phaidra.vetmeduni.ac.at o:3420 DOI 10.1093/sysbio/syad036 DNA Sequences Are as Useful as Protein Sequences for Inferring Deep Phylogenies Inference of deep phylogenies has almost exclusively used protein rather than DNA sequences based on the perception that protein sequences are less prone to homoplasy and saturation or to issues of compositional heterogeneity than DNA sequences. Here, we analyze a model of codon evolution under an idealized genetic code and demonstrate that those perceptions may be misconceptions. We conduct a simulation study to assess the utility of protein versus DNA sequences for inferring deep phylogenies, with protein-coding data generated under models of heterogeneous substitution processes across sites in the sequence and among lineages on the tree, and then analyzed using nucleotide, amino acid, and codon models. Analysis of DNA sequences under nucleotide-substitution models (possibly with the third codon positions excluded) recovered the correct tree at least as often as analysis of the corresponding protein sequences under modern amino acid models. We also applied the different data-analysis strategies to an empirical dataset to infer the metazoan phylogeny. Our results from both simulated and real data suggest that DNA sequences may be as useful as proteins for inferring deep phylogenies and should not be excluded from such analyses. Analysis of DNA data under nucleotide models has a major computational advantage over protein-data analysis, potentially making it feasible to use advanced models that account for among-site and among-lineage heterogeneity in the nucleotide-substitution process in inference of deep phylogenies. eng Codon-Substitution Models; Amino-Acid Substitution; Compositional Heterogeneity; Sister Group; Nucleotide Substitution; Evolutionary Trees; Likelihood Models; Supports Sponges; Mixture-Models; Reconstruction 2024-08-23T08:22:12.422Z LOMv1.0 Author BEGIN:VCARD VERSION:3.0 N:Kapli;Paschalia; FN:Paschalia Kapli X-ORCID:https://orcid.org/0000-0001-8769-8779 END:VCARD BEGIN:VCARD VERSION:3.0 N:Kotari;Ioanna; FN:Ioanna Kotari X-ORCID:https://orcid.org/0000-0002-9939-7444 END:VCARD BEGIN:VCARD VERSION:3.0 N:Telford;Maximilian J.; FN:Maximilian J. Telford X-ORCID:https://orcid.org/0000-0002-3749-5620 END:VCARD BEGIN:VCARD VERSION:3.0 N:Goldman;Nick; FN:Nick Goldman X-ORCID:https://orcid.org/0000-0001-8486-2211 END:VCARD BEGIN:VCARD VERSION:3.0 N:Yang;Ziheng; FN:Ziheng Yang X-ORCID:https://orcid.org/0000-0003-3351-7981 END:VCARD https://w3id.org/kim/hcrt/scheme https://w3id.org/kim/hcrt/text Textdokument Text LOMv1.0 yes https://creativecommons.org/licenses/by-nc/4.0 application/pdf 1862075 https://phaidra.vetmeduni.ac.at/o:3420 https://phaidra.vetmeduni.ac.at/api/object/o:3420/thumbnail LOMv1.0 discipline