def test_bad_generation_time(self):
for generation_time in (-100, -1e-9, 0, float("inf")):
with self.assertRaises(ValueError):
DemeGraph(
description="test",
time_units="years",
generation_time=generation_time,
)
def zigzag():
N1 = 14312
N2 = 1431
g = DemeGraph(
description=
"Sequential exponential increase and decrease of population size.",
doi="10.1038/ng.3015",
time_units="years",
generation_time=30,
)
g.deme(
"ZigZag",
initial_size=N1,
epochs=[
Epoch(start_time=33.33, final_size=N2),
Epoch(start_time=133.33, final_size=N1),
Epoch(start_time=533.33, final_size=N2),
Epoch(start_time=2133.33, final_size=N1),
Epoch(start_time=8533.33, final_size=N2),
Epoch(start_time=34133.33, initial_size=N2),
],
)
return g
def IM(num_demes, N, m, time_units="generations", generation_time=1):
g = DemeGraph(
description="Isolation with migration.",
time_units=time_units,
generation_time=generation_time,
default_Ne=N,
)
for k in range(num_demes):
g.deme(f"D{k}")
g.symmetric_migration(*[deme.id for deme in g.demes], rate=m)
return g
def jacobs_papuans():
N_archaic = 13249
N_DeniAnc = 100
N_ghost = 8516
T_Eu_bottleneck = 1659
g = DemeGraph(
description="Jacobs et al. (2019) archaic admixture into Papuans",
doi="10.1016/j.cell.2019.02.035",
time_units="generations",
generation_time=29,
)
g.deme("ancestral_hominin", start_time=20225, initial_size=32671)
g.deme(
"archaic",
ancestor="ancestral_hominin",
start_time=15090,
initial_size=N_archaic,
)
g.deme("Den1",
ancestor="archaic",
start_time=12500,
initial_size=N_DeniAnc)
g.deme("Den2", ancestor="Den1", start_time=9750, initial_size=N_DeniAnc)
# Altai Denisovan (sampling lineage)
g.deme("DenAltai", ancestor="Den2", initial_size=5083)
# Introgressing Denisovan lineages 1 and 2
g.deme("DenI1", ancestor="Den2", initial_size=N_archaic)
g.deme("DenI2", ancestor="Den1", initial_size=N_archaic)
g.deme("Nea", ancestor="archaic", start_time=3375, initial_size=N_archaic)
# Altai Neanderthal (sampling lineage)
g.deme("NeaAltai", ancestor="Nea", initial_size=826)
# Introgressing Neanderthal lineage
g.deme("NeaI", ancestor="Nea", start_time=883, initial_size=N_archaic)
g.deme("AMH",
ancestor="ancestral_hominin",
start_time=2218,
initial_size=41563)
g.deme("Africa", ancestor="AMH", initial_size=48433)
g.deme(
"Ghost1",
ancestor="AMH",
start_time=1784,
initial_size=N_ghost,
epochs=[
# bottleneck
Epoch(start_time=2119, initial_size=1394),
Epoch(start_time=2218, initial_size=N_ghost),
],
)
g.deme("Ghost2", ancestor="Ghost1", start_time=1758, initial_size=N_ghost)
g.deme("Ghost3", ancestor="Ghost2", initial_size=N_ghost)
g.deme(
"Papua",
ancestor="Ghost1",
initial_size=8834,
# bottleneck
epochs=[Epoch(start_time=1685, initial_size=243)],
)
g.deme(
"Eurasia",
ancestor="Ghost2",
start_time=1293,
initial_size=12971,
# bottleneck
epochs=[Epoch(start_time=T_Eu_bottleneck, initial_size=2231)],
)
g.deme("WestEurasia", ancestor="Eurasia", initial_size=6962)
g.deme("EastAsia", ancestor="Eurasia", initial_size=9025)
g.symmetric_migration("Africa",
"Ghost3",
rate=1.79e-4,
end_time=T_Eu_bottleneck)
g.symmetric_migration("Ghost3", "WestEurasia", rate=4.42e-4)
g.symmetric_migration("WestEurasia", "EastAsia", rate=3.14e-5)
g.symmetric_migration("EastAsia", "Papua", rate=5.72e-5)
g.symmetric_migration("Eurasia",
"Papua",
rate=5.72e-4,
end_time=T_Eu_bottleneck)
g.symmetric_migration("Ghost3",
"Eurasia",
rate=4.42e-4,
end_time=T_Eu_bottleneck)
g.pulse(source="EastAsia", dest="NeaI", proportion=0.002, time=883)
g.pulse(source="Papua", dest="NeaI", proportion=0.002, time=1412)
g.pulse(source="Eurasia", dest="NeaI", proportion=0.011, time=1566)
g.pulse(source="Ghost1", dest="NeaI", proportion=0.024, time=1853)
m_Den_Papuan = 0.04
p = 0.55 # S10.i p. 31
T_Den1_Papuan_mig = 29.8e3 / g.generation_time
T_Den2_Papuan_mig = 45.7e3 / g.generation_time
g.pulse(
source="Papua",
dest="DenI1",
proportion=p * m_Den_Papuan,
time=T_Den1_Papuan_mig,
)
g.pulse(
source="Papua",
dest="DenI2",
proportion=(1 - p) * m_Den_Papuan,
time=T_Den2_Papuan_mig,
)
return g
def browning_america():
g = DemeGraph(
description=
"Browning et al. (2011) model of admixture in the Americas.",
doi="10.1371/journal.pgen.1007385",
time_units="generations",
generation_time=25,
# generation_time_unit="years",
)
g.deme("ancestral", start_time=5920, initial_size=7310)
g.deme("AMH", ancestor="ancestral", start_time=2040, initial_size=14474)
g.deme("AFR", ancestor="AMH", initial_size=14474)
g.deme("OOA", ancestor="AMH", start_time=920, initial_size=1861)
g.deme("EUR", ancestor="OOA", initial_size=34039, final_size=1000)
g.deme("EAS", ancestor="OOA", initial_size=45852, final_size=510)
g.subgraph(
"ADMIX",
ancestors=["AFR", "EUR", "EAS"],
proportions=[1 / 6, 1 / 3, 1 / 2],
end_time=12,
initial_size=54664,
final_size=30000,
)
g.symmetric_migration("AFR", "OOA", rate=15e-5)
g.symmetric_migration("AFR", "EUR", rate=2.5e-5)
g.symmetric_migration("AFR", "EAS", rate=0.78e-5)
g.symmetric_migration("EUR", "EAS", rate=3.11e-5)
return g
def gutenkunst_ooa():
g = DemeGraph(
description="Gutenkunst et al. (2009) three-population model.",
doi="10.1371/journal.pgen.1000695",
time_units="years",
generation_time=25,
)
g.deme("ancestral", start_time=220e3, initial_size=7300)
g.deme("AMH", ancestor="ancestral", start_time=140e3, initial_size=12300)
g.deme("OOA", ancestor="AMH", start_time=21.2e3, initial_size=2100)
g.deme("YRI", ancestor="AMH", initial_size=12300)
g.deme("CEU", ancestor="OOA", initial_size=29725, final_size=1000)
g.deme("CHB", ancestor="OOA", initial_size=54090, final_size=510)
g.symmetric_migration("YRI", "OOA", rate=25e-5 / g.generation_time)
g.symmetric_migration("YRI", "CEU", rate=3e-5 / g.generation_time)
g.symmetric_migration("YRI", "CHB", rate=1.9e-5 / g.generation_time)
g.symmetric_migration("CEU", "CHB", rate=9.6e-5 / g.generation_time)
return g