Catalog

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

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

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

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

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

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

5. which annotation track? (ie. which Annotation object)

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

1. chromosome 22, using

2. the HapMapII genetic map, under

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

4. background selection acting within

5. exons from the Ensembl Havana 104 annotations.

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

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

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

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

Aedes aegypti

ID

AedAeg

Name

Aedes aegypti

Common name

Yellow fever mosquito

Generation time

0.06666666666666667 (Crawford et al., 2017)

Population size

1000000.0 (Crawford et al., 2017)

Genome

ID	Length	Recombination rate	Mutation rate
1	310827022	3.06e-09	3.5e-09
2	474425716	2.49e-09	3.5e-09
3	409777670	2.91e-09	3.5e-09
MT	16790	0	3.5e-09

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

---

Anas platyrhynchos

ID

AnaPla

Name

Anas platyrhynchos

Common name

Mallard

Generation time

4 (Lavretsky et al., 2020)

Population size

156000 (Guo et al., 2021)

Genome

ID	Length	Recombination rate	Mutation rate
1	208326429	1.52e-08	4.83e-09
2	162939446	1.39e-08	4.83e-09
3	119723720	9.38e-09	4.83e-09
4	77626585	1.2e-08	4.83e-09
5	64988622	1.21e-08	4.83e-09
6	39543408	3.04e-08	4.83e-09
7	37812880	2.59e-08	4.83e-09
8	33348632	1.28e-08	4.83e-09
9	26742597	1.34e-08	4.83e-09
10	22933227	2.5e-08	4.83e-09
11	22193879	1.5e-08	4.83e-09
12	22338721	3.15e-08	4.83e-09
13	21714986	1.41e-08	4.83e-09
14	20320564	8.61e-09	4.83e-09
15	18227546	3.79e-09	4.83e-09
16	16053328	3.86e-09	4.83e-09
17	15319648	3.13e-09	4.83e-09
18	13333155	1.58e-09	4.83e-09
19	12198306	1.43e-08	4.83e-09
20	12091001	1.43e-08	4.83e-09
21	8553409	1.43e-08	4.83e-09
22	16160689	1.43e-08	4.83e-09
23	7977799	1.43e-08	4.83e-09
24	7737077	1.43e-08	4.83e-09
25	7574731	1.43e-08	4.83e-09
26	6918023	1.43e-08	4.83e-09
27	6270716	1.43e-08	4.83e-09
28	5960150	1.43e-08	4.83e-09
29	1456683	1.43e-08	4.83e-09
30	1872559	1.43e-08	4.83e-09
Z	81233375	1.43e-08	4.83e-09
31	2637124	1.43e-08	4.83e-09
32	3473573	1.43e-08	4.83e-09
33	2151773	1.43e-08	4.83e-09
34	7214884	1.43e-08	4.83e-09
35	5548691	1.43e-08	4.83e-09
36	3997205	1.43e-08	4.83e-09
37	3148754	1.43e-08	4.83e-09
38	2836164	1.43e-08	4.83e-09
39	2018729	1.43e-08	4.83e-09
40	1354177	1.43e-08	4.83e-09

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

---

Demographic Models

ID	Description
MallardBlackDuck_2L19	North American Mallard/Black Duck split

North American Mallard/Black Duck split

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

Details

ID

MallardBlackDuck_2L19

Description

North American Mallard/Black Duck split

Num populations

3

Populations

Index	ID	Sampling time	Description
0	Mallard	None	Wild North American mallards
1	Black_duck	None	Wild black ducks
2	Ancestral	158076.25	Ancestral population

Citations

• Lavretsky et al., 2019. https://doi.org/10.1111/mec.15343

Demographic Model parameters

Parameter Type (units)	Value	Description
Population size	819,535	Ancestral pop. size
Population size	1,570,000	Mallard pop. size
Population size	1,370,000	Black duck pop. size
Migration rate (x10^-6 per gen.)	0.84	Black-Mallard migration rate
Migration rate (x10^-6 per gen.)	1.10	Mallard-Black migration rate
Epoch Time (gen.)	158076	Mallard/Black split time
Generation time (yrs.)	4	Generation time
Mutation rate (subst/gen)	4.83e-9	Mutation rate

Anolis carolinensis

ID

AnoCar

Name

Anolis carolinensis

Common name

Anole lizard

Generation time

1.5 (Lovern et al., 2004)

Population size

3050000.0 (Pombi et al., 2019)

Genome

ID	Length	Recombination rate	Mutation rate
1	263920458	1e-08	2.1e-10
2	199619895	1e-08	2.1e-10
3	204416410	1e-08	2.1e-10
4	156502444	1e-08	2.1e-10
5	150641573	1e-08	2.1e-10
6	80741955	1e-08	2.1e-10
LGa	7025928	1e-08	2.1e-10
LGb	3271537	1e-08	2.1e-10
LGc	9478905	1e-08	2.1e-10
LGd	1094478	1e-08	2.1e-10
LGf	4257874	1e-08	2.1e-10
LGg	424765	1e-08	2.1e-10
LGh	248369	1e-08	2.1e-10
MT	17223	0	2.1e-10

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

---

Anopheles gambiae

ID

AnoGam

Name

Anopheles gambiae

Common name

Anopheles gambiae

Generation time

0.09090909090909091 (Ag1000G Consortium, 2017)

Population size

1000000.0 (Ag1000G Consortium, 2017)

Genome

ID	Length	Recombination rate	Mutation rate
2L	49364325	1.3e-08	3.5e-09
2R	61545105	1.3e-08	3.5e-09
3L	41963435	1.3e-08	3.5e-09
3R	53200684	1.6e-08	3.5e-09
X	24393108	2.04e-08	3.5e-09
Mt	15363	0	3.5e-09

