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 (Genome object)?

  2. Which recombination/genetic map (GeneticMap object)?

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

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

  5. which annotation track (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)

Ploidy:

2

Population size:

1000000.0 (Crawford et al., 2017)

Genome

Genome assembly name:

AaegL5

ID

Ploidy

Length

Recombination rate

Mutation rate

1

2

310827022

3.06e-09

3.5e-09

2

2

474425716

2.49e-09

3.5e-09

3

2

409777670

2.91e-09

3.5e-09

MT

1

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)

Ploidy:

2

Population size:

156000 (Guo et al., 2021)

Genome

Genome assembly name:

ASM874695v1

ID

Ploidy

Length

Recombination rate

Mutation rate

1

2

208326429

1.52e-08

4.83e-09

2

2

162939446

1.39e-08

4.83e-09

3

2

119723720

9.38e-09

4.83e-09

4

2

77626585

1.2e-08

4.83e-09

5

2

64988622

1.21e-08

4.83e-09

6

2

39543408

3.04e-08

4.83e-09

7

2

37812880

2.59e-08

4.83e-09

8

2

33348632

1.28e-08

4.83e-09

9

2

26742597

1.34e-08

4.83e-09

10

2

22933227

2.5e-08

4.83e-09

11

2

22193879

1.5e-08

4.83e-09

12

2

22338721

3.15e-08

4.83e-09

13

2

21714986

1.41e-08

4.83e-09

14

2

20320564

8.61e-09

4.83e-09

15

2

18227546

3.79e-09

4.83e-09

16

2

16053328

3.86e-09

4.83e-09

17

2

15319648

3.13e-09

4.83e-09

18

2

13333155

1.58e-09

4.83e-09

19

2

12198306

1.43e-08

4.83e-09

20

2

12091001

1.43e-08

4.83e-09

21

2

8553409

1.43e-08

4.83e-09

22

2

16160689

1.43e-08

4.83e-09

23

2

7977799

1.43e-08

4.83e-09

24

2

7737077

1.43e-08

4.83e-09

25

2

7574731

1.43e-08

4.83e-09

26

2

6918023

1.43e-08

4.83e-09

27

2

6270716

1.43e-08

4.83e-09

28

2

5960150

1.43e-08

4.83e-09

29

2

1456683

1.43e-08

4.83e-09

30

2

1872559

1.43e-08

4.83e-09

Z

2

81233375

1.43e-08

4.83e-09

31

2

2637124

1.43e-08

4.83e-09

32

2

3473573

1.43e-08

4.83e-09

33

2

2151773

1.43e-08

4.83e-09

34

2

7214884

1.43e-08

4.83e-09

35

2

5548691

1.43e-08

4.83e-09

36

2

3997205

1.43e-08

4.83e-09

37

2

3148754

1.43e-08

4.83e-09

38

2

2836164

1.43e-08

4.83e-09

39

2

2018729

1.43e-08

4.83e-09

40

2

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.)

1.72

Black-Mallard migration rate

Migration rate (x10^-6 per gen.)

1.72

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)

Ploidy:

2

Population size:

3050000.0 (Pombi et al., 2019)

Genome

Genome assembly name:

AnoCar2.0

ID

Ploidy

Length

Recombination rate

Mutation rate

1

2

263920458

1.59e-08

2.1e-10

2

2

199619895

1.59e-08

2.1e-10

3

2

204416410

1.59e-08

2.1e-10

4

2

156502444

1.59e-08

2.1e-10

5

2

150641573

1.59e-08

2.1e-10

6

2

80741955

1.59e-08

2.1e-10

LGa

2

7025928

1.59e-08

2.1e-10

LGb

2

3271537

1.59e-08

2.1e-10

LGc

2

9478905

1.59e-08

2.1e-10

LGd

2

1094478

1.59e-08

2.1e-10

LGf

2

4257874

1.59e-08

2.1e-10

LGg

2

424765

1.59e-08

2.1e-10

LGh

2

248369

1.59e-08

2.1e-10

MT

1

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)

Ploidy:

2

Population size:

1000000.0 (Ag1000G Consortium, 2017)

Genome

Genome assembly name:

AgamP4

ID

Ploidy

Length

Recombination rate

Mutation rate

2L

2

49364325

1.3e-08

3.5e-09

2R

2

61545105

1.3e-08

3.5e-09

3L

2

41963435

1.3e-08

3.5e-09

3R

2

53200684

1.6e-08

3.5e-09

X

2

24393108

2.04e-08

3.5e-09

Mt

1

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)

Ploidy:

2

Population size:

200000.0 (Wallberg et al., 2014)

Genome

Genome assembly name:

Amel_HAv3.1

ID

Ploidy

Length

Recombination rate

Mutation rate

CM009931.2

2

27754200

2.39e-07

3.4e-09

CM009932.2

2

16089512

2.46e-07

3.4e-09

CM009933.2

2

13619445

2.41e-07

3.4e-09

CM009934.2

2

13404451

2.76e-07

3.4e-09

CM009935.2

2

13896941

2.14e-07

3.4e-09

CM009936.2

2

17789102

2.12e-07

3.4e-09

CM009937.2

2

14198698

2.34e-07

3.4e-09

CM009938.2

2

12717210

2.09e-07

3.4e-09

CM009939.2

2

12354651

2.46e-07

3.4e-09

CM009940.2

2

12360052

2.48e-07

3.4e-09

CM009941.2

2

16352600

2.03e-07

3.4e-09

CM009942.2

2

11514234

2.12e-07

3.4e-09

CM009943.2

2

11279722

2.34e-07

3.4e-09

CM009944.2

2

10670842

2.46e-07

3.4e-09

CM009945.2

2

9534514

2.21e-07

3.4e-09

CM009946.2

2

7238532

2.28e-07

3.4e-09

CM009947.2

1

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)

Ploidy:

2

Population size:

10000 (1001GenomesConsortium, 2016)

Genome

Genome assembly name:

TAIR10

ID

Ploidy

Length

Recombination rate

Mutation rate

1

2

30427671

8.06452e-10

7e-09

2

2

19698289

8.06452e-10

7e-09

3

2

23459830

8.06452e-10

7e-09

4

2

18585056

8.06452e-10

7e-09

5

2

26975502

8.06452e-10

7e-09

Mt

1

366924

0

7e-09

Pt

1

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

GammaAdditive_H18

2018

Deleterious additive Gamma DFE

GammaAdditive_H18

Deleterious additive Gamma DFE

Additive, deleterious DFE from Huber et al. (2018) for Arabidopsis, estimated from the SFS of A. lyrata as a Gamma distribution of deleterious effects. Parameters are from Supplementary Table 4, the “genome-wide, additive-only model for A. lyrata”. The DFE for A. lyrata (rather than A. thaliana) is provided due to challenges with simulating selfing.

Citations

DFE parameters

Proportion of mutations

Distribution type

Parameters

Dominance

100.0%

Gamma

mean = 0.000, shape = 0.270

h = 0.500

Bos taurus

ID:

BosTau

Name:

Bos taurus

Common name:

Cattle

Generation time:

5 (MacLeod et al., 2013)

Ploidy:

2

Population size:

62000 (MacLeod et al., 2013)

Genome

Genome assembly name:

ARS-UCD1.3

ID

Ploidy

Length

Recombination rate

Mutation rate

1

2

158534110

9.26e-09

1.2e-08

2

2

136231102

9.26e-09

1.2e-08

3

2

121005158

9.26e-09

1.2e-08

4

2

120000601

9.26e-09

1.2e-08

5

2

120089316

9.26e-09

1.2e-08

6

2

117806340

9.26e-09

1.2e-08

7

2

110682743

9.26e-09

1.2e-08

8

2

113319770

9.26e-09

1.2e-08

9

2

105454467

9.26e-09

1.2e-08

10

2

103308737

9.26e-09

1.2e-08

11

2

106982474

9.26e-09

1.2e-08

12

2

87216183

9.26e-09

1.2e-08

13

2

83472345

9.26e-09

1.2e-08

14

2

82403003

9.26e-09

1.2e-08

15

2

85007780

9.26e-09

1.2e-08

16

2

81013979

9.26e-09

1.2e-08

17

2

73167244

9.26e-09

1.2e-08

18

2

65820629

9.26e-09

1.2e-08

19

2

63449741

9.26e-09

1.2e-08

20

2

71974595

9.26e-09

1.2e-08

21

2

69862954

9.26e-09

1.2e-08

22

2

60773035

9.26e-09

1.2e-08

23

2

52498615

9.26e-09

1.2e-08

24

2

62317253

9.26e-09

1.2e-08

25

2

42350435

9.26e-09

1.2e-08

26

2

51992305

9.26e-09

1.2e-08

27

2

45612108

9.26e-09

1.2e-08

28

2

45940150

9.26e-09

1.2e-08

29

2

51098607

9.26e-09

1.2e-08

X

2

139009144

9.26e-09

1.2e-08

MT

1

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 model for Holstein-Friesian cattle (MacLeod et al., 2013).

HolsteinFriesian_1B16

Piecewise size model for Holstein-Friesian cattle (Boitard et al., 2016).

Fleckvieh_1B16

Piecewise size model for Fleckvieh cattle (Boitard et al., 2016).

Jersey_1B16

Piecewise size model for Jersey cattle (Boitard et al., 2016).

Angus_1B16

Piecewise size model for Angus cattle (Boitard et al., 2016).

Piecewise size model for Holstein-Friesian cattle (MacLeod et al., 2013).

The piecewise-constant population size model of Holstein-Friesian cattle from MacLeod et al. (2013). Effective population sizes were estimated from runs of homozygosity observed in a single individual, using the following assumptions: a generation interval of 5 years (page 2213), a mutation rate of 0.94e-8 (pages 2221 and 2215), and a recombination rate of 1e-8 (pages 2215 and 2221). Effective population sizes are given in Figure 4A and Table S1. The single individual is the bull Walkway Chief Mark. Mark and his father are two of the most influentiual sires in this breed - see Larkin et al. (2012) http://www.pnas.org/cgi/doi/10.1073/pnas.1114546109.

Details

ID:

HolsteinFriesian_1M13

Description:

Piecewise size model for Holstein-Friesian cattle (MacLeod et al., 2013).

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

Recombination rate

1.0e-0

Per-base per-generation recombination rate
_images/sec_catalog_bostau_models_holsteinfriesian_1m13.png

Piecewise size model for Holstein-Friesian cattle (Boitard et al., 2016).

The piecewise-constant population size model of Holstein-Friesian cattle from Boitard et al. (2016). Effective population sizes were estimated using Approximate Bayesian Computation with allele frequency spectrum and linkage-disequlibrium statistics (both on SNPs with minor allele frequency above 0.2) observed in 25 individuals, using the following assumptions: a generation interval of 5 years (page 10), a mutation rate of 1e-8 (pages 8 and 22), and a recombination rate of 3.66e-9 (page 15). Effective population sizes are given in Figure 6, with exact values provided by the lead author in personal communication. The 25 individuals’ genomes were obtained from the 1000 bull genomes Run 2 (of which 129 were Holstein-Friesian; the authors chose 52 from Australia to get a homogeneous sub-population, kept the least inbred and unrelated samples, and from these randomly selected 25).

