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.

Concatenation of 12 exons and 3'-UTR gene fragments resulted in 7,888 aligned positions for 39 taxa. Concatenation of seven intron gene fragments resulted in 2,532 aligned positions. These two data sets were then further combined resulting in an alignment of 10,420 positions. Of note, analysis of the alignment with Repeatmasker identified a 128-bp insertion in the intron THY as a class 1 retrotransposon, which was common to the genera Triaenops, Cloeotis, Paratrianeops, and Rhinonicteris. jModeltest indicated the most appropriate model of sequence evolution for each individual gene fragment using the Akaike Information Criterion (AIC; see supplementary table S1, Supplementary Material online). Each data set, exons, introns, and exons+introns were analyzed with and without the outliers identified by the Phylo-MCOA analysis. Topologies of trees resulting from the exon+intron and exon+intron-outliers removed data sets were identical ( fig. 2 ). Following the removal of outlying data, minimal changes in posteriors were observed at seven nodes with a resulting average minimal posterior change of À0.00167. Furthermore, maximum observed changes across these seven nodes were also minor, with a maximum increase in posterior values of 0.02 and a maximum decrease of 0.03.