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

---

Demographic Models

ID	Description
GabonAg1000G_1A17	Stairwayplot estimates of N(t) for Gabon sample

Stairwayplot estimates of N(t) for Gabon sample

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

Details

ID

GabonAg1000G_1A17

Description

Stairwayplot estimates of N(t) for Gabon sample

Num populations

1

Populations

Index	ID	Sampling time	Description
0	GAS	0	Gabon gambiae population

Citations

• Ag1000G Consortium, 2017. https://doi.org/10.1038/nature24995

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

Apis mellifera

ID

ApiMel

Name

Apis mellifera

Common name

Apis mellifera (DH4)

Generation time

2 (Nelson et al., 2017)

Population size

200000.0 (Wallberg et al., 2014)

Genome

ID	Length	Recombination rate	Mutation rate
CM009931.2	27754200	2.39e-07	3.4e-09
CM009932.2	16089512	2.46e-07	3.4e-09
CM009933.2	13619445	2.41e-07	3.4e-09
CM009934.2	13404451	2.76e-07	3.4e-09
CM009935.2	13896941	2.14e-07	3.4e-09
CM009936.2	17789102	2.12e-07	3.4e-09
CM009937.2	14198698	2.34e-07	3.4e-09
CM009938.2	12717210	2.09e-07	3.4e-09
CM009939.2	12354651	2.46e-07	3.4e-09
CM009940.2	12360052	2.48e-07	3.4e-09
CM009941.2	16352600	2.03e-07	3.4e-09
CM009942.2	11514234	2.12e-07	3.4e-09
CM009943.2	11279722	2.34e-07	3.4e-09
CM009944.2	10670842	2.46e-07	3.4e-09
CM009945.2	9534514	2.21e-07	3.4e-09
CM009946.2	7238532	2.28e-07	3.4e-09
CM009947.2	16343	0	3.4e-09

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

---

Arabidopsis thaliana

ID

AraTha

Name

Arabidopsis thaliana

Common name

A. thaliana

Generation time

1.0 (Donohue, 2002)

Population size

10000 (1001GenomesConsortium, 2016)

Genome

ID	Length	Recombination rate	Mutation rate
1	30427671	8.06452e-10	7e-09
2	19698289	8.06452e-10	7e-09
3	23459830	8.06452e-10	7e-09
4	18585056	8.06452e-10	7e-09
5	26975502	8.06452e-10	7e-09
Mt	366924	0	7e-09
Pt	154478	0	7e-09

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

---

Genetic Maps

ID	Year	Description
SalomeAveraged_TAIR10	2012	Crossover frequency map averaged over 17 populations

SalomeAveraged_TAIR10

This map is based on the study of crossover frequencies in over 7000 plants in 17 F2 populations derived from crosses between 18 A. thaliana accessions. Salomé et al provide genetic maps for each of these populations. To get a single map for each chromosome, the Haldane map function distances were converted to recombination rates (cM/Mb) for each cross and then averaged across the 17 populations using loess. The map was constructed on genome version TAIR7, and lifted to TAIR10.

Citations

• Salomé et al., 2012. https://doi.org/10.1038/hdy.2011.95

---

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

• Durvasula et al., 2017. https://doi.org/10.1073/pnas.1616736114

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

---

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

• Huber et al., 2018. https://doi.org/10.1038/s41467-018-05281-7

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

---

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

• Huber et al., 2018. https://doi.org/10.1038/s41467-018-05281-7

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

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

• Cheng et al, 2017. http://dx.doi.org/10.1111/tpj.13415

araport_11_CDS

Araport11 exon annotations on TAIR10

Citations

• Cheng et al, 2017. http://dx.doi.org/10.1111/tpj.13415

---

Distribution of Fitness Effects (DFEs)

ID	Year	Description
Gamma_H18	2018	Deleterious Gamma DFE

Gamma_H18

Deleterious Gamma DFE

Citations

• Huber et al., 2018. https://doi.org/10.1038/s41467-018-05281-7

---

Bos taurus

ID

BosTau

Name

Bos taurus

Common name

Cattle

Generation time

5 (MacLeod et al., 2013)

Population size

62000 (MacLeod et al., 2013)

Genome

ID	Length	Recombination rate	Mutation rate
1	158534110	9.26e-09	1.2e-08
2	136231102	9.26e-09	1.2e-08
3	121005158	9.26e-09	1.2e-08
4	120000601	9.26e-09	1.2e-08
5	120089316	9.26e-09	1.2e-08
6	117806340	9.26e-09	1.2e-08
7	110682743	9.26e-09	1.2e-08
8	113319770	9.26e-09	1.2e-08
9	105454467	9.26e-09	1.2e-08
10	103308737	9.26e-09	1.2e-08
11	106982474	9.26e-09	1.2e-08
12	87216183	9.26e-09	1.2e-08
13	83472345	9.26e-09	1.2e-08
14	82403003	9.26e-09	1.2e-08
15	85007780	9.26e-09	1.2e-08
16	81013979	9.26e-09	1.2e-08
17	73167244	9.26e-09	1.2e-08
18	65820629	9.26e-09	1.2e-08
19	63449741	9.26e-09	1.2e-08
20	71974595	9.26e-09	1.2e-08
21	69862954	9.26e-09	1.2e-08
22	60773035	9.26e-09	1.2e-08
23	52498615	9.26e-09	1.2e-08
24	62317253	9.26e-09	1.2e-08
25	42350435	9.26e-09	1.2e-08
26	51992305	9.26e-09	1.2e-08
27	45612108	9.26e-09	1.2e-08
28	45940150	9.26e-09	1.2e-08
29	51098607	9.26e-09	1.2e-08
X	139009144	9.26e-09	1.2e-08
MT	16338	0	1.2e-08

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

---

Demographic Models

ID	Description
HolsteinFriesian_1M13	Piecewise size changes in Holstein-Friesian cattle.

