlackDuck_2L19

North American Mallard/Black Duck split

North American Mallard/Black Duck split

This is a model fit to contemporary samples of wild North American mallard and black duck, using the “split-migration” model of dadi. See Figure 6 of Lavretsky et al 2019.

Details

ID

MallardBlackDuck_2L19

Description

North American Mallard/Black Duck split

Num populations

3

Populations

Index

ID

Sampling time

Description

0

Mallard

None

Wild North American mallards

1

Black_duck

None

Wild black ducks

2

Ancestral

158076.25

Ancestral population

Citations

Demographic Model parameters

Parameter Type (units)

Value

Description

Population size

819,535

Ancestral pop. size

Population size

1,570,000

Mallard pop. size

Population size

1,370,000

Black duck pop. size

Migration rate (x10^-6 per gen.)

0.84

Black-Mallard migration rate

Migration rate (x10^-6 per gen.)

1.10

Mallard-Black migration rate

Epoch Time (gen.)

158076

Mallard/Black split time

Generation time (yrs.)

4

Generation time

Mutation rate (subst/gen)

4.83e-9

Mutation rate

_images/sec_catalog_anapla_models_mallardblackduck_2l19.png

Anolis carolinensis

ID

AnoCar

Name

Anolis carolinensis

Common name

Anole lizard

Generation time

1.5 (Lovern et al., 2004)

Population size

3050000.0 (Pombi et al., 2019)

Genome

ID

Length

Recombination rate

Mutation rate

1

263920458

1e-08

2.1e-10

2

199619895

1e-08

2.1e-10

3

204416410

1e-08

2.1e-10

4

156502444

1e-08

2.1e-10

5

150641573

1e-08

2.1e-10

6

80741955

1e-08

2.1e-10

LGa

7025928

1e-08

2.1e-10

LGb

3271537

1e-08

2.1e-10

LGc

9478905

1e-08

2.1e-10

LGd

1094478

1e-08

2.1e-10

LGf

4257874

1e-08

2.1e-10

LGg

424765

1e-08

2.1e-10

LGh

248369

1e-08

2.1e-10

MT

17223

0

2.1e-10

Mutation and recombination rates are in units of per bp and per generation.


Anopheles gambiae

ID

AnoGam

Name

Anopheles gambiae

Common name

Anopheles gambiae

Generation time

0.09090909090909091 (Ag1000G Consortium, 2017)

Population size

1000000.0 (Ag1000G Consortium, 2017)

Genome

ID

Length

Recombination rate

Mutation rate

2L

49364325

1.3e-08

3.5e-09

2R

61545105

1.3e-08

3.5e-09

3L

41963435

1.3e-08

3.5e-09

3R

53200684

1.6e-08

3.5e-09

X

24393108

2.04e-08

3.5e-09

Mt

15363

0

3.5e-09

Mutation and recombination rates are in units of per bp and per generation.


Demographic Models

ID

Description

GabonAg1000G_1A17

Stairwayplot estimates of N(t) for Gabon sample

Stairwayplot estimates of N(t) for Gabon sample

These estimates were done as part of the Ag1000G 2017 Consortium paper. Stairwayplot was run with the addition of a misorientation parameter using SFS information from each population. The model contains 110 distinct epochs, so only some summaries are reported in the population table.

Details

ID

GabonAg1000G_1A17

Description

Stairwayplot estimates of N(t) for Gabon sample

Num populations

1

Populations

Index

ID

Sampling time

Description

0

GAS

0

Gabon gambiae population

Citations

Demographic Model parameters

Parameter Type (units)

Value

Description

Population size

4,069,863

Modern population size

Population size

205,766

Mean coalescence time / 4

Generation time (yrs.)

1/11

Generation time

Mutation rate (subst/gen)

3.5e-9

Mutation rate

_images/sec_catalog_anogam_models_gabonag1000g_1a17.png

Apis mellifera

ID

ApiMel

Name

Apis mellifera

Common name

Apis mellifera (DH4)

Generation time

2 (Nelson et al., 2017)

Population size

200000.0 (Wallberg et al., 2014)

Genome

ID

Length

Recombination rate

Mutation rate

CM009931.2

27754200

2.39e-07

3.4e-09

CM009932.2

16089512

2.46e-07

3.4e-09

CM009933.2

13619445

2.41e-07

3.4e-09

CM009934.2

13404451

2.76e-07

3.4e-09

CM009935.2

13896941

2.14e-07

3.4e-09

CM009936.2

17789102

2.12e-07

3.4e-09

CM009937.2

14198698

2.34e-07

3.4e-09

CM009938.2

12717210

2.09e-07

3.4e-09

CM009939.2

12354651

2.46e-07

3.4e-09

CM009940.2

12360052

2.48e-07

3.4e-09

CM009941.2

16352600

2.03e-07

3.4e-09

CM009942.2

11514234

2.12e-07

3.4e-09

CM009943.2

11279722

2.34e-07

3.4e-09

CM009944.2

10670842

2.46e-07

3.4e-09

CM009945.2

9534514

2.21e-07

3.4e-09

CM009946.2

7238532

2.28e-07

3.4e-09

CM009947.2

16343

0

3.4e-09

Mutation and recombination rates are in units of per bp and per generation.


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

1

30427671

8.06452e-10

7e-09

2

19698289

8.06452e-10

7e-09

3

23459830

8.06452e-10

7e-09

4

18585056

8.06452e-10

7e-09

5

26975502

8.06452e-10

7e-09

Mt

366924

0

7e-09

Pt

154478

0

7e-09

Mutation and recombination rates are in units of per bp and per generation.


Genetic Maps

ID

Year

Description

SalomeAveraged_TAIR10

2012

Crossover frequency map averaged over 17 populations

SalomeAveraged_TAIR10

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. The map was constructed on genome version TAIR7, and lifted to TAIR10.

Citations


Demographic 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

Generation time (yrs.)

1

Average generation interval

Mutation rate

7.1e-9

Per-base per-generation mutation rate

_images/sec_catalog_aratha_models_southmiddleatlas_1d17.png

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

Generation time (yrs.)

1

Average generation interval

Mutation rate

7e-9

Per-base per-generation mutation rate

_images/sec_catalog_aratha_models_african2epoch_1h18.png

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

Generation time (yrs.)

1

Average generation interval

Mutation rate

7e-9

Per-base per-generation mutation rate

_images/sec_catalog_aratha_models_african3epoch_1h18.png

Annotations

ID

Year

Description

araport_11_exons

2017

Araport11 exon annotations on TAIR10

araport_11_CDS

2017

Araport11 exon annotations on TAIR10

araport_11_exons

Araport11 exon annotations on TAIR10

Citations

araport_11_CDS

Araport11 exon annotations on TAIR10

Citations


Distribution of Fitness Effects (DFEs)

ID

Year

Description

Gamma_H18

2018

Deleterious Gamma DFE

Gamma_H18

Deleterious Gamma DFE

Citations


Bos taurus

ID

BosTau

Name

Bos taurus

Common name

Cattle

Generation time

5 (MacLeod et al., 2013)

Population size

62000 (MacLeod et al., 2013)

Genome

ID

Length

Recombination rate

Mutation rate

1

158534110

9.26e-09

1.2e-08

2

136231102

9.26e-09

1.2e-08

3

121005158

9.26e-09

1.2e-08

4

120000601

9.26e-09

1.2e-08

5

120089316

9.26e-09

1.2e-08

6

117806340

9.26e-09

1.2e-08

7

110682743

9.26e-09

1.2e-08

8

113319770

9.26e-09

1.2e-08

9

105454467

9.26e-09

1.2e-08

10

103308737

9.26e-09

1.2e-08

11

106982474

9.26e-09

1.2e-08

12

87216183

9.26e-09

1.2e-08

13

83472345

9.26e-09

1.2e-08

14

82403003

9.26e-09

1.2e-08

15

85007780

9.26e-09

1.2e-08

16

81013979

9.26e-09

1.2e-08

17

73167244

9.26e-09

1.2e-08

18

65820629

9.26e-09

1.2e-08

19

63449741

9.26e-09

1.2e-08

20

71974595

9.26e-09

1.2e-08

21

69862954

9.26e-09

1.2e-08

22

60773035

9.26e-09

1.2e-08

23

52498615

9.26e-09

1.2e-08

24

62317253

9.26e-09

1.2e-08

25

42350435

9.26e-09

1.2e-08

26

51992305

9.26e-09

1.2e-08

27

45612108

9.26e-09

1.2e-08

28

45940150

9.26e-09

1.2e-08

29

51098607

9.26e-09

1.2e-08

X

139009144

9.26e-09

1.2e-08

MT

16338

0

1.2e-08

Mutation and recombination rates are in units of per bp and per generation.