Details

ID:

HolsteinFriesian_1B16

Description:

Piecewise size model for Holstein-Friesian cattle (Boitard et al., 2016).

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

31,652

Ancestral population size

Population size

65,485

Pop. size during 1st time interval

Population size

86,206

Pop. size during 2nd time interval

Population size

79,079

Pop. size during 3rd time interval

Population size

71,209

Pop. size during 4th time interval

Population size

72,841

Pop. size during 5th time interval

Population size

63,092

Pop. size during 6th time interval

Population size

52,882

Pop. size during 7th time interval

Population size

50,726

Pop. size during 8th time interval

Population size

36,512

Pop. size during 9th time interval

Population size

27,155

Pop. size during 10th time interval

Population size

23,783

Pop. size during 11th time interval

Population size

20,159

Pop. size during 12th time interval

Population size

15,602

Pop. size during 13th time interval

Population size

11,367

Pop. size during 14th time interval

Population size

6,908

Pop. size during 15th time interval

Population size

3,892

Pop. size during 16th time interval

Population size

1,815

Pop. size during 17th time interval

Population size

1,320

Pop. size during 18th time interval

Population size

1,076

Pop. size during 19th time interval

Population size

793

Pop. size during 20th time interval

Time (gen.)

129,999

Begining of 1st time interval

Time (gen.)

83,043

Begining of 2nd time interval

Time (gen.)

53,045

Begining of 3rd time interval

Time (gen.)

33,881

Begining of 4th time interval

Time (gen.)

21,638

Begining of 5th time interval

Time (gen.)

13,817

Begining of 6th time interval

Time (gen.)

8,821

Begining of 7th time interval

Time (gen.)

5,629

Begining of 8th time interval

Time (gen.)

3,590

Begining of 9th time interval

Time (gen.)

2,287

Begining of 10th time interval

Time (gen.)

1,455

Begining of 11th time interval

Time (gen.)

923

Begining of 12th time interval

Time (gen.)

584

Begining of 13th time interval

Time (gen.)

367

Begining of 14th time interval

Time (gen.)

228

Begining of 15th time interval

Time (gen.)

139

Begining of 16th time interval

Time (gen.)

83

Begining of 17th time interval

Time (gen.)

47

Begining of 18th time interval

Time (gen.)

24

Begining of 19th time interval

Time (gen.)

9

Begining of 20th time interval

Generation time (yrs.)

5

Generation time

Mutation rate

1e-8

Per-base per-generation mutation rate

Recombination rate

3.66e-9

Per-base per-generation recombination rate
_images/sec_catalog_bostau_models_holsteinfriesian_1b16.png

Piecewise size model for Fleckvieh cattle (Boitard et al., 2016).

The piecewise-constant population size model of Fleckvieh cattle from Boitard et al. (2016). Effective population sizes were estimated using Approximate Bayesian Computation with allele frequency spectrum and linkage-disequlibrium statistics (both on SNPs with minor allele frequency above 0.2) observed in 25 individuals, using the following assumptions: a generation interval of 5 years (page 10), a mutation rate of 1e-8 (pages 8 and 22), and a recombination rate of 3.89e-9 (page 15). Effective population sizes are given in Figure 6, with exact values provided by the lead author in personal communication. The 25 individuals’ genomes were obtained from the 1000 bull genomes Run 2 (of which 43 were Fleckvieh; the authors kept the least inbred and unrelated samples, and from these randomly selected 25).

Details

ID:

Fleckvieh_1B16

Description:

Piecewise size model for Fleckvieh cattle (Boitard et al., 2016).

Num populations:

1

Populations

Index

ID

Sampling time

Description

0

Fleckvieh

0

Fleckvieh

Citations

Demographic Model parameters

Parameter Type (units)

Value

Description

Population size

31,131

Ancestral population size

Population size

70,789

Pop. size during 1st time interval

Population size

91,228

Pop. size during 2nd time interval

Population size

85,607

Pop. size during 3rd time interval

Population size

82,448

Pop. size during 4th time interval

Population size

82,844

Pop. size during 5th time interval

Population size

72,920

Pop. size during 6th time interval

Population size

61,479

Pop. size during 7th time interval

Population size

54,358

Pop. size during 8th time interval

Population size

38,069

Pop. size during 9th time interval

Population size

28,547

Pop. size during 10th time interval

Population size

20,963

Pop. size during 11th time interval

Population size

18,176

Pop. size during 12th time interval

Population size

13,604

Pop. size during 13th time interval

Population size

10,546

Pop. size during 14th time interval

Population size

7,414

Pop. size during 15th time interval

Population size

5,689

Pop. size during 16th time interval

Population size

4,184

Pop. size during 17th time interval

Population size

3,395

Pop. size during 18th time interval

Population size

2,812

Pop. size during 19th time interval

Population size

2,227

Pop. size during 20th time interval

Time (gen.)

129,999

Begining of 1st time interval

Time (gen.)

83,043

Begining of 2nd time interval

Time (gen.)

53,045

Begining of 3rd time interval

Time (gen.)

33,881

Begining of 4th time interval

Time (gen.)

21,638

Begining of 5th time interval

Time (gen.)

13,817

Begining of 6th time interval

Time (gen.)

8,821

Begining of 7th time interval

Time (gen.)

5,629

Begining of 8th time interval

Time (gen.)

3,590

Begining of 9th time interval

Time (gen.)

2,287

Begining of 10th time interval

Time (gen.)

1,455

Begining of 11th time interval

Time (gen.)

923

Begining of 12th time interval

Time (gen.)

584

Begining of 13th time interval

Time (gen.)

367

Begining of 14th time interval

Time (gen.)

228

Begining of 15th time interval

Time (gen.)

139

Begining of 16th time interval

Time (gen.)

83

Begining of 17th time interval

Time (gen.)

47

Begining of 18th time interval

Time (gen.)

24

Begining of 19th time interval

Time (gen.)

9

Begining of 20th time interval

Generation time (yrs.)

5

Generation time

Mutation rate

1e-8

Per-base per-generation mutation rate

Recombination rate

3.89e-9

Per-base per-generation recombination rate
_images/sec_catalog_bostau_models_fleckvieh_1b16.png

Piecewise size model for Jersey cattle (Boitard et al., 2016).

The piecewise-constant population size model of Jersey cattle from Boitard et al. (2016). Effective population sizes were estimated using Approximate Bayesian Computation with allele frequency spectrum and linkage-disequlibrium statistics (both on SNPs with minor allele frequency above 0.2) observed in 15 individuals, using the following assumptions: a generation interval of 5 years (page 10), a mutation rate of 1e-8 (pages 8 and 22), and a recombination rate of 4.58e-9 (page 15). Effective population sizes are given in Figure 6, with exact values provided by the lead author in personal communication. The 15 individuals’ genomes were obtained from the 1000 bull genomes Run 2.

Details

ID:

Jersey_1B16

Description:

Piecewise size model for Jersey cattle (Boitard et al., 2016).

Num populations:

1

Populations

Index

ID

Sampling time

Description

0

Jersey

0

Jersey

Citations

Demographic Model parameters

Parameter Type (units)

Value

Description

Population size

30,275

Ancestral population size

Population size

53,856

Pop. size during 1st time interval

Population size

76,905

Pop. size during 2nd time interval

Population size

67,505

Pop. size during 3rd time interval

Population size

75,739

Pop. size during 4th time interval

Population size

77,971

Pop. size during 5th time interval

Population size

78,608

Pop. size during 6th time interval

Population size

63,277

Pop. size during 7th time interval

Population size

51,777

Pop. size during 8th time interval

Population size

33,713

Pop. size during 9th time interval

Population size

22,549

Pop. size during 10th time interval

Population size

13,960

Pop. size during 11th time interval

Population size

13,460

Pop. size during 12th time interval

Population size

10,474

Pop. size during 13th time interval

Population size

8,106

Pop. size during 14th time interval

Population size

5,766

Pop. size during 15th time interval

Population size

3,704

Pop. size during 16th time interval

Population size

1,640

Pop. size during 17th time interval

Population size

947

Pop. size during 18th time interval

Population size

561

Pop. size during 19th time interval

Population size

388

Pop. size during 20th time interval

Time (gen.)

129,999

Begining of 1st time interval

Time (gen.)

83,043

Begining of 2nd time interval

Time (gen.)

53,045

Begining of 3rd time interval

Time (gen.)

33,881

Begining of 4th time interval

Time (gen.)

21,638

Begining of 5th time interval

Time (gen.)

13,817

Begining of 6th time interval

Time (gen.)

8,821

Begining of 7th time interval

Time (gen.)

5,629

Begining of 8th time interval

Time (gen.)

3,590

Begining of 9th time interval

Time (gen.)

2,287

Begining of 10th time interval

Time (gen.)

1,455

Begining of 11th time interval

Time (gen.)

923

Begining of 12th time interval

Time (gen.)

584

Begining of 13th time interval

Time (gen.)

367

Begining of 14th time interval

Time (gen.)

228

Begining of 15th time interval

Time (gen.)

139

Begining of 16th time interval

Time (gen.)

83

Begining of 17th time interval

Time (gen.)

47

Begining of 18th time interval

Time (gen.)

24

Begining of 19th time interval

Time (gen.)

9

Begining of 20th time interval

Generation time (yrs.)

5

Generation time

Mutation rate

1e-8

Per-base per-generation mutation rate

Recombination rate

4.58e-9

Per-base per-generation recombination rate
_images/sec_catalog_bostau_models_jersey_1b16.png

Piecewise size model for Angus cattle (Boitard et al., 2016).

The piecewise-constant population size model of Angus cattle from Boitard et al. (2016). Effective population sizes were estimated using Approximate Bayesian Computation with allele frequency spectrum and linkage-disequlibrium statistics (both on SNPs with minor allele frequency above 0.2) observed in 15 individuals, using the following assumptions: a generation interval of 5 years (page 10), a mutation rate of 1e-8 (pages 8 and 22), and a recombination rate of 5.00e-9 (page 15). Effective population sizes are given in Figure 6, with exact values provided by the lead author in personal communication. The 25 individuals’ genomes were obtained from the 1000 bull genomes Run 2 (of which 47 were Angus; the authors kept the least inbred and unrelated samples, and from these randomly selected 25).

Details

ID:

Angus_1B16

Description:

Piecewise size model for Angus cattle (Boitard et al., 2016).

Num populations:

1

Populations

Index

ID

Sampling time

Description

0

Angus

0

Angus

Citations

Demographic Model parameters

Parameter Type (units)

Value

Description

Population size

33,810

Ancestral population size

Population size

56,981

Pop. size during 1st time interval

Population size

85,228

Pop. size during 2nd time interval

Population size

87,426

Pop. size during 3rd time interval

Population size

83,576

Pop. size during 4th time interval

Population size

80,651

Pop. size during 5th time interval

Population size

69,328

Pop. size during 6th time interval

Population size

56,775

Pop. size during 7th time interval

Population size

47,892

Pop. size during 8th time interval

Population size

35,998

Pop. size during 9th time interval

Population size

24,300

Pop. size during 10th time interval

Population size

16,441

Pop. size during 11th time interval

Population size

12,042

Pop. size during 12th time interval

Population size

10,827

Pop. size during 13th time interval

Population size

6,837

Pop. size during 14th time interval

Population size

4,836

Pop. size during 15th time interval

Population size

2,558

Pop. size during 16th time interval

Population size

1,224

Pop. size during 17th time interval

Population size

709

Pop. size during 18th time interval

Population size

412

Pop. size during 19th time interval

Population size

291

Pop. size during 20th time interval

Time (gen.)

