Horizontal Gene Transfer Resets Codon Usage Bias Within 500 Generations. Experimental Evolution in Escherichia coli We present a comprehensive quantitative analysis that challenges conventional understanding.
Gene trees frequently conflict with species trees, but the magnitude, predictors, and functional distribution of this disagreement remain poorly quantified for most clades. We reconstructed a species tree from 150 fungal genomes using ASTRAL-III and compared it against individual maximum-likelihood gene trees for 2,000 single-copy orthologs identified via OrthoFinder.
Horizontal gene transfer (HGT) disrupts the codon usage signature of recipient genomes, leaving persistent compositional scars detectable as outliers in the GC3–Nc space. We formalise the GC3 deviation score — the normalised absolute distance of a gene's third-codon-position GC content from its host genome mean — as a lightweight, single-feature HGT candidate detector, and benchmark it against curated alien-gene lists across four bacterial genomes: E.