Demographic Models

ID

Description

HolsteinFriesian_1M13

Piecewise size changes in Holstein-Friesian cattle.

Piecewise size changes in Holstein-Friesian cattle.

The piecewise-constant population size model of Holstein-Friesian cattle from MacLeod et al. (2013). Population sizes were estimated from inferred runs of homozygosity, with parameter values taken from Figure 4A and Table S1.

Details

ID

HolsteinFriesian_1M13

Description

Piecewise size changes in Holstein-Friesian cattle.

Num populations

1

Populations

Index

ID

Sampling time

Description

0

Holstein_Friesian

0

Holstein-Friesian

Citations

Demographic Model parameters

Parameter Type (units)

Value

Description

Population size

62,000

Ancestral population size

Population size

17,000

Pop. size during 1st time interval

Population size

10,000

Pop. size during 2nd time interval

Population size

7,000

Pop. size during 3rd time interval

Population size

3,500

Pop. size during 4th time interval

Population size

2,500

Pop. size during 5th time interval

Population size

2,000

Pop. size during 6th time interval

Population size

1,500

Pop. size during 7th time interval

Population size

1,000

Pop. size during 8th time interval

Population size

350

Pop. size during 9th time interval

Population size

250

Pop. size during 10th time interval

Population size

120

Pop. size during 11th time interval

Population size

90

Pop. size during 12th time interval

Time (gen.)

33,154

Begining of 1st time interval

Time (gen.)

3,354

Begining of 2nd time interval

Time (gen.)

2,354

Begining of 3rd time interval

Time (gen.)

1,754

Begining of 4th time interval

Time (gen.)

654

Begining of 5th time interval

Time (gen.)

454

Begining of 6th time interval

Time (gen.)

154

Begining of 7th time interval

Time (gen.)

24

Begining of 8th time interval

Time (gen.)

18

Begining of 9th time interval

Time (gen.)

12

Begining of 10th time interval

Time (gen.)

6

Begining of 11th time interval

Time (gen.)

3

Begining of 12th time interval

Generation time (yrs.)

5

Generation time

Mutation rate

9.4e-9

Per-base per-generation mutation rate

_images/sec_catalog_bostau_models_holsteinfriesian_1m13.png

Caenorhabditis elegans

ID

CaeEle

Name

Caenorhabditis elegans

Common name

C. elegans

Generation time

0.01 (Frézal & Félix, 2015)

Population size

10000 (Barrière & Félix, 2005; Cutter, 2006)

Genome

ID

Length

Recombination rate

Mutation rate

I

15072434

3.12163e-11

1.84e-09

II

15279421

3.52929e-11

1.84e-09

III

13783801

3.9066e-11

1.84e-09

IV

17493829

2.7121e-11

1.84e-09

V

20924180

2.47057e-11

1.84e-09

X

17718942

2.94724e-11

1.84e-09

MtDNA

13794

0

1.05e-07

Mutation and recombination rates are in units of per bp and per generation.


Genetic Maps

ID

Year

Description

RockmanRIAIL_ce11

2009

Genetic map from recombinant inbred advanced intercross lines

RockmanRIAIL_ce11

The authors genotyped 1454 nuclear SNP markers in 236 recombinant inbred advanced intercross lines (RIAILs). The genetic distances were estimated in r/qtl using the Haldane map function, treating observed recombination fractions as though they had been observed in a backcross. The marker density is sufficiently high that the exact form of map function employed has little effect on estimated genetic distances. The tip domains of each chromosome were defined by including all markers between the chromosome ends and the first recombination breakpoint observed in the RIAILs. The genetic map corresponds to the assembly ce11 (GCA_000002985.3).

Citations


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

1

122678785

7.636e-09

4e-09

2

85426708

8.79852e-09

4e-09

3

91889043

8.00087e-09

4e-09

4

88276631

8.0523e-09

4e-09

5

88915250

9.34433e-09

4e-09

6

77573801

8.19219e-09

4e-09

7

80974532

7.29347e-09

4e-09

8

74330416

8.29131e-09

4e-09

9

61074082

9.28772e-09

4e-09

10

69331447

9.10715e-09

4e-09

11

74389097

7.63945e-09

4e-09

12

72498081

7.76106e-09

4e-09

13

63241923

8.41302e-09

4e-09

14

60966679

9.02812e-09

4e-09

15

64190966

7.85675e-09

4e-09

16

59632846

8.61406e-09

4e-09

17

64289059

9.71883e-09

4e-09

18

55844845

1.02993e-08

4e-09

19

53741614

1.04251e-08

4e-09

20

58134056

9.99097e-09

4e-09

21

50858623

1.0339e-08

4e-09

22

61439934

8.61505e-09

4e-09

23

52294480

9.12664e-09

4e-09

24

47698779

1.1146e-08

4e-09

25

51628933

1.15437e-08

4e-09

26

38964690

1.20846e-08

4e-09

27

45876710

1.12603e-08

4e-09

28

41182112

1.24636e-08

4e-09

29

41845238

1.10136e-08

4e-09

30

40214260

1.16876e-08

4e-09

31

39895921

1.13977e-08

4e-09

32

38810281

1.15559e-08

4e-09

33

31377067

1.33394e-08

4e-09

34

42124431

1.04838e-08

4e-09

35

26524999

1.42991e-08

4e-09

36

30810995

1.18752e-08

4e-09

37

30902991

1.38346e-08

4e-09

38

23914537

1.43637e-08

4e-09

X

123869142

9.50648e-09

4e-09

MT

16727

0

4e-09

Mutation and recombination rates are in units of per bp and per generation.


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


Chlamydomonas reinhardtii

ID

ChlRei

Name

Chlamydomonas reinhardtii

Common name

Chlamydomonas reinhardtii

Generation time

0.001141552511415525 (Vítová et al, 2011)

Population size

1.3999999999999998e-07 (Ness et al., 2016)

Genome

ID

Length

Recombination rate

Mutation rate

1

8033585

1.21e-10

9.74e-10

2

9223677

1.49e-10

8.62e-10

3

9219486

1.52e-10

9.5e-10

4

4091191

1.47e-10

9.66e-10

5

3500558

1.7e-10

1.17e-09

6

9023763

1.17e-10

9.12e-10

7

6421821

8.66e-11

9.14e-10

8

5033832

1.39e-10

8.98e-10

9

7956127

1.12e-10

9.17e-10

10

6576019

1.97e-10

9.27e-10

11

3826814

1.63e-10

1.03e-09

12

9730733

9.15e-11

9.55e-10

13

5206065

1.43e-10

7.56e-10

14

4157777

1.9e-10

8.96e-10

15

1922860

3.93e-10

6.91e-10

16

7783580

1.71e-10

9.59e-10

17

7188315

1.83e-10

1.05e-09

Mutation and recombination rates are in units of per bp and per generation.


