{ "time_units": "generations", "generation_time": 1, "doi": [ "https://doi.org/10.1016/j.cell.2019.02.035", "https://doi.org/10.1038/nature18299" ], "description": "A ten population model of out-of-Africa, including two pulses of\nDenisovan admixture into Papuans, and several pulses of Neandertal\nadmixture into non-Africans.\nMost parameters are from Jacobs et al. (2019), Table S5 and Figure S5.\nThis model is an extension of one from Malaspinas et al. (2016), thus\nsome parameters are inherited from there.\n", "metadata": {}, "demes": [ { "name": "YRI", "description": "", "start_time": "Infinity", "epochs": [ { "end_time": 20225.0, "start_size": 32671.0, "end_size": 32671.0, "size_function": "constant", "selfing_rate": 0, "cloning_rate": 0 }, { "end_time": 2218.0, "start_size": 41563.0, "end_size": 41563.0, "size_function": "constant", "selfing_rate": 0, "cloning_rate": 0 }, { "end_time": 0, "start_size": 48433.0, "end_size": 48433.0, "size_function": "constant", "selfing_rate": 0, "cloning_rate": 0 } ], "proportions": [], "ancestors": [] }, { "name": "DenA", "description": "", "start_time": 20225.0, "epochs": [ { "end_time": 15090.0, "start_size": 13249.0, "end_size": 13249.0, "size_function": "constant", "selfing_rate": 0, "cloning_rate": 0 }, { "end_time": 12500.0, "start_size": 100.0, "end_size": 100.0, "size_function": "constant", "selfing_rate": 0, "cloning_rate": 0 }, { "end_time": 9750.0, "start_size": 100.0, "end_size": 100.0, "size_function": "constant", "selfing_rate": 0, "cloning_rate": 0 }, { "end_time": 0, "start_size": 5083.0, "end_size": 5083.0, "size_function": "constant", "selfing_rate": 0, "cloning_rate": 0 } ], "proportions": [ 1 ], "ancestors": [ "YRI" ] }, { "name": "NeaA", "description": "", "start_time": 15090.0, "epochs": [ { "end_time": 3375.0, "start_size": 13249.0, "end_size": 13249.0, "size_function": "constant", "selfing_rate": 0, "cloning_rate": 0 }, { "end_time": 0, "start_size": 826.0, "end_size": 826.0, "size_function": "constant", "selfing_rate": 0, "cloning_rate": 0 } ], "proportions": [ 1 ], "ancestors": [ "DenA" ] }, { "name": "Den2", "description": "", "start_time": 12500.0, "epochs": [ { "end_time": 0, "start_size": 13249.0, "end_size": 13249.0, "size_function": "constant", "selfing_rate": 0, "cloning_rate": 0 } ], "proportions": [ 1 ], "ancestors": [ "DenA" ] }, { "name": "Den1", "description": "", "start_time": 9750.0, "epochs": [ { "end_time": 0, "start_size": 13249.0, "end_size": 13249.0, "size_function": "constant", "selfing_rate": 0, "cloning_rate": 0 } ], "proportions": [ 1 ], "ancestors": [ "DenA" ] }, { "name": "Nea1", "description": "", "start_time": 3375.0, "epochs": [ { "end_time": 0, "start_size": 13249.0, "end_size": 13249.0, "size_function": "constant", "selfing_rate": 0, "cloning_rate": 0 } ], "proportions": [ 1 ], "ancestors": [ "NeaA" ] }, { "name": "Ghost", "description": "", "start_time": 2218.0, "epochs": [ { "end_time": 2119.0, "start_size": 1394.0, "end_size": 1394.0, "size_function": "constant", "selfing_rate": 0, "cloning_rate": 