Ghost Lineages Highly Influence the Interpretation of Introgression Tests.

Area of Science:

• Evolutionary Biology
• Genomics
• Bioinformatics

Background:

• Horizontal gene flow events like introgression are common in evolutionary history.
• These events often involve extinct or unknown lineages, termed "ghost lineages."
• The impact of ghost lineages on detecting gene flow is often underestimated.

Purpose of the Study:

• To quantify the influence of ghost lineages on introgression detection.
• To evaluate the effect of ghost lineages on the D-statistic method for inferring gene flow.
• To assess the reliability of current methods when ghost lineages are present.

Main Methods:

• Utilized simulated data to model evolutionary scenarios.
• Applied the D-statistic method to analyze introgression.
• Varied conditions to test the impact of absent lineages.

Main Results:

• Ghost lineages can lead to incorrect identification of gene flow donors and recipients.
• The use of distant outgroups, typically recommended, exacerbates error rates.
• Simulations demonstrated false interpretations under common evolutionary conditions.

Conclusions:

• Ghost lineages significantly impact the accuracy of gene flow detection.
• Introgression from ghost lineages should be systematically considered in evolutionary analyses.
• Current methods may require re-evaluation to account for these absent lineages.