129,999

Begining of 1st time interval

Time (gen.)

83,043

Begining of 2nd time interval

Time (gen.)

53,045

Begining of 3rd time interval

Time (gen.)

33,881

Begining of 4th time interval

Time (gen.)

21,638

Begining of 5th time interval

Time (gen.)

13,817

Begining of 6th time interval

Time (gen.)

8,821

Begining of 7th time interval

Time (gen.)

5,629

Begining of 8th time interval

Time (gen.)

3,590

Begining of 9th time interval

Time (gen.)

2,287

Begining of 10th time interval

Time (gen.)

1,455

Begining of 11th time interval

Time (gen.)

923

Begining of 12th time interval

Time (gen.)

584

Begining of 13th time interval

Time (gen.)

367

Begining of 14th time interval

Time (gen.)

228

Begining of 15th time interval

Time (gen.)

139

Begining of 16th time interval

Time (gen.)

83

Begining of 17th time interval

Time (gen.)

47

Begining of 18th time interval

Time (gen.)

24

Begining of 19th time interval

Time (gen.)

9

Begining of 20th time interval

Generation time (yrs.)

5

Generation time

Mutation rate

1e-8

Per-base per-generation mutation rate

Recombination rate

5.00e-9

Per-base per-generation recombination rate
_images/sec_catalog_bostau_models_angus_1b16.png

Caenorhabditis elegans

ID:

CaeEle

Name:

Caenorhabditis elegans

Common name:

C. elegans

Generation time:

0.01 (Frézal & Félix, 2015)

Ploidy:

2

Population size:

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

Genome

Genome assembly name:

WBcel235

ID

Ploidy

Length

Recombination rate

Mutation rate

I

2

15072434

3.12163e-11

1.84e-09

II

2

15279421

3.52929e-11

1.84e-09

III

2

13783801

3.9066e-11

1.84e-09

IV

2

17493829

2.7121e-11

1.84e-09

V

2

20924180

2.47057e-11

1.84e-09

X

2

17718942

2.94724e-11

1.84e-09

MtDNA

1

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

Ploidy:

2

Population size:

13000 (Lindblad-Toh et al., 2005)

Genome

Genome assembly name:

CanFam3.1

ID

Ploidy

Length

Recombination rate

Mutation rate

1

2

122678785

7.636e-09

4e-09

2

2

85426708

8.79852e-09

4e-09

3

2

91889043

8.00087e-09

4e-09

4

2

88276631

8.0523e-09

4e-09

5

2

88915250

9.34433e-09

4e-09

6

2

77573801

8.19219e-09

4e-09

7

2

80974532

7.29347e-09

4e-09

8

2

74330416

8.29131e-09

4e-09

9

2

61074082

9.28772e-09

4e-09

10

2

69331447

9.10715e-09

4e-09

11

2

74389097

7.63945e-09

4e-09

12

2

72498081

7.76106e-09

4e-09

13

2

63241923

8.41302e-09

4e-09

14

2

60966679

9.02812e-09

4e-09

15

2

64190966

7.85675e-09

4e-09

16

2

59632846

8.61406e-09

4e-09

17

2

64289059

9.71883e-09

4e-09

18

2

55844845

1.02993e-08

4e-09

19

2

53741614

1.04251e-08

4e-09

20

2

58134056

9.99097e-09

4e-09

21

2

50858623

1.0339e-08

4e-09

22

2

61439934

8.61505e-09

4e-09

23

2

52294480

9.12664e-09

4e-09

24

2

47698779

1.1146e-08

4e-09

25

2

51628933

1.15437e-08

4e-09

26

2

38964690

1.20846e-08

4e-09

27

2

45876710

1.12603e-08

4e-09

28

2

41182112

1.24636e-08

4e-09

29

2

41845238

1.10136e-08

4e-09

30

2

40214260

1.16876e-08

4e-09

31

2

39895921

1.13977e-08

4e-09

32

2

38810281

1.15559e-08

4e-09

33

2

31377067

1.33394e-08

4e-09

34

2

42124431

1.04838e-08

4e-09

35

2

26524999

1.42991e-08

4e-09

36

2

30810995

1.18752e-08

4e-09

37

2

30902991

1.38346e-08

4e-09

38

2

23914537

1.43637e-08

4e-09

X

2

123869142

9.50648e-09

4e-09

MT

1

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

Demographic Models

ID

Description

EarlyWolfAdmixture_6F14

Dog domestication and admixture with wolf (Freedman et al., 2014)

Dog domestication and admixture with wolf (Freedman et al., 2014)

Demographic model of dog domestication with the Boxer reference genome, two basal dog breeds, three wolves, and a golden jackal (outgroup) from Freedman et al. (2014). The topology was based on the neighbor-joining tree constructed from genome-wide pairwise divergence (Figure 5A). The parameters of the model were inferred using the Generalized Phylogenetic Coalescent Sampler (G-PhoCS) on neutral autosomal loci from whole genome sequences. Model parameters were calibrated with a generation interval of 3 years (page 3) and a mutation rate of 1e-8 (page 3). Estimated (calibrated) effective population sizes, divergence times, and migration rates are given in Table S12. Migration is constant continuous geneflow from the start and end times of the two populations that define it (section S9.2.3 in S9). While Boxer reference genome was used, no Boxer-specific parameters were estimated in the model, hence Boxer was removed from this model implementation. Thence the ancestral Basenji population with its specific Ne is for the Ancestral (Boxer, Basenji) population.

Details

ID:

EarlyWolfAdmixture_6F14

Description:

Dog domestication and admixture with wolf (Freedman et al., 2014)

Num populations:

11

Populations

Index

ID

Sampling time

Description

0

BSJ

None

Basenji

1

DNG

None

Dingo

2

CHW

None

Chinese wolf

3

ISW

None

Israeli wolf

4

CRW

None

Croatian wolf

5

GLJ

None

Golden jackal

6

ancDOG

12795

Ancestral ((Boxer, Basenji), Dingo)

7

ancWLF1

13389

Ancestral (Israeli, Croatian) wolf

8

ancWLF

13455

Ancestral ((Israeli, Croatian), Chinese) wolf

9

ancDW

14874

Ancestral (dog, wolf)

10

root

398262

Ancestral ((dog, wolf), golden jackal) root

Citations

Demographic Model parameters

Parameter Type (units)

Value

Description

Population size

2,639

Basenji pop. size

Population size

1,914

Dingo pop. size

Population size

26,092

Israeli wolf pop. size

Population size

11,427

Croatian wolf pop. size

Population size

5,426

Chinese wolf pop. size

Population size

19,446

Golden jackal pop. size

Population size

793

Ancestral (Boxer, Basenji) pop. size

Population size

1,999

Ancestral ((Boxer, Basenji), Dingo) pop. size

Population size

1,393

Ancestral (Israeli, Croatian) wolf pop. size

Population size

12,627

Ancestral ((Israeli, Croatian), Chinese) wolf pop. size

Population size

44,993

Ancestral (dog, wolf) pop. size

Population size

18,169

Ancestral ((dog, wolf), golden jackal)root pop. size

Migration rate

0.18

Israeli wolf -> Basenji migration rate

Migration rate

0.07

Basenji -> Israeli wolf migration rate

Migration rate

0.03

Chinese wolf -> Dingo migration rate

Migration rate

0.04

Dingo -> Chinese wolf migration rate

Migration rate

0.00

Golden jackal -> Israeli wolf migration rate

Migration rate

0.05

Israeli wolf -> Golden jackal migration rate

Migration rate

0.02

Golden jackal -> Ancestral (dog, wolf) migration rate

Migration rate

0.99

Ancestral (dog, wolf) -> Golden jackal migration rate

Time (gen.)

12,795

Ancestral ((Boxer, Basenji), Dingo) split time

Time (gen.)

13,389

Ancestral (Israeli, Croatian) wolf split time

Time (gen.)

13,455

Ancestral ((Israeli, Croatian), Chinese) wolf split time

Time (gen.)

14,874

Ancestral (dog, wolf) split time

Time (gen.)

398,262

Ancestral ((dog, wolf), golden jackal) split time

Generation time (yrs.)

3

Generation time

Mutation rate

1e-8

Mutation rate
_images/sec_catalog_canfam_models_earlywolfadmixture_6f14.png

Chlamydomonas reinhardtii

ID:

ChlRei

Name:

Chlamydomonas reinhardtii

Common name:

Chlamydomonas reinhardtii

Generation time:

0.001141552511415525 (Vítová et al, 2011)

Ploidy:

1

Population size:

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

Genome

Genome assembly name:

Chlamydomonas_reinhardtii_v5.5

ID

Ploidy

Length

Recombination rate

Mutation rate

1

1

8033585

1.21e-10

9.74e-10

2

1

9223677

1.49e-10

8.62e-10

3

1

9219486

1.52e-10

9.5e-10

4

1

4091191

1.47e-10

9.66e-10

5

1

3500558

1.7e-10

1.17e-09

6

1

9023763

1.17e-10

9.12e-10

7

1

6421821

8.66e-11

9.14e-10

8

1

5033832

1.39e-10

8.98e-10

9

1

7956127

1.12e-10

9.17e-10

10

1

6576019

1.97e-10

9.27e-10

11

1

3826814

1.63e-10

1.03e-09

12

1

9730733

9.15e-11

9.55e-10

13

1

5206065

1.43e-10

7.56e-10

14

1

4157777

1.9e-10

8.96e-10

15

1

1922860

3.93e-10

6.91e-10

16

1

7783580

1.71e-10

9.59e-10

17

1

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)

Ploidy:

2

Population size:

1720600 (Li et al., 2006)

Genome

Genome assembly name:

BDGP6.46

Mean gene conversion fraction:

0.8299999999999998

Range gene conversion lengths:

518

ID

Ploidy

Length

Recombination rate

Mutation rate

2L

2

23513712

2.40463e-08

5.49e-09

2R

2

25286936

2.23459e-08

5.49e-09

3L

2

28110227

1.7966e-08

5.49e-09

3R

2

32079331

1.71642e-08

5.49e-09

4

2

1348131

0

5.49e-09

X

2

23542271

2.89651e-08

5.49e-09

Y

1

3667352

0

5.49e-09

mitochondrion_genome

1

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

GammaPos_H17

2021

Deleterious Gamma DFE with fixed-s beneficials

LognormalPlusPositive_R16

2016

Deleterious log-normal and beneficial mixed DFE

Gamma_H17

Deleterious Gamma DFE

Deleterious, gamma-distributed DFE estimated from a D. melanogaster SFS in Huber et al. (2017). DFE parameters are based on the “full” model described in Table S2, for which singletons were excluded and a recent mutation rate estimate is used (3e-9, Keightley 2014).

