Saturation and base composition bias explain phylogenomic conflict in Plasmodium

Area of Science:

• Molecular evolution
• Genomics
• Parasitology

Background:

• Current Plasmodium phylogenetics relies on limited single-gene analyses, hindering a comprehensive understanding of its evolution.
• Genome-based advances offer potential for improved insights into disease mechanisms and drug development.

Purpose of the Study:

• To develop and analyze a genome-scale dataset of 100 orthologous genes for robust Plasmodium phylogeny reconstruction.
• To minimize systematic errors in phylogenetic analysis using a large-scale dataset.

Main Methods:

• Analysis of 100 putative orthologous genes from genome comparisons.
• Evaluation of gene congruence, optimality criteria, and molecular evolution models.
• Application of codon position-specific rate partitioning and amino acid alignment analyses.

Main Results:

• Plasmodium genes exhibit saturation in substitutions and base frequency bias at third-codon positions.
• Molecular evolution models accounting for codon position and amino acid alignments best addressed sequence characteristics.
• Expanded taxon sampling and advanced models improved, but did not fully eliminate, phylogenetic accuracy.

Conclusions:

• Genome-scale phylogenetic analysis is essential for resolving Plasmodium evolutionary history.
• Advanced molecular evolution models and expanded taxon sampling are critical for accurate Plasmodium phylogeny.
• Accurate Plasmodium phylogeny is vital for understanding disease mechanisms and guiding drug development.