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- Title
LDJump: Estimating variable recombination rates from population genetic data.
- Authors
Hermann, Philipp; Heissl, Angelika; Tiemann‐Boege, Irene; Futschik, Andreas
- Abstract
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 accurate, 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.
- Subjects
POPULATION genetics; GENOTYPES; BIOINFORMATICS; BIOLOGICAL evolution; HUMAN genome
- Publication
Molecular Ecology Resources, 2019, Vol 19, Issue 3, p623
- ISSN
1755-098X
- Publication type
Article
- DOI
10.1111/1755-0998.12994