Data and code from: An evolutionary framework for characterizing noncoding regions of DNA
Year: 2026
Type: dataset
Abstract: Quantifying the evolutionary forces acting on protein-coding sequences has long been a central goal of molecular evolutionary biology, facilitated by the distinction between synonymous and nonsynonymous substitutions embodied in the dN/dS framework. Comparable quantitative approaches for structured non-protein-coding sequences are less well developed, despite the strong functional constraints imposed by nucleic acid secondary structure. Here, an analogous framework is developed for analyzing the evolution of structured RNAs by distinguishing classes of nucleotide change according to their consequences for paired and unpaired positions. We introduce ωRNA, a measure of the relative evolutionary dynamics of pair-disrupting change, and ρcomp, a complementary parameter describing compensatory restoration of nucleotide pairing. Because both pair disruption and compensatory restoration can arise under the underlying nucleotide substitution process, the framework is extended using phylogenetic stochastic mapping and parametric simulation to obtain molecule-specific evolutionary expectations. This yields two model-aware quantities: ωRNA*, the observed pair-disruption statistic relative to its model-derived expectation, and Δρcomp, the excess compensatory-restoration signal above its corresponding expectation. The approach is demonstrated and validated using mitochondrial tRNAs across a 482-taxon drosophilid phylogeny. Individual tRNAs occupy markedly different regions of ωRNA*–Δρcomp evolutionary space, ranging from strong suppression of pair disruption accompanied by substantial excess compensatory restoration to pair-disruption dynamics near their model-derived expectation. These results demonstrate that preservation of RNA secondary structure can arise through different combinations of suppression of disruptive change and compensatory restoration. The ωRNA/ρcomp framework provides a phylogenetically explicit approach for quantifying these complementary dimensions of molecular evolution in structured nucleic acids.
Source: DRYAD
Author: DeSalle, Rob
Institution: American Museum of Natural History
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7202203622