Piecewise size changes in Holstein-Friesian cattle.

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

Details

ID

HolsteinFriesian_1M13

Description

Piecewise size changes in Holstein-Friesian cattle.

Num populations

1

Populations

Index	ID	Sampling time	Description
0	Holstein_Friesian	0	Holstein-Friesian

Citations

• MacLeod et al., 2013. https://doi.org/10.1093/molbev/mst125

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

Caenorhabditis elegans

ID

CaeEle

Name

Caenorhabditis elegans

Common name

C. elegans

Generation time

0.01 (Frézal & Félix, 2015)

Population size

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

Genome

ID	Length	Recombination rate	Mutation rate
I	15072434	3.12163e-11	1.84e-09
II	15279421	3.52929e-11	1.84e-09
III	13783801	3.9066e-11	1.84e-09
IV	17493829	2.7121e-11	1.84e-09
V	20924180	2.47057e-11	1.84e-09
X	17718942	2.94724e-11	1.84e-09
MtDNA	13794	0	1.05e-07

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

---

Genetic Maps

ID	Year	Description
RockmanRIAIL_ce11	2009	Genetic map from recombinant inbred advanced intercross lines

RockmanRIAIL_ce11

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

Citations

• Rockman & Kruglyak, 2009. https://doi.org/10.1371/journal.pgen.1000419

---

Canis familiaris

ID

CanFam

Name

Canis familiaris

Common name

Dog

Generation time

3

Population size

13000 (Lindblad-Toh et al., 2005)

Genome

ID	Length	Recombination rate	Mutation rate
1	122678785	7.636e-09	4e-09
2	85426708	8.79852e-09	4e-09
3	91889043	8.00087e-09	4e-09
4	88276631	8.0523e-09	4e-09
5	88915250	9.34433e-09	4e-09
6	77573801	8.19219e-09	4e-09
7	80974532	7.29347e-09	4e-09
8	74330416	8.29131e-09	4e-09
9	61074082	9.28772e-09	4e-09
10	69331447	9.10715e-09	4e-09
11	74389097	7.63945e-09	4e-09
12	72498081	7.76106e-09	4e-09
13	63241923	8.41302e-09	4e-09
14	60966679	9.02812e-09	4e-09
15	64190966	7.85675e-09	4e-09
16	59632846	8.61406e-09	4e-09
17	64289059	9.71883e-09	4e-09
18	55844845	1.02993e-08	4e-09
19	53741614	1.04251e-08	4e-09
20	58134056	9.99097e-09	4e-09
21	50858623	1.0339e-08	4e-09
22	61439934	8.61505e-09	4e-09
23	52294480	9.12664e-09	4e-09
24	47698779	1.1146e-08	4e-09
25	51628933	1.15437e-08	4e-09
26	38964690	1.20846e-08	4e-09
27	45876710	1.12603e-08	4e-09
28	41182112	1.24636e-08	4e-09
29	41845238	1.10136e-08	4e-09
30	40214260	1.16876e-08	4e-09
31	39895921	1.13977e-08	4e-09
32	38810281	1.15559e-08	4e-09
33	31377067	1.33394e-08	4e-09
34	42124431	1.04838e-08	4e-09
35	26524999	1.42991e-08	4e-09
36	30810995	1.18752e-08	4e-09
37	30902991	1.38346e-08	4e-09
38	23914537	1.43637e-08	4e-09
X	123869142	9.50648e-09	4e-09
MT	16727	0	4e-09

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

---

Genetic Maps

ID	Year	Description
Campbell2016_CanFam3_1	2016	Pedigree-based crossover map from 237 individuals

Campbell2016_CanFam3_1

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

Citations

• Campbell et al., 2016. https://doi.org/10.1534/g3.116.034678

---

Chlamydomonas reinhardtii

ID

ChlRei

Name

Chlamydomonas reinhardtii

Common name

Chlamydomonas reinhardtii

Generation time

0.001141552511415525 (Vítová et al, 2011)

Population size

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

Genome

ID	Length	Recombination rate	Mutation rate
1	8033585	1.21e-10	9.74e-10
2	9223677	1.49e-10	8.62e-10
3	9219486	1.52e-10	9.5e-10
4	4091191	1.47e-10	9.66e-10
5	3500558	1.7e-10	1.17e-09
6	9023763	1.17e-10	9.12e-10
7	6421821	8.66e-11	9.14e-10
8	5033832	1.39e-10	8.98e-10
9	7956127	1.12e-10	9.17e-10
10	6576019	1.97e-10	9.27e-10
11	3826814	1.63e-10	1.03e-09
12	9730733	9.15e-11	9.55e-10
13	5206065	1.43e-10	7.56e-10
14	4157777	1.9e-10	8.96e-10
15	1922860	3.93e-10	6.91e-10
16	7783580	1.71e-10	9.59e-10
17	7188315	1.83e-10	1.05e-09

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

---

Drosophila melanogaster

ID

DroMel

Name

Drosophila melanogaster

Common name

D. melanogaster

Generation time

0.1 (Li et al., 2006)

Population size

1720600 (Li et al., 2006)

Genome

Mean gene conversion fraction

0.8299999999999998

Range gene conversion lengths

518

ID	Length	Recombination rate	Mutation rate
2L	23513712	2.40463e-08	5.49e-09
2R	25286936	2.23459e-08	5.49e-09
3L	28110227	1.7966e-08	5.49e-09
3R	32079331	1.71642e-08	5.49e-09
4	1348131	0	5.49e-09
X	23542271	2.89651e-08	5.49e-09
Y	3667352	0	5.49e-09
mitochondrion_genome	19524	0	5.49e-09

