CASTLES

CASTLES estimates branch lengths on species trees in substitution units under an extended multispecies coalescent (MSC) framework to account for gene tree heterogeneity and substitution rate variation.

Key Features:

• Derivation of expected gene tree branch lengths: Computes expected values of gene tree branch lengths in substitution units under a coalescent-based model.
• Extended multispecies coalescent (MSC): Implements an extension of the MSC that accommodates substitutions with varying rates across the species tree.
• Use of estimated gene trees: Leverages estimated gene trees as input to infer species tree branch lengths from the derived expectations.
• Output in substitution units: Produces species tree branch length estimates explicitly expressed in substitution units for downstream analyses.
• Handles incomplete lineage sorting and genomic heterogeneity: Accounts for heterogeneity in evolutionary histories across the genome, including effects of incomplete lineage sorting.
• Improved computational performance: Reports improvements in speed and accuracy relative to previous branch length estimation techniques.

Scientific Applications:

• Estimating diversification dates: Provides branch lengths in substitution units useful for converting to divergence time estimates.
• Characterizing selection pressures: Supplies branch length information that can inform analyses of selection across lineages.
• Understanding adaptive evolution: Enables comparative analyses that require accurate branch length estimates to detect adaptive changes.
• Comparative genomics and phylogenomics: Supports downstream comparative genomic and phylogenomic analyses that depend on reliable species tree branch lengths.
• Species tree reconstruction for evolutionary inference: Improves the precision of species tree reconstructions used in diverse evolutionary studies.

Methodology:

Derives expected gene tree branch lengths in substitution units under an extended multispecies coalescent (MSC) model that accommodates substitutions with varying rates across the species tree, and uses estimated gene trees to estimate species tree branch lengths from those expectations.