  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 https://github.com/rachelss/SISRS.
