The role of interdomain horizontal gene transfer (iHGT) in eukaryotic genome evolution remains a subject of ongoing debate. Numerous studies have reported prokaryote-to-eukaryote transfer events, yet the extent to which these inferences are sensitive to taxon sampling and methodological choices remains unclear. In this study, we performed an independent phylogenetic analysis of the 1,138 candidate genes previously proposed by Katz (2015), using updated homology searches, expanded taxon sampling, and different iHGT detection pipelines. Under the interpretative framework applied here, approximately 30% of candidates exhibited phylogenetic support for iHGT. The remaining candidates were classified as inconclusive, as their phylogenetic patterns were broader or ambiguous and compatible with alternative evolutionary scenarios, including cyanobacterial affinity consistent with endosymbiotic gene transfer, differential gene loss, incomplete lineage sorting, absent or limited donor representation. In many cases, the recovery of homologs from additional eukaryotic major clades transformed apparently lineage-restricted genes into multi-clade distributions, illustrating the strong influence of taxon sampling on iHGT inference. These findings underscore the sensitivity of horizontal gene transfer detection to database completeness, analytical thresholds, and evolutionary context. Rather than providing a definitive count of transfer events, this study highlights how expanding genomic resources and methodological choices shape interpretations of interdomain gene transfer in eukaryotes.
Aguirre-Carvajal et al. (2026) studied this question.