Serine codon usage bias in deep phylogenomics: pancrustacean relationships as a case study. Syst Biol

Abstract.—Phylogenomic analyses of ancient relationships are usually performed using amino acid data, but it is unclear whether amino acids or nucleotides should be preferred. With the 2-fold aim of addressing this problem and clarifying pancrustacean relationships, we explored the signals in the 62 protein-coding genes carefully assembled by Regier et al. in 2010.With reference to thepancrustaceans, thisdata set infers ahighly supportednucleotide tree that is substantiallydifferent to the corresponding, butpoorly supported, aminoacidone.Weshowthat thediscrepancybetween thenucleotide-basedand the amino acids-based trees is caused by substitutions within synonymous codon families (especially those of serine—TCN and AGY). We show that different arthropod lineages are differentially biased in their usage of serine, arginine, and leucin