Phylogenomic Analyses Elucidate the Evolutionary Relationships of Bats

Molecular phylogenetics has rapidly established the evolutionary positions of most major mammal groups [1, 2], yet analyses have repeatedly failed to agree on that of bats (order Chiroptera) [3–6]. Moreover, the relationship among the major bat lineages has proven equally contentious, with ongoing disagreements about whether echolocating bats are paraphyletic [7–9] or a true group [10] having profound implications for whether echolocation evolved once or possibly multiple times. By generating new bat genome data and applying model-based phylogenomic analyses designed to accommodate heterogeneous evolutionary processes [4, 11], we show that—contrary to recent suggestions—bats are not closely related to odd-toed ungulates but instead have a more ancient origin as sister group to a large clade of carnivores, ungulates, and cetaceans. Additionally, we provide the first genome-scale support showing that laryngeal echolocating bats are not a true group and that this paraphyly is robust to their position within mammals. We suggest that earlier disagreements in the literature may reflect model misspecification, long-branch artifacts, poor taxonomic coverage, and differences in the phylogenetic markers used. These findings are a timely reminder of the relevance of experimental design and careful statistical analysis as we move into the phylogenomic era. •Bats are a sister group of a clade of carnivores, ungulates, and cetaceans•Genome-scale analyses show that echolocating bats are not a true group•Previous conflicting results likely stem from a mixed signal among loci