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.

The Rhinolophidae form a fully supported monophyletic group but intrafamilial relationships are less well resolved than for the Hipposideridae (see supplementary table S2, Supplementary Material online). Generally, the analyses produced a topology that provided either no structure at the base of the crown group Rhinolophidae or a strict division between the African/European clade, comprising R. hipposideros, R. ferrumequinum, and R. euryale versus the Asian clade, comprising all other Rhinolophus spp. However, the African/ European clade, when recovered, grouped together with relatively low support approximately 60 BSS/0.6 PP. For all analyses using the CAT model in PhyloBayes, a topology with no structure at the base of the crown group Rhinolophidae was supported. Uniquely, the intron data set with outliers included under a BEAST analysis provided an alternative topology in which R. hipposideros was the basal clade; however, this was poorly supported, 0.38 PP. The association of Asian taxa was supported across all BA 0.88-1.0 PP, whereas ML analyses provided variable support depending on the data set. The exon and exon+introns data sets strongly support the association of the Asian taxa, 98-100 BSS; however, less support for this association is found in the introns analyses 63-65 BSS.