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 determine the position of Anthops within our tree, a separate analysis was carried out on a subset of data, comprising only Hipposideridae species. The analysis was constrained to include only Hipposideridae species as it was important to maximize the number of confidently aligned positions available in this reduced intron data set to accurately determine the position of Anthops. Each gene fragment was aligned separately using T-Coffee (Notredame et al. 2000) , all resulting ambiguous alignment regions were removed, and fragments were subsequently concatenated. jModeltest was used to determine the most appropriate model of sequence evolution for the concatenated alignment and AIC indicated a TVM + G model was best. Bayesian analysis was carried out in BEAST and analyzed as above. As TVM + G is not directly implemented in BEAST, our analysis was run under the next most complicated model GTR+G.