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 examine differences between different data types (exons vs. introns), single gene fragments were divided by data type and concatenated to form distinct data sets for further analysis: 1) exons, 2) introns, and 3) exons+introns. Preliminary analysis revealed topological incongruence between intron and exon data. Topological incongruence may be due to factors such as incomplete lineage sorting, hybridization, or different mutation rates, therefore it is optimal to identify these data and remove them to assess the true evolutionary signal in a data set (de Vienne et al. 2012) . Given that our data comprised of introns and exons, which evolve at differential rates, we performed a search for outlying data using Phylo-MCOA (de Vienne et al. 2012) with default settings on individual gene trees to resolve the topological incongruence observed between exon and intron data in preliminary analysis. A small number of sequences (0.67%; 5/741; supplementary table S1, Supplementary Material online) were identified as outlying data and were removed 327 Overcoming Impediments to Resolution . doi:10.1093/molbev/msu329 MBE to optimize each single gene alignment. jModeltest was rerun as before for each gene fragment to obtain an appropriate model of sequence evolution, there was no change from previous results (supplementary table S1, Supplementary Material online). To evaluate the effect of removing outliers, we analyzed our data with and without outliers resulting in a total of six data sets for further phylogenetic analysis: 1) exons, 2) introns, 3) exons+introns, 4) exons-outliers removed, 5) introns-outliers removed, and 6) exons+introns-outliers removed. The steps taken to optimize the alignment of each data set were then evaluated using the GUIDANCE web server (Penn et al. 2010) , which reported that each position of our alignments were confidently aligned with regard to tree uncertainty. A comparison of the observed change in posteriors obtained from BEAST runs for exon+intron and exon+intron-outliers removed data sets was used to evaluate the effect of removing outliers.