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Spatial structure alters the site frequency spectrum produced by hitchhiking

View ORCID ProfileJiseon Min, Misha Gupta, Michael M. Desai, Daniel B. Weissman
doi: https://doi.org/10.1101/2022.06.08.495311
Jiseon Min
1Department of Molecular and Cellular Biology, Harvard University
2NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard University
3Quantitative Biology Initiative, Harvard University
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  • ORCID record for Jiseon Min
Misha Gupta
4Department of Organismic and Evolutionary Biology, Harvard University
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Michael M. Desai
2NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard University
3Quantitative Biology Initiative, Harvard University
4Department of Organismic and Evolutionary Biology, Harvard University
5Department of Physics, Harvard University
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Daniel B. Weissman
6Department of Physics, Emory University
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  • For correspondence: daniel.weissman@emory.edu
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ABSTRACT

The reduction of genetic diversity due to genetic hitchhiking is widely used to find past selective sweeps from sequencing data, but very little is known about how spatial structure affects hitchhiking. We use mathematical modeling and simulations to find the unfolded site frequency spectrum (SFS) left by hitchhiking in the genomic region of a sweep in a population occupying a one-dimensional range. For such populations, sweeps spread as Fisher waves, rather than logistically. We find that this leaves a characteristic three-part SFS at loci very close to the swept locus. Very low frequencies are dominated by recent mutations that occurred after the sweep and are unaffected by hitchhiking. At moderately low frequencies, there is a transition zone primarily composed of alleles that briefly “surfed” on the wave of the sweep before falling out of the wavefront, leaving a spectrum close to that expected in well-mixed populations. However, for moderate-to-high frequencies, there is a distinctive scaling regime of the SFS produced by alleles that drifted to fixation in the wavefront and then were carried throughout the population. For loci slightly farther away from the swept locus on the genome, recombination is much more effective at restoring diversity in one-dimensional populations than it is in well-mixed ones. We find that these signatures of space can be strong even in apparently well-mixed populations with negligible spatial genetic differentiation, suggesting that spatial structure may frequently distort the signatures of hitchhiking in natural populations.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted June 10, 2022.
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Spatial structure alters the site frequency spectrum produced by hitchhiking
Jiseon Min, Misha Gupta, Michael M. Desai, Daniel B. Weissman
bioRxiv 2022.06.08.495311; doi: https://doi.org/10.1101/2022.06.08.495311
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Spatial structure alters the site frequency spectrum produced by hitchhiking
Jiseon Min, Misha Gupta, Michael M. Desai, Daniel B. Weissman
bioRxiv 2022.06.08.495311; doi: https://doi.org/10.1101/2022.06.08.495311

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