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Qc bonobo ghost #1370

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Sep 25, 2022
Merged

Qc bonobo ghost #1370

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2 changes: 1 addition & 1 deletion stdpopsim/catalog/PanTro/demographic_models.py
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Original file line number Diff line number Diff line change
Expand Up @@ -187,7 +187,7 @@ def _bonobo_ghost():
time=T_bonobo_resize2,
initial_size=N_anc_bonobo2,
growth_rate=0.0,
population_id=1,
population_id=2,
),
msprime.MassMigration(
time=T_bonobo_split,
Expand Down
201 changes: 201 additions & 0 deletions stdpopsim/qc/PanTro.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,201 @@
import msprime
import stdpopsim

_species = stdpopsim.get_species("PanTro")


def KuhlwilmPan():
id = "PanTro"
populations = [
stdpopsim.Population(id="western", description=""),
stdpopsim.Population(id="central", description=""),
stdpopsim.Population(id="bonobo", description=""),
stdpopsim.Population(id="ghost", description=""),
]
citations = [
stdpopsim.Citation(
author="Kuhlwilm et al.",
year="2019",
doi="",
reasons={stdpopsim.CiteReason.DEM_MODEL},
)
]

generation_time = 25
mutation_rate = 1.2e-8 # per bp per generation

# parameter value definitions based on published values
# these are parameters from Table S3, B7 in Kuhlwilm et al., 2019
# corresponding to Table S4, Column H: "ABC flow AT"
Ne_west = 10100
Ne_cent = 73000
Ne_bonobo = 33500
Ne_ghost = 10000

Ne_WAnc = 11000
Ne_BAnc = 3900
Ne_BonAnc = 11100
Ne_CAnc = 103100
Ne_ChimpAnc = 10100
Ne_PanAnc = 14200
Ne_Anc = 10000

m_W_C = 57.5 / 4000
m_C_W = 89.7 / 4000
m_C_B = 14.5 / 4000
m_B_C = 21.7 / 4000
m_B_gh = 68 / 4000
m_Ch_B = 0.0004 / 4000
m_B_Ch = 0.0004 / 4000

T_chimp_ex = 1.00075 * 4000
T_bon_ex = 1.5505 * 4000
T_west_re = 2.61 * 4000
T_bon_re = 3.08 * 4000
T_cent_re = 3.78 * 4000
T_ghost_ex = 5 * 4000
T_ChimpAnc = 7 * 4000
T_PanAnc = 19.9 * 4000
T_BonAnc_re = 19.875 * 4000
T_Anc = 33.01 * 4000
T_Anc_ex = 12 * 4000
T_Anc_ex_stop = 15 * 4000

return stdpopsim.DemographicModel(
id=id,
description=id,
long_description=id,
populations=populations,
citations=citations,
generation_time=generation_time,
mutation_rate=mutation_rate,
population_configurations=[
msprime.PopulationConfiguration(
initial_size=Ne_west, metadata=populations[0].asdict()
),
msprime.PopulationConfiguration(
initial_size=Ne_cent, metadata=populations[1].asdict()
),
msprime.PopulationConfiguration(
initial_size=Ne_bonobo, metadata=populations[2].asdict()
),
msprime.PopulationConfiguration(
initial_size=Ne_ghost, metadata=populations[3].asdict()
),
],
demographic_events=[
msprime.MassMigration(
time=T_chimp_ex,
source=0,
destination=1,
proportion=m_W_C,
),
msprime.MassMigration(
time=T_chimp_ex,
source=1,
destination=0,
proportion=m_C_W,
),
msprime.MassMigration(
time=T_bon_ex,
source=1,
destination=2,
proportion=m_C_B,
),
msprime.MassMigration(
time=T_bon_ex,
source=2,
destination=1,
proportion=m_B_C,
),
msprime.PopulationParametersChange(
time=T_west_re,
initial_size=Ne_WAnc,
growth_rate=0.0,
population_id=0,
),
msprime.PopulationParametersChange(
time=T_bon_re,
initial_size=Ne_BAnc,
growth_rate=0.0,
population_id=2,
),
msprime.PopulationParametersChange(
time=T_cent_re,
initial_size=Ne_CAnc,
growth_rate=0.0,
population_id=1,
),
msprime.MassMigration(
time=T_ghost_ex,
source=2,
destination=3,
proportion=m_B_gh,
),
msprime.MassMigration(
time=T_ChimpAnc,
source=0,
destination=1,
proportion=1.0,
),
msprime.PopulationParametersChange(
time=T_ChimpAnc,
initial_size=Ne_ChimpAnc,
growth_rate=0.0,
population_id=1,
),
msprime.MigrationRateChange(
time=T_Anc_ex,
rate=m_Ch_B,
matrix_index=(2, 1),
),
msprime.MigrationRateChange(
time=T_Anc_ex,
rate=m_B_Ch,
matrix_index=(1, 2),
),
msprime.MigrationRateChange(
time=T_Anc_ex_stop,
rate=0,
matrix_index=(2, 1),
),
msprime.MigrationRateChange(
time=T_Anc_ex_stop,
rate=0,
matrix_index=(1, 2),
),
msprime.PopulationParametersChange(
time=T_BonAnc_re,
initial_size=Ne_BonAnc,
growth_rate=0.0,
population_id=2,
),
msprime.MassMigration(
time=T_PanAnc,
source=1,
destination=2,
proportion=1.0,
),
msprime.PopulationParametersChange(
time=T_PanAnc,
initial_size=Ne_PanAnc,
growth_rate=0.0,
population_id=2,
),
msprime.MassMigration(
time=T_Anc,
source=2,
destination=3,
proportion=1.0,
),
msprime.PopulationParametersChange(
time=T_Anc,
initial_size=Ne_Anc,
growth_rate=0.0,
population_id=3,
),
],
)


_species.get_demographic_model("BonoboGhost_4K19").register_qc(KuhlwilmPan())
1 change: 1 addition & 0 deletions stdpopsim/qc/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,3 +6,4 @@
from . import HomSap # NOQA
from . import PonAbe # NOQA
from . import PapAnu # NOQA
from . import PanTro # NOQA