phyloConverge

phyloConverge performs scalable, fine-grained local convergence analysis of genomic elements to identify rate-accelerated conserved noncoding elements and reveal patterns in convergent evolution of regulatory elements.

Key Features:

• Flexible length scale analysis: phyloConverge analyzes genomic elements at flexible length scales, from entire CNE units down to transcription factor motif-level subregions.
• CNE-level scoring: The method detects convergent regression of entire conserved noncoding element units and distinguishes subterranean-associated coding region regression specific to ocular functions from regulatory element regression enriched for neuronal phenotypes and developmental processes.
• Transcription factor motif-level scoring: phyloConverge dissects elements into subregions with uneven convergence signals and demonstrates modular adaptation of CNEs with high functional specificity.
• Genome-wide scalability: The method performs high-resolution convergence analysis at genome-wide scale.

Scientific Applications:

• Convergent evolution of regulatory elements: phyloConverge identifies rate-accelerated conserved noncoding elements with high specificity and statistical robustness relative to competing methods, overcoming limitations of convergence analysis on regulatory elements due to modular composition and rapid turnover of transcription factor motifs.
• Subterranean mammal adaptation: The method benchmarks convergent subterranean mammal adaptation to detect convergent regression patterns in both coding and regulatory genomic elements.
• Modular adaptation dissection: phyloConverge reveals how CNEs undergo modular adaptation with high functional specificity through analysis of subregions with uneven convergence signals.

Methodology:

phyloConverge uses a phylogenetic method to perform local convergence analysis of genomic elements, scoring at both CNE-level and transcription factor motif-level to detect rate-accelerated elements.