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Genetic variability under the seed bank coalescent

Jochen Blath, Bjarki Eldon, Adrián González Casanova, Noemi Kurt, Maite Wilke-Berenguer
doi: https://doi.org/10.1101/017244
Jochen Blath
1TU Berlin, Institute für Mathematik, 10623 Berlin, Germany
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Bjarki Eldon
1TU Berlin, Institute für Mathematik, 10623 Berlin, Germany
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  • For correspondence: eldon@math.tu-berlin.de
Adrián González Casanova
1TU Berlin, Institute für Mathematik, 10623 Berlin, Germany
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Noemi Kurt
1TU Berlin, Institute für Mathematik, 10623 Berlin, Germany
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Maite Wilke-Berenguer
1TU Berlin, Institute für Mathematik, 10623 Berlin, Germany
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Abstract

We analyse patterns of genetic variability of populations in the presence of a large seed bank with the help of a new coalescent structure called the seed bank coalescent. This ancestral process appears naturally as scaling limit of the genealogy of large populations that sustain seed banks, if the seed bank size and individual dormancy times are of the same order as the active population. Mutations appear as Poisson processes on the active lineages, and potentially at reduced rate also on the dormant lineages. The presence of ‘dormant’ lineages leads to qualitatively altered times to the most recent common ancestor and non-classical patterns of genetic diversity. To illustrate this we provide a Wright-Fisher model with seed bank component and mutation, motivated from recent models of microbial dormancy, whose genealogy can be described by the seed bank coalescent. Based on our coalescent model, we derive recursions for the expectation and variance of the time to most recent common ancestor, number of segregating sites, pairwise differences, and singletons. Estimates (obtained by simulations) of the distributions of commonly employed distance statistics, in the presence and absence of a seed bank, are compared. The effect of a seed bank on the expected site-frequency spectrum is also investigated using simulations. Our results indicate that the presence of a large seed bank considerably alters the distribution of some distance statistics, as well as the site-frequency spectrum. Thus, one should be able to detect the presence of a large seed bank in genetic data.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted March 30, 2015.
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Genetic variability under the seed bank coalescent
Jochen Blath, Bjarki Eldon, Adrián González Casanova, Noemi Kurt, Maite Wilke-Berenguer
bioRxiv 017244; doi: https://doi.org/10.1101/017244
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Genetic variability under the seed bank coalescent
Jochen Blath, Bjarki Eldon, Adrián González Casanova, Noemi Kurt, Maite Wilke-Berenguer
bioRxiv 017244; doi: https://doi.org/10.1101/017244

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