Statistical tools for seed bank detection

DOI10.1016/J.TPB.2020.01.001MaRDI QIDQ1984656zbMATH OpenOpenAlexWikidataFDO

Authors Jochen Blath, Eugenio Buzzoni, Jere Koskela, Maite Wilke-Berenguer

Publication date 7 April 2020

Published in Theoretical Population Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1907.13549, http://wrap.warwick.ac.uk/132017/1/WRAP-statistical-tools-seed-bank-Koskela-2020.pdf

zbMATH Keywords

coalescentmodel selectionpopulation structuresampling formulaseed banksite frequency spectrum

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Genetics and epigenetics (92D10)

Abstract: In this article, we derive statistical tools to analyze and distinguish the patterns of genetic variability produced by classical and recent population genetic models related to seed banks. In particular, we are concerned with models described by the Kingman coalescent (K), models exhibiting so-called weak seed banks described by a time-changed Kingman coalescent (W), models with so-called strong seed bank described by the seed bank coalescent (S) and the classical two-island model by Wright, described by the structured coalescent (TI). As the presence of a (strong) seed bank should stratify a population, we expect it to produce a signal roughly comparable to the presence of population structure. We begin with a brief analysis of Wright's $F_{ST}$, which is a classical but crude measure for population structure, followed by a derivation of the expected site frequency spectrum (SFS) in the infinite sites model based on 'phase-type distribution calculus' as recently discussed by Hobolth et al. (2019). Both the $F_{ST}$ and the SFS can be readily computed under various population models, they discard statistical signal. Hence we also derive exact likelihoods for the full sampling probabilities, which can be achieved via recursions and a Monte Carlo scheme both in the infinite alleles and the infinite sites model. We employ a pseudo-marginal Metropolis-Hastings algorithm of Andrieu and Roberts (2009) to provide a method for simultaneous model selection and parameter inference under the so-called infinitely-many sites model, which is the most relevant in real applications. It turns out that this full likelihood method can reliably distinguish among the model classes (K, W), (S) and (TI) on the basis of simulated data even from moderate sample sizes. It is also possible to infer mutation rates, and in particular determine whether mutation is taking place in the (strong) seed bank.

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Cited in

(8)

• Separation of timescales for the seed bank diffusion and its jump-diffusion limit
• The seed bank coalescent with simultaneous switching
• A new coalescent for seed-bank models
• Sequential Methods for Monitoring Declining Quality, with Application to the Long-Term Storage of Seeds
• Dormancy in stochastic population models
• The TMRCA of general genealogies in populations with deterministically varying size
• Phase-type distributions in mathematical population genetics: an emerging framework
• The impact of genetic diversity statistics on model selection between coalescents

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