{"doi":"10.1101/2023.12.07.570590","title":"Phylogenomics reveals an almost perfect polytomy among the almost ungulates ( <i>Paenungulata</i> )","abstract":"Abstract 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.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2023,"id":395461,"datarank":0.23151115830702176,"base_score":1.3862943611198906,"endowment":1.3862943611198906,"self_citation_contribution":0.20794415416798362,"citation_network_contribution":0.02356700413903814,"self_endowment_contribution":0.20794415416798362,"citer_contribution":0.02356700413903814,"corpus_percentile":null,"corpus_rank":null,"citation_count":3,"citer_count":2,"citers_with_citation_signal":1,"citers_with_endowment":1,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9506,"is_data_producer":true,"deposit_databanks":{"Dryad":["10.5061/dryad.5dv41nsbc"]},"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":635235,"name":"David Enard","orcid":"0000-0003-2634-8016","position":1,"is_corresponding":false},{"id":596087,"name":"Vincent J. Lynch","orcid":"0000-0001-5311-3824","position":2,"is_corresponding":false},{"id":999779,"name":"Jacob D. Bowman","orcid":null,"position":0,"is_corresponding":true}],"reference_count":111,"raw_metadata":null,"created_at":"2026-07-19T01:19:22.857556Z","pmid":"38106080","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}