Redlich, R. | Search bioRxiv

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↗

bioRxiv2019

Subcortical Shape Alterations in Major Depressive Disorder: Findings from the ENIGMA Major Depressive Disorder Working Group

Alterations in regional subcortical brain volumes have been widely investigated as part of the efforts of an international consortium, ENIGMA, to determine reliable structural brain signatures for Major Depressive Disorder (MDD). Given that subcortical structures are comprised of distinct subfields, we sought to build significantly from prior work to precisely map localized MDD-related differences in subcortical regions using shape analysis. In this meta-analysis of subcortical shape from the ENIGMA-MDD working group, we compared 1,781 patients with MDD and 2,953 healthy controls (CTL) on individual measures of shape metrics (thickness and surface area) on the surface of seven bilateral subcortical structures: nucleus accumbens, amygdala, caudate, hippocampus, pallidum, putamen, and thalamus. Harmonized data processing and statistical analyses were conducted locally at each site, and findings were aggregated by meta-analysis. Relative to CTL, patients with MDD had lower surface area in the subiculum of the hippocampus, the basolateral amygdala, and the nucleus accumbens shell. Relative to CTL, patients with adolescent-onset MDD ([≤] 21 years) had lower thickness and surface area of the subiculum of the hippocampus and the basolateral amygdala. Relative to first-episode MDD, recurrent MDD patients had lower thickness and surface area in the CA1 of the hippocampus and the basolateral amygdala. Our results suggest that previously reported MDD-associated volumetric differences may be localized to specific subfields of these structures that have been shown to be sensitive to the effects of stress, with important implications for mapping treatments to patients based on specific neural targets and key clinical features.

neuroscience↗