How and Why Overcome the Impediments to Resolution: Lessons from rhinolophid and hipposiderid Bats

Foley, Nicole M.; Thong, Vu Dinh; Soisook, Pipat; Goodman, Steven M.; Armstrong, Kyle N.; Jacobs, David S.; Puechmaille, Sébastien J.; Teeling, Emma C.

To elucidate possible systematic bias obscuring the phylogenetic signals, we investigated the effects of removing outlying data on phylogenetic reconstruction and compared the relative resolving power of intron and exon data for our tree. We show that removal of outlying data had no effect on tree topology and only a minimal effect on posterior probabilities. Furthermore, our analyses show that intron data provides better nodal support for our tree than exon data sets of similar size. Phylogenetic analyses resulted in a well-resolved phylogeny, which settles, for the first time, the phylogenetic controversies surrounding the Hipposideridae. A combination of phylogenetic analyses and divergence time estimates support the elevation of Hipposideridae and Rhinonycteridae to family level. Biogeographic analysis revealed that the Rhinolophidae, Hipposideridae, and Rhinonycteridae originated in Africa. The largest genus of the Hipposideridae, Hipposideros, is paraphyletic, and our study shows that Anthops ornatus may represent a species of Hipposideros. Our resolved phylogeny provides the foundation essential for "systematic surveillance" of emerging bat-based novel coronaviruses. Although they have been underrepresented in previous studies, our phylogenetic results suggest members of the Rhinonycteridae may represent excellent candidates in which to survey to expand our knowledge of the diversity of coronaviruses, especially those related to the Betacoronavirusb group, which includes the SARS-CoV. In this way, our phylogeny provides guidance to better predict and manage these human-lethal zoonotic diseases. These analyses also highlight these three bat families as separate Evolutionary Significant Units, with their own morphological peculiarities, long phylogenetic history, and patterns of dispersal, warranting differential conservation management strategies in the future.