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Statistical tools for seed bank detection

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Blath, Jochen, Buzzoni, Eugenio, Koskela, Jere and Wilke-Berenguer, Maite (2020) Statistical tools for seed bank detection. Theoretical Population Biology, 132 . pp. 1-15. doi:10.1016/j.tpb.2020.01.001 ISSN 0040-5809.

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Official URL: https://doi.org/10.1016/j.tpb.2020.01.001

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Abstract

We derive statistical tools to analyze the patterns of genetic variability produced by models related to seed banks; in particular the Kingman coalescent, its time-changed counterpart describing so-called weak seed banks, the strong seed bank coalescent, and the two-island structured coalescent. As (strong) seed banks stratify a population, we expect them to produce a signal comparable to population structure. We present tractable formulas for Wright’s and the expected site frequency spectrum for these models, and show that they can distinguish between some models for certain ranges of parameters. We then use pseudo-marginal MCMC to show that the full likelihood can reliably distinguish between all models in the presence of parameter uncertainty under moderate stratification, and point out statistical pitfalls arising from stratification that is either too strong or too weak. We further show that it is possible to infer parameters, and in particular determine whether mutation is taking place in the (strong) seed bank.

Item Type: Journal Article
Divisions: Faculty of Science, Engineering and Medicine > Science > Statistics
Journal or Publication Title: Theoretical Population Biology
Publisher: Academic Press
ISSN: 0040-5809
Official Date: April 2020
Dates:
DateEvent
April 2020Published
13 January 2020Available
3 January 2020Accepted
Volume: 132
Page Range: pp. 1-15
DOI: 10.1016/j.tpb.2020.01.001
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Restricted or Subscription Access
Date of first compliant deposit: 15 January 2020
Date of first compliant Open Access: 13 January 2021
Funder: Funded by DFG Priority Programme 1590 "Probabilistic Structures in Evolution" project 1105/5-1, by DFG RTG 1845, by the BMS Berlin Mathematical School, and by EPSRC grant EP/R044732/1.
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