Inferring recombination patterns in African populations

Abstract

Although several high-resolution recombination maps exist for European-descent populations, the recombination landscape of African populations remains relatively understudied. Given that there is high genetic divergence among groups in Africa, it is possible that recombination hotspots also diverge significantly. Both limitations and opportunities exist for developing recombination maps for these populations. In this review, we discuss various recombination inference methods, and the strengths and weaknesses of these methods in analyzing recombination in African-descent populations. Furthermore, we provide a decision tree and recommendations for which inference method to use in various research contexts. Establishing an appropriate methodology for recombination rate inference in a particular study will improve the accuracy of various downstream analyses including but not limited to local ancestry inference, haplotype phasing, fine-mapping of GWAS loci and genome assemblies.

Figure 1

A decision tree for recombination inference method selection. The figure is an extreme oversimplification and serves only as a starting point. Use the series of questions to find the recombination rate inference method that would be the most likely fit for a given use case. The questions should not necessarily exclude any method, but serve as a guide. For many use cases there will be more than one appropriate method.