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lizard recomb rate estimate #1654

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19 changes: 15 additions & 4 deletions stdpopsim/catalog/AnoCar/species.py
Original file line number Diff line number Diff line change
Expand Up @@ -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,
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2 changes: 1 addition & 1 deletion tests/test_AnoCar.py
Original file line number Diff line number Diff line change
Expand Up @@ -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"],
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