AncestryGrapher toolkit: Python command-line pipelines to visualize global– and local– ancestry inferences from the RFMix2 software

Abstract

Summary: Admixture is a fundamental process that has shaped patterns of genetic variation and the risk for disease in human populations. Here, we introduce the AncestryGrapher toolkit for visualizing inferred global– and local– ancestry by the RFMix v.2 software. Currently, there is no straightforward method to summarize population ancestry results from RFMix analysis. Results: To demonstrate the utility of our method, we applied the AncestryGrapher toolkit to the output files of RFMix v.2 to visualize the global and local ancestry of individuals in the Mozabite Berber population from North Africa. Our results showed that the Mozabite Berbers derived their ancestry from the Middle East, Europe, and sub-Saharan Africa (global ancestry). Furthermore, we found that the population origin of ancestry varied considerably along chromosomes. More specifically, we observed variance in ancestry along chromosome 2 (local ancestry), in the genomic region containing the common genetic polymorphisms associated with lactase persistence, a trait known to be under strong positive selection. This finding indicates that the demographic process of admixture has influenced patterns of allelic variation in addition to natural selection. Overall, the AncestryGrapher toolkit facilitates the exploration, interpretation, and reporting of ancestry patterns in human populations. Availability and implementation: The AncestryGrapher toolkit is free and open source on https://github.com/alisi1989/RFmix2-Pipeline-to-plot.