0 }, { "end_time": 0, "start_size": 8516.0, "end_size": 8516.0, "size_function": "constant", "selfing_rate": 0, "cloning_rate": 0 } ], "proportions": [ 1 ], "ancestors": [ "YRI" ] }, { "name": "Papuan", "description": "", "start_time": 1784.0, "epochs": [ { "end_time": 1685.0, "start_size": 243.0, "end_size": 243.0, "size_function": "constant", "selfing_rate": 0, "cloning_rate": 0 }, { "end_time": 0, "start_size": 8834.0, "end_size": 8834.0, "size_function": "constant", "selfing_rate": 0, "cloning_rate": 0 } ], "proportions": [ 1 ], "ancestors": [ "Ghost" ] }, { "name": "CHB", "description": "", "start_time": 1758.0, "epochs": [ { "end_time": 1659.0, "start_size": 2231.0, "end_size": 2231.0, "size_function": "constant", "selfing_rate": 0, "cloning_rate": 0 }, { "end_time": 1293.0, "start_size": 12971.0, "end_size": 12971.0, "size_function": "constant", "selfing_rate": 0, "cloning_rate": 0 }, { "end_time": 0, "start_size": 9025.0, "end_size": 9025.0, "size_function": "constant", "selfing_rate": 0, "cloning_rate": 0 } ], "proportions": [ 1 ], "ancestors": [ "Ghost" ] }, { "name": "CEU", "description": "", "start_time": 1293.0, "epochs": [ { "end_time": 0, "start_size": 6962.0, "end_size": 6962.0, "size_function": "constant", "selfing_rate": 0, "cloning_rate": 0 } ], "proportions": [ 1 ], "ancestors": [ "CHB" ] } ], "migrations": [ { "rate": 0.000179, "start_time": 1659.0, "end_time": 0, "source": "YRI", "dest": "Ghost" }, { "rate": 0.000179, "start_time": 1659.0, "end_time": 0, "source": "Ghost", "dest": "YRI" }, { "rate": 0.000572, "start_time": 1659.0, "end_time": 1293.0, "source": "CHB", "dest": "Papuan" }, { "rate": 0.000572, "start_time": 1659.0, "end_time": 1293.0, "source": "Papuan", "dest": "CHB" }, { "rate": 5.72e-05, "start_time": 1293.0, "end_time": 0, "source": "CHB", "dest": "Papuan" }, { "rate": 5.72e-05, "start_time": 1293.0, "end_time": 0, "source": "Papuan", "dest": "CHB" }, { "rate": 0.000442, "start_time": 1659.0, "end_time": 1293.0, "source": "CHB", "dest": "Ghost" }, { "rate": 0.000442, "start_time": 1659.0, "end_time": 1293.0, "source": "Ghost", "dest": "CHB" }, { "rate": 3.14e-05, "start_time": 1293.0, "end_time": 0, "source": "CEU", "dest": "CHB" }, { "rate": 3.14e-05, "start_time": 1293.0, "end_time": 0, "source": "CHB", "dest": "CEU" }, { "rate": 0.000442, "start_time": 1293.0, "end_time": 0, "source": "CEU", "dest": "Ghost" }, { "rate": 0.000442, "start_time": 1293.0, "end_time": 0, "source": "Ghost", "dest": "CEU" } ], "pulses": [ { "sources": [ "Nea1" ], "dest": "Ghost", "time": 1853.0, "proportions": [ 0.024 ] }, { "sources": [ "Den2" ], "dest": "Papuan", "time": 1575.8620689655172, "proportions": [ 0.018 ] }, { "sources": [ "Nea1" ], "dest": "CHB", "time": 1566.0, "proportions": [ 0.011 ] }, { "sources": [ "Nea1" ], "dest": "Papuan", "time": 1412.0, "proportions": [ 0.002 ] }, { "sources": [ "Den1" ], "dest": "Papuan", "time": 1027.5862068965516, "proportions": [ 0.022 ] }, { "sources": [ "Nea1" ], "dest": "CHB", "time": 883.0, "proportions": [ 0.002 ] } ] }