Inferring the demographic history from DNA sequences: An importance sampling approach based on non-homogeneous processes

S. Ait Kaci Azzou, F. Larribe and S. Froda

Theoretical Population Biology, 2016, vol. 111, issue C, 16-27

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.

Keywords: Non-homogeneous processes; Importance sampling; Effective population size; Calibrated skywis plot; Coalescent process (search for similar items in EconPapers)
Date: 2016
References: View references in EconPapers View complete reference list from CitEc
Citations:

Downloads: (external link)
http://www.sciencedirect.com/science/article/pii/S004058091630020X
Full text for ScienceDirect subscribers only

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:eee:thpobi:v:111:y:2016:i:c:p:16-27

DOI: 10.1016/j.tpb.2016.05.004

Access Statistics for this article

Theoretical Population Biology is currently edited by Jeremy Van Cleve

More articles in Theoretical Population Biology from Elsevier
Bibliographic data for series maintained by Catherine Liu ().