Phylogeny-aware simulations suggest a low impact of unsampled lineages in the inference of gene flow during eukaryogenesis

Gene phylogenies are broadly used to analyse events of horizontal gene transfer, namely, their presence, the potential donor and acceptor lineages, and their relative timing. Recent phylogenomics analyses have reconstructed a relative chronology of gene acquisitions in the lineage leading to the eukaryotes, revealing waves of acquisition from different donors before and after the mitochondrial endosymbiosis. However, a recognised caveat is the potential biases introduced by the presence of incomplete taxon sampling resulting in so-called “ghost” lineages. Here, we assessed the robustness of the gene phylogeny-based branch length ratio method in the inference of the relative ordering of gene acquisition events during eukaryogenesis. We introduce a novel simulation framework that populates a known dated Tree of Life with plausible “ghost” lineages and simulates their gene transfers to the lineage leading to the last eukaryotic common ancestor. Our simulations suggest a generally low probability of misinterpreting the relative order of gene acquisitions from distinct ghost donors. However, we identify specific problematic phylogenetic placements where unsampled lineages are more likely to produce misleading results. Overall, our approach offers valuable guidance for the interpretation of future work on eukaryogenesis, and can be readily adapted to other evolutionary scenarios.