Do Alignment and Trimming Methods Matter for Phylogenomic (UCE) Analyses?

Area of Science:

• Molecular Phylogenetics
• Bioinformatics
• Evolutionary Biology

Background:

• Sequence alignment is critical in molecular phylogenetics, potentially influencing gene tree topologies.
• The impact of alignment methods and trimming on large-scale phylogenomic analyses remains unclear.
• Potential biases from alignment may amplify across many genes or become negligible.

Purpose of the Study:

• To investigate the impact of 12 alignment and trimming method combinations on phylogenomic analyses.
• To assess how different methods affect alignment properties like length, informative sites, and missing data.
• To evaluate the recovery of well-established clades using concatenated and species-tree methods.

Main Methods:

• Tested 12 combinations of DNA sequence alignment and trimming methods.
• Utilized ultraconserved elements (UCEs) phylogenomic data from squamate reptiles, birds, and tetrapods.
• Analyzed data using concatenated (RAxML) and species-tree (ASTRAL-III) methods on full and subsampled datasets.

Main Results:

• Different alignment and trimming methods significantly altered alignment characteristics (length, informative sites).
• These variations had minimal impact on recovering well-established clades and their support values.
• Phylogenetic method choice strongly influenced results; concatenated analyses showed superior clade recovery and support.

Conclusions:

• Alignment and trimming method choice has limited effect on robust clade recovery in phylogenomics.
• Concatenated analyses are generally more effective than species-tree methods for recovering established clades.
• Recommendations for "best practices" in alignment and trimming are suggested.