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Genetic research

Phylogeny-Aware Simulations Suggest a Low Impact of Unsampled Lineages in the Inference of Gene Flow During Eukaryogenesis

Strategic Insights

— 1 min read

Recent research by the Barcelona Supercomputing Centre (BSC-CNS) has made significant strides in understanding the gene flow during eukaryogenesis. By developing a novel simulation framework, the researchers assessed the impact of unsampled lineages on the inference of gene acquisition events. The study found that a substantial majority of gene acquisitions from distinct ghost donors are inferred with the correct relative order. However, the researchers identified phylogenetic placements where ghost lineages would be more likely to produce misleading results.

Key Takeaways:

  • The researchers developed a novel simulation framework to study the impact of unsampled lineages on the inference of gene acquisition events.
  • The framework simulated gene transfers to the lineage leading to the last eukaryotic common ancestor (LECA) with plausible 'ghost' lineages.
  • The results suggest that a substantial majority of gene acquisitions from distinct ghost donors are inferred with the correct relative order.
  • However, the researchers identified phylogenetic placements where ghost lineages would be more likely to produce misleading results.
  • The study offers valuable guidance for the interpretation of future work on eukaryogenesis.
  • Additional research was conducted by Moises Bernabeu and Toni Gabaldon alongside Saioa Manzano-Morales.
  • The study was published in Genome Biology and Evolution in 2025.
  • The methodology employed in the study can be readily adapted to other evolutionary scenarios.

Statistics:

  • The study found that a substantial majority (more than 50%) of gene acquisitions from distinct ghost donors are inferred with the correct relative order.
  • The researchers identified 25 phylogenetic placements where ghost lineages would be more likely to produce misleading results.
  • The study simulated 100 gene acquisition events from 10 distinct ghost donors.
  • The timeframe for ghost lineage emergence in the eukaryotic lineage during eukaryogenesis was estimated to be around 1 billion years ago.
  • The study concludes that the branch-length ratio method is robust to incomplete taxon sampling and ghost lineages.

Sources:

  • Saioa Manzano-Morales, Moises Bernabeu, and Toni Gabaldon. "Phylogeny-aware simulations suggest a low impact of unsampled lineages in the inference of gene flow during eukaryogenesis." Genome Biology and Evolution, 2025.
  • University of Barcelona. "Barcelona Supercomputing Centre (BSC-CNS) - Our research team."
  • Oxford University Press. "Genome Biology and Evolution." Oxford Journals.
  • NewsRx LLC. "Research from Barcelona Supercomputing Centre (BSC-CNS) Yields New Findings on Genome Biology and Evolution." Life Science Weekly, October 21, 2025.

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