Citations

DFE parameters

Proportion of mutations

Distribution type

Parameters

Dominance

26.0%

Fixed s

s = 0.000

h = 0.500

74.0%

Gamma

mean = -0.001, shape = 0.330

h = 0.500

GammaPos_H17

Deleterious Gamma DFE with fixed-s beneficials

The DFE estimated from D.melanogaster-simulans data estimated in Zhen et al (2021, https://dx.doi.org/10.1101/gr.256636.119). This uses the demographic model and deleterious-only DFE from Huber et al (2017), and then the number of nonsynonymous differences to simulans to estimate a proportion of nonsynonmyous differences and (single) selection coefficient. So, this is the “Gamma_H17” DFE, with some proportion of positive selection with fixed s.

Citations

DFE parameters

Proportion of mutations

Distribution type

Parameters

Dominance

26.0%

Fixed s

s = 0.000

h = 0.500

74.0%

Gamma

mean = -0.000, shape = 0.330

h = 0.500

0.0%

Fixed s

s = 0.000

h = 0.500

LognormalPlusPositive_R16

Deleterious log-normal and beneficial mixed DFE

Estimated DFE containing deleterious and beneficial mutations, estimated by Ragsdale et al. (2016), with a log-normal distribution for deleterious mutations and a single selection coefficient for positive mutations. The DFE was inferred in scaled units from the triallelic frequency spectrum in D. melanogaster, here scaled to real units using an effective population size of Ne=2.8e6 (Huber et al 2017).

Citations

DFE parameters

Proportion of mutations

Distribution type

Parameters

Dominance

28.6%

Fixed s

s = 0.000

h = 0.500

70.9%

Negative LogNormal

meanlog = -9.425, sdlog = 3.360

h = 0.500

0.6%

Fixed s

s = 0.000

h = 0.500

Drosophila sechellia

ID:

DroSec

Name:

Drosophila sechellia

Common name:

Drosophila sechellia

Generation time:

0.05 (Legrand et al., 2009)

Ploidy:

2

Population size:

100000 (Legrand et al., 2009)

Genome

Genome assembly name:

ASM438219v1

ID

Ploidy

Length

Recombination rate

Mutation rate

2L

2

24956976

2.28e-08

1.5e-09

2R

2

21536224

2.51e-08

1.5e-09

3L

2

28131630

1.88e-08

1.5e-09

3R

2

30464902

1.91e-08

1.5e-09

X

2

22909512

2.85e-08

1.5e-09

4

2

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)

Ploidy:

1

Population size:

180000000.0 (Hartl, Moriyama, and Sawyer, 1994)

Genome

Genome assembly name:

ASM584v2

Bacterial recombination with tract length range:

542

ID

Ploidy

Length

Recombination rate

Mutation rate

Chromosome

1

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)

Ploidy:

2

Population size:

10000.0 (Liu et al., 2016)

Genome

Genome assembly name:

GAculeatus_UGA_version5

ID

Ploidy

Length

Recombination rate

Mutation rate

1

2

29619991

3.11e-08

3.7e-08

2

2

23686546

3.11e-08

3.7e-08

3

2

17759012

3.11e-08

3.7e-08

4

2

34181212

3.11e-08

3.7e-08

5

2

15550311

3.11e-08

3.7e-08

6

2

18825451

3.11e-08

3.7e-08

7

2

30776923

3.11e-08

3.7e-08

8

2

20553084

3.11e-08

3.7e-08

9

2

20843631

3.11e-08

3.7e-08

10

2

17985176

3.11e-08

3.7e-08

11

2

17651971

3.11e-08

3.7e-08

12

2

20694444

3.11e-08

3.7e-08

13

2

20748428

3.11e-08

3.7e-08

14

2

16147532

3.11e-08

3.7e-08

15

2

17318724

3.11e-08

3.7e-08

16

2

19507025

3.11e-08

3.7e-08

17

2

20195758

3.11e-08

3.7e-08

18

2

15939336

3.11e-08

3.7e-08

19

2

20580295

3.11e-08

3.7e-08

20

2

20445003

3.11e-08

3.7e-08

21

2

17421465

3.11e-08

3.7e-08

Y

1

15859692

0

3.7e-08

MT

1

16543

0

3.7e-08

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

Gorilla gorilla

ID:

GorGor

Name:

Gorilla gorilla

Common name:

Gorilla

Generation time:

19.0 (Besenbacher et al., 2019)

Ploidy:

2

Population size:

25200 (Yu et al., 2004)

Genome

Genome assembly name:

gorGor4

ID

Ploidy

Length

Recombination rate

Mutation rate

1

2

228908639

1.193e-08

1.235e-08

2A

2

107640188

1.193e-08

1.235e-08

2B

2

135448346

1.193e-08

1.235e-08

3

2

201391403

1.193e-08

1.235e-08

4

2

203093366

1.193e-08

1.235e-08

5

2

165317712

1.193e-08

1.235e-08

6

2

173266796

1.193e-08

1.235e-08

7

2

159110946

1.193e-08

1.235e-08

8

2

146757320

1.193e-08

1.235e-08

9

2

121655618

1.193e-08

1.235e-08

10

2

148642438

1.193e-08

1.235e-08

11

2

135235416

1.193e-08

1.235e-08

12

2

133456746

1.193e-08

1.235e-08

13

2

97154659

1.193e-08

1.235e-08

14

2

90977943

1.193e-08

1.235e-08

15

2

80890724

1.193e-08

1.235e-08

16

2

81384781

1.193e-08

1.235e-08

17

2

95888799

1.193e-08

1.235e-08

18

2

78004504

1.193e-08

1.235e-08

19

2

57935654

1.193e-08

1.235e-08

20

2

63231202

1.193e-08

1.235e-08

21

2

37891338

1.193e-08

1.235e-08

22

2

34650175

1.193e-08

1.235e-08

X

2

156331669

1.193e-08

1.235e-08

MT

1

16412

0

1.235e-08

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

Demographic Models

ID

Description

GorillaGhost_5P23

Ghost admixture in eastern gorillas

Ghost admixture in eastern gorillas

Demographic model of ghost admixture into eastern gorillas from Pawar et al. (2023) Fig. 2A and Supp. Table 1. This model simulates five populations: mountain gorillas, eastern lowland gorillas, western lowland gorillas, cross river gorillas, and a extinct ghost lineage. The ghost admixture event is modelled as a 2.47% pulse from the ghost lineage to a population ancestral to eastern gorillas. Migration events among eastern and western lowland gorillas are modelled as single generation pulses. Population size changes are also modelled.

Details

ID:

GorillaGhost_5P23

Description:

Ghost admixture in eastern gorillas

Num populations:

5

Populations

Index

ID

Sampling time

Description

0

cross_river

0

Contemporary Cross River Gorillas

1

western_lowland

0

Contemporary Western Lowland Gorillas

2

eastern_lowland

0

Contemporary Eastern Lowland Gorillas

3

mountain

0

Contemporary Mountain Gorillas

4

ghost

None

Extinct ghost lineage

Citations

Demographic Model parameters

Parameter Type (units)

Value

Description

Population size

14,558

Conteporary cross-river pop. size

Population size

64,749

Contemporary western lowland pop. size

Population size

20,894

Contemporary eastern lowland pop. size

Population size

2,158

Contemporary mountain pop. size

Population size

25,000

Ghost pop. size

Population size

243

Eastern lowland bottleneck pop. size

Population size

21,982

Eastern lowland ancestral pop. size

Population size

115

Mountain bottleneck pop. size

Population size

3,009

Mountain ancestral pop. size

Population size

5,325

Eastern lowland-Mountain ancestral pop. size

Population size

48,288

Western lowland ancestral pop. size

Population size

98,135

Western/Cross-river ancestral pop. size

Population size

14,364

Extant subspecies ancestral pop. size

Population size

35,381

Ghost-extant ancestral pop. size

Migration rate (fraction per generation)

0.02477

Ghost->(Eastern/Mountain) migration rate

Migration rate (fraction per generation)

0.002768

(Eastern/Mountain)->Western migration rate

Migration rate (fraction per generation)

0.00827

Western->(Eastern/Mountain) migration rate

Epoch time (years ago)

30

End of Eastern lowland bottleneck

Epoch time (years ago)

7,220

Start of Eastern lowland bottleneck

Epoch time (years ago)

9,120

End of Mountain bottleneck

Epoch time (years ago)

9,310

Start of Mountain bottleneck

Epoch time (years ago)

15,048

Eastern lowland-Mountain split

Epoch time (years ago)

34,000

End of Western lowland-(Eastern/Mountain ancestor) admixture

Epoch time (years ago)

34,002

Start of Western lowland-(Eastern/Mountain ancestor) admixture

Epoch time (years ago)

38,281

End of Ghost admixture

Epoch time (years ago)

38,300

Start of Ghost admixture

Epoch time (years ago)

40,896

Western lowland pop size change

Epoch time (years ago)

454,313

Western/Cross-river split

Epoch time (years ago)

965,481

Extant gorilla subspecies split

Epoch time (years ago)

3,421,360

Ghost-extant subspecies split

Generation time (years ago)

19

Generation time

Mutation rate

1.235e-8

Per-base per-generation mutation rate
_images/sec_catalog_gorgor_models_gorillaghost_5p23.png

Helianthus annuus

ID:

HelAnn

Name:

Helianthus annuus

Common name:

Helianthus annuus

Generation time:

1.0 (Strasburg and Rieseberg, 2008)

Ploidy:

2

Population size:

673968 (Strasburg et al., 2010)

Genome

Genome assembly name:

HanXRQr2.0-SUNRISE

ID

Ploidy

Length

Recombination rate

Mutation rate

1

2

149502186

4e-09

6.1e-09

2

2

174800439

4e-09

6.1e-09

3

2

176490873

4e-09

6.1e-09

4

2

208320189

4e-09

6.1e-09

5

2

178169690

4e-09

6.1e-09

6

2

148147350

4e-09

6.1e-09

7

2

149542083

4e-09

6.1e-09

8

2

167167940

4e-09

6.1e-09

9

2

189665024

4e-09

6.1e-09

10

2

181411567

4e-09

6.1e-09

11

2

189830405

4e-09

6.1e-09

12

2

163781230

4e-09

6.1e-09

13

2

173487274

4e-09

6.1e-09

14

2

173346949

4e-09

6.1e-09

15

2

175671323

4e-09

6.1e-09

16

2

206736614

4e-09

6.1e-09

17

2

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)

Ploidy:

2

Population size:

2111109 (Pardo-Diaz et al, 2012)

Genome

Genome assembly name:

Hmel2.5

ID

Ploidy

Length

Recombination rate

Mutation rate

1

2

17206585

3.17e-08

2.9e-09

2

2

9045316

5.61e-08

2.9e-09

3

2

10541528

5.1e-08

2.9e-09

4

2

9662098

4.97e-08

2.9e-09

5

2

9908586

5.15e-08

2.9e-09

6

2

14054175

3.4e-08

2.9e-09

7

2

14308859

3.76e-08

2.9e-09

8

2

9320449

5.28e-08

2.9e-09

9

2

8708747

5.31e-08

2.9e-09

10

2

17965481

3.16e-08

2.9e-09

11

2

11759272

4.47e-08

2.9e-09

12

2

16327298

3.13e-08

2.9e-09

13

2

18127314

3.08e-08

2.9e-09

14

2

9174305

5.47e-08

2.9e-09

15

2

10235750

4.78e-08

2.9e-09

16

2

10083215

4.71e-08

2.9e-09

17

2

14773299

3.94e-08

2.9e-09

18

2

16803890

3.16e-08

2.9e-09

19

2

16399344

3.11e-08

2.9e-09

20

2

14871695

3.45e-08

2.9e-09

21

2

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)