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

---

Genetic Maps

ID	Year	Description
ComeronCrossover_dm6	2012	Crossover map from meioses products of 8 lab crosses
ComeronCrossoverV2_dm6	2012	Crossover map from meioses products of 8 lab crosses

ComeronCrossover_dm6

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

Citations

• Comeron et al, 2012. https://doi.org/10.1371/journal.pgen.1002905

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

• Comeron et al, 2012. https://doi.org/10.1371/journal.pgen.1002905

---

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

• Sheehan and Song, 2016. https://doi.org/10.1371/journal.pcbi.1004845

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

---

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

• Li et al., 2006. https://doi.org/10.1371/journal.pgen.0020166

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

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

• Hoskins et al, 2014. https://doi.org/10.1101/gr.185579.114

FlyBase_BDGP6.32.51_CDS

FlyBase CDS annotations on BDGP6

Citations

• Hoskins et al, 2014. https://doi.org/10.1101/gr.185579.114

---

Distribution of Fitness Effects (DFEs)

ID	Year	Description
Gamma_H17	2017	Deleterious Gamma DFE
LognormalPlusPositive_R16	2016	Deleterious log-normal and beneficial mixed DFE

Gamma_H17

Deleterious Gamma DFE

Citations

• Huber et al., 2017. https://doi.org/10.1073/pnas.1619508114

LognormalPlusPositive_R16

Deleterious log-normal and beneficial mixed DFE

Citations

• Ragsdale et al., 2016. https://doi.org/10.1534/genetics.115.184812

---

Drosophila sechellia

ID

DroSec

Name

Drosophila sechellia

Common name

Drosophila sechellia

Generation time

0.05 (Legrand et al., 2009)

Population size

100000 (Legrand et al., 2009)

Genome

ID	Length	Recombination rate	Mutation rate
2L	24956976	2.28e-08	1.5e-09
2R	21536224	2.51e-08	1.5e-09
3L	28131630	1.88e-08	1.5e-09
3R	30464902	1.91e-08	1.5e-09
X	22909512	2.85e-08	1.5e-09
4	1277805	0	1.5e-09

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

---

Escherichia coli

ID

EscCol

Name

Escherichia coli

Common name

E. coli

Generation time

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

Population size

180000000.0 (Hartl, Moriyama, and Sawyer, 1994)

Genome

Bacterial recombination with tract length range

542

ID	Length	Recombination rate	Mutation rate
Chromosome	4641652	8.9e-11	8.9e-11

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

---

Gasterosteus aculeatus

ID

GasAcu

Name

Gasterosteus aculeatus

Common name

Three-spined stickleback

Generation time

2 (Liu et al., 2016)

Population size

10000.0 (Liu et al., 2016)

Genome

ID	Length	Recombination rate	Mutation rate
1	29619991	3.11e-08	3.7e-08
2	23686546	3.11e-08	3.7e-08
3	17759012	3.11e-08	3.7e-08
4	34181212	3.11e-08	3.7e-08
5	15550311	3.11e-08	3.7e-08
6	18825451	3.11e-08	3.7e-08
7	30776923	3.11e-08	3.7e-08
8	20553084	3.11e-08	3.7e-08
9	20843631	3.11e-08	3.7e-08
10	17985176	3.11e-08	3.7e-08
11	17651971	3.11e-08	3.7e-08
12	20694444	3.11e-08	3.7e-08
13	20748428	3.11e-08	3.7e-08
14	16147532	3.11e-08	3.7e-08
15	17318724	3.11e-08	3.7e-08
16	19507025	3.11e-08	3.7e-08
17	20195758	3.11e-08	3.7e-08
18	15939336	3.11e-08	3.7e-08
19	20580295	3.11e-08	3.7e-08
20	20445003	3.11e-08	3.7e-08
21	17421465	3.11e-08	3.7e-08
Y	15859692	0	3.7e-08
MT	16543	0	3.7e-08

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

---

Helianthus annuus

ID

HelAnn

Name

Helianthus annuus

Common name

Helianthus annuus

Generation time

1.0 (Strasburg and Rieseberg, 2008)

Population size

673968 (Strasburg et al., 2010)

Genome

ID	Length	Recombination rate	Mutation rate
1	149502186	4e-09	6.1e-09
2	174800439	4e-09	6.1e-09
3	176490873	4e-09	6.1e-09
4	208320189	4e-09	6.1e-09
5	178169690	4e-09	6.1e-09
6	148147350	4e-09	6.1e-09
7	149542083	4e-09	6.1e-09
8	167167940	4e-09	6.1e-09
9	189665024	4e-09	6.1e-09
10	181411567	4e-09	6.1e-09
11	189830405	4e-09	6.1e-09
12	163781230	4e-09	6.1e-09
13	173487274	4e-09	6.1e-09
14	173346949	4e-09	6.1e-09
15	175671323	4e-09	6.1e-09
16	206736614	4e-09	6.1e-09
17	195042445	4e-09	6.1e-09

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

---

Heliconius melpomene

ID

HelMel

Name

Heliconius melpomene

Common name

Heliconius melpomene

Generation time

0.0958904109589041 (Pardo-Diaz et al, 2012)

Population size

2111109 (Pardo-Diaz et al, 2012)

