mallard demographic model

docs/parameter_tables/AnaPla/MallardBlackDuck_2L19.csv

@@ -0,0 +1,8 @@
+Population size,"2,940,000",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

stdpopsim/catalog/AnaPla/__init__.py

@@ -2,3 +2,4 @@
 Catalog definitions for AnaPla (Ensembl ID='anas_platyrhynchos')
 """
 from . import species  # noqa: F401
+from . import demographic_models  # noqa: F401

stdpopsim/catalog/AnaPla/demographic_models.py

@@ -0,0 +1,69 @@
+import msprime
+
+import stdpopsim
+
+_species = stdpopsim.get_species("AnaPla")
+
+
+def _mallard_black_split():
+    id = "MallardBlackDuck_2L19"
+    description = "North American Mallard/Black Duck split"
+    long_description = """
+        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.
+    """
+    T = 632305 / 4  # in generations, not years
+    N_BlackDuck = 1.57e6
+    N_Mallard = 1.37e6
+    # personal communication from Joshua Brown 13 Apr 2021:
+    # "Based on the contemporary dataset, the ancestral population size
+    # "for the Black duck/Mallard dadi model was 819535."
+    N_Anc = 819535
+    # the migration rate is reported as 2.82 in each direction.  From the dadi
+    # manual, m12 is "the fraction of individuals each generation in pop 1 that
+    # are new migrants from pop 2, times the 2Nref". To convert back to real
+    # time units (fraction replaced per generation) we divide by 2 * N_anc.
+    m = 2.82 / (2 * N_Anc)
+
+    model = msprime.Demography()
+    model.add_population(
+        initial_size=N_Mallard,
+        name="Mallard",
+        description="Wild North American mallards",
+    )
+    model.add_population(
+        initial_size=N_BlackDuck,
+        name="Black_duck",
+        description="Wild black ducks",
+    )
+    model.add_population(
+        initial_size=N_Anc,
+        name="Ancestral",
+        description="Ancestral population",
+    )
+    model.set_symmetric_migration_rate(populations=["Mallard", "Black_duck"], rate=m)
+
+    model.add_population_split(
+        time=T, derived=["Mallard", "Black_duck"], ancestral="Ancestral"
+    )
+
+    return stdpopsim.DemographicModel(
+        id=id,
+        description=description,
+        long_description=long_description,
+        citations=[
+            stdpopsim.Citation(
+                author="Lavretsky et al.",
+                year=2019,
+                doi="https://doi.org/10.1111/mec.15343",
+                reasons={stdpopsim.CiteReason.DEM_MODEL},
+            )
+        ],
+        generation_time=4,
+        model=model,
+        # mutation_rate=4.83e-9,
+    )
+
+
+_species.add_demographic_model(_mallard_black_split())