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Recombination rate placeholder used for AnoCar #1365

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nspope opened this issue Sep 20, 2022 · 2 comments · May be fixed by #1654
Open

Recombination rate placeholder used for AnoCar #1365

nspope opened this issue Sep 20, 2022 · 2 comments · May be fixed by #1654
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@petrelharp
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Version 0.2.1

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@nspope
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nspope commented Sep 20, 2022 •
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stdpopsim/stdpopsim/catalog/AnoCar/species.py

Lines 23 to 26 in eccf60c

# 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

Is there a better placeholder that could be used here -- e.g. from another Anolis or reptile?
@nspope nspope added this to the Version 0.2.0 milestone Sep 20, 2022
@andrewkern
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i did some searching and can't find anything other than 4Nr estimates...

@andrewkern
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wait! I just found this paper: https://doi.org/10.1093/gbe/evaa161

they get a sex averaged rate of 1.59 cM/MB which would be 1.59e-8...

I'll draft a PR

@andrewkern andrewkern linked a pull request Jan 17, 2025 that will close this issue
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lizard recomb rate estimate andrewkern/stdpopsim
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@petrelharp @nspope @andrewkern