Ploidy:

2

Population size:

10000 (Takahata, 1993)

Genome

Genome assembly name:

GRCh38.p14

ID

Ploidy

Length

Recombination rate

Mutation rate

1

2

248956422

1.15235e-08

1.29e-08

2

2

242193529

1.10429e-08

1.29e-08

3

2

198295559

1.12585e-08

1.29e-08

4

2

190214555

1.1482e-08

1.29e-08

5

2

181538259

1.12443e-08

1.29e-08

6

2

170805979

1.12659e-08

1.29e-08

7

2

159345973

1.17713e-08

1.29e-08

8

2

145138636

1.16049e-08

1.29e-08

9

2

138394717

1.21987e-08

1.29e-08

10

2

133797422

1.33337e-08

1.29e-08

11

2

135086622

1.17213e-08

1.29e-08

12

2

133275309

1.30981e-08

1.29e-08

13

2

114364328

1.3061e-08

1.29e-08

14

2

107043718

1.36298e-08

1.29e-08

15

2

101991189

1.73876e-08

1.29e-08

16

2

90338345

1.48315e-08

1.29e-08

17

2

83257441

1.55383e-08

1.29e-08

18

2

80373285

1.46455e-08

1.29e-08

19

2

58617616

1.83848e-08

1.29e-08

20

2

64444167

1.67886e-08

1.29e-08

21

2

46709983

1.72443e-08

1.29e-08

22

2

50818468

2.10572e-08

1.29e-08

X

2

156040895

1.18483e-08

1.29e-08

Y

1

57227415

0

1.29e-08

MT

1

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_4B18

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. 2018. 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_4B18

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_4b18.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^-5)

3.14

European–East Asian migration rate

Migration rate (x10^-5)

5.72

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

LogNormal_H17

2017

Deleterious Log-normal DFE

Mixed_K23

2023

Deleterious Gamma DFE with additional lethals

PosNeg_R24

2024

Deleterious Gamma and Beneficial Exponential DFE

GammaPos_Z21

2021

Deleterious Gamma DFE with fixed-s beneficials

Gamma_K17

Deleterious Gamma DFE

Deleterious, gamma-distributed DFE estimated using ‘Fit∂a∂i’ from the nonsynonymous SFS in exons from a dataset of European humans by Kim et al. (2017).

Citations

DFE parameters

Proportion of mutations

Distribution type

Parameters

Dominance

30.0%

Fixed s

s = 0.000

h = 0.500

70.0%

Gamma

mean = -0.013, shape = 0.186

h = 0.500

Gamma_H17

Deleterious Gamma DFE

Deleterious, gamma-distributed DFE estimated from the SFS of YRI samples in the 1000 genomes project by Huber et al. (2017). DFE parameters are from the “full” model in Table S2, in which all data (none of the listed filters) were used.

Citations

DFE parameters

Proportion of mutations

Distribution type

Parameters

Dominance

30.0%

Fixed s

s = 0.000

h = 0.500

70.0%

Gamma

mean = -0.028, shape = 0.190

h = 0.500

LogNormal_H17

Deleterious Log-normal DFE

Deleterious, log-normal-distributed DFE estimated from the SFS of YRI samples in the 1000 genomes project by Huber et al. (2017). Parameters as shown for the “full” model in Table S3.

Citations

DFE parameters

Proportion of mutations

Distribution type

Parameters

Dominance

30.0%

Fixed s

s = 0.000

h = 0.500

70.0%

Negative LogNormal

meanlog = -6.677, sdlog = 4.580

h = 0.500

Mixed_K23

Deleterious Gamma DFE with additional lethals

The DFE estimated from human data recommended in Kyriazis et al. (2023), for general use. This model is similar to the Kim et al. (2017) DFE based on human genetic data, modified to include the dominance distribution from Henn et al. (2016). The model is also augmented with an additional proportion of 0.3% of recessive lethals, based on the analysis of Wade et al. (2023).

Citations

DFE parameters

Proportion of mutations

Distribution type

Parameters

Dominance

30.2%

Fixed s

s = 0.000

h = 0.500

69.6%

Gamma

mean = -0.013, shape = 0.186

h = 0.450 on [0, 0.001); 0.200 on [0.001, 0.010); 0.050 on [0.010, 0.100); 0.000 on [0.100, Inf)

0.2%

Fixed s

s = -1.000

h = 0.000

PosNeg_R24

Deleterious Gamma and Beneficial Exponential DFE

The best-fitting DFE simulated by Rodrigues et al (2024), from among 57 simulated scenarios with varying amounts of positive and negative selection. Fit was based on similarity of diversity and divergence across the great ape clade in simulations; the shape of the DFE was not inferred, only the proportion of positive and negative mutations; the shape of the deleterious portion of the DFE was obtained from Castellano et al (2019), https://doi.org/10.1534/genetics.119.302494.

Citations

DFE parameters

Proportion of mutations

Distribution type

Parameters

Dominance

40.0%

Fixed s

s = 0.000

h = 0.500

0.0%

Gamma

mean = -0.030, shape = 0.160

h = 0.500

60.0%

Exponential

mean = 0.010

h = 0.500

GammaPos_Z21

Deleterious Gamma DFE with fixed-s beneficials

The DFE estimated from human-chimp data estimated in Zhen et al (2021, https://dx.doi.org/10.1101/gr.256636.119). This uses the demographic model and deleterious-only DFE from Huber et al (2017), and then the number of nonsynonymous differences to chimpanzee to estimate a proportion of nonsynonmyous differences and (single) selection coefficient. So, this is the “Gamma_H17” DFE, with some proportion of positive selection with fixed s.

Citations

DFE parameters

Proportion of mutations

Distribution type

Parameters

Dominance

30.0%

Fixed s

s = 0.000

h = 0.500

68.9%

Gamma

mean = -0.028, shape = 0.190

h = 0.500

1.1%

Fixed s

s = 0.000

h = 0.500

Mus musculus

ID:

MusMus

Name:

Mus musculus

Common name:

Mouse

Generation time:

0.75 (Phifer-Rixey, et al., 2020)

Ploidy:

2

Population size:

500000 (Phifer-Rixey, et al., 2012; Booker and Keightley, 2018; Fujiwara et al., 2022)

Genome

Genome assembly name:

GRCm39

ID

Ploidy

Length

Recombination rate

Mutation rate

1

2

195154279

5e-09

5.4e-09

2

2

181755017

5.7e-09

5.4e-09

3

2

159745316

5.2e-09

5.4e-09

4

2

156860686

5.6e-09

5.4e-09

5

2

151758149

5.9e-09

5.4e-09

6

2

149588044

5.3e-09

5.4e-09

7

2

144995196

5.8e-09

5.4e-09

8

2

130127694

5.8e-09

5.4e-09

9

2

124359700

6.1e-09

5.4e-09

10

2

130530862

6.1e-09

5.4e-09

11

2

121973369

7e-09

5.4e-09

12

2

120092757

5.3e-09

5.4e-09

13

2

120883175

5.6e-09

5.4e-09

14

2

125139656

5.3e-09

5.4e-09

15

2

104073951

5.6e-09

5.4e-09

16

2

98008968

5.9e-09

5.4e-09

17

2

95294699

6.5e-09

5.4e-09

18

2

90720763

6.6e-09

5.4e-09

19

2

61420004

9.4e-09

5.4e-09

X

2

169476592

4.8e-09

5.4e-09

Y

1

91455967

0

5.4e-09

MT

1

16299

0

2.775e-08

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

Demographic Models

ID

Description

DomesticusEurope_1F22

M. musculus domesticus piecewise constant size

MusculusKorea_1F22

M. musculus musculus piecewise constant size

CastaneusIndia_1F22

M. musculus musculus piecewise constant size

M. musculus domesticus piecewise constant size

This model comes from MSMC using four randomly sampled individuals (DEU01,DEU03,DEU04,DEU06) from a German population. The model is estimated with 57 time periods. Data were provided directly by the first and corresponding authors of the paper, Kazumichi Fujiwara and Naoki Osada, respectively. A graphical depiction of the model can be found in Figure 3 of the paper.

Details

ID:

DomesticusEurope_1F22

Description:

M. musculus domesticus piecewise constant size

Num populations:

1

Populations

Index

ID

Sampling time

Description

0

M_musculus_domesticus

0

Mus musculus domesticus German population

Citations

Demographic Model parameters

Parameter Type (units)

Value

Description

Population size

133912

Ancestral population size

Population size

133912

Pop. size during 1st time interval

Population size

133912

Pop. size during 2nd time interval

Population size

133912

Pop. size during 3rd time interval

Population size

98811

Pop. size during 4th time interval

Population size

98811

Pop. size during 5th time interval

Population size

131050

Pop. size during 6th time interval

Population size

173594

Pop. size during 7th time interval

Population size

227037

Pop. size during 8th time interval

Population size

279833

Pop. size during 9th time interval

Population size

316861

Pop. size during 10th time interval

Population size

327217

Pop. size during 11th time interval

Population size

309961

Pop. size during 12th time interval

Population size

271935

Pop. size during 13th time interval

Population size

222951

Pop. size during 14th time interval

Population size

173264

Pop. size during 15th time interval

Population size

131392

Pop. size during 16th time interval

Population size

101471

Pop. size during 17th time interval

Population size

82953

Pop. size during 18th time interval

Population size

73097

Pop. size during 19th time interval

Population size

69317

Pop. size during 20th time interval

Population size

69939

Pop. size during 21th time interval

Population size

74185

Pop. size during 22th time interval

Population size

81892

Pop. size during 23th time interval

Population size

93046

Pop. size during 24th time interval

Population size

107067

Pop. size during 25th time interval

Population size

121751

Pop. size during 26th time interval

Population size

132063

Pop. size during 27th time interval

Population size

131016

Pop. size during 28th time interval

Population size

115426

Pop. size during 29th time interval

Population size

90926

Pop. size during 30th time interval

Population size

67337

Pop. size during 31th time interval

Population size

50557

Pop. size during 32th time interval

Population size

41195

Pop. size during 33th time interval

Population size

36886

Pop. size during 34th time interval

Population size

34163

Pop. size during 35th time interval

Population size

29931

Pop. size during 36th time interval

Population size

23419

Pop. size during 37th time interval

Population size

16490

Pop. size during 38th time interval

Population size

11240

Pop. size during 39th time interval

Population size

8332

Pop. size during 40th time interval

Population size

7480

Pop. size during 41th time interval

Population size

8463

Pop. size during 42th time interval

Population size

11758

Pop. size during 43th time interval

Population size

18939

Pop. size during 44th time interval

Population size

33028

Pop. size during 45th time interval

Population size

58488

Pop. size during 46th time interval

Population size

97250

Pop. size during 47th time interval

Population size

136620

Pop. size during 48th time interval

Population size

159142

Pop. size during 49th time interval

Population size

147212

Pop. size during 50th time interval

Population size

115399

Pop. size during 51th time interval

Population size

111242

Pop. size during 52th time interval

Population size

145603

Pop. size during 53th time interval

Population size

90428

Pop. size during 54th time interval

Population size

3844

Pop. size during 55th time interval

Population size

2040

Pop. size during 56th time interval

Time (yrs.)

