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.

Previous molecular phylogenies have mainly focused on the relationship between a limited number of Hipposideridae genera and have predominantly used mitochondrial data (Wang et al. 2003; Li et al. 2007; Gu et al. 2008; Murray et al. 2012) . The phylogeny of Eick et al. (2005) focused on interfamilial relationships among bats and was constructed using slower evolving nuclear introns. Herein, we generated a data set comprising differentially evolving nuclear exons and introns to ascertain the familial status of the Hipposideridae and to elucidate the intergeneric phylogenetic relationships of the speciose and presumed rapidly diversifying genera Rhinolophus and Hipposideros. We hypothesize that slower evolving exons should provide resolution of deeper nodes, following their successful use in resolving phylogenies focusing on deep time scales at interordinal level in mammals ) and interfamilial levels in bats (Teeling et al. 2002 (Teeling et al. , 2003 (Teeling et al. , 2005 Miller-Butterworth et al. 2007; Lack et al. 2010) and that faster evolving introns should provide resolution of more recent nodes in a tree, following their widespread use in resolving intergeneric and species level relationships (Lim et al. 2008; Stoffberg et al. 2010; Puechmaille et al. 2011; Salicini et al. 2011) . In this study, we test the validity of these assumptions and the resolving power of exons and introns.