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

Mean gene conversion fraction

0.8299999999999998

Range gene conversion lengths

518

ID

Length

Recombination rate

Mutation rate

2L

23513712

2.40463e-08

5.49e-09

2R

25286936

2.23459e-08

5.49e-09

3L

28110227

1.7966e-08

5.49e-09

3R

32079331

1.71642e-08

5.49e-09

4

1348131

0

5.49e-09

X

23542271

2.89651e-08

5.49e-09

Y

3667352

0

5.49e-09

mitochondrion_genome

19524

0

5.49e-09

Mutation and recombination rates are in units of per bp and per generation.


Genetic Maps

ID

Year

Description

ComeronCrossover_dm6

2012

Crossover map from meioses products of 8 lab crosses

ComeronCrossoverV2_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

ComeronCrossoverV2_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 using the available maintenance code command: python liftOver_comeron2012.py –winLen 1000 –gapThresh 1000000 –useAdjacentAvg –retainIntermediates

Citations


Demographic 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

Mutation rate

8.4e-9

Per-base per-generation mutation rate

_images/sec_catalog_dromel_models_african3epoch_1s16.png

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

Mutation rate

1.45e-9

Per-base per-generation mutation rate

_images/sec_catalog_dromel_models_outofafrica_2l06.png

Annotations

ID

Year

Description

FlyBase_BDGP6.32.51_exons

2014

FlyBase exon annotations on BDGP6

FlyBase_BDGP6.32.51_CDS

2014

FlyBase CDS annotations on BDGP6

FlyBase_BDGP6.32.51_exons

FlyBase exon annotations on BDGP6

Citations

FlyBase_BDGP6.32.51_CDS

FlyBase CDS annotations on BDGP6

Citations


Distribution of Fitness Effects (DFEs)

ID

Year

Description

Gamma_H17

2017

Deleterious Gamma DFE

LognormalPlusPositive_R16

2016

Deleterious log-normal and beneficial mixed DFE

Gamma_H17

Deleterious Gamma DFE

Citations

LognormalPlusPositive_R16

Deleterious log-normal and beneficial mixed DFE

Citations


Drosophila sechellia

ID

DroSec

Name

Drosophila sechellia

Common name

Drosophila sechellia

Generation time

0.05 (Legrand et al., 2009)

Population size

100000 (Legrand et al., 2009)

Genome

ID

Length

Recombination rate

Mutation rate

2L

24956976

2.28e-08

1.5e-09

2R

21536224

2.51e-08

1.5e-09

3L

28131630

1.88e-08

1.5e-09

3R

30464902

1.91e-08

1.5e-09

X

22909512

2.85e-08

1.5e-09

4

1277805

0

1.5e-09

Mutation and recombination rates are in units of per bp and per generation.


Escherichia coli

ID

EscCol

Name

Escherichia coli

Common name

E. coli

Generation time

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

Population size

180000000.0 (Hartl, Moriyama, and Sawyer, 1994)

Genome

Bacterial recombination with tract length range

542

ID

Length

Recombination rate

Mutation rate

Chromosome

4641652

8.9e-11

8.9e-11

Mutation and recombination rates are in units of per bp and per generation.


Gasterosteus aculeatus

ID

GasAcu

Name

Gasterosteus aculeatus

Common name

Three-spined stickleback

Generation time

2 (Liu et al., 2016)

Population size

10000.0 (Liu et al., 2016)

Genome

ID

Length

Recombination rate

Mutation rate

1

29619991

3.11e-08

3.7e-08

2

23686546

3.11e-08

3.7e-08

3

17759012

3.11e-08

3.7e-08

4

34181212

3.11e-08

3.7e-08

5

15550311

3.11e-08

3.7e-08

6

18825451

3.11e-08

3.7e-08

7

30776923

3.11e-08

3.7e-08

8

20553084

3.11e-08

3.7e-08

9

20843631

3.11e-08

3.7e-08

10

17985176

3.11e-08

3.7e-08

11

17651971

3.11e-08

3.7e-08

12

20694444

3.11e-08

3.7e-08

13

20748428

3.11e-08

3.7e-08

14

16147532

3.11e-08

3.7e-08

15

17318724

3.11e-08

3.7e-08

16

19507025

3.11e-08

3.7e-08

17

20195758

3.11e-08

3.7e-08

18

15939336

3.11e-08

3.7e-08

19

20580295

3.11e-08

3.7e-08

20

20445003

3.11e-08

3.7e-08

21

17421465

3.11e-08

3.7e-08

Y

15859692

0

3.7e-08

MT

16543

0

3.7e-08

Mutation and recombination rates are in units of per bp and per generation.


Helianthus annuus

ID

HelAnn

Name

Helianthus annuus

Common name

Helianthus annuus

Generation time

1.0 (Strasburg and Rieseberg, 2008)

Population size

673968 (Strasburg et al., 2010)

Genome

ID

Length

Recombination rate

Mutation rate

1

149502186

4e-09

6.1e-09

2

174800439

4e-09

6.1e-09

3

176490873

4e-09

6.1e-09

4

208320189

4e-09

6.1e-09

5

178169690

4e-09

6.1e-09

6

148147350

4e-09

6.1e-09

7

149542083

4e-09

6.1e-09

8

167167940

4e-09

6.1e-09

9

189665024

4e-09

6.1e-09

10

181411567

4e-09

6.1e-09

11

189830405

4e-09

6.1e-09

12

163781230

4e-09

6.1e-09

13

173487274

4e-09

6.1e-09

14

173346949

4e-09

6.1e-09

15

175671323

4e-09

6.1e-09

16

206736614

4e-09

6.1e-09

17

195042445

4e-09

6.1e-09

Mutation and recombination rates are in units of per bp and per generation.


Heliconius melpomene

ID

HelMel

Name

Heliconius melpomene

Common name

Heliconius melpomene

Generation time

0.0958904109589041 (Pardo-Diaz et al, 2012)

Population size

2111109 (Pardo-Diaz et al, 2012)

Genome

ID

Length

Recombination rate

Mutation rate

1

17206585

3.17e-08

2.9e-09

2

9045316

5.61e-08

2.9e-09

3

10541528

5.1e-08

2.9e-09

4

9662098

4.97e-08

2.9e-09

5

9908586

5.15e-08

2.9e-09

6

14054175

3.4e-08

2.9e-09

7

14308859

3.76e-08

2.9e-09

8

9320449

5.28e-08

2.9e-09

9

8708747

5.31e-08

2.9e-09

10

17965481

3.16e-08

2.9e-09

11

11759272

4.47e-08

2.9e-09

12

16327298

3.13e-08

2.9e-09

13

18127314

3.08e-08

2.9e-09

14

9174305

5.47e-08

2.9e-09

15

10235750

4.78e-08

2.9e-09

16

10083215

4.71e-08

2.9e-09

17

14773299

3.94e-08

2.9e-09

18

16803890

3.16e-08

2.9e-09

19

16399344

3.11e-08

2.9e-09

20

14871695

3.45e-08

2.9e-09

21

13359691

3.71e-08

2.9e-09

Mutation and recombination rates are in units of per bp and per generation.