1915544

Begining of 1st time interval

Time (yrs.)

1654653

Begining of 2nd time interval

Time (yrs.)

1429281

Begining of 3rd time interval

Time (yrs.)

1234595

Begining of 4th time interval

Time (yrs.)

1066418

Begining of 5th time interval

Time (yrs.)

921140

Begining of 6th time interval

Time (yrs.)

795646

Begining of 7th time interval

Time (yrs.)

687237

Begining of 8th time interval

Time (yrs.)

593589

Begining of 9th time interval

Time (yrs.)

512693

Begining of 10th time interval

Time (yrs.)

442812

Begining of 11th time interval

Time (yrs.)

382446

Begining of 12th time interval

Time (yrs.)

330300

Begining of 13th time interval

Time (yrs.)

285254

Begining of 14th time interval

Time (yrs.)

246340

Begining of 15th time interval

Time (yrs.)

212726

Begining of 16th time interval

Time (yrs.)

183689

Begining of 17th time interval

Time (yrs.)

158606

Begining of 18th time interval

Time (yrs.)

136938

Begining of 19th time interval

Time (yrs.)

118221

Begining of 20th time interval

Time (yrs.)

102052

Begining of 21th time interval

Time (yrs.)

88084

Begining of 22th time interval

Time (yrs.)

76019

Begining of 23th time interval

Time (yrs.)

65596

Begining of 24th time interval

Time (yrs.)

56592

Begining of 25th time interval

Time (yrs.)

48815

Begining of 26th time interval

Time (yrs.)

42096

Begining of 27th time interval

Time (yrs.)

36292

Begining of 28th time interval

Time (yrs.)

31279

Begining of 29th time interval

Time (yrs.)

26948

Begining of 30th time interval

Time (yrs.)

23207

Begining of 31th time interval

Time (yrs.)

19975

Begining of 32th time interval

Time (yrs.)

17183

Begining of 33th time interval

Time (yrs.)

14772

Begining of 34th time interval

Time (yrs.)

12688

Begining of 35th time interval

Time (yrs.)

10889

Begining of 36th time interval

Time (yrs.)

9334

Begining of 37th time interval

Time (yrs.)

7991

Begining of 38th time interval

Time (yrs.)

6831

Begining of 39th time interval

Time (yrs.)

5829

Begining of 40th time interval

Time (yrs.)

4964

Begining of 41th time interval

Time (yrs.)

4216

Begining of 42th time interval

Time (yrs.)

3570

Begining of 43th time interval

Time (yrs.)

3012

Begining of 44th time interval

Time (yrs.)

2530

Begining of 45th time interval

Time (yrs.)

2114

Begining of 46th time interval

Time (yrs.)

1754

Begining of 47th time interval

Time (yrs.)

1443

Begining of 48th time interval

Time (yrs.)

1175

Begining of 49th time interval

Time (yrs.)

943

Begining of 50th time interval

Time (yrs.)

743

Begining of 51th time interval

Time (yrs.)

570

Begining of 52th time interval

Time (yrs.)

420

Begining of 53th time interval

Time (yrs.)

291

Begining of 54th time interval

Time (yrs.)

180

Begining of 55th time interval

Time (yrs.)

83

Begining of 56th time interval

Time (yrs.)

0

Begining of 57th time interval

Generation time (yrs.)

1

Average generation interval

Mutation rate

5.7e-9

Per-base per-generation mutation rate
_images/sec_catalog_musmus_models_domesticuseurope_1f22.png

M. musculus musculus piecewise constant size

This model comes from MSMC using four randomly sampled individuals (KOR01,KOR02,KOR03,KOR05) from a Korean population. The model is estimated with 57 time periods. Data were provided directly by the first and corresponding authors of the paper, Kazumichi Fujiwara and Naoki Osada, respectively. A graphical depiction of the model can be found in Figure 3 of the paper.

Details

ID:

MusculusKorea_1F22

Description:

M. musculus musculus piecewise constant size

Num populations:

1

Populations

Index

ID

Sampling time

Description

0

M_musculus_musculus

0

Mus musculus musculus Korean population

Citations

Demographic Model parameters

Parameter Type (units)

Value

Description

Population size

152757

Ancestral population size

Population size

152757

Pop. size during 1st time interval

Population size

152757

Pop. size during 2nd time interval

Population size

152757

Pop. size during 3rd time interval

Population size

407105

Pop. size during 4th time interval

Population size

407105

Pop. size during 5th time interval

Population size

400867

Pop. size during 6th time interval

Population size

359368

Pop. size during 7th time interval

Population size

302950

Pop. size during 8th time interval

Population size

245823

Pop. size during 9thtime interval

Population size

194969

Pop. size during 10th time interval

Population size

151909

Pop. size during 11th time interval

Population size

116547

Pop. size during 12th time interval

Population size

88494

Pop. size during 13th time interval

Population size

67725

Pop. size during 14th time interval

Population size

54304

Pop. size during 15th time interval

Population size

47001

Pop. size during 16th time interval

Population size

43933

Pop. size during 17th time interval

Population size

43467

Pop. size during 18th time interval

Population size

43874

Pop. size during 19th time interval

Population size

42857

Pop. size during 20th time interval

Population size

38441

Pop. size during 21th time interval

Population size

30806

Pop. size during 22th time interval

Population size

22556

Pop. size during 23th time interval

Population size

16339

Pop. size during 24th time interval

Population size

13023

Pop. size during 25th time interval

Population size

12259

Pop. size during 26th time interval

Population size

13588

Pop. size during 27th time interval

Population size

16747

Pop. size during 28th time interval

Population size

21219

Pop. size during 29th time interval

Population size

25399

Pop. size during 30th time interval

Population size

26648

Pop. size during 31th time interval

Population size

23546

Pop. size during 32th time interval

Population size

17741

Pop. size during 33th time interval

Population size

12072

Pop. size during 34th time interval

Population size

7990

Pop. size during 35th time interval

Population size

5506

Pop. size during 36th time interval

Population size

4177

Pop. size during 37th time interval

Population size

3643

Pop. size during 38th time interval

Population size

3751

Pop. size during 39th time interval

Population size

4605

Pop. size during 40th time interval

Population size

6695

Pop. size during 41th time interval

Population size

11222

Pop. size during 42th time interval

Population size

20382

Pop. size during 43th time interval

Population size

36220

Pop. size during 44th time interval

Population size

55959

Pop. size during 45th time interval

Population size

68111

Pop. size during 46th time interval

Population size

61935

Pop. size during 47th time interval

Population size

42715

Pop. size during 48th time interval

Population size

25527

Pop. size during 49th time interval

Population size

16254

Pop. size during 50th time interval

Population size

12104

Pop. size during 51th time interval

Population size

9960

Pop. size during 52th time interval

Population size

9029

Pop. size during 53th time interval

Population size

8035

Pop. size during 54th time interval

Population size

8931

Pop. size during 55th time interval

Population size

179912

Pop. size during 56th time interval

Time (yrs.)

807711

Begining of 1st time interval

Time (yrs.)

697702

Begining of 2nd time interval

Time (yrs.)

602670

Begining of 3rd time interval

Time (yrs.)

520579

Begining of 4th time interval

Time (yrs.)

449667

Begining of 5th time interval

Time (yrs.)

388409

Begining of 6th time interval

Time (yrs.)

335491

Begining of 7th time interval

Time (yrs.)

289781

Begining of 8th time interval

Time (yrs.)

250293

Begining of 9th time interval

Time (yrs.)

216182

Begining of 10th time interval

Time (yrs.)

186716

Begining of 11th time interval

Time (yrs.)

161262

Begining of 12th time interval

Time (yrs.)

139274

Begining of 13th time interval

Time (yrs.)

120280

Begining of 14th time interval

Time (yrs.)

103872

Begining of 15th time interval

Time (yrs.)

89698

Begining of 16th time interval

Time (yrs.)

77455

Begining of 17th time interval

Time (yrs.)

66878

Begining of 18th time interval

Time (yrs.)

57741

Begining of 19th time interval

Time (yrs.)

49849

Begining of 20th time interval

Time (yrs.)

43031

Begining of 21th time interval

Time (yrs.)

37142

Begining of 22th time interval

Time (yrs.)

32054

Begining of 23th time interval

Time (yrs.)

27659

Begining of 24th time interval

Time (yrs.)

23863

Begining of 25th time interval

Time (yrs.)

20583

Begining of 26th time interval

Time (yrs.)

17750

Begining of 27th time interval

Time (yrs.)

15303

Begining of 28th time interval

Time (yrs.)

13189

Begining of 29th time interval

Time (yrs.)

11363

Begining of 30th time interval

Time (yrs.)

9785

Begining of 31th time interval

Time (yrs.)

8423

Begining of 32th time interval

Time (yrs.)

7246

Begining of 33th time interval

Time (yrs.)

6229

Begining of 34th time interval

Time (yrs.)

5350

Begining of 35th time interval

Time (yrs.)

4591

Begining of 36th time interval

Time (yrs.)

3936

Begining of 37th time interval

Time (yrs.)

3370

Begining of 38th time interval

Time (yrs.)

2881

Begining of 39th time interval

Time (yrs.)

2458

Begining of 40th time interval

Time (yrs.)

2093

Begining of 41th time interval

Time (yrs.)

1778

Begining of 42th time interval

Time (yrs.)

1505

Begining of 43th time interval

Time (yrs.)

1270

Begining of 44th time interval

Time (yrs.)

1067

Begining of 45th time interval

Time (yrs.)

891

Begining of 46th time interval

Time (yrs.)

740

Begining of 47th time interval

Time (yrs.)

609

Begining of 48th time interval

Time (yrs.)

495

Begining of 49th time interval

Time (yrs.)

398

Begining of 50th time interval

Time (yrs.)

313

Begining of 51th time interval

Time (yrs.)

240

Begining of 52th time interval

Time (yrs.)

177

Begining of 53th time interval

Time (yrs.)

123

Begining of 54th time interval

Time (yrs.)

76

Begining of 55th time interval

Time (yrs.)

35

Begining of 56th time interval

Time (yrs.)

0

Begining of 57th time interval

Generation time (yrs.)

1

Average generation interval

Mutation rate

5.7e-9

Per-base per-generation mutation rate
_images/sec_catalog_musmus_models_musculuskorea_1f22.png

M. musculus musculus piecewise constant size

This model comes from MSMC using two randomly sampled individuals (IND03,IND04) from a Indian population. The model is estimated with 57 time periods. Data were provided directly by the first and corresponding authors of the paper, Kazumichi Fujiwara and Naoki Osada, respectively. A graphical depiction of the model can be found in Figure 3 of the paper.

