Phylogenomics reveals an almost perfect polytomy among the almost ungulates (Paenungulata)

Abstract

AbstractPhylogenetic studies have resolved most relationships amongEutherianOrders. However, the branching order of elephants (Proboscidea), hyraxes (Hyracoidea), and sea cows (Sirenia) (i.e., thePaenungulata) has remained uncertain since at least 1758, when Linnaeus grouped elephants and manatees into a single Order (Bruta) to the exclusion of hyraxes. Subsequent morphological, molecular, and large-scale phylogenomic datasets have reached conflicting conclusions on the branching order withinPaenungulates. We use a phylogenomic dataset of alignments from 13,388 protein-coding genes across 261Eutherianmammals to infer phylogenetic relationships withinPaenungulates. We find that gene trees almost equally support the three alternative resolutions ofPaenungulaterelationships and that despite strong support for aProboscidea+Hyracoideasplit in the multispecies coalescent (MSC) tree, there is significant evidence for gene tree uncertainty, incomplete lineage sorting, and introgression amongProboscidea,Hyracoidea, andSirenia. Indeed, only 8-10% of genes have statistically significant phylogenetic signal to reject the hypothesis of aPaenungulatepolytomy. These data indicate little support for any resolution for the branching orderProboscidea,Hyracoidea, andSireniawithinPaenungulataand suggest thatPaenungulatamay be as close to a real, or at least unresolvable, polytomy as possible.