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QC for OutOfAfrica_4J17 #1246

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May 13, 2022
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QC for OutOfAfrica_4J17 #1246

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90be49b
Implement Jouganous 2017 QC
jeffspence May 13, 2022
2356eed
switch to old msprime API for population splits
jeffspence May 13, 2022
0826dd9
clean up formatting with black
jeffspence May 13, 2022
0294f0e
More reformatting
jeffspence May 13, 2022
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96 changes: 96 additions & 0 deletions stdpopsim/qc/HomSap.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1258,6 +1258,102 @@ def ZigZag():
_species.get_demographic_model("Zigzag_1S14").register_qc(ZigZag())


def JouganousOOA2017():
"""
Four population OOA model from Jouganous et al. 2017, fit to the
SFS using moments. The populations are YRI, CEU, CHB, and JPT.
The model is shown in Figure 3 and the parameters are taken from
table 4.
The model includes population splits, directional migration and
exponential growth in the various populations. The model was fit
using data from 20 samples from each population and assumes a
mutation rate of 1.44e-8 per generation and a generation time
of 29 years.
"""
id = "QC-OutOfAfrica_4J17"

N_A = 11293
N_AF = 23721
N_B = 2831
N_EU0 = 2512
r_EU = 0.0016
N_AS0 = 1019
r_AS = 0.0026
N_JP0 = 4384
r_JP = 0.0129
m_AF_B = 16.8e-5
m_AF_EU = 1.14e-5
m_AF_AS = 0.56e-5
m_EU_AS = 4.75e-5
m_CH_JP = 3.3e-5
T_AF_y = 357e3
T_AF_g = int(T_AF_y / 29)
T_B_y = 119e3
T_B_g = int(T_B_y / 29)
T_EU_AS_y = 46e3
T_EU_AS_g = int(T_EU_AS_y / 29)
T_CH_JP_y = 9e3
T_CH_JP_g = int(T_CH_JP_y / 29)

N_curr_CEU = N_EU0 * math.exp(T_EU_AS_g * r_EU)
N_curr_CHB = N_AS0 * math.exp(T_EU_AS_g * r_AS)
N_curr_JPT = N_JP0 * math.exp(T_CH_JP_g * r_JP)

de = msprime.Demography()
de.add_population(name="YRI", initial_size=N_AF, initially_active=True)
de.add_population(
name="CEU", initial_size=N_curr_CEU, growth_rate=r_EU, initially_active=True
)
de.add_population(
name="CHB", initial_size=N_curr_CHB, growth_rate=r_AS, initially_active=True
)
de.add_population(
name="JPT", initial_size=N_curr_JPT, growth_rate=r_JP, initially_active=True
)

de.set_symmetric_migration_rate(["YRI", "CEU"], m_AF_EU)
de.set_symmetric_migration_rate(["YRI", "CHB"], m_AF_AS)
de.set_symmetric_migration_rate(["CEU", "CHB"], m_EU_AS)
de.set_symmetric_migration_rate(["CHB", "JPT"], m_CH_JP)

de.add_mass_migration(time=T_CH_JP_g, source="JPT", dest="CHB", proportion=1)
de.add_symmetric_migration_rate_change(
time=T_CH_JP_g, populations=["CHB", "JPT"], rate=0
)
de.add_mass_migration(time=T_EU_AS_g, source="CHB", dest="CEU", proportion=1)
de.add_symmetric_migration_rate_change(
time=T_EU_AS_g, populations=["CEU", "CHB"], rate=0
)
de.add_symmetric_migration_rate_change(
time=T_EU_AS_g, populations=["YRI", "CHB"], rate=0
)

de.add_population_parameters_change(
time=T_EU_AS_g, initial_size=N_B, growth_rate=0, population="CEU"
)
de.add_symmetric_migration_rate_change(
time=T_EU_AS_g, populations=["CEU", "YRI"], rate=m_AF_B
)
de.add_mass_migration(time=T_B_g, source="CEU", dest="YRI", proportion=1)
de.add_symmetric_migration_rate_change(
time=T_B_g, populations=["CEU", "YRI"], rate=0
)
de.add_population_parameters_change(time=T_AF_g, initial_size=N_A, population="YRI")

return stdpopsim.DemographicModel(
id=id,
description=id,
long_description=id,
generation_time=29,
model=de,
mutation_rate=1.44e-8,
population_id_map=None,
)


_species.get_demographic_model("OutOfAfrica_4J17").register_qc(JouganousOOA2017())


def Boyko2008():
"""
African-American two-epoch instantaneous growth model from Boyko et al
Expand Down