Biology subjects

Tene, M.

Publications and source records attributed to Tene, M..

3 recordsLinked to original sources

bioRxiv2026

RERconverge Update: Runtime Reduction and Analysis Function Overhaul

MotivationConvergent evolution, or the independent acquisition of similar phenotypes in distinct lineages, provides a powerful framework for investigating genomic changes associated with a phenotype. This paper details an update to RERconverge, a powerful R package that tests for associations between gene relative evolutionary rates (RERs) and convergent phenotypes to infer genomic regions associated with traits or selective pressures. We introduce new customizable analysis choices and scalable and efficient algorithms that can process larger genomic datasets, a critical improvement as genomic data become available for more species. ResultsModifications to core functions in the RERconverge pipeline resulted in an immense speedup (by a factor of up to 28.6). The function that tests for associations between phenotypes and RERs has been expanded to include two new analytical methods for outlier control; we also provide here a summary of the statistical tests users can perform, along with their use cases. Availability and implementationThe code and walkthrough vignettes for the package are available at https://github.com/nclark-lab/RERconverge. ContactNathan L. Clark nclark@pitt.edu; Maria Chikina mchikina@pitt.edu

genomics↗

bioRxiv2025

Diet-Related Molecular Evolution Differs between Vertivores, Invertivores, and Combined Carnivores

Mammals have repeatedly evolved specialized diets, including a variety of predatory diets targeting different prey animals. Prior research has found differences in positive selection, gene family evolution and gene functional loss linked with diet, but has focused primarily on trophic level classifications of herbivory, carnivory, and omnivory. Here we divide "carnivores" into vertivores and invertivores, due to the differences in nutrient composition of those food sources. We find significant differences in evolutionary conservation of multiple genes and GO categories between vertivores and invertivores. Conservation relative to herbivores differs among vertivores, invertivores, and the combination of all carnivores. Lineages with predatory diets have increased conservation in lipid and amino acid metabolism relative to herbivores. Notably, we find that results in the combined carnivore-herbivore comparison are much more similar to those of the invertivore-herbivore comparison than the vertivore-herbivore comparison, which suggests that prior studies on carnivory may have been detecting signatures of selection related to invertivory.

genetics↗

bioRxiv2023

RERconverge Expansion: Using Relative Evolutionary Rates to Study Complex Categorical Trait Evolution

Comparative genomics approaches seek to associate evolutionary genetic changes with the evolution of phenotypes across a phylogeny. Many of these methods, including our evolutionary rates based method, RERconverge, lack the capability of analyzing non-ordinal, multicategorical traits. To address this limitation, we introduce an expansion to RERconverge that associates shifts in evolutionary rates with the convergent evolution of multi-categorical traits. The categorical RERconverge expansion includes methods for performing categorical ancestral state reconstruction, statistical tests for associating relative evolutionary rates with categorical variables, and a new method for performing phylogenetic permulations on multi-categorical traits. In addition to demonstrating our new method on a three-category diet phenotype, we compare its performance to naive pairwise binary RERconverge analyses and two existing methods for comparative genomic analyses of categorical traits: phylogenetic simulations and a phylogenetic signal based method. We also present a diagnostic analysis of the new permulations approach demonstrating how the method scales with the number of species and the number of categories included in the analysis. Our results show that our new categorical method outperforms phylogenetic simulations at identifying genes and enriched pathways significantly associated with the diet phenotype and that the new ancestral reconstruction drives an improvement in our ability to capture diet-related enriched pathways. Our categorical permulations were able to account for non-uniform null distributions and correct for non-independence in gene rank during pathway enrichment analysis. The categorical expansion to RERconverge will provide a strong foundation for applying the comparative method to categorical traits on larger data sets with more species and more complex trait evolution.

bioinformatics↗