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.

Alternative topology tests, Kishino-Hasegawa (KH), Shimodaira-Hasegawa (SH), approximately unbiased (AU), were carried out to test a number of competing hypotheses and alternative topologies arising from our data, results are summarized in table 2. The statistical tests were unable to differentiate between the phylogenetic hypothesis in which H. vittatus and H. commersoni fall outside a clade containing the sister taxa Aselliscus and Coelops and all other Hipposideros spp. (KH P = 0.104, SH P = 0.104, and AU P = 0.89) and the hypothesis in which H. commersoni and H. vittatus are sister taxa to Aselliscus stoliczkanus and Coelops frithii (KH P = 0.896, SH P = 0.896, and AU P = 0.911). The paraphyly of Hipposideros is strongly supported by our phylogenetic analyses; statistical tests also rejected the alternative hypothesis in which Hipposideros is monophyletic (KH P = 0.037, SH P = 0.037, and AU P = 0.018). Four alternative topologies of Rhinolophidae arising from our data were tested. Topology tests could not reject the hypothesis in which R. hipposideros was basal (KH P = 0.363, SH P = 0.784, and AU P = 0.37). The topology in which the R. trifoliatus and R. luctus was the basal clade was rejected by the AU (P = 0.022) and KH (P = 0.047) tests, but the SH test (P = 0.268) was unable to reject this hypothesis. The topology in which R. pearsoni is basal was also rejected (KH P = 0.000, SH P = 0.000, and AU P = 0.00). The topology arising from the consensus tree, which supports a basal division between European/African versus Asian clades, could not be rejected in favor of any other topology tested (KH P = 0.637, SH P = 0.911, and AU P = 0.765).