Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics.

Area of Science:

• Phylogenomics
• Evolutionary Biology
• Computational Biology

Background:

• Recent criticisms have questioned the validity and implementation of the multispecies coalescent (MSC) model in phylogenomics.
• Specific concerns include data alignment errors, gene tree rooting issues, and violated assumptions of the MSC model, such as neutrality and the use of transcriptomes.
• These criticisms suggest that current "species tree" methods may yield unreliable evolutionary conclusions.

Purpose of the Study:

• To address and refute criticisms leveled against the multispecies coalescent (MSC) model in phylogenomic analyses.
• To evaluate the impact of reported data errors on study conclusions and the validity of MSC model assumptions.
• To demonstrate the robustness and superiority of MSC models over alternative methods like concatenation, particularly in challenging evolutionary scenarios.

Main Methods:

• Re-analysis of previously published phylogenomic datasets (Song et al., 2012; Xi et al., 2014) to assess the impact of reported errors.
• Computer simulations to test the performance of MSC models versus concatenation under various evolutionary conditions, including incomplete lineage sorting (ILS) and data subsampling.
• Theoretical evaluation of criticisms regarding MSC model assumptions and their application in phylogenomics.

Main Results:

• Identified data errors and specific analytical methods had minimal impact on the conclusions of the criticized studies.
• Computer simulations demonstrated that MSC models are robust to ILS and data subsampling, while concatenation methods produce erratic and unreliable results.
• Criticisms regarding MSC model assumptions, such as neutrality and the use of transcriptomes, were shown to be based on misunderstandings or misapplications.

Conclusions:

• The multispecies coalescent (MSC) model is a valuable and robust tool for inferring species trees in phylogenomics.
• Concatenation methods exhibit significant limitations and can produce misleading results, especially with incomplete lineage sorting.
• MSC models, when viewed as a part of a broader network framework, offer a powerful approach for understanding evolutionary history and gene tree heterogeneity.