Genome

ID	Length	Recombination rate	Mutation rate
1	17206585	3.17e-08	2.9e-09
2	9045316	5.61e-08	2.9e-09
3	10541528	5.1e-08	2.9e-09
4	9662098	4.97e-08	2.9e-09
5	9908586	5.15e-08	2.9e-09
6	14054175	3.4e-08	2.9e-09
7	14308859	3.76e-08	2.9e-09
8	9320449	5.28e-08	2.9e-09
9	8708747	5.31e-08	2.9e-09
10	17965481	3.16e-08	2.9e-09
11	11759272	4.47e-08	2.9e-09
12	16327298	3.13e-08	2.9e-09
13	18127314	3.08e-08	2.9e-09
14	9174305	5.47e-08	2.9e-09
15	10235750	4.78e-08	2.9e-09
16	10083215	4.71e-08	2.9e-09
17	14773299	3.94e-08	2.9e-09
18	16803890	3.16e-08	2.9e-09
19	16399344	3.11e-08	2.9e-09
20	14871695	3.45e-08	2.9e-09
21	13359691	3.71e-08	2.9e-09

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

---

Homo sapiens

ID

HomSap

Name

Homo sapiens

Common name

Human

Generation time

30 (Tremblay and Vézina, 2000)

Population size

10000 (Takahata, 1993)

Genome

ID	Length	Recombination rate	Mutation rate
1	248956422	1.15235e-08	1.29e-08
2	242193529	1.10429e-08	1.29e-08
3	198295559	1.12585e-08	1.29e-08
4	190214555	1.1482e-08	1.29e-08
5	181538259	1.12443e-08	1.29e-08
6	170805979	1.12659e-08	1.29e-08
7	159345973	1.17713e-08	1.29e-08
8	145138636	1.16049e-08	1.29e-08
9	138394717	1.21987e-08	1.29e-08
10	133797422	1.33337e-08	1.29e-08
11	135086622	1.17213e-08	1.29e-08
12	133275309	1.30981e-08	1.29e-08
13	114364328	1.3061e-08	1.29e-08
14	107043718	1.36298e-08	1.29e-08
15	101991189	1.73876e-08	1.29e-08
16	90338345	1.48315e-08	1.29e-08
17	83257441	1.55383e-08	1.29e-08
18	80373285	1.46455e-08	1.29e-08
19	58617616	1.83848e-08	1.29e-08
20	64444167	1.67886e-08	1.29e-08
21	46709983	1.72443e-08	1.29e-08
22	50818468	2.10572e-08	1.29e-08
X	156040895	1.18483e-08	1.29e-08
Y	57227415	0	1.29e-08
MT	16569	0	1.29e-08

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

---

Genetic Maps

ID	Year	Description
HapMapII_GRCh37	2007	HapMap Phase II lifted over to GRCh37
HapMapII_GRCh38	2007	HapMap Phase II lifted over to GRCh37 then lifted over to GRCh38
DeCodeSexAveraged_GRCh36	2010	Sex averaged map from deCode family study
DeCodeSexAveraged_GRCh38	2010	Sex averaged map from deCode family study
PyrhoACB_GRCh38	2019	Pyrho population-specific map for ACB
PyrhoASW_GRCh38	2019	Pyrho population-specific map for ASW
PyrhoBEB_GRCh38	2019	Pyrho population-specific map for BEB
PyrhoCDX_GRCh38	2019	Pyrho population-specific map for CDX
PyrhoCEU_GRCh38	2019	Pyrho population-specific map for CEU
PyrhoCHB_GRCh38	2019	Pyrho population-specific map for CHB
PyrhoCHS_GRCh38	2019	Pyrho population-specific map for CHS
PyrhoCLM_GRCh38	2019	Pyrho population-specific map for CLM
PyrhoESN_GRCh38	2019	Pyrho population-specific map for ESN
PyrhoFIN_GRCh38	2019	Pyrho population-specific map for FIN
PyrhoGBR_GRCh38	2019	Pyrho population-specific map for GBR
PyrhoGIH_GRCh38	2019	Pyrho population-specific map for GIH
PyrhoGWD_GRCh38	2019	Pyrho population-specific map for GWD
PyrhoIBS_GRCh38	2019	Pyrho population-specific map for IBS
PyrhoITU_GRCh38	2019	Pyrho population-specific map for ITU
PyrhoJPT_GRCh38	2019	Pyrho population-specific map for JPT
PyrhoKHV_GRCh38	2019	Pyrho population-specific map for KHV
PyrhoLWK_GRCh38	2019	Pyrho population-specific map for LWK
PyrhoMSL_GRCh38	2019	Pyrho population-specific map for MSL
PyrhoMXL_GRCh38	2019	Pyrho population-specific map for MXL
PyrhoPEL_GRCh38	2019	Pyrho population-specific map for PEL
PyrhoPJL_GRCh38	2019	Pyrho population-specific map for PJL
PyrhoPUR_GRCh38	2019	Pyrho population-specific map for PUR
PyrhoSTU_GRCh38	2019	Pyrho population-specific map for STU
PyrhoTSI_GRCh38	2019	Pyrho population-specific map for TSI
PyrhoYRI_GRCh38	2019	Pyrho population-specific map for YRI

HapMapII_GRCh37

This genetic map is from the Phase II Hapmap project and based on 3.1 million genotyped SNPs from 270 individuals across four populations (YRI, CEU, CHB and JPT). Genome wide recombination rates were estimated using LDHat. This version of the HapMap genetic map was lifted over to GRCh37 (and adjusted in regions where the genome assembly had rearranged) for use in the 1000 Genomes project. Please see the README file on the 1000 Genomes download site for details of these adjustments. ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/working/20110106_recombination_hotspots

