RADpainter and fineRADstructure Population Inference from RADseq Data

作者：Malinsky Milan^*; Trucchi Emiliano; Lawson Daniel John; Falush Daniel^*

来源：Molecular Biology and Evolution, 2018, 35(5): 1284-1290.

DOI：10.1093/molbev/msy023

• population structure
• RAD-seq
• inference

Powerful approaches to inferring recent or current population structure based on nearest neighbor haplotype "coancestry" have so far been inaccessible to users without high quality genome-wide haplotype data. With a boom in nonmodel 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-siteassociated 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; last accessed February 24, 2018). Finally, with two example data sets, we illustrate its use, benefits, and robustness to missing RAD alleles in double digest RAD sequencing.

• 出版日期2018-5