Generation of high-resolution a priori Y-chromosome phylogenies using “next-generation” sequencing data

An approach for generating high-resolution a priori maximum parsimony Y-chromosome (chrY) phylogenies based on SNP and small INDEL variant data from massively-parallel short-read (next-generation) sequencing data is described; the tree-generation methodology produces annotations localizing mutations to individual branches of the tree, along with indications of mutation placement uncertainty in cases for which \"no-calls\" (through lack of mapped reads or otherwise) at particular site precludes a precise placement of the mutation. The approach leverages careful variant site filtering and a novel iterative reweighting procedure to generate high-accuracy trees while considering variants in regi