LDJump : Estimating variable recombination rates from population genetic data

Philipp Hermann, Angelika Heissl, Irene Tiemann‐Boege, Andreas Futschik
2019 Molecular Ecology Resources  
As recombination plays an important role in evolution, its estimation and the identification of hotspot positions is of considerable interest. We propose a novel approach for estimating population recombination rates based on genotyping or sequence data that involves a sequential multiscale change point estimator. Our method also permits demography to be taken into account. It uses several summary statistics within a regression model fitted on suitable scenarios. Our proposed method is
more » ... computationally fast, and provides a parsimonious solution by ensuring a type I error control against too many changes in the recombination rate. An application to human genome data suggests a good congruence between our estimated and experimentally identified hotspots. Our method is implemented in the R-package LDJump, which is freely available at https://github.com/PhHermann/LDJump.
doi:10.1111/1755-0998.12994 pmid:30666785 pmcid:PMC6519033 fatcat:m277ya45qnetvdxp3gqet3tmcy