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Fixing removal of the Boxer
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@gregorgorjanc
gregorgorjanc committed Dec 31, 2024
1 parent 6f1c850 commit 607ae85
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Showing 2 changed files with 54 additions and 42 deletions.
28 changes: 14 additions & 14 deletions docs/parameter_tables/CanFam/EarlyWolfAdmixture_6F14.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -4,25 +4,25 @@ Population size,"26,092",Israeli wolf pop. size
Population size,"11,427",Croatian wolf pop. size
Population size,"5,426",Chinese wolf pop. size
Population size,"19,446",Golden jackal pop. size
Population size,"793",Ancestral Basenji pop. size
Population size,"1,999",Ancestral Basenji-Dingo pop. size
Population size,"1,393",Ancestral Israeli-Croatian wolf pop. size
Population size,"12,627",Ancestral (Israeli-Croatian)-Chinese wolf pop. size
Population size,"44,993",Ancestral dog-wolf pop. size
Population size,"18,169",Ancestral (dog-wolf)-golden jackal (root) pop. size
Population size,"793",Ancestral (Boxer, Basenji) pop. size
Population size,"1,999",Ancestral ((Boxer, Basenji), Dingo) pop. size
Population size,"1,393",Ancestral (Israeli, Croatian) wolf pop. size
Population size,"12,627",Ancestral ((Israeli, Croatian), Chinese) wolf pop. size
Population size,"44,993",Ancestral (dog, wolf) pop. size
Population size,"18,169",Ancestral ((dog, wolf), golden jackal)root pop. size
Migration rate,0.18,Israeli wolf -> Basenji migration rate
Migration rate,0.07,Basenji -> Israeli wolf migration rate
Migration rate,0.03,Chinese wolf -> Dingo migration rate
Migration rate,0.04,Dingo -> Chinese wolf migration rate
Migration rate,0.00,Golden jackal -> Israeli wolf migration rate
Migration rate,0.05,Israeli wolf -> Golden jackal migration rate
Migration rate,0.02,Golden jackal -> Ancestral dog-wolf migration rate
Migration rate,0.99,Ancestral dog-wolf -> Golden jackal migration rate
Time (gen.),"12,102",Ancestral Basenji split time
Time (gen.),"12,795",Ancestral Basenji-Dingo split time
Time (gen.),"13,389",Ancestral Israeli-Croatian wolf split time
Time (gen.),"13,455",Ancestral (Israeli-Croatian)-Chinese wolf split time
Time (gen.),"14,874",Ancestral dog-wolf split time
Time (gen.),"398,262",Ancestral (dog-wolf)-golden jackal split time
Migration rate,0.02,Golden jackal -> Ancestral (dog, wolf) migration rate
Migration rate,0.99,Ancestral (dog, wolf) -> Golden jackal migration rate
Time (gen.),"12,102",Ancestral (Boxer, Basenji) split time
Time (gen.),"12,795",Ancestral ((Boxer, Basenji), Dingo) split time
Time (gen.),"13,389",Ancestral (Israeli, Croatian) wolf split time
Time (gen.),"13,455",Ancestral ((Israeli, Croatian), Chinese) wolf split time
Time (gen.),"14,874",Ancestral (dog, wolf) split time
Time (gen.),"398,262",Ancestral ((dog, wolf), golden jackal) split time
Generation time (yrs.),3,Generation time
Mutation rate,1e-8,Mutation rate
68 changes: 40 additions & 28 deletions stdpopsim/catalog/CanFam/demographic_models.py
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Original file line number Diff line number Diff line change
Expand Up @@ -32,8 +32,8 @@ def _dog_wolf_admixture():
end times of the two populations that define it (section S9.2.3 in S9).
While Boxer reference genome was used, no Boxer-specific parameters
were estimated in the model, hence Boxer was removed from this model
implementation. Boxer coalesced with Basenji, so Ancestral Basenji
population here is ancestral population to Boxer and Basenji.
implementation. Thence the ancestral Basenji population with its specific
Ne is for the Ancestral (Boxer, Basenji) population.
"""
citations = [
stdpopsim.Citation(
Expand All @@ -48,26 +48,27 @@ def _dog_wolf_admixture():
mutation_rate = 1e-8 # page 3

