Kehui Liu
Shanjun Deng
Xionglei He
State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
More InformationCorresponding author: E-mail address: hexiongl@mail.sysu.edu.cn (Xionglei He)
Received Date: 2020-12-07
Accepted Date:2021-03-05
Rev Recd Date:2021-02-23
Available Online: 2021-04-09 Publish Date:2021-03-20
Abstract
Abstract
Conventional coalescent inferences of population history make the critical assumption that the population under examination is panmictic. However, most populations are structured. This complicates the prevailing coalescent analyses and sometimes leads to inaccurate estimates. To develop a coalescent method unhampered by population structure, we perform two analyses. First, we demonstrate that the coalescent probability of two randomly sampled alleles from the immediate preceding generation (one generation back) is independent of population structure. Second, motivated by this finding, we propose a new coalescent method: i-coalescent analysis. The i-coalescent analysis computes the instantaneous coalescent rate?by using a phylogenetic tree of sampled alleles. Using simulated data, we broadly demonstrate the capability of i-coalescent analysis to accurately reconstruct population size dynamics of highly structured populations, although we find this method often requires larger sample sizes for structured populations than for panmictic populations. Overall, our results indicate i-coalescent analysis to be a useful tool, especially for the inference of population histories with intractable structure such as the developmental history of cell populations in the organs of complex organisms.Keywords: Coalescent,
Population structure,
Demographic history,
Population size,
Phylogenetic tree
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