arisim_remnants: Ari-like Simulated genetic data for the Remnants Scenario
In danjlawson/badMIXTURE: Validating Structure With Chromosome Painting

Description Usage Format References

Simulated data set to represent the genetics of the Ari people, as reported in van Dorp et al PLoS Genetics 2015 11(8): e1005397, and followed up in Falush, van Dorp & Lawson http://biorxiv.org/content/early/2016/07/28/066431.

This dataset was simulated to understand the Ari people, who are culturally split into "Blacksmiths" and "Cultivators". There was much discussion whether the Blacksmiths were a better representative of an ancient African population, or whether they were simply marginalised and hence had experienced genetic drift that made them look different to other populations. Package badMIXTURE allows you to test exactly this.

This simulation follows the so-called "Remnants" scenario, in which the truth is that the "Ari Blacksmiths" (Population 13) are the last remnants of an ancient population mixed with a recent one, whilst the "Ari Cultivators" (population 5) are admixed between these and other modern populations. The mixture solution (arisim_remnants$mix produced with ADMIXTURE, Alexander, Novembre & Lange 2009, Genome Research 19:1655-1664) gets this wrong but the residual plots (arisim_remnants$data produced with ChromoPainter, Lawson, Hellenthal, Myers & Falush 2012, PLoS Genetics, e1002453) highlight this.

See compareMixtureToData) and the examples within for how to understand this data.