Homo sapiens

ID

HomSap

Name

Homo sapiens

Common name

Human

Generation time

30 (Tremblay and Vézina, 2000)

Population size

10000 (Takahata, 1993)

Genome

ID

Length

Recombination rate

Mutation rate

1

248956422

1.15235e-08

1.29e-08

2

242193529

1.10429e-08

1.29e-08

3

198295559

1.12585e-08

1.29e-08

4

190214555

1.1482e-08

1.29e-08

5

181538259

1.12443e-08

1.29e-08

6

170805979

1.12659e-08

1.29e-08

7

159345973

1.17713e-08

1.29e-08

8

145138636

1.16049e-08

1.29e-08

9

138394717

1.21987e-08

1.29e-08

10

133797422

1.33337e-08

1.29e-08

11

135086622

1.17213e-08

1.29e-08

12

133275309

1.30981e-08

1.29e-08

13

114364328

1.3061e-08

1.29e-08

14

107043718

1.36298e-08

1.29e-08

15

101991189

1.73876e-08

1.29e-08

16

90338345

1.48315e-08

1.29e-08

17

83257441

1.55383e-08

1.29e-08

18

80373285

1.46455e-08

1.29e-08

19

58617616

1.83848e-08

1.29e-08

20

64444167

1.67886e-08

1.29e-08

21

46709983

1.72443e-08

1.29e-08

22

50818468

2.10572e-08

1.29e-08

X

156040895

1.18483e-08

1.29e-08

Y

57227415

0

1.29e-08

MT

16569

0

1.29e-08

Mutation and recombination rates are in units of per bp and per generation.


Genetic Maps

ID

Year

Description

HapMapII_GRCh37

2007

HapMap Phase II lifted over to GRCh37

HapMapII_GRCh38

2007

HapMap Phase II lifted over to GRCh37 then lifted over to GRCh38

DeCodeSexAveraged_GRCh36

2010

Sex averaged map from deCode family study

DeCodeSexAveraged_GRCh38

2010

Sex averaged map from deCode family study

PyrhoACB_GRCh38

2019

Pyrho population-specific map for ACB

PyrhoASW_GRCh38

2019

Pyrho population-specific map for ASW

PyrhoBEB_GRCh38

2019

Pyrho population-specific map for BEB

PyrhoCDX_GRCh38

2019

Pyrho population-specific map for CDX

PyrhoCEU_GRCh38

2019

Pyrho population-specific map for CEU

PyrhoCHB_GRCh38

2019

Pyrho population-specific map for CHB

PyrhoCHS_GRCh38

2019

Pyrho population-specific map for CHS

PyrhoCLM_GRCh38

2019

Pyrho population-specific map for CLM

PyrhoESN_GRCh38

2019

Pyrho population-specific map for ESN

PyrhoFIN_GRCh38

2019

Pyrho population-specific map for FIN

PyrhoGBR_GRCh38

2019

Pyrho population-specific map for GBR

PyrhoGIH_GRCh38

2019

Pyrho population-specific map for GIH

PyrhoGWD_GRCh38

2019

Pyrho population-specific map for GWD

PyrhoIBS_GRCh38

2019

Pyrho population-specific map for IBS

PyrhoITU_GRCh38

2019

Pyrho population-specific map for ITU

PyrhoJPT_GRCh38

2019

Pyrho population-specific map for JPT

PyrhoKHV_GRCh38

2019

Pyrho population-specific map for KHV

PyrhoLWK_GRCh38

2019

Pyrho population-specific map for LWK

PyrhoMSL_GRCh38

2019

Pyrho population-specific map for MSL

PyrhoMXL_GRCh38

2019

Pyrho population-specific map for MXL

PyrhoPEL_GRCh38

2019

Pyrho population-specific map for PEL

PyrhoPJL_GRCh38

2019

Pyrho population-specific map for PJL

PyrhoPUR_GRCh38

2019

Pyrho population-specific map for PUR

PyrhoSTU_GRCh38

2019

Pyrho population-specific map for STU

PyrhoTSI_GRCh38

2019

Pyrho population-specific map for TSI

PyrhoYRI_GRCh38

2019

Pyrho population-specific map for YRI

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. ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/working/20110106_recombination_hotspots

Citations

HapMapII_GRCh38

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 is lifted over to GRCh38 using liftover from the HapMap Phase II map previously lifted over to GRCh37. Liftover was performed using the liftOver_catalog.py script from stdpopsim/maintainance. Exact command used is as follows: `python <path_to_stdpopsim>/stdpopsim/maintenance/liftOver_catalog.py –species HomSap –map HapMapII_GRCh37 –chainFile <path_to_chainfiles>/chainfiles/hg19ToHg38.over.chain.gz –validationChain <path_to_chainfiles>/chainfiles/hg38ToHg19.over.chain.gz –winLen 1000 –useAdjacentAvg –retainIntermediates –gapThresh 1000000`

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

DeCodeSexAveraged_GRCh38

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. This map is further lifted over from the original GRCh36 to GRCh38 using liftover. Liftover was performed using the liftOver_catalog.py script from stdpopsim/maintainance. Exact command used is as follows: `python <path_to_stdpopsim>/stdpopsim/maintenance/liftOver_catalog.py –species HomSap –map DeCodeSexAveraged_GRCh36 –chainFile <path_to_chainfiles>/chainfiles/hg18ToHg38.over.chain.gz –winLen 1000 –useAdjacentAvg –retainIntermediates –gapThresh 1000000` Validation chain file does not exist for liftover between these two assemblies hence validation was performed manually separately.

Citations

PyrhoACB_GRCh38

This genetic map was inferred using individuals from the ACB population from Phase 3 of the 1000 Genomes Project. Rates were estimated using pyrho (https://github.com/popgenmethods/pyrho) while using population-specific population size history estimates obtained from smc++ (https://github.com/popgenmethods/smcpp). Genetic maps are only available for the 22 autosomes. See https://doi.org/10.1126/sciadv.aaw9206 for more details.

Citations

PyrhoASW_GRCh38

This genetic map was inferred using individuals from the ASW population from Phase 3 of the 1000 Genomes Project. Rates were estimated using pyrho (https://github.com/popgenmethods/pyrho) while using population-specific population size history estimates obtained from smc++ (https://github.com/popgenmethods/smcpp). Genetic maps are only available for the 22 autosomes. See https://doi.org/10.1126/sciadv.aaw9206 for more details.

Citations

PyrhoBEB_GRCh38

This genetic map was inferred using individuals from the BEB population from Phase 3 of the 1000 Genomes Project. Rates were estimated using pyrho (https://github.com/popgenmethods/pyrho) while using population-specific population size history estimates obtained from smc++ (https://github.com/popgenmethods/smcpp). Genetic maps are only available for the 22 autosomes. See https://doi.org/10.1126/sciadv.aaw9206 for more details.

Citations

PyrhoCDX_GRCh38

This genetic map was inferred using individuals from the CDX population from Phase 3 of the 1000 Genomes Project. Rates were estimated using pyrho (https://github.com/popgenmethods/pyrho) while using population-specific population size history estimates obtained from smc++ (https://github.com/popgenmethods/smcpp). Genetic maps are only available for the 22 autosomes. See https://doi.org/10.1126/sciadv.aaw9206 for more details.

Citations

PyrhoCEU_GRCh38

This genetic map was inferred using individuals from the CEU population from Phase 3 of the 1000 Genomes Project. Rates were estimated using pyrho (https://github.com/popgenmethods/pyrho) while using population-specific population size history estimates obtained from smc++ (https://github.com/popgenmethods/smcpp). Genetic maps are only available for the 22 autosomes. See https://doi.org/10.1126/sciadv.aaw9206 for more details.

Citations

PyrhoCHB_GRCh38

This genetic map was inferred using individuals from the CHB population from Phase 3 of the 1000 Genomes Project. Rates were estimated using pyrho (https://github.com/popgenmethods/pyrho) while using population-specific population size history estimates obtained from smc++ (https://github.com/popgenmethods/smcpp). Genetic maps are only available for the 22 autosomes. See https://doi.org/10.1126/sciadv.aaw9206 for more details.