Citations

• The International HapMap Consortium, 2007. https://doi.org/10.1038/nature06258

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

• The International HapMap Consortium, 2007. https://doi.org/10.1038/nature06258

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

• Kong et al, 2010. https://doi.org/10.1038/nature09525

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

• Kong et al, 2010. https://doi.org/10.1038/nature09525

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

• Spence and Song, 2019. https://doi.org/10.1126/sciadv.aaw9206

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

• Spence and Song, 2019. https://doi.org/10.1126/sciadv.aaw9206

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

• Spence and Song, 2019. https://doi.org/10.1126/sciadv.aaw9206

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

• Spence and Song, 2019. https://doi.org/10.1126/sciadv.aaw9206

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

• Spence and Song, 2019. https://doi.org/10.1126/sciadv.aaw9206

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

• Spence and Song, 2019. https://doi.org/10.1126/sciadv.aaw9206

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

• Spence and Song, 2019. https://doi.org/10.1126/sciadv.aaw9206

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

• Spence and Song, 2019. https://doi.org/10.1126/sciadv.aaw9206

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

• Spence and Song, 2019. https://doi.org/10.1126/sciadv.aaw9206

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

• Spence and Song, 2019. https://doi.org/10.1126/sciadv.aaw9206

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

• Spence and Song, 2019. https://doi.org/10.1126/sciadv.aaw9206

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

• Spence and Song, 2019. https://doi.org/10.1126/sciadv.aaw9206

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

• Spence and Song, 2019. https://doi.org/10.1126/sciadv.aaw9206

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

• Spence and Song, 2019. https://doi.org/10.1126/sciadv.aaw9206

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

• Spence and Song, 2019. https://doi.org/10.1126/sciadv.aaw9206

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

• Spence and Song, 2019. https://doi.org/10.1126/sciadv.aaw9206

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

• Spence and Song, 2019. https://doi.org/10.1126/sciadv.aaw9206

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

• Spence and Song, 2019. https://doi.org/10.1126/sciadv.aaw9206

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

• Spence and Song, 2019. https://doi.org/10.1126/sciadv.aaw9206

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

• Spence and Song, 2019. https://doi.org/10.1126/sciadv.aaw9206

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

• Spence and Song, 2019. https://doi.org/10.1126/sciadv.aaw9206

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

• Spence and Song, 2019. https://doi.org/10.1126/sciadv.aaw9206

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

• Spence and Song, 2019. https://doi.org/10.1126/sciadv.aaw9206

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

• Spence and Song, 2019. https://doi.org/10.1126/sciadv.aaw9206

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

• Spence and Song, 2019. https://doi.org/10.1126/sciadv.aaw9206

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

• Spence and Song, 2019. https://doi.org/10.1126/sciadv.aaw9206

---

Demographic Models

ID	Description
OutOfAfricaExtendedNeandertalAdmixturePulse_3I21	Three population out-of-Africa with an extended pulse of Neandertal admixture into Europeans
OutOfAfrica_3G09	Three population out-of-Africa
OutOfAfrica_2T12	Two population out-of-Africa
Africa_1T12	African population
AmericanAdmixture_4B11	American admixture
OutOfAfricaArchaicAdmixture_5R19	Three population out-of-Africa with archaic admixture
Zigzag_1S14	Periodic growth and decline.
AncientEurasia_9K19	Multi-population model of ancient Eurasia
PapuansOutOfAfrica_10J19	Out-of-Africa with archaic admixture into Papuans
AshkSub_7G19	Ashkenazi Jewish with substructure and European admixture
OutOfAfrica_4J17	4 population out of Africa
Africa_1B08	African-americans population
AncientEurope_4A21	Multi-population model of ancient Europe

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

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

Details

ID

OutOfAfricaExtendedNeandertalAdmixturePulse_3I21

Description

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

Num populations

3

Populations

Index	ID	Sampling time	Description
0	YRI	0	1000 Genomes YRI (Yoruba)
1	CEU	0	1000 Genomes CEU (Utah Residents (CEPH) with Northern and Western European Ancestry)
2	NEA	0	Neandertals

Citations

• Iasi et al., 2021. https://doi.org/10.1093/molbev/msab210

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

---

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

• Gutenkunst et al., 2009. https://doi.org/10.1371/journal.pgen.1000695

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

---

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

• Tennessen et al., 2012. https://doi.org/10.1126/science.1219240

• Fu et al., 2013. https://doi.org/10.1038/nature11690

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

---

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

• Tennessen et al., 2012. https://doi.org/10.1126/science.1219240

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

---

American admixture

Demographic model for American admixture, taken from Browning et al. 2011. This model extends the Gravel et al. (2011) model of African/European/Asian demographic history to simulate an admixed population with admixture occurring 12 generations ago. The admixed population had an initial size of 30,000 and grew at a rate of 5% per generation, with 1/6 of the population of African ancestry, 1/3 European, and 1/2 Asian. Note that this demographic model was not inferred, and the mutation rate that Browning et al. used for simulation is smaller than used for inferring the model, so the mutation rate provided here is that from Gravel et al.

Details

ID

AmericanAdmixture_4B11

Description

American admixture

Num populations

4

Populations

Index	ID	Sampling time	Description
0	AFR	0	Contemporary African population
1	EUR	0	Contemporary European population
2	ASIA	0	Contemporary Asian population
3	ADMIX	0	Modern admixed population

