{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Bernabeu M"],"funding":["European Research Council"],"pagination":["evaf190"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12573248"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["17(11)"],"pubmed_abstract":["The topologies of gene trees are broadly used to infer horizontal gene transfer events and characterize the potential donor and acceptor partners. Additionally, ratios between branch lengths in the gene tree can inform about the timing of transfers relative to each other. Using this approach, recent studies have proposed a relative chronology of gene acquisitions in the lineage leading to the last eukaryotic common ancestor. However, a recognized caveat of the branch-length ratio method are potential biases due to incomplete taxon sampling resulting in so-called \"ghost\" lineages. Here, we assessed the effect of ghost lineages on the inference of the relative ordering of gene acquisition events during eukaryogenesis. For this, we used a novel simulation framework that populates a dated Tree"],"journal":["Genome biology and evolution"],"pubmed_title":["Phylogeny-aware Simulations Suggest a Low Impact of Unsampled Lineages in the Inference of Gene Flow During Eukaryogenesis."],"pmcid":["PMC12573248"],"funding_grant_id":["724173"],"pubmed_authors":["Bernabeu M","Manzano-Morales S","Gabaldon T"],"additional_accession":[]},"is_claimable":false,"name":"Phylogeny-aware Simulations Suggest a Low Impact of Unsampled Lineages in the Inference of Gene Flow During Eukaryogenesis.","description":"The topologies of gene trees are broadly used to infer horizontal gene transfer events and characterize the potential donor and acceptor partners. Additionally, ratios between branch lengths in the gene tree can inform about the timing of transfers relative to each other. Using this approach, recent studies have proposed a relative chronology of gene acquisitions in the lineage leading to the last eukaryotic common ancestor. However, a recognized caveat of the branch-length ratio method are potential biases due to incomplete taxon sampling resulting in so-called \"ghost\" lineages. Here, we assessed the effect of ghost lineages on the inference of the relative ordering of gene acquisition events during eukaryogenesis. For this, we used a novel simulation framework that populates a dated Tree","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Oct","modification":"2026-06-05T10:42:35.33Z","creation":"2026-05-16T03:08:02.152Z"},"accession":"S-EPMC12573248","cross_references":{"pubmed":["41063607"],"doi":["10.1093/gbe/evaf190"]}}