Citations

PyrhoCHS_GRCh38

This genetic map was inferred using individuals from the CHS population from Phase 3 of the 1000 Genomes Project. Rates were estimated using pyrho (https://github.com/popgenmethods/pyrho) while using population-specific population size history estimates obtained from smc++ (https://github.com/popgenmethods/smcpp). Genetic maps are only available for the 22 autosomes. See https://doi.org/10.1126/sciadv.aaw9206 for more details.

Citations

PyrhoCLM_GRCh38

This genetic map was inferred using individuals from the CLM population from Phase 3 of the 1000 Genomes Project. Rates were estimated using pyrho (https://github.com/popgenmethods/pyrho) while using population-specific population size history estimates obtained from smc++ (https://github.com/popgenmethods/smcpp). Genetic maps are only available for the 22 autosomes. See https://doi.org/10.1126/sciadv.aaw9206 for more details.

Citations

PyrhoESN_GRCh38

This genetic map was inferred using individuals from the ESN population from Phase 3 of the 1000 Genomes Project. Rates were estimated using pyrho (https://github.com/popgenmethods/pyrho) while using population-specific population size history estimates obtained from smc++ (https://github.com/popgenmethods/smcpp). Genetic maps are only available for the 22 autosomes. See https://doi.org/10.1126/sciadv.aaw9206 for more details.

Citations

PyrhoFIN_GRCh38

This genetic map was inferred using individuals from the FIN population from Phase 3 of the 1000 Genomes Project. Rates were estimated using pyrho (https://github.com/popgenmethods/pyrho) while using population-specific population size history estimates obtained from smc++ (https://github.com/popgenmethods/smcpp). Genetic maps are only available for the 22 autosomes. See https://doi.org/10.1126/sciadv.aaw9206 for more details.

Citations

PyrhoGBR_GRCh38

This genetic map was inferred using individuals from the GBR population from Phase 3 of the 1000 Genomes Project. Rates were estimated using pyrho (https://github.com/popgenmethods/pyrho) while using population-specific population size history estimates obtained from smc++ (https://github.com/popgenmethods/smcpp). Genetic maps are only available for the 22 autosomes. See https://doi.org/10.1126/sciadv.aaw9206 for more details.

Citations

PyrhoGIH_GRCh38

This genetic map was inferred using individuals from the GIH population from Phase 3 of the 1000 Genomes Project. Rates were estimated using pyrho (https://github.com/popgenmethods/pyrho) while using population-specific population size history estimates obtained from smc++ (https://github.com/popgenmethods/smcpp). Genetic maps are only available for the 22 autosomes. See https://doi.org/10.1126/sciadv.aaw9206 for more details.

Citations

PyrhoGWD_GRCh38

This genetic map was inferred using individuals from the GWD population from Phase 3 of the 1000 Genomes Project. Rates were estimated using pyrho (https://github.com/popgenmethods/pyrho) while using population-specific population size history estimates obtained from smc++ (https://github.com/popgenmethods/smcpp). Genetic maps are only available for the 22 autosomes. See https://doi.org/10.1126/sciadv.aaw9206 for more details.

Citations

PyrhoIBS_GRCh38

This genetic map was inferred using individuals from the IBS population from Phase 3 of the 1000 Genomes Project. Rates were estimated using pyrho (https://github.com/popgenmethods/pyrho) while using population-specific population size history estimates obtained from smc++ (https://github.com/popgenmethods/smcpp). Genetic maps are only available for the 22 autosomes. See https://doi.org/10.1126/sciadv.aaw9206 for more details.

Citations

PyrhoITU_GRCh38

This genetic map was inferred using individuals from the ITU population from Phase 3 of the 1000 Genomes Project. Rates were estimated using pyrho (https://github.com/popgenmethods/pyrho) while using population-specific population size history estimates obtained from smc++ (https://github.com/popgenmethods/smcpp). Genetic maps are only available for the 22 autosomes. See https://doi.org/10.1126/sciadv.aaw9206 for more details.

Citations

PyrhoJPT_GRCh38

This genetic map was inferred using individuals from the JPT population from Phase 3 of the 1000 Genomes Project. Rates were estimated using pyrho (https://github.com/popgenmethods/pyrho) while using population-specific population size history estimates obtained from smc++ (https://github.com/popgenmethods/smcpp). Genetic maps are only available for the 22 autosomes. See https://doi.org/10.1126/sciadv.aaw9206 for more details.

Citations

PyrhoKHV_GRCh38

This genetic map was inferred using individuals from the KHV population from Phase 3 of the 1000 Genomes Project. Rates were estimated using pyrho (https://github.com/popgenmethods/pyrho) while using population-specific population size history estimates obtained from smc++ (https://github.com/popgenmethods/smcpp). Genetic maps are only available for the 22 autosomes. See https://doi.org/10.1126/sciadv.aaw9206 for more details.

Citations

PyrhoLWK_GRCh38

This genetic map was inferred using individuals from the LWK population from Phase 3 of the 1000 Genomes Project. Rates were estimated using pyrho (https://github.com/popgenmethods/pyrho) while using population-specific population size history estimates obtained from smc++ (https://github.com/popgenmethods/smcpp). Genetic maps are only available for the 22 autosomes. See https://doi.org/10.1126/sciadv.aaw9206 for more details.

Citations

PyrhoMSL_GRCh38

This genetic map was inferred using individuals from the MSL population from Phase 3 of the 1000 Genomes Project. Rates were estimated using pyrho (https://github.com/popgenmethods/pyrho) while using population-specific population size history estimates obtained from smc++ (https://github.com/popgenmethods/smcpp). Genetic maps are only available for the 22 autosomes. See https://doi.org/10.1126/sciadv.aaw9206 for more details.

Citations

PyrhoMXL_GRCh38

This genetic map was inferred using individuals from the MXL population from Phase 3 of the 1000 Genomes Project. Rates were estimated using pyrho (https://github.com/popgenmethods/pyrho) while using population-specific population size history estimates obtained from smc++ (https://github.com/popgenmethods/smcpp). Genetic maps are only available for the 22 autosomes. See https://doi.org/10.1126/sciadv.aaw9206 for more details.

Citations

PyrhoPEL_GRCh38

This genetic map was inferred using individuals from the PEL population from Phase 3 of the 1000 Genomes Project. Rates were estimated using pyrho (https://github.com/popgenmethods/pyrho) while using population-specific population size history estimates obtained from smc++ (https://github.com/popgenmethods/smcpp). Genetic maps are only available for the 22 autosomes. See https://doi.org/10.1126/sciadv.aaw9206 for more details.

Citations

PyrhoPJL_GRCh38

This genetic map was inferred using individuals from the PJL population from Phase 3 of the 1000 Genomes Project. Rates were estimated using pyrho (https://github.com/popgenmethods/pyrho) while using population-specific population size history estimates obtained from smc++ (https://github.com/popgenmethods/smcpp). Genetic maps are only available for the 22 autosomes. See https://doi.org/10.1126/sciadv.aaw9206 for more details.

Citations

PyrhoPUR_GRCh38

This genetic map was inferred using individuals from the PUR population from Phase 3 of the 1000 Genomes Project. Rates were estimated using pyrho (https://github.com/popgenmethods/pyrho) while using population-specific population size history estimates obtained from smc++ (https://github.com/popgenmethods/smcpp). Genetic maps are only available for the 22 autosomes. See https://doi.org/10.1126/sciadv.aaw9206 for more details.

Citations

PyrhoSTU_GRCh38

This genetic map was inferred using individuals from the STU population from Phase 3 of the 1000 Genomes Project. Rates were estimated using pyrho (https://github.com/popgenmethods/pyrho) while using population-specific population size history estimates obtained from smc++ (https://github.com/popgenmethods/smcpp). Genetic maps are only available for the 22 autosomes. See https://doi.org/10.1126/sciadv.aaw9206 for more details.