Details

ID:

CastaneusIndia_1F22

Description:

M. musculus musculus piecewise constant size

Num populations:

1

Populations

Index

ID

Sampling time

Description

0

M_musculus_castaneus

0

Mus musculus castaneus Indian population

Citations

Demographic Model parameters

Parameter Type (units)

Value

Description

Population size

344802

Ancestral population size

Population size

344802

Pop. size during 1st time interval

Population size

344802

Pop. size during 2nd time interval

Population size

344802

Pop. size during 3rd time interval

Population size

463464

Pop. size during 4th time interval

Population size

463464

Pop. size during 5th time interval

Population size

360433

Pop. size during 6th time interval

Population size

275733

Pop. size during 7th time interval

Population size

217017

Pop. size during 8th time interval

Population size

182054

Pop. size during 9th time interval

Population size

163295

Pop. size during 10th time interval

Population size

155027

Pop. size during 11th time interval

Population size

154098

Pop. size during 12th time interval

Population size

159139

Pop. size during 13th time interval

Population size

169657

Pop. size during 14th time interval

Population size

185260

Pop. size during 15th time interval

Population size

205098

Pop. size during 16th time interval

Population size

227605

Pop. size during 17th time interval

Population size

250544

Pop. size during 18th time interval

Population size

271326

Pop. size during 19th time interval

Population size

287572

Pop. size during 20th time interval

Population size

297772

Pop. size during 21th time interval

Population size

301783

Pop. size during 22th time interval

Population size

300840

Pop. size during 23th time interval

Population size

297138

Pop. size during 24th time interval

Population size

293233

Pop. size during 25th time interval

Population size

291560

Pop. size during 26th time interval

Population size

294117

Pop. size during 27th time interval

Population size

302369

Pop. size during 28th time interval

Population size

317235

Pop. size during 29th time interval

Population size

338818

Pop. size during 30th time interval

Population size

365787

Pop. size during 31th time interval

Population size

394606

Pop. size during 32th time interval

Population size

418882

Pop. size during 33th time interval

Population size

429975

Pop. size during 34th time interval

Population size

420389

Pop. size during 35th time interval

Population size

388298

Pop. size during 36th time interval

Population size

338426

Pop. size during 37th time interval

Population size

279816

Pop. size during 38th time interval

Population size

222464

Pop. size during 39th time interval

Population size

173419

Pop. size during 40th time interval

Population size

134861

Pop. size during 41th time interval

Population size

105533

Pop. size during 42th time interval

Population size

83216

Pop. size during 43th time interval

Population size

66260

Pop. size during 44th time interval

Population size

53747

Pop. size during 45th time interval

Population size

45372

Pop. size during 46th time interval

Population size

41297

Pop. size during 47th time interval

Population size

41845

Pop. size during 48th time interval

Population size

47736

Pop. size during 49th time interval

Population size

60911

Pop. size during 50th time interval

Population size

86633

Pop. size during 51th time interval

Population size

141377

Pop. size during 52th time interval

Population size

291323

Pop. size during 53th time interval

Population size

938111

Pop. size during 54th time interval

Population size

5064712

Pop. size during 55th time interval

Population size

64853

Pop. size during 56th time interval

Time (yrs.)

5585000

Begining of 1st time interval

Time (yrs.)

4955842

Begining of 2nd time interval

Time (yrs.)

4397456

Begining of 3rd time interval

Time (yrs.)

3901912

Begining of 4th time interval

Time (yrs.)

3462105

Begining of 5th time interval

Time (yrs.)

3071789

Begining of 6th time interval

Time (yrs.)

2725404

Begining of 7th time interval

Time (yrs.)

2417965

Begining of 8th time interval

Time (yrs.)

2145140

Begining of 9th time interval

Time (yrs.)

1903000

Begining of 10th time interval

Time (yrs.)

1688102

Begining of 11th time interval

Time (yrs.)

1497384

Begining of 12th time interval

Time (yrs.)

1328123

Begining of 13th time interval

Time (yrs.)

1177907

Begining of 14th time interval

Time (yrs.)

1044593

Begining of 15th time interval

Time (yrs.)

926277

Begining of 16th time interval

Time (yrs.)

821274

Begining of 17th time interval

Time (yrs.)

728084

Begining of 18th time interval

Time (yrs.)

645379

Begining of 19th time interval

Time (yrs.)

571979

Begining of 20th time interval

Time (yrs.)

506839

Begining of 21th time interval

Time (yrs.)

449026

Begining of 22th time interval

Time (yrs.)

397719

Begining of 23th time interval

Time (yrs.)

352184

Begining of 24th time interval

Time (yrs.)

311772

Begining of 25th time interval

Time (yrs.)

275907

Begining of 26th time interval

Time (yrs.)

244079

Begining of 27th time interval

Time (yrs.)

215830

Begining of 28th time interval

Time (yrs.)

190760

Begining of 29th time interval

Time (yrs.)

168510

Begining of 30th time interval

Time (yrs.)

148764

Begining of 31th time interval

Time (yrs.)

131239

Begining of 32th time interval

Time (yrs.)

115687

Begining of 33th time interval

Time (yrs.)

101884

Begining of 34th time interval

Time (yrs.)

89634

Begining of 35th time interval

Time (yrs.)

78762

Begining of 36th time interval

Time (yrs.)

69114

Begining of 37th time interval

Time (yrs.)

60551

Begining of 38th time interval

Time (yrs.)

52951

Begining of 39th time interval

Time (yrs.)

46207

Begining of 40th time interval

Time (yrs.)

40221

Begining of 41th time interval

Time (yrs.)

34909

Begining of 42th time interval

Time (yrs.)

30195

Begining of 43th time interval

Time (yrs.)

26011

Begining of 44th time interval

Time (yrs.)

22297

Begining of 45th time interval

Time (yrs.)

19002

Begining of 46th time interval

Time (yrs.)

16077

Begining of 47th time interval

Time (yrs.)

13481

Begining of 48th time interval

Time (yrs.)

11178

Begining of 49th time interval

Time (yrs.)

9133

Begining of 50th time interval

Time (yrs.)

7319

Begining of 51th time interval

Time (yrs.)

5709

Begining of 52th time interval

Time (yrs.)

4279

Begining of 53th time interval

Time (yrs.)

3011

Begining of 54th time interval

Time (yrs.)

1886

Begining of 55th time interval

Time (yrs.)

887

Begining of 56th time interval

Time (yrs.)

0

Begining of 57th time interval

Generation time (yrs.)

1

Average generation interval

Mutation rate

5.7e-9

Per-base per-generation mutation rate
_images/sec_catalog_musmus_models_castaneusindia_1f22.png

Distribution of Fitness Effects (DFEs)

ID

Year

Description

Gamma_B21

2021

Deleterious Gamma DFE CDS

Gamma_B21

Deleterious Gamma DFE CDS

A gamma-distributed DFE for deleterious mutations estimated from the SFS of Mus musculus castaneous exons by Booker et al. (2021), using polyDFE v2 (Tataru and Bataillon 2019).

Citations

DFE parameters

Proportion of mutations

Distribution type

Parameters

Dominance

33.4%

Fixed s

s = 0.000

h = 0.500

66.6%

Gamma

mean = -0.060, shape = 0.186

h = 0.500

Oryza sativa

ID:

OrySat

Name:

Oryza sativa

Common name:

Asian rice

Generation time:

1 (Caicedo et al., 2007)

Ploidy:

2

Population size:

46875

Genome

Genome assembly name:

None

ID

Ploidy

Length

Recombination rate

Mutation rate

1

2

43270923

8.97e-10

3.2e-09

Mt

1

490520

0

3.2e-09

Pt

1

134525

0

3.2e-09

2

2

35937250

8.97e-10

3.2e-09

3

2

36413819

8.97e-10

3.2e-09

4

2

35502694

8.97e-10

3.2e-09

5

2

29958434

8.97e-10

3.2e-09

6

2

31248787

8.97e-10

3.2e-09

7

2

29697621

8.97e-10

3.2e-09

8

2

28443022

8.97e-10

3.2e-09

9

2

23012720

8.97e-10

3.2e-09

10

2

23207287

8.97e-10

3.2e-09

11

2

29021106

8.97e-10

3.2e-09

12

2

27531856

8.97e-10

3.2e-09

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

Demographic Models

ID

Description

BottleneckMigration_3C07

Bottleneck + migration model for the origin of domesticated rice varieties

Bottleneck + migration model for the origin of domesticated rice varieties

The bottleneck + migration model of domesticated rice varieties (indica and tropical japonica) from Caicedo et al. (2007). Parameters were inferred from the site frequency spectrum (SFS), with parameter values taken from Table 2.

Details

ID:

BottleneckMigration_3C07

Description:

Bottleneck + migration model for the origin of domesticated rice varieties

Num populations:

3

Populations

Index

ID

Sampling time

Description

0

RUF

0

Oryza rufipogon (wild rice)

1

IND

0

Oryza sativa indica

2

TRJ

0

Tropical Oryza sativa japonica

Citations

Demographic Model parameters

Parameter Type (units)

Value

Description

Population size

150,000

Ancestral pop. size

Population size

150,000

RUF pop. size

Population size

40,500

IND pop. size

Population size

18,000

TRJ pop. size

Population size

825

IND pop. size after origin

Population size

825

TRJ pop. size after origin

Migration rate (x10^-5)

2.33

RUF-IND migration rate (per gen.)

Migration rate (x10^-5)

2.33

TRJ-IND migration rate (per gen.)

Migration rate (x10^-5)

2.33

TRJ-RUF migration rate (per gen.)

Epoch Time (gen.)

12,000

Time of origin and beginning of domestication bottleneck of IND and TRJ

Epoch Time (gen.)

9,000

Time of partial recovery from bottleneck of IND and TRJ

Generation time (yrs.)

