Ghost lineages can invalidate or even reverse findings regarding gene flow.

Area of Science:

• Evolutionary biology
• Genomics
• Phylogenetics

Background:

• Horizontal gene flow (HGF), introgression, and endosymbiosis are key drivers of evolutionary innovation.
• Current HGF detection methods analyze genomic signatures, particularly their impact on phylogenetic tree branch lengths.
• Existing methods often assume minimal influence from unsampled taxa (ghost lineages).

Purpose of the Study:

• To investigate the impact of unsampled taxa on the reliability of HGF detection methods.
• To re-evaluate conclusions drawn from previous studies that did not account for ghost lineages.

Main Methods:

• Simulations were used to model evolutionary scenarios with varying numbers of sampled and unsampled taxa.
• Reanalysis of existing datasets was performed to assess the influence of ghost lineages on prior findings.

Main Results:

• The influence of ghost lineages can significantly alter or even reverse conclusions drawn from HGF detection methods.
• Studies assuming limited ghost lineages may yield unfounded or inaccurate evolutionary interpretations.
• The impact of unsampled taxa is substantial, even when compared to sampled ones.

Conclusions:

• The assumption of minimal ghost lineage influence is often invalid.
• Recognizing and incorporating the impact of ghost lineages is crucial for accurate evolutionary inference.
• Future phylogenetic and HGF studies must account for the pervasive effect of unsampled taxa.