diff --git a/stdpopsim/catalog/AnoCar/species.py b/stdpopsim/catalog/AnoCar/species.py index 03819668f..e83eff0e1 100644 --- a/stdpopsim/catalog/AnoCar/species.py +++ b/stdpopsim/catalog/AnoCar/species.py @@ -20,10 +20,21 @@ }, ) -# No recombination rate yet for this species. -# Author of BourgeoisEtAl is sending the recombination map -# Placeholder rate of 1cM/Mb used -_recombo_rate = 1e-8 +_YurchenkoEtAl = stdpopsim.Citation( + doi="https://doi.org/10.1093/gbe/evaa161", + year=2020, + author="Yurchenko et al.", + reasons={stdpopsim.CiteReason.REC_RATE}, +) + +# Recombination rate from Yurchenko et al. +# which was calculated from a linkage map +# from a different lizard species, Zootoca vivipara +# the "common lizard" +# they estimated male and female recombination rates +# at 1.49 cM/Mb and 1.69 cM/Mb, respectively +# we can use the average of the two +_recombo_rate = 1.59e-8 _recombination_rate = { "1": _recombo_rate, diff --git a/tests/test_AnoCar.py b/tests/test_AnoCar.py index c6e7df13a..5447176d3 100644 --- a/tests/test_AnoCar.py +++ b/tests/test_AnoCar.py @@ -28,7 +28,7 @@ class TestGenomeData(test_species.GenomeTestBase): genome = stdpopsim.get_species("AnoCar").genome - rec_rate = 1e-8 # placeholder as we wait for map + rec_rate = 1.59e-8 # placeholder as we wait for map @pytest.mark.parametrize( ["name", "rate"],