A metaanalysis of bat phylogenetics and positive selection based on genomes and transcriptomes from 18 species

Hawkins, John A.; Kaczmarek, Maria E.; Müller, Marcel A.; Drosten, Christian; Press, William H.; Sawyer, Sara L.

Finally, we have analyzed positive selection of genes during the speciation of bats, on a genome-wide basis. Previously, work aimed at describing adaptive evolution in bats primarily focused on their unique traits, selecting families of genes to study for selection. These studies can broadly be divided into two categories, those that dealt with specific life traits, such as echolocation or metabolism related to frugivory (24, (64) (65) (66) (67) (68) (69) (70) (71) (72) (73) , and those that were related to pathogens or immunity (74) (75) (76) (77) (78) (79) (80) . There are three studies that used larger datasets, two of which used whole-genome data (13, 23, 24) . Unlike our study, Tsagkogeorga et al. (13) used genome-wide data to ask which genes might explain the alternative subordinal topologies supported by their data. Similarly, the Shen et al. (24) study was specifically interested in energy metabolism in bats due to their energy-expensive mode of locomotion, flight. Finally, Zhang et al. (23) used whole-genome data available from two distantly related bats, along with orthologs from a number of mammals, and inferred adaptive evolution in the innate immune pathway and DNA damage checkpoint path-way. Our work, in comparison, includes more Chiropteran species and a holistic analysis of selection in the bat genome. The addition of more species, and the generation of a high-confidence tree for these species, gives us better resolution for detecting adaptive evolution specifically within Chiroptera (81) .