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.

A combination of state-of-the-art phylogenetic methods, divergence time estimates, and biogeographical analyses were employed to elucidate the evolutionary history of the Hipposideridae and Rhinolophidae and to explore the reasons for any phylogenetic incongruence. A comparative diversification analysis focusing on Rhinolophus and Hipposideros was used to elucidate if the diversification patterns of these speciose lineages are similar through time. In particular, we explore potential impediments to phylogenetic resolution in our data by examining the effects of removing outlying data and compare the resolving abilities of exons and introns. Our phylogeny also addresses the following outstanding phylogenetic questions: 1) Do hipposiderid bats represent an independent family or a subfamily of the Rhinolophidae? 2) Is Hipposideros a monophyletic genus? 3) When did hipposiderid and rhinolophid bats diverge and where did they originate? 4) Which species or clade is the most basal lineage of the Rhinolophidae? Finally, we explore the use of our phylogeny for future systematic surveying for novel emergent coronaviruses and for the on-going conservation of these species.