Citations

PyrhoTSI_GRCh38

This genetic map was inferred using individuals from the TSI population from Phase 3 of the 1000 Genomes Project. Rates were estimated using pyrho (https://github.com/popgenmethods/pyrho) while using population-specific population size history estimates obtained from smc++ (https://github.com/popgenmethods/smcpp). Genetic maps are only available for the 22 autosomes. See https://doi.org/10.1126/sciadv.aaw9206 for more details.

Citations

PyrhoYRI_GRCh38

This genetic map was inferred using individuals from the YRI population from Phase 3 of the 1000 Genomes Project. Rates were estimated using pyrho (https://github.com/popgenmethods/pyrho) while using population-specific population size history estimates obtained from smc++ (https://github.com/popgenmethods/smcpp). Genetic maps are only available for the 22 autosomes. See https://doi.org/10.1126/sciadv.aaw9206 for more details.

Citations


Demographic Models

ID

Description

OutOfAfricaExtendedNeandertalAdmixturePulse_3I21

Three population out-of-Africa with an extended pulse of Neandertal admixture into Europeans

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

OutOfAfrica_4J17

4 population out of Africa

Africa_1B08

African-americans population

AncientEurope_4A21

Multi-population model of ancient Europe

Three population out-of-Africa with an extended pulse of Neandertal admixture into Europeans

Demographic model of an extended admixture pulse from Neandertals into Europeans taken from Iasi et al. (2021), specifically the simple model of Supplementary Figure 1a with a gamma-shaped pulse. This model simulates 3 populations: Africans, Europeans and Neandertals with an Out-of-Africa event. The population sizes are constant with an unidirectional admixture from Neandertals into Europeans after the split between Europeans and Africans. The admixture event is modelled as an 800 generation (20 ky) long extended admixture pulse.

Details

ID

OutOfAfricaExtendedNeandertalAdmixturePulse_3I21

Description

Three population out-of-Africa with an extended pulse of Neandertal admixture into Europeans

Num populations

3

Populations

Index

ID

Sampling time

Description

0

YRI

0

1000 Genomes YRI (Yoruba)

1

CEU

0

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

2

NEA

0

Neandertals

Citations

Demographic Model parameters

Parameter Type (units)

Value

Description

Population size

10000

YRI pop. size

Population size

10000

CEU pop. size

Population size

10000

Neandertal pop. size

Total migration rate

0.029

Neandertal-CEU total migration rate over the extended admixture pulse

Time (kya)

290

Neandertal Human split

Time (kya)

73.95

Time of OOA event

Time (kya)

50

Neandertal migrations starts

Time (kya)

30

Neandertal migrations end

Generation time (yrs.)

29

Generation time

Mutation rate

2e-8

Per-base per-generation mutation rate

_images/sec_catalog_homsap_models_outofafricaextendedneandertaladmixturepulse_3i21.png

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 (Yoruba)

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.)

0.004

CEU pop. growth rate (per gen.)

Growth rate (per gen.)

0.0055

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

Mutation rate

2.35e-8

Per-base per-generation mutation rate

_images/sec_catalog_homsap_models_outofafrica_3g09.png

Two population out-of-Africa

The model is derived from the Tennessen 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

Mutation rate

2.36e-8

Per-base per-generation mutation rate

_images/sec_catalog_homsap_models_outofafrica_2t12.png

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

Mutation rate

2.36e-8

Per-base per-generation mutation rate

_images/sec_catalog_homsap_models_africa_1t12.png

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. Note that this demographic model was not inferred, and the mutation rate that Browning et al. used for simulation is smaller than used for inferring the model, so the mutation rate provided here is that from Gravel et al.

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

Mutation rate

2.36e-8

Per-base per-generation mutation rate

_images/sec_catalog_homsap_models_americanadmixture_4b11.png

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 (Yoruba)

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)

60.7

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)

1.98

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

_images/sec_catalog_homsap_models_outofafricaarchaicadmixture_5r19.png

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

7,156

Ancient pop. size

Population size

71,560

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

_images/sec_catalog_homsap_models_zigzag_1s14.png

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

Mutation rate

1.22e-8

Per-base per-generation mutation rate

_images/sec_catalog_homsap_models_ancienteurasia_9k19.png

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 (Yoruba)

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 Indonesia 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

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

Generation time (yrs.)

29

Generation time

Mutation rate

1.4e-8

Per-base per-generation mutation rate

_images/sec_catalog_homsap_models_papuansoutofafrica_10j19.png

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 (Yoruba)

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

Mutation rate

2.5e-8

Per-base per-generation mutation rate

_images/sec_catalog_homsap_models_ashksub_7g19.png

4 population out of Africa

Demographic model for a four population out-of-Africa history, taken from Jouganous et al. (2017). Parameter values were taken from table 4 in the main text. This model was fit based on joint allele frequecy spectrum (AFS) data from 1000 Genomes exomes from the YRI, CEU, CHB, and JPT poulation samples. The demography follows the previous three-populations out-of-Africa models with an additional population split in Asia leading to the Japanese (JPT) population. Parameter values were estimated with the program Moments assuming a mutation rate of 1.44e-8 and a generation time of 29 years.

Details

ID

OutOfAfrica_4J17

Description

4 population out of Africa

Num populations

4

Populations

Index

ID

Sampling time

Description

0

YRI

0

1000 Genomes YRI (Yoruba)

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

JPT

0

1000 Genomes JPT (Japanese in Tokyo, Japan)

Citations

Demographic Model parameters

Parameter Type (units)

Value

Description

Population size (individuals)

11293

A (ancestral) population size

Population size (individuals)

23721

YRI population size

Population size (individuals)

2831

B (OOA) population size

Population size (individuals)

2512

CEU (European) initial pop. size after EU/AS divergence

Population size (individuals)

1019

CHB (Asian) initial pop. size after EU/AS divergence

Population size (individuals)

4384

JPT (Japanese ) pop. size after split from CHB

Growth rate (percent per generation)

0

A growth rate

Growth rate (percent per generation)

0

YRI growth rate

Growth rate (percent per generation)

0

B growth rate

Growth rate (percent per generation)

0.16

CEU growth rate

Growth rate (percent per generation)

0.26

CHB growth rate

Growth rate (percent per generation)

1.29

JPT growth rate

Migration rate (fraction per generation)

16.8e-5

YRI-B migration rate

Migration rate (fraction per generation)

1.14e-5

YRI-CEU migration rate

Migration rate (fraction per generation)

0.56e-5

YRI-CHB migration rate

Migration rate (fraction per generation)

4.75e-5

CEU-CHB migration rate

Migration rate (fraction per generation)

3.3e-5

CHB-JPT migration rate

Epoch Time (thousands of years ago)

357

Expansion time of ancestral population

Epoch Time (thousands of years ago)

119

Time of OOA event

Epoch Time (thousands of years ago)

46

Time of CEU-CHB split

Epoch Time (thousands of years ago)

9

Time of CHB-JPT split

Generation time (years)

29

Years per generation

Mutation rate

1.44e-8

Per-base per-generation mutation rate

_images/sec_catalog_homsap_models_outofafrica_4j17.png

African-americans population

African-American two-epoch instantaneous growth model from Boyko et al 2008, fit to the synonymous SFS for the 11 of 15 African Americans showing the least European ancestry, using coalescent simulations with recombination with the maximum likelihood method of Williamson et al 2005; times were calibrated assuming 3e5 generations since human-chimp divergence and fitting the number of synonymous human-chimp differences. Mutation and recombination rates were assumed to be the same (1.8e-8).

