diff --git a/stdpopsim/catalog/HomSap/demographic_models.py b/stdpopsim/catalog/HomSap/demographic_models.py index 656193884..84838bc1b 100644 --- a/stdpopsim/catalog/HomSap/demographic_models.py +++ b/stdpopsim/catalog/HomSap/demographic_models.py @@ -1824,9 +1824,11 @@ def _ancient_europe(): id="Pop0", description="1000GenomesEUR/BronzeAge/Neolithic/Anatolian/WestAsian/Basal", ), - stdpopsim.Population(id="Pop1", description="Yamnaya/CHG"), - stdpopsim.Population(id="Pop2", description="WHG/NorthernEuropean"), - stdpopsim.Population(id="Pop3", description="EHG"), + stdpopsim.Population(id="Pop1", description="Yamnaya/CHG", sampling_time=140), + stdpopsim.Population( + id="Pop2", description="WHG/NorthernEuropean", sampling_time=200 + ), + stdpopsim.Population(id="Pop3", description="EHG", sampling_time=180), ] citations = [ stdpopsim.Citation( diff --git a/stdpopsim/qc/HomSap.py b/stdpopsim/qc/HomSap.py index b29ed5b71..6b1fbcbfb 100644 --- a/stdpopsim/qc/HomSap.py +++ b/stdpopsim/qc/HomSap.py @@ -1639,6 +1639,13 @@ def extended_pulse( def PearsonAncientEurope(): + """ + Demographic history of ancient Europe from Allentoft et al. 2022. It + describes population splits and migration pulses for four main branches + in Fig. S3i.1 in Supplementary Information (Part I) found at + https://www.biorxiv.org/content/10.1101/2022.05.04.490594v2.supplementary-material + The branches are colored (black, red, yellow and purple). + """ id = "QC-AncientEurope_4A21" dgraph = demes.loads(_ancient_europe_demes_str) model = msprime.Demography.from_demes(dgraph) @@ -1646,7 +1653,8 @@ def PearsonAncientEurope(): id=id, description=id, long_description=id, - generation_time=None, + generation_time=29, # TODO: not clear where this came from, + # but it is not necessary, given the times are in generations already model=model, mutation_rate=1.25e-8, )