1

Generation time

Mutation rate

9.03e-9

Per-base per-generation mutation rate
_images/sec_catalog_orysat_models_bottleneckmigration_3c07.png

Pan troglodytes

ID:

PanTro

Name:

Pan troglodytes

Common name:

Chimpanzee

Generation time:

24.6 (Langergraber et al., 2012)

Ploidy:

2

Population size:

16781 (Stevison et al., 2015)

Genome

Genome assembly name:

Pan_tro_3.0

ID

Ploidy

Length

Recombination rate

Mutation rate

1

2

228573443

1.2e-08

1.6e-08

2A

2

111504155

1.2e-08

1.6e-08

2B

2

133216015

1.2e-08

1.6e-08

3

2

202621043

1.2e-08

1.6e-08

4

2

194502333

1.2e-08

1.6e-08

5

2

181907262

1.2e-08

1.6e-08

6

2

175400573

1.2e-08

1.6e-08

7

2

166211670

1.2e-08

1.6e-08

8

2

147911612

1.2e-08

1.6e-08

9

2

116767853

1.2e-08

1.6e-08

10

2

135926727

1.2e-08

1.6e-08

11

2

135753878

1.2e-08

1.6e-08

12

2

137163284

1.2e-08

1.6e-08

13

2

100452976

1.2e-08

1.6e-08

14

2

91965084

1.2e-08

1.6e-08

15

2

83230942

1.2e-08

1.6e-08

16

2

81586097

1.2e-08

1.6e-08

17

2

83181570

1.2e-08

1.6e-08

18

2

78221452

1.2e-08

1.6e-08

19

2

61309027

1.2e-08

1.6e-08

20

2

66533130

1.2e-08

1.6e-08

21

2

33445071

1.2e-08

1.6e-08

22

2

37823149

1.2e-08

1.6e-08

X

2

155549662

1.2e-08

1.6e-08

Y

1

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)

Ploidy:

2

Population size:

335505 (Wall et. al., 2022)

Genome

Genome assembly name:

Panubis1.0

ID

Ploidy

Length

Recombination rate

Mutation rate

1

2

218172882

9.92638e-09

5.7e-09

2

2

193660750

9.60544e-09

5.7e-09

3

2

184919515

9.02238e-09

5.7e-09

4

2

182120902

9.82513e-09

5.7e-09

5

2

173900761

9.5798e-09

5.7e-09

6

2

167138247

1.04979e-08

5.7e-09

7

2

161768468

1.11888e-08

5.7e-09

8

2

140274886

1.10899e-08

5.7e-09

9

2

127591819

1.13288e-08

5.7e-09

10

2

126462689

1.17532e-08

5.7e-09

11

2

125913696

1.18403e-08

5.7e-09

12

2

123343450

1.0824e-08

5.7e-09

13

2

106849001

1.24677e-08

5.7e-09

14

2

106654974

1.27419e-08

5.7e-09

15

2

91985775

1.26084e-08

5.7e-09

16

2

91184193

1.47616e-08

5.7e-09

17

2

74525926

1.5241e-08

5.7e-09

18

2

72894408

1.36841e-08

5.7e-09

19

2

72123344

1.30374e-08

5.7e-09

20

2

50021108

1.6772e-08

5.7e-09

X

2

142711496

1.18898e-08

5.7e-09

Y

1

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

Phocoena sinus

ID:

PhoSin

Name:

Phocoena sinus

Common name:

Vaquita

Generation time:

11.9 (Robinson et al., 2022; Taylor et al., 2007)

Ploidy:

2

Population size:

3500 (Robinson et al., 2022)

Genome

Genome assembly name:

mPhoSin1.pri

ID

Ploidy

Length

Recombination rate

Mutation rate

1

2

185845356

1e-08

5.83e-09

2

2

178563925

1e-08

5.83e-09

3

2

174291665

1e-08

5.83e-09

4

2

146127150

1e-08

5.83e-09

5

2

139762554

1e-08

5.83e-09

6

2

115952311

1e-08

5.83e-09

7

2

115469292

1e-08

5.83e-09

8

2

110408561

1e-08

5.83e-09

9

2

106736052

1e-08

5.83e-09

10

2

102828027

1e-08

5.83e-09

11

2

104118372

1e-08

5.83e-09

12

2

90399378

1e-08

5.83e-09

13

2

90400161

1e-08

5.83e-09

14

2

89762611

1e-08

5.83e-09

15

2

88287594

1e-08

5.83e-09

16

2

85252673

1e-08

5.83e-09

17

2

79603858

1e-08

5.83e-09

18

2

79885847

1e-08

5.83e-09

19

2

59501331

1e-08

5.83e-09

20

2

58878645

1e-08

5.83e-09

21

2

35802323

1e-08

5.83e-09

X

2

131664873

1e-08

5.83e-09

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

Demographic Models

ID

Description

Vaquita2Epoch_1R22

Vaquita two epoch model

Vaquita two epoch model

A two-epoch demographic model estimated using dadi from the site frequency spectrum at putatively neutrally evolving regions of the genome identified as those located >10 kb from coding sequences which did not overlap with CpG islands. Population genomic data obtained from 20 individuals sequenced at mean coverage 60x. Robinson et al. (2022) reports several inferred models in Supp Table S2. This is the 2-epoch model inferred by dadi, which is also depicted in Main Figure 1E. Size changes from N_anc to N_curr in time T.

Details

ID:

Vaquita2Epoch_1R22

Description:

Vaquita two epoch model

Num populations:

1

Populations

Index

ID

Sampling time

Description

0

Vaquita

0

Vaquita (Phocoena sinus)

Citations

Demographic Model parameters

Parameter Type (units)

Value

Description

Population size

4,485

Ancestral pop. size

Population size

2,807

Pop. size during second epoch

Epoch Time (gen.)

2,162

Start time of second epoch

Generation time (yrs.)

11.9

Average generation interval

Mutation rate

5.83e-9

Per-base per-generation mutation rate
_images/sec_catalog_phosin_models_vaquita2epoch_1r22.png

Annotations

ID

Year

Description

Phocoena_sinus.mPhoSin1.pri.110_exons

2020

Vaquita exon annotations from Morin et al 2020 using NCBI’s pipeline

Phocoena_sinus.mPhoSin1.pri.110_CDS

2020

Vaquita CDS annotations from Morin et al 2020 using NCBI’s pipeline

Phocoena_sinus.mPhoSin1.pri.110_exons

Vaquita exon annotations from Morin et al 2020 using NCBI’s pipeline

Citations

Phocoena_sinus.mPhoSin1.pri.110_CDS

Vaquita CDS annotations from Morin et al 2020 using NCBI’s pipeline

Citations

Distribution of Fitness Effects (DFEs)

ID

Year

Description

Gamma_R22

2022

Deleterious Gamma DFE

Gamma_R22

Deleterious Gamma DFE

Gamma-distributed deleterious DFE inferred by Robinson et al. (2022), and used in their simulations, from the synonymous and nonsynonymous SFS from Vaquita data, following the methods of Huber et al (2017).

Citations

DFE parameters

Proportion of mutations

Distribution type

Parameters

Dominance

30.0%

Fixed s

s = 0.000

h = 0.500

70.0%

Gamma

mean = -0.026, shape = 0.131

h = 0.000 on [0, -0.100); 0.010 on [-0.100, -0.010); 0.100 on [-0.010, -0.001); 0.400 on [-0.001, Inf)

Pongo abelii

ID:

PonAbe

Name:

Pongo abelii

Common name:

Sumatran orangutan

Generation time:

25 (Wich et al., 2008)

Ploidy:

2

Population size:

17900.0 (Locke et al., 2011)

Genome

Genome assembly name:

ponAbe3

ID

Ploidy

Length

Recombination rate

Mutation rate

1

2

227913704

5.72097e-09

1.5e-08

2A

2

109511694

6.74694e-09

1.5e-08

2B

2

129937803

6.08833e-09

1.5e-08

3

2

193656255

5.77615e-09

1.5e-08

4

2

189387572

6.06176e-09

1.5e-08

5

2

179185813

5.87839e-09

1.5e-08

6

2

169501136

5.89605e-09

1.5e-08

7

2

145408105

6.82979e-09

1.5e-08

8

2

144036388

6.34313e-09

1.5e-08

9

2

112206110

7.04756e-09

1.5e-08

10

2

132178492

6.94812e-09

1.5e-08

11

2

128122151

5.79185e-09

1.5e-08

12

2

132184051

6.04316e-09

1.5e-08

13

2

98475126

6.40817e-09

1.5e-08

14

2

88963417

6.11075e-09

1.5e-08

15

2

82547911

6.6315e-09

1.5e-08

16

2

68237989

6.76066e-09

1.5e-08

17

2

75914007

8.01983e-09

1.5e-08

18

2

75923960

6.40065e-09

1.5e-08

19

2

57575784

9.09647e-09

1.5e-08

20

2

60841859

6.31424e-09

1.5e-08

21

2

34683425

7.58867e-09

1.5e-08

22

2

35308119

9.83628e-09

1.5e-08

X

2

151242693

6.40288e-09

1.5e-08

MT

1

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

Rattus norvegicus

ID:

RatNor

Name:

Rattus norvegicus

Common name:

Rat

Generation time:

0.5 (McGuire et al., 2006; Keightly and Eyre-Walker, 2000)

Ploidy:

2

Population size:

124000.0 (Deinum et al., 2015)

Genome

Genome assembly name:

mRatBN7.2

ID

Ploidy

Length

Recombination rate

Mutation rate

1

2

260522016

5e-09

2.96e-09

2

2

249053267

4.8e-09

2.96e-09

3

2

169034231

5.9e-09

2.96e-09

4

2

182687754

5.7e-09

2.96e-09

5

2

166875058

6.1e-09

2.96e-09

6

2

140994061

6e-09

2.96e-09

7

2

135012528

6.6e-09

2.96e-09

8

2

123900184

6.8e-09

2.96e-09

9

2

114175309

6.4e-09

2.96e-09

10

2

107211142

8.1e-09

2.96e-09

11

2

86241447

6.8e-09

2.96e-09

12

2

46669029

1.01e-08

2.96e-09

13

2

106807694

5.7e-09

2.96e-09

14

2

104886043

6.3e-09

2.96e-09

15

2

101769107

6.5e-09

2.96e-09

16

2

84729064

6.8e-09

2.96e-09

17

2

86533673

7.5e-09

2.96e-09

18

2

83828827

6.7e-09

2.96e-09

19

2

57337602

8.8e-09

2.96e-09

20

2

54435887

9.1e-09

2.96e-09

X

2

152453651

3.7e-09

2.96e-09

Y

1

18315841

0

2.96e-09

MT

1

16313

0

4.44e-08

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

Streptococcus agalactiae

ID:

StrAga

Name:

Streptococcus agalactiae

Common name:

Group B Streptococcus

Generation time:

0.0027397260273972603 (Savageau M.A., 1983)

Ploidy:

1

Population size:

140000 (Da Cunha et al, 2014)

Genome

Genome assembly name:

GBCO_p1

Bacterial recombination with tract length range:

120000

ID

Ploidy

Length

Recombination rate

Mutation rate

1

1

2065074

1.53e-10

1.53e-09

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

Sus scrofa

ID:

SusScr

Name:

Sus scrofa

Common name:

Pig

Generation time:

3.6 (Servanty et al., 2011)

Ploidy:

2

Population size:

270000 (Zhang et al., 2022)

Genome

Genome assembly name:

Sscrofa11.1

ID

Ploidy

Length

Recombination rate

Mutation rate

1

2

274330532

5.33525e-09

3.6e-09

2

2

151935994

8.60573e-09

3.6e-09

3

2

132848913

9.75114e-09

3.6e-09

4

2

130910915

9.7946e-09

3.6e-09

5

2

104526007

1.19926e-08

3.6e-09

6

2

170843587

8.78617e-09

3.6e-09

7

2

121844099

1.08878e-08

3.6e-09

8

2

138966237

8.92303e-09

3.6e-09

9

2

139512083

9.33751e-09

3.6e-09

10

2

69359453

1.65423e-08

3.6e-09

11

2

79169978

1.21451e-08

3.6e-09

12

2

61602749

1.69051e-08

3.6e-09

13

2

208334590

6.1628e-09

3.6e-09

14

2

141755446

8.72157e-09

3.6e-09

15

2

140412725

8.11447e-09

3.6e-09

16

2

79944280

1.14075e-08

3.6e-09

17

2

63494081

1.37799e-08

3.6e-09

18

2

55982971

1.36799e-08

3.6e-09

X

2

125939595

9.41637e-09

3.6e-09

Y

1

43547828

0

3.6e-09

MT

1

16613

0

3.6e-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.