diff --git a/docs/parameter_tables/CanFam/EarlyWolfAdmixture_6F14.csv b/docs/parameter_tables/CanFam/EarlyWolfAdmixture_6F14.csv index d8ac01b70..f6727567f 100644 --- a/docs/parameter_tables/CanFam/EarlyWolfAdmixture_6F14.csv +++ b/docs/parameter_tables/CanFam/EarlyWolfAdmixture_6F14.csv @@ -10,18 +10,18 @@ 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.),"12,795","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" +Migration rate,0.18,"Israeli wolf -> Basenji total migration rate" +Migration rate,0.07,"Basenji -> Israeli wolf total migration rate" +Migration rate,0.03,"Chinese wolf -> Dingo total migration rate" +Migration rate,0.04,"Dingo -> Chinese wolf total migration rate" +Migration rate,0.00,"Golden jackal -> Israeli wolf total migration rate" +Migration rate,0.05,"Israeli wolf -> Golden jackal total migration rate" +Migration rate,0.02,"Golden jackal -> Ancestral (dog, wolf) total migration rate" +Migration rate,0.99,"Ancestral (dog, wolf) -> Golden jackal total migration rate" +Time (yrs.),"12,795","Ancestral ((Boxer, Basenji), Dingo) split time" +Time (yrs.),"13,389","Ancestral (Israeli, Croatian) wolf split time" +Time (yrs.),"13,455","Ancestral ((Israeli, Croatian), Chinese) wolf split time" +Time (yrs.),"14,874","Ancestral (dog, wolf) split time" +Time (yrs.),"398,262","Ancestral ((dog, wolf), golden jackal) split time" Generation time (yrs.),3,Generation time Mutation rate,1e-8,Mutation rate diff --git a/stdpopsim/catalog/CanFam/demographic_models.py b/stdpopsim/catalog/CanFam/demographic_models.py index c64eaf434..3ade38d6a 100644 --- a/stdpopsim/catalog/CanFam/demographic_models.py +++ b/stdpopsim/catalog/CanFam/demographic_models.py @@ -28,9 +28,14 @@ def _dog_wolf_admixture(): a mutation rate of 1e-8 (page 3). Estimated (calibrated) effective population sizes, divergence times, and migration rates are given in Table S12. - Migration is constant continuous geneflow from the start and - 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 + Migration is continuous gene flow between the start and end + times of the two populations that define each migration band, + and are reported as reverse-time migration rates + (in the sense of msprime's migration rates; Section S9.2.3 in S9). + The values reported in Table S12 are total migration rates inferred by + G-PhoCS, equal to the per-generation migration rate multiplied by the + duration of the migration band. + While Boxer reference genome was used, no Boxer-specific parameters were estimated in the model, hence Boxer was removed from this model implementation. Thence the ancestral Basenji population with its specific Ne is for the Ancestral (Boxer, Basenji) population. @@ -62,25 +67,29 @@ def _dog_wolf_admixture(): N_ancDW = 44993 # (dog, wolf) N_root = 18169 # ((dog, wolf), golden jackal)root - # Estimated (calibrated) divergence times, from Table S12 - 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 + # Estimated (calibrated) divergence times in years, from Table S12 + # so divide by the generation time to convert to generations + T_ancDOG1 = 12102 / generation_time # (Boxer, Basenji) + T_ancDOG = 12795 / generation_time # ((Boxer, Basenji), Dingo) + T_ancWLF1 = 13389 / generation_time # (Israeli, Croatian) wolf + T_ancWLF = 13455 / generation_time # ((Israeli, Croatian), Chinese) wolf + T_ancDW = 14874 / generation_time # (dog, wolf) + T_ancroot = 398262 / generation_time # ((dog, wolf), golden jackal)root - # Migration rates, from Table S12 - # migration is constant continuous geneflow from the start and end times of - # the two populations that define it. See section S9.2.3 in S9. - m_ISW_BSJ = 0.18 - m_BSJ_ISW = 0.07 - m_CHW_DNG = 0.03 - m_DNG_CHW = 0.04 - m_GLJ_ISW = 0 - m_ISW_GLJ = 0.05 - m_GLJ_ancDW = 0.02 - m_ancDW_GLJ = 0.99 + # Total migration rates, from Table S12 + # migration is constant continuous gene flow from the start and end times of + # the two populations that define it, see section S9.2.3 in S9, where + # total migration rate = per-gen migration rate * duration of migration band + # so, total migration rate / duration of migration band, equals the + # per-gen migration rate + m_ISW_BSJ = 0.18 / T_ancDOG1 + m_BSJ_ISW = 0.07 / T_ancDOG1 + m_CHW_DNG = 0.03 / T_ancDOG + m_DNG_CHW = 0.04 / T_ancDOG + m_GLJ_ISW = 0 / T_ancWLF1 + m_ISW_GLJ = 0.05 / T_ancWLF1 + m_GLJ_ancDW = 0.02 / (T_ancroot - T_ancDW) + m_ancDW_GLJ = 0.99 / (T_ancroot - T_ancDW) model = msprime.Demography() model.add_population(