Efficient Identification of Phylogenetically Informative Alignment Sites via Sparse Learning

Abstract

Identifying phylogenetically informative sites in multiple sequence alignments is critical for accurate tree reconstruction and efficient data curation in phylogenomics. Existing approaches that measure phylogenetic information often rely on predefined topologies or heuristic criteria, limiting their generality and interpretability. Here, we introduce a novel, topology-agnostic framework for quantifying site-wise phylogenetic information using sparse learning via Lasso (Least Absolute Shrinkage and Selection Operator) regression. By modeling site log-likelihoods as predictors of the tree likelihood across a large ensemble of random topologies, our approach isolates the minimal subset of sites that meaningfully contribute to phylogenetic signal. We validate the method using both simulated and empirical mammalian datasets, demonstrating that Lasso-selected sites yield topologies nearly identical to those inferred from full alignments. For computational efficiency, we show that a simple entropy-based proxy (Shannon H [≥] 0.5) approximates Lasso results with high fidelity, enabling rapid site-level assessments. Importantly, our definition of phylogenetically informative sites provides an objective metric that can serve as a gold standard to evaluate commonly used alignment filtering tools. These findings establish sparse learning as a principled, scalable, and practical approach for assessing and optimizing phylogenetic data.