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.

It is important to recognize the limitations of the methods used herein for divergence time estimation and biogeographic analysis. Caution must be taken when interpreting results provided by divergence time estimates given that errors can be introduced through the use of fossil calibrations as fossils based on limited characters can be incorrectly classified (Parham et al. 2012) , and stratigraphic layers can be assigned to incorrect geological times. This is particularly applicable to bats which have a poor and limited fossil record (Teeling et al. 2005; Eiting and Gunnell 2009) . Although the oldest fossil attributable to a lineage can provide a minimum age in a soft bound analysis, choosing a maximum bound is more difficult, here we use the stratigraphic bounding method of Meredith et al. (2011) to standardize the way in which maximum boundaries are chosen across the tree. Area coding is one of the key manners contributing to error in biogeographic reconstruction. Springer et al. (2011) showed that including information regarding the provenance of the oldest fossil 325 Overcoming Impediments to Resolution . doi:10.1093/molbev/msu329 MBE attributable to a clade produced very different results than only coding for the extant geographical distribution of a species. Including fossil taxa introduces error in the form of taphonomy and sampling bias. In particular, with regard to the fossil record of the Hipposideridae, the inclusion of fossil data to biogeographic analysis would introduce a European/ Australian bias based on the majority of species ascribed to this group to date (McKenna and Bell 1997; Hand and Kirsch 1998) . To overcome the limitations inherent in the bat fossil record, we use only the distribution of extant taxa in our analysis. Furthermore, taxonomic sampling remains a problem inherent in biogeographic analyses. Our phylogeny comprises representatives from all Hipposideridae, Rhinolophidae, and Rhinonycteridae genera. Our taxonomic sampling of Rhinolophidae does not include any Sub-Saharan African representatives, and so this may hinder a definitive biogeographic analysis of this family. However, a recent study of Emballonura bats has shown that the basal clade of a group can drastically impact its biogeographical reconstruction (Ruedi et al. 2012) . Although the basal clade of the Rhinolophidae remains unresolved, our reconstruction is the first to include all previously recovered basal candidates for this group as a strategy to minimize the impacts of partial taxonomic sampling of this group.