Conflict between Amino Acid and Nucleotide Characters

Area of Science:

• Molecular Evolution
• Phylogenetics
• Bioinformatics

Background:

• Phylogenetic analyses traditionally favor slowly evolving characters like amino acid replacements.
• Amino acids are composite characters influenced by the degenerate genetic code, increasing susceptibility to convergent evolution.
• Previous studies have overlooked the potential phylogenetic utility of silent, or synonymous, nucleotide substitutions.

Purpose of the Study:

• To compare the phylogenetic informativeness of silent nucleotide substitutions versus amino acid replacement substitutions.
• To investigate the impact of composite characters and convergence on phylogenetic tree reconstruction using amino acid data.
• To assess the reliability of amino acid-based phylogenies in seed plants.

Main Methods:

• Analysis of the atpB and rbcL genes from 567 seed plant species.
• Phylogenetic tree construction using both nucleotide (silent substitutions) and amino acid (replacement substitutions) datasets.
• Comparison of resulting phylogenetic trees with independent biological evidence.

Main Results:

• Silent nucleotide substitutions provide more accurate phylogenetic signals than amino acid replacements.
• Phylogenetic artifacts, including composite characters and convergence, cause amino acid-based trees to conflict with nucleotide-based trees.
• Amino acid trees showed discordance with independent evidence, highlighting potential inaccuracies.

Conclusions:

• Coding nucleotide sequences solely as amino acid characters offers limited phylogenetic benefit.
• Relying on amino acid data for phylogenetic inference can yield misleading evolutionary relationships.
• Silent nucleotide substitutions are a more reliable character type for reconstructing evolutionary history in seed plants.