biostudies-literatureUnknownBowman JNIA NIH HHSPhylogenetic studies have resolved most relationships among <i>Eutherian</i> Orders. However, the branching order of elephants (<i>Proboscidea</i>), hyraxes (<i>Hyracoidea</i>), and sea cows (<i>Sirenia</i>) (i.e., the <i>Paenungulata</i>) has remained uncertain since at least 1758, when Linnaeus grouped elephants and manatees into a single Order (<i>Bruta</i>) to the exclusion of hyraxes. Subsequent morphological, molecular, and large-scale phylogenomic datasets have reached conflicting conclusions on the branching order within <i>Paenungulates</i>. We use a phylogenomic dataset of alignments from 13,388 protein-coding genes across 261 <i>Eutherian</i> mammals to infer phylogenetic relationships within <i>Paenungulates</i>. We find that gene trees almost equally support the three alternatbioRxiv : the preprint server for biology2023.12.07.570590https://www.ebi.ac.uk/biostudies/studies/S-EPMC10723481biostudies-literaturePhylogenomics reveals an almost perfect polytomy among the almost ungulates (<i>Paenungulata</i>).PMC10723481R56 AG071860Enard DBowman JLynch VJfalsePhylogenomics reveals an almost perfect polytomy among the almost ungulates (<i>Paenungulata</i>).Phylogenetic studies have resolved most relationships among <i>Eutherian</i> Orders. However, the branching order of elephants (<i>Proboscidea</i>), hyraxes (<i>Hyracoidea</i>), and sea cows (<i>Sirenia</i>) (i.e., the <i>Paenungulata</i>) has remained uncertain since at least 1758, when Linnaeus grouped elephants and manatees into a single Order (<i>Bruta</i>) to the exclusion of hyraxes. Subsequent morphological, molecular, and large-scale phylogenomic datasets have reached conflicting conclusions on the branching order within <i>Paenungulates</i>. We use a phylogenomic dataset of alignments from 13,388 protein-coding genes across 261 <i>Eutherian</i> mammals to infer phylogenetic relationships within <i>Paenungulates</i>. We find that gene trees almost equally support the three alternat2023-01-01T00:00:00Z2023 Dec2025-04-22T01:59:02.406Z2024-12-04T01:25:14.75ZS-EPMC107234813810608010.1101/2023.12.07.570590