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

Phylogenetic studies have resolved most relationships among Eutherian Orders. However, the branching order of elephants ( Proboscidea ), hyraxes ( Hyracoidea ), and sea cows ( Sirenia ) (i.e., the Paenungulata ) 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 within Paenungulates . We use a phylogenomic dataset of alignments from 13,388 protein-coding genes across 261 Eutherian mammals to infer phylogenetic relationships within Paenungulates . We find that gene trees almost equally support the three alternative resolutions of Paenungulate relationships and that despite strong support for a Proboscidea + Hyracoidea split in the multispecies coalescent (MSC) tree, there is significant evidence for gene tree uncertainty, incomplete lineage sorting, and introgression among Proboscidea , Hyracoidea , and Sirenia . Indeed, only 8-10% of genes have statistically significant phylogenetic signal to reject the hypothesis of a Paenungulate polytomy. These data indicate little support for any resolution for the branching order Proboscidea , Hyracoidea , and Sirenia within Paenungulata and suggest that Paenungulata may be as close to a real, or at least unresolvable, polytomy as possible.