Robust estimation of recent effective population size from number of independent origins in soft sweeps
File(s)msz081(1).pdf (1.71 MB)
Published version
Author(s)
Khatri, Bhavin S
Burt, Austin
Type
Journal Article
Abstract
Estimating recent effective population size is of great importance in characterising and predicting the evolution of natural populations. Methods based on nucleotide diversity may underestimate current day effective population sizes due to historical bottlenecks, whilst methods that reconstruct demographic history typically only detect long-term variations. However, soft selective sweeps, which leave a fingerprint of mutational history by recurrent mutations on independent haplotype backgrounds, holds promise of an estimate more representative of recent population history. Here we present a simple and robust method of estimation based only on knowledge of the number of independent recurrent origins and the current frequency of the beneficial allele in a population sample, independent of the strength of selection and age of the mutation. Using a forward time theoretical framework, we show the mean number of origins is a function of θ=2Nμ and current allele frequency, through a simple equation, and the distribution is approximately Poisson. This estimate is robust to whether mutants pre-existed before selection arose, and is equally accurate for diploid populations with incomplete dominance. For fast (e.g., seasonal) demographic changes compared to time scale for fixation of the mutant allele, and for moderate peak-to-trough ratios, we show our constant population size estimate can be used to bound the maximum and minimum population size. Applied to the Vgsc gene of Anopheles gambiae, we estimate an effective population size of roughly 6×107, and including seasonal demographic oscillations, a minimum effective population size greater than 3×107 and a maximum less than 6×109, suggesting a mean ~109.
Date Issued
2019-09-01
Date Acceptance
2019-03-24
Citation
Molecular Biology and Evolution, 2019, 36 (9), pp.2040-2052
ISSN
1537-1719
Publisher
Oxford University Press (OUP)
Start Page
2040
End Page
2052
Journal / Book Title
Molecular Biology and Evolution
Volume
36
Issue
9
Copyright Statement
© The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Sponsor
Bill & Melinda Gates Foundation
Silicon Valley Community Foundation
Identifier
https://www.ncbi.nlm.nih.gov/pubmed/30968124
PII: 5435963
Grant Number
OPP1141988
N/A
Subjects
Anopheles
Effective population size
demographic oscillations
recurrent mutation
soft sweeps
Publication Status
Published
Coverage Spatial
United States
Date Publish Online
2019-04-09