Impact of Phylogenetic Method Choice on Indel Analyses in HIV-1 Subtype B

Area of Science:

• Genomics
• Evolutionary Biology
• Bioinformatics

Background:

• Insertions and deletions (indels) are key drivers of genome evolution.
• Accurate detection and interpretation of indels in phylogenetic studies are challenging.
• Methodological choices in bioinformatics tools can influence evolutionary inferences.

Purpose of the Study:

• To investigate how different multiple sequence alignment (MSA) and ancestral sequence reconstruction (ASR) tools affect indel pattern reconstruction.
• To understand the impact of tool selection on indel detection in HIV-1 subtype B.
• To emphasize the importance of choosing appropriate tools for accurate phylogenetic analyses.

Main Methods:

• Comparative analysis of five MSA tools (MAFFT, PRANK+F, IndelMaP, ProPIP, Historian) and five ASR tools (GRASP, FastML, IndelMaP, ARPIP, Historian).
• Evaluation of inferred indel events, including rates, lengths, and positions.
• Focus on the env gene and its V1 variable loop in HIV-1 subtype B.

Main Results:

• All tested methods could reconstruct known variable regions in the HIV-1 env gene.
• The selection of MSA tools had a greater impact on indel conservation and interpretation than ASR tools.
• Indel detection accuracy is highly dependent on the chosen MSA method.

Conclusions:

• The choice of MSA tool is critical for accurate indel detection in phylogenetic studies.
• Context-specific MSA tool selection is necessary for reliable evolutionary inferences.
• Findings provide insights for improving phylogenetic accuracy in HIV-1 and other genomic studies.