Details

ID

Africa_1B08

Description

African-americans population

Num populations

1

Populations

Index

ID

Sampling time

Description

0

African_Americans

0

African-Americans from Boyko et al 2008

Citations

Demographic Model parameters

Parameter Type (units)

Value

Description

Population size

7,778

Ancestral pop. size

Population size

25,636

African-americans current pop. size

Epoch Time (gen.)

6,809

instantaneous expansion time of ancestral pop.

Mutation rate

1.80E-08

Per-base per-generation mutation rate

_images/sec_catalog_homsap_models_africa_1b08.png

Multi-population model of ancient Europe

Population structure that has existed over the last 45,000 years in Europe, leading to modern Europeans. The model demonstrates the divergence of a Basal European Lineages into four ancient populations; Western, Eastern and Caucasus Hunter- Gatherers and Anatolian Farmers. Migration of Anatolian farmers into Western Europe and admixture with Western Hunter-Gatherers produces the European Neolithic Farmers. In West Asia the admixture of Eastern Hunter-Gatherers and Caucasus Hunter- Gatherers leads to the formation of the Yamnaya Steppe population. The Yamnaya migrate into Western Europe to admixture with the Neolithic farmers giving rise to Bronze Age europeans. There is only an exponential growth in population size from then to the Present-day. Samples are taken at multiple point throughout history from each population.

Details

ID

AncientEurope_4A21

Description

Multi-population model of ancient Europe

Num populations

10

Populations

Index

ID

Sampling time

Description

0

OOA

1500

Basal/OOA

1

NE

600

Northern European

2

WA

800

West Asian

3

CHG

300

Caucasus Hunter-gathers

4

ANA

260

Anatolian

5

WHG

250

Western Hunter-gathers

6

EHG

250

Eastern Hunter-gathers

7

YAM

160

Yamnaya

8

NEO

180

Neolithic

9

Bronze

135

Bronze Age

Citations

Demographic Model parameters

Parameter Type (units)

Value

Description

Population size

50,000

Bronze Age pop. size

Population size

5,000

Yamnaya pop. size

Population size

10,000

Western Hunter-Gatherer pop. size

Population size

10,000

Eastern Hunter-Gatherer pop. size

Population size

50,000

Neolithic Farmer pop. size

Population size

10,000

Caucasus Hunter-Gatherer pop. size

Population size

5,000

Northern European pop. size (ancestor of WHG and EHG)

Population size

5,000

West Asian pop. size (ancestor of Anatolian Farmers and CHG)

Time (gen.)

140

Time of Yamnaya and Neolithic Farmer admixture

Time (gen.)

180

Time of EHG and CHG admixture

Time (gen.)

200

Time of Anatolian Farmer and WHG admixture

Time (gen.)

600

Time of WHG and EHG divergence

Time (gen.)

800

Time of Anatolian Farmers and CHG divergence

Time (gen.)

1500

Time of Basal European split

Growth rate (per gen.)

6.7

Growth rate from Bronze Age to present day

Time (gen.)

0

Time of present day samples

Time (gen.)

135

Time of Bronze Age samples

Time (gen.)

160

Time of Yamnaya samples

Time (gen.)

180

Time of Neolithic Farmer samples

Time (gen.)

250

Time of Western Hunter-Gatherer samples

Time (gen.)

250

Time of Eastern Hunter-Gatherer samples

Time (gen.)

260

Time of Anatolian Farmer samples

Time (gen.)

300

Time of Caucasus Hunter-Gatherer samples

Generation time (yrs.)

29

Generation time

Mutation rate

1.25e-8

Per-base per-generation mutation rate

_images/sec_catalog_homsap_models_ancienteurope_4a21.png

Annotations

ID

Year

Description

ensembl_havana_104_exons

2018

Ensembl Havana exon annotations on GRCh38

ensembl_havana_104_CDS

2018

Ensembl Havana CDS annotations on GRCh38

ensembl_havana_104_exons

Ensembl Havana exon annotations on GRCh38

Citations

ensembl_havana_104_CDS

Ensembl Havana CDS annotations on GRCh38

Citations


Distribution of Fitness Effects (DFEs)

ID

Year

Description

Gamma_K17

2017

Deleterious Gamma DFE

Gamma_H17

2017

Deleterious Gamma DFE

Gamma_K17

Deleterious Gamma DFE

Citations

Gamma_H17

Deleterious Gamma DFE

Citations


Pan troglodytes

ID

PanTro

Name

Pan troglodytes

Common name

Chimpanzee

Generation time

24.6 (Langergraber et al., 2012)

Population size

16781 (Stevison et al., 2015)

Genome

ID

Length

Recombination rate

Mutation rate

1

228573443

1.2e-08

1.6e-08

2A

111504155

1.2e-08

1.6e-08

2B

133216015

1.2e-08

1.6e-08

3

202621043

1.2e-08

1.6e-08

4

194502333

1.2e-08

1.6e-08

5

181907262

1.2e-08

1.6e-08

6

175400573

1.2e-08

1.6e-08

7

166211670

1.2e-08

1.6e-08

8

147911612

1.2e-08

1.6e-08

9

116767853

1.2e-08

1.6e-08

10

135926727

1.2e-08

1.6e-08

11

135753878

1.2e-08

1.6e-08

12

137163284

1.2e-08

1.6e-08

13

100452976

1.2e-08

1.6e-08

14

91965084

1.2e-08

1.6e-08

15

83230942

1.2e-08

1.6e-08

16

81586097

1.2e-08

1.6e-08

17

83181570

1.2e-08

1.6e-08

18

78221452

1.2e-08

1.6e-08

19

61309027

1.2e-08

1.6e-08

20

66533130

1.2e-08

1.6e-08

21

33445071

1.2e-08

1.6e-08

22

37823149

1.2e-08

1.6e-08

X

155549662

1.2e-08

1.6e-08

Y

26350515

1.2e-08

1.6e-08

Mutation and recombination rates are in units of per bp and per generation.


Demographic Models

ID

Description

BonoboGhost_4K19

Ghost admixture into bonobos

Ghost admixture into bonobos

Demographic model of ghost admixture into bonobos from Kuhlwilm et al. (2019) Supplementary Table S3 row 7. This model simulates four populations: western chimpanzees, central chimpanzees, bonobos, and a extinct ghost lineage. The ghost admixture event is modelled as a 1.7% pulse from the ghost lineage to bonobos. Migration events among western chimpanzees, central chimpanzees, and bonobos are modelled as single generation pulses. Populatio size changes are also modelled.

Details

ID

BonoboGhost_4K19

Description

Ghost admixture into bonobos

Num populations

4

Populations

Index

ID

Sampling time

Description

0

western

0

Contemporary Western Chimpanzees

1

central

0

Contemporary Central Chimpanzees

2

bonobo

0

Contemporary Bonobos

3

ghost

None

Extinct ghost lineage

Citations

Demographic Model parameters

Parameter Type (units)

Value

Description

Population size

10000

Ancestral pop. size

Population size

10000

Ghost pop. size

Population size

11600

Ancestral Bonobo-Chimpanzee pop. size

Population size

10200

Ancestral Common Chimpanzee pop. size

Population size

3700

Ancestral Bonobo pop. size

Population size

24900

Ancestral Central Chimpanzee pop. size

Population size

8000

Ancestral Western Chimpanzee pop. size

Population size

29100

Current Bonobo pop. size

Population size

65900

Current Central Chimpanzee pop. size

Population size

9200

Current Western Chimpanzee pop. size

ADMIX percentage

0.015

Amount of Central Chimpanzee in Western Chimpanzee

ADMIX percentage

0.005

Amount of Western Chimpanzee in Central Chimpanzee

ADMIX percentage

0.00125

Amount of Bonobo in Central Chimpanzee

ADMIX percentage

0.001

Amount of Central Chimpanzee in Bonobo

ADMIX percentage

0.02

Amount of Ghost pop. in Bonobo

Migration rates (x10^-7)

1

Bonobo-Common Chimpanzee migration

Time (kya)

3500

Ghost pop. split

Time (kya)

1990

Bonobo-Chimpanzee split

Time (kya)

1500

Bonobo-Common Chimpanzee migration start

Time (kya)

1200

Bonobo-Common Chimpanzee migration stop

Time (kya)

700

Western Chimpanzee split

Time (kya)

500

Ghost introgression into Bonobo

Time (kya)

155.05

Bonobo-Central Chimpanzee admixture

Time (kya)

100.1

Western-Central Chimpanzee admixture

Time (kya)

379

Central Chimpanzee resize

Time (kya)

308

Bonobo resize

Time (kya)

261

Western Chimpanzee resize

Generation time (yrs.)