Citations

• Browning et al., 2018. http://dx.doi.org/10.1371/journal.pgen.1007385

• Gravel et al., 2011. https://doi.org/10.1073/pnas.1019276108

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

---

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

• Ragsdale and Gravel, 2019. https://doi.org/10.1371/journal.pgen.1008204

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

---

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

• Schiffels and Durbin, 2014. https://doi.org/10.1038/ng.3015

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

---

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

• Kamm et al., 2019. https://doi.org/10.1080/01621459.2019.1635482

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

---

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

• Jacobs et al., 2019. https://doi.org/10.1016/j.cell.2019.02.035

• Malaspinas et al., 2016. https://doi.org/10.1038/nature18299

Demographic Model parameters

Parameter Type (units)	Value	Description
Population size	48,433	African pop. size
Population size	6,962	European pop. size
Population size	9,025	East Asian pop. size
Population size	8,834	Papuan pop. size
Population size	5,083	Altai Denisovan pop. size
Population size	826	Altai Neandertal pop. size
Population size	13,249	Introgressing Denisovan D1 pop. size
Population size	13,249	Introgressing Denisovan D2 pop. size
Population size	13,249	Introgressing Neandertal pop. size
Population size	8,516	Ghost (out-of-Africa lineage) pop. size
Population size	12,971	(European + East Asian) pop. size before divergence
Population size	41,563	(Ghost + African) pop. size before divergence
Population size	13,249	(Denisovan + Neandertal) pop. size before divergence
Population size	32,671	(Human + Archaic) pop. size before divergence
Population size	100	(Altai Denisovan + Introgressing Denisovan D1) pop. size before divergence
Population size	100	(Altai Denisovan + Introgressing Denisovan D2) pop. size before divergence
Population size	13,249	(Altai Neandertal + Introgressing Neandertal) pop. size before divergence
Time (yrs.)	37,497	Time of European and East Asian split
Time (yrs.)	50,982	Time of Ghost and (European + East Asian) split
Time (yrs.)	51,736	Time of Ghost and Papuan split
Time (yrs.)	64,322	Time of Ghost and African split
Time (yrs.)	97,875	Time of Altai Neandertal and Introgressing Neandertal split
Time (yrs.)	282,750	Time of Altai Denisovan and Introgressing Denisovan D1 split
Time (yrs.)	362,500	Time of Altai Denisovan and Introgressing Denisovan D2 split
Time (yrs.)	437,610	Time of Denisovan and Neandertal split
Time (yrs.)	586,525	Time of Human and Archaic split
Population size	2,231	(European + East Asian) bottleneck pop. size
Population size	243	Papuan bottleneck pop. size
Population size	1,394	Ghost (out-of-Africa) bottleneck pop. size
Time (yrs.)	48,111	Time of the (European + East Asian) bottleneck
Time (yrs.)	48,865	Time of the Papuan bottleneck
Time (yrs.)	61,451	Time of the Ghost (out-of-Africa) bottleneck
ADMIX percentage	2.2	Amount of Denisovan D1 admixture in Papaun pop.
ADMIX percentage	1.8	Amount of Denisovan D2 admixture in Papaun pop.
ADMIX percentage	2.4	Amount of Neandertal admixture in Ghost pop.
ADMIX percentage	1.1	Amount of Neandertal admixture in (European + East Asian) pop.
ADMIX percentage	0.2	Amount of Neandertal admixture in Papuan pop.
ADMIX percentage	0.2	Amount of Neandertal admixture in East Asian pop.
Time (yrs.)	29,800	Time of Denisovan D1 to Papuan admixture
Time (yrs.)	45,700	Time of Denisovan D2 to Papuan admixture
Time (yrs.)	53,737	Time of Neandertal to Ghost admixture
Time (yrs.)	45,414	Time of Neandertal to (European + East Asian) admixture
Time (yrs.)	40,948	Time of Neandertal to Papuan admixture
Time (yrs.)	25,607	Time of Neandertal to East Asian admixture
Migration rate (x10^-4)	1.79	Ghost–African migration rate
Migration rate (x10^-4)	4.42	Ghost–European migration rate
Migration rate (x10^-4)	31.4	European–East Asian migration rate
Migration rate (x10^-4)	57.2	East Asian–Papuan migration rate
Migration rate (x10^-4)	5.72	(European + East Asian)–Papuan migration rate
Migration rate (x10^-4)	4.42	(European + East Asian)–Ghost migration rate
Time (yrs.)	37,497	(European + East Asian)–Papuan migration begins
Time (yrs.)	37,497	(European + East Asian)–Ghost migration begins
Generation time (yrs.)	29	Generation time
Mutation rate	1.4e-8	Per-base per-generation mutation rate

---

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

• Gladstein and Hammer, 2019. https://doi.org/10.1093/molbev/msz047

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

---

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

• Jouganous et al., 2017. https://doi.org/10.1534/genetics.117.200493

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

---

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

• Boyko et al., 2008. https://doi.org/10.1371/journal.pgen.1000083

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

---

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

• Allentoft et al., 2022. https://doi.org/10.1101/2022.05.04.490594

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

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

• Hunt et al, 2018. https://doi.org/10.1093/database/bay119

ensembl_havana_104_CDS

Ensembl Havana CDS annotations on GRCh38

Citations

• Hunt et al, 2018. https://doi.org/10.1093/database/bay119

---

Distribution of Fitness Effects (DFEs)

ID	Year	Description
Gamma_K17	2017	Deleterious Gamma DFE
Gamma_H17	2017	Deleterious Gamma DFE

Gamma_K17

Deleterious Gamma DFE

Citations

• Kim et al., 2017. https://doi.org/10.1534/genetics.116.197145

Gamma_H17

Deleterious Gamma DFE

Citations

• Huber et al., 2017. https://doi.org/10.1073/pnas.1619508114

---

Pan troglodytes

ID

PanTro

Name

Pan troglodytes

Common name

Chimpanzee

Generation time

24.6 (Langergraber et al., 2012)

Population size

16781 (Stevison et al., 2015)

