MapGL

MapGL infers evolutionary gain and loss of short genomic sequence features to enable phylogenetic analysis of cis-regulatory element turnover across eutherian genomes.

Key Features:

• Targeted sequence features: Infers gain and loss events for short genomic sequence features, specifically cis-regulatory elements.
• Phylogenetic algorithm: Implements phylogenetic maximum parsimony for ancestral-state reconstruction.
• Ancestral-state reconstruction: Reconstructs ancestral presence/absence states by minimizing the number of evolutionary changes.
• Phylogenetic scope: Supports analysis across a wide range of phylogenetic topologies and evolutionary distances.
• Taxonomic application: Applied to comparative analyses of eutherian genomes.
• Evolutionary context: Places species-specific sequence features within an explicit phylogenetic framework to assess regulatory sequence turnover.

Scientific Applications:

• Comparative genomics: Elucidates shared and divergent regulatory sequence content between species using phylogenetic inference.
• Regulatory sequence turnover: Quantifies gain and loss of cis-regulatory elements to study turnover dynamics.
• Phenotypic divergence: Investigates how genomic sequence gain and loss contribute to species-specific phenotypic differences.
• Genome evolution and regulatory biology: Supports studies on genome evolution, regulatory element evolution, and the genetic basis of adaptation.

Methodology:

Uses phylogenetic maximum parsimony to reconstruct ancestral states by minimizing the number of evolutionary changes.