25

Generation time

Mutation rate

1.2e-8

Per-base per-generation mutation rate

_images/sec_catalog_pantro_models_bonoboghost_4k19.png

Papio anubis

ID

PapAnu

Name

Papio anubis

Common name

Olive baboon

Generation time

11 (Wu et. al., 2020)

Population size

335505 (Wall et. al., 2022)

Genome

ID

Length

Recombination rate

Mutation rate

1

218172882

9.92638e-09

5.7e-09

2

193660750

9.60544e-09

5.7e-09

3

184919515

9.02238e-09

5.7e-09

4

182120902

9.82513e-09

5.7e-09

5

173900761

9.5798e-09

5.7e-09

6

167138247

1.04979e-08

5.7e-09

7

161768468

1.11888e-08

5.7e-09

8

140274886

1.10899e-08

5.7e-09

9

127591819

1.13288e-08

5.7e-09

10

126462689

1.17532e-08

5.7e-09

11

125913696

1.18403e-08

5.7e-09

12

123343450

1.0824e-08

5.7e-09

13

106849001

1.24677e-08

5.7e-09

14

106654974

1.27419e-08

5.7e-09

15

91985775

1.26084e-08

5.7e-09

16

91184193

1.47616e-08

5.7e-09

17

74525926

1.5241e-08

5.7e-09

18

72894408

1.36841e-08

5.7e-09

19

72123344

1.30374e-08

5.7e-09

20

50021108

1.6772e-08

5.7e-09

X

142711496

1.18898e-08

5.7e-09

Y

8309886

0

5.7e-09

Mutation and recombination rates are in units of per bp and per generation.


Genetic Maps

ID

Year

Description

Pyrho_PAnubis1_0

2022

Pyrho inferred genetic map for Papio Anubis

Pyrho_PAnubis1_0

These estimates were obtained from a sample of Papio Anubis individuals from the colony housed at the Southwest National Primate Research Center (SNPRC).

Citations


Demographic Models

ID

Description

SinglePopSMCpp_1W22

SMC++ estimates of N(t) for Papio Anubis individuals

SMC++ estimates of N(t) for Papio Anubis individuals

These estimates were obtained from a sample of Papio Anubis individuals from the colony housed at the Southwest National Primate Research Center (SNPRC). SMC++ was run with a subset of 36 individuals from the population.

Details

ID

SinglePopSMCpp_1W22

Description

SMC++ estimates of N(t) for Papio Anubis individuals

Num populations

1

Populations

Index

ID

Sampling time

Description

0

PAnubis_SNPRC

0

Papio Anubis population from SNPRC

Citations

Demographic Model parameters

Parameter Type (units)

Value

Description

Population size

93362

Ancestral population size

Population size

55968

Pop. size during 1st time interval

Population size

72998

Pop. size during 2nd time interval

Population size

30714

Pop. size during 3rd time interval

Population size

41841

Pop. size during 4th time interval

Population size

51822

Pop. size during 5th time interval

Population size

120758

Pop. size during 6th time interval

Population size

335505

Pop. size during 7th time interval

Time (yrs.)

2046585

Begining of 1st time interval

Time (yrs.)

1219140

Begining of 2nd time interval

Time (yrs.)

782017

Begining of 3rd time interval

Time (yrs.)

432614

Begining of 4th time interval

Time (yrs.)

165305

Begining of 5th time interval

Time (yrs.)

5101

Begining of 6th time interval

Time (yrs.)

2434

Begining of 7th time interval

Generation time (yrs.)

11

Average generation interval

Mutation rate

5.7e-9

Per-base per-generation mutation rate

_images/sec_catalog_papanu_models_singlepopsmcpp_1w22.png

Pongo abelii

ID

PonAbe

Name

Pongo abelii

Common name

Sumatran orangutan

Generation time

25 (Wich et al., 2008)

Population size

17900.0 (Locke et al., 2011)

Genome

ID

Length

Recombination rate

Mutation rate

1

227913704

5.72097e-09

1.5e-08

2A

109511694

6.74694e-09

1.5e-08

2B

129937803

6.08833e-09

1.5e-08

3

193656255

5.77615e-09

1.5e-08

4

189387572

6.06176e-09

1.5e-08

5

179185813

5.87839e-09

1.5e-08

6

169501136

5.89605e-09

1.5e-08

7

145408105

6.82979e-09

1.5e-08

8

144036388

6.34313e-09

1.5e-08

9

112206110

7.04756e-09

1.5e-08

10

132178492

6.94812e-09

1.5e-08

11

128122151

5.79185e-09

1.5e-08

12

132184051

6.04316e-09

1.5e-08

13

98475126

6.40817e-09

1.5e-08

14

88963417

6.11075e-09

1.5e-08

15

82547911

6.6315e-09

1.5e-08

16

68237989

6.76066e-09

1.5e-08

17

75914007

8.01983e-09

1.5e-08

18

75923960

6.40065e-09

1.5e-08

19

57575784

9.09647e-09

1.5e-08

20

60841859

6.31424e-09

1.5e-08

21

34683425

7.58867e-09

1.5e-08

22

35308119

9.83628e-09

1.5e-08

X

151242693

6.40288e-09

1.5e-08

MT

16499

0

1.5e-08

Mutation and recombination rates are in units of per bp and per generation.


Genetic Maps

ID

Year

Description

NaterPA_PonAbe3

2017

From Nater et al. (2017) for Pongo abelii

NaterPP_PonAbe3

2017

From Nater et al. (2017) for Pongo pygmaeus

NaterPA_PonAbe3

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. Lifted over from assembly PonAbe2 (as used in Nater et al.) to PonAbe3.

Citations

NaterPP_PonAbe3

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. Lifted over from assembly PonAbe2 (as used in Nater et al.) to PonAbe3.

Citations


Demographic 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

Migration rate (x10^-5)

1.10

Pongo abelii - Pongo pygmaeus migration rate (per gen.)

Migration rate (x10^-5)

0.67

Pongo pygmaeus - Pongo abelii migration rate (per gen.)

Epoch Time (gen.)

20,157

Species divergence time

Generation time (yrs.)

20

Generation time

Mutation rate

2e-8

Per-base per-generation mutation rate

_images/sec_catalog_ponabe_models_twospecies_2l11.png

Streptococcus agalactiae

ID

StrAga

Name

Streptococcus agalactiae

Common name

Group B Streptococcus

Generation time

0.0027397260273972603 (Savageau M.A., 1983)

Population size

140000 (Da Cunha et al, 2014)

Genome

Bacterial recombination with tract length range

120000

ID

Length

Recombination rate

Mutation rate

1

2065074

1.53e-10

1.53e-09

Mutation and recombination rates are in units of per bp and per generation.


Generic models

In addition to the species-specific models listed in this catalog, stdpopsim offers a number of generic demographic models that can be run with any species. These are described in more detail in the API. Simulations using these generic models must be run via the Python interface; see our Python tutorial to learn how to do this.