A Composite Genome Approach to Identify Phylogenetically Informative Data from Next-Generation Sequencing
Rachel S. Schwartz, Kelly Harkins, Anne C. Stone, Reed A. Cartwright
(Submitted on 16 May 2013 (v1), last revised 12 Nov 2014 (this version, v3))

We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS, avoids the time consuming steps of de novo whole genome assembly, genome-genome alignment, and annotation. For simulations SISRS is able to identify large numbers of loci containing variable sites with phylogenetic signal. For genomic data from apes, SISRS identified thousands of variable sites, from which we produced an accurate phylogeny. Finally, we used SISRS to identify phylogenetic markers that we used to estimate the phylogeny of placental mammals. We recovered phylogenies from multiple datasets that were consistent with previous conflicting estimates of the relationships among mammals. SISRS is open source and freely available at this https URL