Data from: When outgroups fail; phylogenomics of rooting the emerging pathogen, Coxiella burnetii

Rooting phylogenies is critical for understanding evolution, yet the
importance, intricacies and difficulties of rooting are often overlooked.
For rooting, polymorphic characters among the group of interest (ingroup)
must be compared to those of a relative (outgroup) that diverged before
the last common ancestor (LCA) of the ingroup. Problems arise if an
outgroup does not exist, is unknown, or is so distant that few characters
are shared, in which case duplicated genes originating before the LCA can
be used as proxy outgroups to root diverse phylogenies. Here, we describe
a genome-wide expansion of this technique that can be used to solve
problems at the other end of the evolutionary scale: where ingroup
individuals are all very closely related to each other, but the next
closest relative is very distant. We used shared orthologous single
nucleotide polymorphisms (SNPs) from 10 whole genome sequences of Coxiella
burnetii, the causative agent of Q fever in humans, to create a robust,
but unrooted phylogeny. To maximize the number of characters informative
about the rooting, we searched entire genomes for polymorphic duplicated
regions where orthologs of each paralog could be identified so that the
paralogs could be used to root the tree. Recent radiations, such as those
of emerging pathogens, often pose rooting challenges due to a lack of
ingroup variation and large genomic differences with known outgroups.
Using a phylogenomic approach, we created a robust, rooted phylogeny for
C. burnetii.