RADpainter and fineRADstructure: population inference from RADseq data

Abstract

Powerful approaches to inferring recent or current population structure based on nearest neighbour haplotype coancestry have so far been inaccessible to users without high quality genome-wide haplotype data. With a boom in non-model organism genomics, there is a pressing need to bring these methods to communities without access to such data. Here we present RADpainter, a new program designed to infer the coancestry matrix from restriction-site-associated DNA sequencing (RADseq) data. We combine this program together with a previously published MCMC clustering algorithm into fineRADstructure - a complete, easy to use, and fast population inference package for RADseq data (https://github.com/millanek/fineRADstructure). Finally, with two example datasets, we illustrate its use, benefits, and robustness to missing RAD alleles in double digest RAD sequencing.