We are excited to share our new preprint describing the inclusion of selection models to stdpopsim, our community-maintained library with an extensive catalog of population genetic models. 1/n www.biorxiv.org/content/10.1... - ThreadSky

mufernando.bsky.social • 69 days ago

We are excited to share our new preprint describing the inclusion of selection models to stdpopsim, our community-maintained library with an extensive catalog of population genetic models. 1/n
https://www.biorxiv.org/content/10.1101/2025.03.23.644823v1

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mufernando.bsky.social•69 days ago

Now, it is possible to simulate under various modes of selection, including background selection and selective sweeps. This can be used in conjunction with our catalog of species-specific recombination maps and demographic histories. 2/n

mufernando.bsky.social•69 days ago

We take the new functionalities for a spin and investigate: (i) the effects of background selection on demographic inference methods, (ii) the estimation of DFEs, and (iii) detection of sweeps along realistic looking chromosomes, with recombination rate variation and background selection. 3/n

mufernando.bsky.social•69 days ago

I mostly contributed with the analysis of power to detect sweeps along realistic chromosomes. We introduced beneficial mutations in the center of 5cM chunks along human chromosome 1. These sweeps were compared to neutral mutations and mutations with background selection acting on exons. 4/n

mufernando.bsky.social•69 days ago

We found that the power to detect sweep can vary dramatically along the chromosome, what is mostly driven by variation in recombination rates. SweepFinder 2's CLR was was the least affected by recombination rate variation, but overall it's power is not as high as diploSHIC. 5/n

mufernando.bsky.social•69 days ago

Curiously, using a background selection null model for sweep detection did not impact power very much, suggesting that the effects of realistic background selection might not be as similar to sweeps as previously thought. Recapitulating Dan Schrider's findings from 2020 Genetics. 6/n

mufernando.bsky.social•69 days ago

We hope you take our library and its new additions for a spin soon. And we would be ecstatic for you to join our efforts in the next phase of stdpopsim! n/n

sagitaninta.bsky.social•16 days ago

Why does the three human populations all have the same true DFE? (Fig 3C)

mufernando.bsky.social•16 days ago

hi @sagitaninta.bsky.social! we wanted to compare the performance of different DFE inference methods across different human populations (each with unique demographies). for this reason, we assumed the same DFE for all three human populations.

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