Abstract：
:In Ait Kaci Azzou et al. (2015) we introduced an Importance Sampling (IS) approach for estimating the demographic history of a sample of DNA sequences, the skywis plot. More precisely, we proposed a new nonparametric estimate of a population size that changes over time. We showed on simulated data that the skywis plot can work well in typical situations where the effective population size does not undergo very steep changes. In this paper, we introduce an iterative procedure which extends the previous method and gives good estimates under such rapid variations. In the iterative calibrated skywis plot we approximate the effective population size by a piecewise constant function, whose values are re-estimated at each step. These piecewise constant functions are used to generate the waiting times of non homogeneous Poisson processes related to a coalescent process with mutation under a variable population size model. Moreover, the present IS procedure is based on a modified version of the Stephens and Donnelly (2000) proposal distribution. Finally, we apply the iterative calibrated skywis plot method to a simulated data set from a rapidly expanding exponential model, and we show that the method based on this new IS strategy correctly reconstructs the demographic history.
journal_name
Theor Popul Bioljournal_title
Theoretical population biologyauthors
Ait Kaci Azzou S,Larribe F,Froda Sdoi
10.1016/j.tpb.2016.05.004subject
Has Abstractpub_date
2016-10-01 00:00:00pages
16-27eissn
0040-5809issn
1096-0325pii
S0040-5809(16)30020-Xjournal_volume
111pub_type
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