# Estimated (calibrated) effective population sizes, from Table S12
# no N_BOX provided in the paper
N_BSJ = 2639
N_DNG = 1914
N_ISW = 26092
N_CRW = 11427
N_CHW = 5426
N_GLJ = 19446
N_ancDOG1 = 793
N_ancDOG = 1999
N_ancWLF1 = 1393
N_ancWLF = 12627
N_ancDW = 44993
N_root = 18169
N_ancDOG1 = 793 # (Boxer, Basenji)
N_ancDOG = 1999 # ((Boxer, Basenji), Dingo)
N_ancWLF1 = 1393 # (Israeli, Croatian) wolf
N_ancWLF = 12627 # ((Israeli, Croatian), Chinese) wolf
N_ancDW = 44993 # (dog, wolf)
N_root = 18169 # ((dog, wolf), golden jackal)root

# Estimated (calibrated) divergence times, from Table S12
T_ancDOG1 = 12102
T_ancDOG = 12795
T_ancWLF1 = 13389
T_ancWLF = 13455
T_ancDW = 14874
T_ancroot = 398262
T_ancDOG1 = 12102 # (Boxer, Basenji)
T_ancDOG = 12795 # ((Boxer, Basenji), Dingo)
T_ancWLF1 = 13389 # (Israeli, Croatian) wolf
T_ancWLF = 13455 # ((Israeli, Croatian), Chinese) wolf
T_ancDW = 14874 # (dog, wolf)
T_ancroot = 398262 # ((dog, wolf), golden jackal)root

# Migration rates, from Table S12
# migration is constant continuous geneflow from the start and end times of
Expand All @@ -86,6 +87,8 @@ def _dog_wolf_admixture():
initial_size=N_BSJ,
name="BSJ",
description="Basenji",
initially_active=True,
# need initially_active=True due to the removal of Boxer
)
model.add_population(
initial_size=N_DNG,
Expand All @@ -112,36 +115,36 @@ def _dog_wolf_admixture():
name="GLJ",
description="Golden jackal",
)
model.add_population(
initial_size=N_ancDOG1,
name="ancDOG1",
description="Ancestral Basenji",
# we removed Boxer above
)
# model.add_population(
# initial_size=N_ancDOG1,
# name="ancDOG1",
# description="Ancestral (Boxer, Basenji)",
# )
# commenting ancDOG1 pop due to the removal of Boxer
model.add_population(
initial_size=N_ancDOG,
name="ancDOG",
description="Ancestral Basenji-Dingo",
description="Ancestral ((Boxer, Basenji), Dingo)",
)
model.add_population(
initial_size=N_ancWLF1,
name="ancWLF1",
description="Ancestral Israeli-Croatian wolf",
description="Ancestral (Israeli, Croatian) wolf",
)
model.add_population(
initial_size=N_ancWLF,
name="ancWLF",
description="Ancestral (Israeli-Croatian)-Chinese wolf",
description="Ancestral ((Israeli, Croatian), Chinese) wolf",
)
model.add_population(
initial_size=N_ancDW,
name="ancDW",
description="Ancestral dog-wolf",
description="Ancestral (dog, wolf)",
)
model.add_population(
initial_size=N_root,
name="root",
description="Ancestral (dog-wolf)-golden jackal (root)",
description="Ancestral ((dog, wolf), golden jackal)root",
)

model.set_migration_rate(rate=m_ISW_BSJ, source="BSJ", dest="ISW")
Expand All @@ -153,10 +156,19 @@ def _dog_wolf_admixture():
model.set_migration_rate(rate=m_GLJ_ancDW, source="ancDW", dest="GLJ")
model.set_migration_rate(rate=m_ancDW_GLJ, source="GLJ", dest="ancDW")

model.add_population_split(time=T_ancDOG1, derived=["BSJ"], ancestral="ancDOG1")
# we removed Boxer above
# model.add_population_split(
# time=T_ancDOG1, derived=["BOX", "BSJ"], ancestral="ancDOG1"
# )
# commenting out pop split above due to the removal of Boxer and
# instead changing Ne below for "Ancestral (Boxer, Basenji)"
model.add_population_parameters_change(
time=T_ancDOG1,
initial_size=N_ancDOG1,
population="BSJ",
)
# In the paper, the below split is (ancDOG1, DNG)ancDOG
model.add_population_split(
time=T_ancDOG, derived=["ancDOG1", "DNG"], ancestral="ancDOG"
time=T_ancDOG, derived=["BSJ", "DNG"], ancestral="ancDOG"
)
model.add_population_split(
time=T_ancWLF1, derived=["ISW", "CRW"], ancestral="ancWLF1"
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