codon congruence

codon congruence ranks codons and orthologous genes by their phylogenetic signal to evaluate evolutionary relationships using parsimony analysis across 12,337 species and 25,727 orthologous genes.

Key Features:

• Extensive Dataset Analysis: Examines each codon within orthologs to determine specific codon usage for each of 12,337 species across 25,727 orthologous genes, identifying 890,814 parsimony-informative codons.
• Phylogenetic Signal Ranking: Compares species that use particular codons with those that do not to assess congruence of codon usage with species relationships in the Open Tree of Life (OTL).
• Statistical Evaluation: Calculates the statistical probability that observed codon usages align with phylogenetic trees by chance and identifies 25,771 codons with no parallelisms or reversals when mapped to the OTL.
• Phylogenetic Conservation Evidence: Demonstrates phylogenetic conservation of codon usage across archaea, bacteria, plants, mammals, and other vertebrates, reporting codon usages are 1,109 times more likely to align with OTL species relationships than expected by random chance.
• Framework for Tree Hypothesis Testing: Provides a framework for testing alternative tree hypotheses, exemplified by confirming turtle placement as sister to archosaurs using the OTL.

Scientific Applications:

• Evolutionary Biology Research: Aids understanding of evolutionary relationships and codon usage patterns across diverse taxa.
• Phylogenetic Analysis: Supports phylogenetic studies by providing codon-level evidence that can be compared to established species trees.
• Genomic Studies: Enables testing hypotheses about orthologous gene evolution and codon-usage conservation across genomes.

Methodology:

Parsimony-based analysis of codon usage across 12,337 species and 25,727 orthologous genes, mapping parsimony-informative codons to the Open Tree of Life and performing statistical assessments of congruence and probability of alignment by chance.