The deterministic effects of alignment bias in phylogenetic inference

Area of Science:

• Bioinformatics
• Computational Biology
• Evolutionary Biology

Background:

• Sequence alignment is crucial for molecular phylogenetics.
• Alignment errors can introduce systematic biases in phylogenetic inference.
• Four alignment methods were compared: progressive pairwise, simultaneous multiple, local pairwise, and direct optimization.

Discussion:

• Direct optimization (implied alignments) showed extreme behavior, supporting correct trees in easy simulations and incorrect trees in long-branch-attraction scenarios.
• Direct optimization increased interdependence between partitions with different histories, complicating recombination detection.
• Simultaneous alignment performed robustly across various simulations.

Key Insights:

• Alignment method choice significantly influences phylogenetic tree reconstruction.
• Direct optimization's integrated approach can amplify biases and obscure evolutionary signals.
• Simultaneous alignment offers a more reliable approach by considering alignment uncertainty.

Outlook:

• Future phylogenetic studies should prioritize methods that account for alignment uncertainty.
• Simultaneous alignment, integrated with biological context, is recommended for robust phylogenetic analyses.
• Further research into optimizing simultaneous alignment parameters could enhance its performance.