diff --git a/stdpopsim/catalog/ChlRei/species.py b/stdpopsim/catalog/ChlRei/species.py index d33c9dc4a..7c9da0f40 100644 --- a/stdpopsim/catalog/ChlRei/species.py +++ b/stdpopsim/catalog/ChlRei/species.py @@ -2,13 +2,13 @@ from . import genome_data -# IMPORTANT: these are recombination rate values with the rate of sex +# IMPORTANT: These are recombination rate values with the rate of sex # incorporated - e.g. they are lower than the physical recombination rates on account # of being the 'realized' recombination rates in nature, since C. reinhardtii only # undergoes sex/recombination once every ~840 generations (Hasan and Ness 2020). -# when simulating natural populations with these values, the infrequency -# of sex should be implicitly taken into account. otherwise, to get estimates -# of physical rates, divide all values by 0.001194. see Discussion of Hasan +# When simulating natural populations with these values, the infrequency +# of sex should be implicitly taken into account. Otherwise, to get estimates +# of physical rates, divide all values by 0.001194. See Discussion of Hasan # and Ness 2020 for more details _recombination_rate = { "1": 1.21e-10, @@ -30,26 +30,24 @@ "17": 1.83e-10, } -_overall_rate = 9.63 * 1e-10 # SNM rate -# there is also an indel mutation rate in Ness 2015 if that is eventually supported _mutation_rate = { - "1": _overall_rate, - "2": _overall_rate, - "3": _overall_rate, - "4": _overall_rate, - "5": _overall_rate, - "6": _overall_rate, - "7": _overall_rate, - "8": _overall_rate, - "9": _overall_rate, - "10": _overall_rate, - "11": _overall_rate, - "12": _overall_rate, - "13": _overall_rate, - "14": _overall_rate, - "15": _overall_rate, - "16": _overall_rate, - "17": _overall_rate, + "1": 9.74e-10, + "2": 8.62e-10, + "3": 9.5e-10, + "4": 9.66e-10, + "5": 1.17e-9, + "6": 9.12e-10, + "7": 9.14e-10, + "8": 8.98e-10, + "9": 9.17e-10, + "10": 9.27e-10, + "11": 1.03e-9, + "12": 9.55e-10, + "13": 7.56e-10, + "14": 8.96e-10, + "15": 6.91e-10, + "16": 9.59e-10, + "17": 1.05e-9, } _genome = stdpopsim.Genome.from_data( @@ -66,13 +64,13 @@ stdpopsim.Citation( author="Hasan and Ness", year=2020, - doi="https://doi.org/10.1093/gbe/evaa057", + doi="https://doi.org/10.6084/m9.figshare.14608239.v1", reasons={stdpopsim.CiteReason.REC_RATE}, ), stdpopsim.Citation( author="Ness et al", year=2015, - doi="https://doi.org/10.1101/gr.191494.115", + doi="https://doi.org/10.6084/m9.figshare.14700156.v1", reasons={stdpopsim.CiteReason.MUT_RATE}, ), ],