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The bounded coalescent model : conditioning a genealogy on a minimum root date

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Carson, Jake, Ledda, A., Ferretti, L., Keeling, Matthew James and Didelot, Xavier (2022) The bounded coalescent model : conditioning a genealogy on a minimum root date. Journal of Theoretical Biology, 548 . 111186. doi:10.1016/j.jtbi.2022.111186 ISSN 0022-5193.

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Official URL: https://doi.org/10.1016/j.jtbi.2022.111186

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Abstract

The coalescent model represents how individuals sampled from a population may have originated from a last common ancestor. The bounded coalescent model is obtained by conditioning the coalescent model such that the last common ancestor must have existed after a certain date. This conditioned model arises in a variety of applications, such as speciation, horizontal gene transfer or transmission analysis, and yet the bounded coalescent model has not been previously analysed in detail. Here we describe a new algorithm to simulate from this model directly, without resorting to rejection sampling. We show that this direct simulation algorithm is more computationally efficient than the rejection sampling approach. We also show how to calculate the probability of the last common ancestor occurring after a given date, which is required to compute the probability density of realisations under the bounded coalescent model. Our results are applicable in both the isochronous (when all samples have the same date) and heterochronous (where samples can have different dates) settings. We explore the effect of setting a bound on the date of the last common ancestor, and show that it affects a number of properties of the resulting phylogenies. All our methods are implemented in a new R package called BoundedCoalescent which is freely available online.

Item Type: Journal Article
Subjects: G Geography. Anthropology. Recreation > GN Anthropology
Q Science > QH Natural history
Divisions: Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- )
Faculty of Science, Engineering and Medicine > Science > Mathematics
Faculty of Science, Engineering and Medicine > Science > Statistics
Library of Congress Subject Headings (LCSH): Human beings -- Phylogeny, Genealogy, Human population genetics
Journal or Publication Title: Journal of Theoretical Biology
Publisher: Elsevier
ISSN: 0022-5193
Official Date: 7 September 2022
Dates:
DateEvent
7 September 2022Published
10 June 2022Available
2 June 2022Accepted
Volume: 548
Article Number: 111186
DOI: 10.1016/j.jtbi.2022.111186
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Open Access (Creative Commons)
Date of first compliant deposit: 14 June 2022
Date of first compliant Open Access: 14 June 2022
RIOXX Funder/Project Grant:
Project/Grant IDRIOXX Funder NameFunder ID
NIHR200892[NIHR] National Institute for Health Researchhttp://dx.doi.org/10.13039/501100000272

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