Genome

ID	Length	Recombination rate	Mutation rate
1	228573443	1.2e-08	1.6e-08
2A	111504155	1.2e-08	1.6e-08
2B	133216015	1.2e-08	1.6e-08
3	202621043	1.2e-08	1.6e-08
4	194502333	1.2e-08	1.6e-08
5	181907262	1.2e-08	1.6e-08
6	175400573	1.2e-08	1.6e-08
7	166211670	1.2e-08	1.6e-08
8	147911612	1.2e-08	1.6e-08
9	116767853	1.2e-08	1.6e-08
10	135926727	1.2e-08	1.6e-08
11	135753878	1.2e-08	1.6e-08
12	137163284	1.2e-08	1.6e-08
13	100452976	1.2e-08	1.6e-08
14	91965084	1.2e-08	1.6e-08
15	83230942	1.2e-08	1.6e-08
16	81586097	1.2e-08	1.6e-08
17	83181570	1.2e-08	1.6e-08
18	78221452	1.2e-08	1.6e-08
19	61309027	1.2e-08	1.6e-08
20	66533130	1.2e-08	1.6e-08
21	33445071	1.2e-08	1.6e-08
22	37823149	1.2e-08	1.6e-08
X	155549662	1.2e-08	1.6e-08
Y	26350515	1.2e-08	1.6e-08

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

---

Demographic Models

ID	Description
BonoboGhost_4K19	Ghost admixture into bonobos

Ghost admixture into bonobos

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

Details

ID

BonoboGhost_4K19

Description

Ghost admixture into bonobos

Num populations

4

Populations

Index	ID	Sampling time	Description
0	western	0	Contemporary Western Chimpanzees
1	central	0	Contemporary Central Chimpanzees
2	bonobo	0	Contemporary Bonobos
3	ghost	None	Extinct ghost lineage

Citations

• Kuhlwilm et al. 2019, 2019. https://doi.org/10.1038/s41559-019-0881-7

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

Papio anubis

ID

PapAnu

Name

Papio anubis

Common name

Olive baboon

Generation time

11 (Wu et. al., 2020)

Population size

335505 (Wall et. al., 2022)

Genome

ID	Length	Recombination rate	Mutation rate
1	218172882	9.92638e-09	5.7e-09
2	193660750	9.60544e-09	5.7e-09
3	184919515	9.02238e-09	5.7e-09
4	182120902	9.82513e-09	5.7e-09
5	173900761	9.5798e-09	5.7e-09
6	167138247	1.04979e-08	5.7e-09
7	161768468	1.11888e-08	5.7e-09
8	140274886	1.10899e-08	5.7e-09
9	127591819	1.13288e-08	5.7e-09
10	126462689	1.17532e-08	5.7e-09
11	125913696	1.18403e-08	5.7e-09
12	123343450	1.0824e-08	5.7e-09
13	106849001	1.24677e-08	5.7e-09
14	106654974	1.27419e-08	5.7e-09
15	91985775	1.26084e-08	5.7e-09
16	91184193	1.47616e-08	5.7e-09
17	74525926	1.5241e-08	5.7e-09
18	72894408	1.36841e-08	5.7e-09
19	72123344	1.30374e-08	5.7e-09
20	50021108	1.6772e-08	5.7e-09
X	142711496	1.18898e-08	5.7e-09
Y	8309886	0	5.7e-09

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

---

Genetic Maps

ID	Year	Description
Pyrho_PAnubis1_0	2022	Pyrho inferred genetic map for Papio Anubis

Pyrho_PAnubis1_0

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

Citations

• Wall et. al., 2022. https://doi.org/10.1093/gbe/evac040

---

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

• Wall et. al., 2022. https://doi.org/10.1093/gbe/evac040

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

Pongo abelii

ID

PonAbe

Name

Pongo abelii

Common name

Sumatran orangutan

Generation time

25 (Wich et al., 2008)

Population size

17900.0 (Locke et al., 2011)

Genome

ID	Length	Recombination rate	Mutation rate
1	227913704	5.72097e-09	1.5e-08
2A	109511694	6.74694e-09	1.5e-08
2B	129937803	6.08833e-09	1.5e-08
3	193656255	5.77615e-09	1.5e-08
4	189387572	6.06176e-09	1.5e-08
5	179185813	5.87839e-09	1.5e-08
6	169501136	5.89605e-09	1.5e-08
7	145408105	6.82979e-09	1.5e-08
8	144036388	6.34313e-09	1.5e-08
9	112206110	7.04756e-09	1.5e-08
10	132178492	6.94812e-09	1.5e-08
11	128122151	5.79185e-09	1.5e-08
12	132184051	6.04316e-09	1.5e-08
13	98475126	6.40817e-09	1.5e-08
14	88963417	6.11075e-09	1.5e-08
15	82547911	6.6315e-09	1.5e-08
16	68237989	6.76066e-09	1.5e-08
17	75914007	8.01983e-09	1.5e-08
18	75923960	6.40065e-09	1.5e-08
19	57575784	9.09647e-09	1.5e-08
20	60841859	6.31424e-09	1.5e-08
21	34683425	7.58867e-09	1.5e-08
22	35308119	9.83628e-09	1.5e-08
X	151242693	6.40288e-09	1.5e-08
MT	16499	0	1.5e-08

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

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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

• Nater et al., 2017. https://doi.org/10.1016/j.cub.2017.09.047

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

• Nater et al., 2017. https://doi.org/10.1016/j.cub.2017.09.047

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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

• Locke et al., 2011. http://doi.org/10.1038/nature09687

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

Streptococcus agalactiae

ID

StrAga

Name

Streptococcus agalactiae

Common name

Group B Streptococcus

Generation time

0.0027397260273972603 (Savageau M.A., 1983)

Population size

140000 (Da Cunha et al, 2014)

Genome

Bacterial recombination with tract length range

120000

ID	Length	Recombination rate	Mutation rate
1	2065074	1.53e-10	1.53e-09

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

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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.

• stdpopsim.PiecewiseConstantSize()

• stdpopsim.IsolationWithMigration()