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popsim-consortium / stdpopsim

A library of standard population genetic models
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aratha generation_time/population_size values and citations #293

Closed jeromekelleher closed 4 years ago

jeromekelleher commented 4 years ago

We need citations for the generation time and population size in A thaliana. These are defined here

Can someone who knows about these things propose the correct values and citations for these please?

andrewkern commented 4 years ago

i asked twitter today about this https://twitter.com/pastramimachine/status/1203721175349653504?s=20

overwhelming the answer was 1 gen / yr. and an appropriate citation https://doi.org/10.1890/0012-9658(2002)083[1006:GTINSO]2.0.CO;2

jeromekelleher commented 4 years ago

Great, thanks @andrewkern, we have generation time sorted in #296

Any takers for A thal. population size citation?

gtsambos commented 4 years ago

Any takers for A thal. population size citation?

One of the researchers in my lab who did a postdoc on arabidopsis said it should be more like 10 000 rather than 1000, but like with the human data, it's a bit hard to find a non-population-specific estimate

gtsambos commented 4 years ago

How about this one: (disclaimer: the person I consulted, Ashley Farlow, was an author on this paper)

Alonso-Blanco, C., et al (2016). 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana. Cell, 166(2), 481–491. https://doi.org/10.1016/j.cell.2016.05.063

See figure 4A for estimation of coalescence rates over time. It does look like 10^3 is a better estimate.

EDIT: oops, I meant 10^4. See the present-day values of the curves in that figure -- the estimated recent coalescence rate in non-Iberian samples (which were taken from locations around Europe)

I don't know if this is estimate is as 'explicit' as you want it to be for this resource -- in any case, it sounds like no-one else has ideas and this urgently needs to be part of the release? I'll submit a pull request and we can update the citation if we get any better info later on

gtsambos commented 4 years ago

Also, I was notified about this paper, which seems to use a bit more data and models a bigger range of arabidopsis populations than the ones currently in the catalog.

Hsu, C.‐W., Lo, C.‐Y. and Lee, C.‐R. (2019), On the postglacial spread of human commensal Arabidopsis thaliana: journey to the East. New Phytol, 222: 1447-1457 https://doi.org/10.1111/nph.15682

jeromekelleher commented 4 years ago

Thanks for chasing this @gtsambos, this is perfect.