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.

Our results show that removal of outlying data had no effect on the overall tree topology and had a very minimal effect on posterior probabilities with a minor average posterior change of À 0.00167. Minor decreases (maximum decrease 0.03) in PP occurred at three nodes. It would be expected that phylogenetic trees that contain both old and young divergences would be best resolved by a combination of exon and intron data. In theory, exon data, which are slower evolving, should be best suited to resolve deep nodes in a tree and faster evolving intron data should better resolve young nodes. In contrast to these expectations, our analyses show there is no significant difference in the relationship between node height and posteriors for intron data ( fig. 6 ), yet exons showed poorer support for most of the oldest nodes in our phylogeny. When omitting incongruent nodes, introns systematically outperform exons in terms of nodal support. This cannot be explained by differences in fragment length as our comparisons were carried out on data sets of similar length with both jack-knifed sites and gene fragments. Rather, in line with previous studies (Chojnowski et al. 2008) , we argue that for an equal fragment size and the time frame investigated (~60 Ma), introns carry more phylogenetic signal than exons and are less prone to gene tree conflicts (Romiguier et al. 2013 ). Because of their faster substitution rate, introns evolve more quickly than exons and, hence, can provide more phylogenetic information. However, because they evolve faster, introns should also saturate faster but in a time frame of approximately 60 Ma, as investigated by Chojnowski et al. (2008) , saturation of the phylogenetic signal was not an issue for introns. This may stem from the alignment process, whereby highly variable and divergent intronic sites are removed from analyses given the difficulty in ascertaining homology for these positions. Throughout plants, invertebrates, and vertebrates, it has been shown that introns tend to have a lower GC content than exons (Amit et al. 2012) . This conserved characteristic of genome evolution has important consequences for accurate phylogenetic reconstructions as it has been shown that regions of the genome, which are GC rich have a higher amount of gene tree conflict and have greater difficulties in reconstructing well-supported consensus nodes in the placental mammal tree (Romiguier et al. 2013) . This is particularly important in the context of future phylogenomic studies as to date phylogenomic tree reconstructions have typically used only coding regions (Parker et al. 2013; Seim et al. 2013; Zhang et al. 2013) . A recent study, particularly focused on echolocating mammals, revealed that many coding gene sequences show signs of convergent evolution and, hence, provide phylogenetic signals that are incongruent with the true species tree (Parker et al. 2013) . Although this remains to be tested, we predict that introns should be less prone to convergent evolution and should therefore provide better data to resolve species trees, especially when aligned optimally. The incongruence in tree topology observed between analysis of intron and exon data in our study highlights the importance of using a combination of markers in phylogenetic studies.