Prediction of local convergent shifts in evolutionary rates with phyloConverge.

ABSTRACT:

Motivation

Convergence analysis can characterize genetic elements underlying morphological adaptations. However, its performance on regulatory elements is limited due to their modular composition of transcription factor motifs, which have rapid turnover and experience different evolutionary pressures.

Results

We introduce phyloConverge, a phylogenetic method that performs scalable, fine-grained local convergence analysis of genomic elements at flexible length scales. Using a benchmarking case of convergent subterranean mammal adaptation, phyloConverge identifies rate-accelerated conserved noncoding elements (CNEs) with high specificity and statistical robustness relative to competing methods. From CNE-level scoring, we detect the convergent regression of entire CNE units and

SUBMITTER: Saputra E 

PROVIDER: S-EPMC12275462 | biostudies-literature | 2025 Jul

REPOSITORIES: biostudies-literature