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.

In most evolutionary studies, the unit of analysis is the orthologous multiple sequence alignment. Ideally, one creates a Significance This work represents a large, order-wide evolutionary analysis of the order Chiroptera (bats). Our pipeline for assembling sequence data and curating orthologous multiple sequence alignments includes methods for improving results when combining genomic and transcriptomic data sources. The resulting phylogenetic tree divides the order Chiroptera into Yinpterochiroptera and Yangochiroptera, in disagreement with the previous division into Megachiroptera and Microchiroptera and in agreement with some other recent molecular studies, and also provides evidence for other contested branch placements. We also performed a genome-wide analysis of positive selection and found 181 genes with signatures of positive selection. Enrichment analysis shows these positively selected genes to be primarily related to immune responses but also, surprisingly, collagen formation. set of alignments representing each gene, each of which includes the correct ortholog from each species under analysis. However, accurately assembling short reads, identifying orthologs, and curating/vetting multiple sequence alignments from transcriptomic and genomic data are difficult tasks in an evolving field (17) . In previous studies of bats that employed highthroughput sequencing data, these bioinformatic issues were partially addressed by collecting most of the data at the same time with similar methods: whole-genome sequencing in the case of Tsagkogeorga et al. (13) or transcriptomes in the case of Lei and Dong (15) . However, the complexities of creating high-quality orthologous sequence alignments are compounded when public data from multiple sources are combined because these datasets have been collected with a variety of methods and from either chromosomal DNA or transcribed RNA. These issues may, in part, explain why the phylogenies of bats that have been created to date agree on much of the history of Chiroptera but differ in many ways as well.