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.