resolving discrepancy between nucleotides and amino acids in deep-level arthropod phylogenomics differentiating serine codons in 21-amino-acid models解决差异核苷酸和氨基酸在深层节肢动物phylogenomics区分丝氨酸在21-amino-acid密码子模型.pdfVIP

Resolving Discrepancy between Nucleotides and Amino Acids in Deep-Level Arthropod Phylogenomics: Differentiating Serine Codons in 21-Amino-Acid Models 1 2 3 ¤ Andreas Zwick *, Jerome C. Regier *, Derrick J. Zwickl * 1 Department of Entomology, State Museum of Natural History, Stuttgart, Germany, 2 Institute for Bioscience and Biotechnology Research and Department of Entomology, University of Maryland, College Park, Maryland, United States of America, 3 Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America Abstract Background: In a previous study of higher-level arthropod phylogeny, analyses of nucleotide sequences from 62 protein- coding nuclear genes for 80 panarthopod species yielded significantly higher bootstrap support for selected nodes than did amino acids. This study investigates the cause of that discrepancy. Methodology/Principal Findings: The hypothesis is tested that failure to distinguish the serine residues encoded by two disjunct clusters of codons (TCN, AGY) in amino acid analyses leads to this discrepancy. In one test, the two clusters of serine codons (Ser1, Ser2) are conceptually translated as separate amino acids. Analysis of the resulting 21-amino-acid data matrix shows striking increases in bootstrap support, in some cases matching that in nucleotide analyses. In a second approach, nucleotide and 20-amino-acid data sets are artificially altered through targeted deletions, modifications, and replacements, revealing the pivotal contributions of distinct Ser1 and Ser2 codons. We confirm that previous methods of coding nonsynonymous nucleotide change are robust and computationally efficient by introducing two new degeneracy coding methods. We demonstrate for degeneracy coding that neith