Phylogenetic inference using non-redundant coding of dependent characters vs. alternative approaches when applied to protein-coding genes

Simmons MP, Zhang LB, Müller KF

Research article (journal)


Contemporary molecular phylogenetic analyses often encompass a broad range of taxonomic diversity while maintaining high levels of sampling within each major taxon. To help maximize phylogenetic signal in such studies, one may analyse multiple levels of characters simultaneously. We test the performance of both the original and the modified versions of non-redundant coding of dependent characters (NRCDC) relative to commonly applied alternative character-sampling strategies using codon-based simulations under a range of conditions. Both original and modified NRCDC generally outperformed other character-sampling strategies that only sampled characters at one level (nucleotides or amino acids) over a broader range of simulation parameters than any of the alternative character-sampling strategies with respect to both overall success of resolution and averaged overall success of resolution in the parsimony-based analyses. Based on theoretical considerations and the results of our simulations, we encourage application and further testing of modified NRCDC in parsimony-based molecular phylogenetic analyses that sample exons of protein-coding genes. We expect that modified NRCDC will generally increase both accuracy and branch-support over commonly applied alternative character-sampling strategies when analysed using the same phylogenetic inference method, particularly in studies that sample both closely and distantly related taxa with clades representing both ancient and recent divergences.

Details zur Publikation

Pages: 11
Release year: 2010
Language in which the publication is writtenEnglish