A Hierarchical Haplotype-Based Distance for Genome-Wide Phylogenetic Reconstruction

Phylogenetic reconstruction is a central problem in computational biology, typically addressed through sequence alignments and distance- or character-based inference methods. Recent advances in sequencing technologies have enabled the generation of large-scale haplotype-resolved datasets, motivating the development of phylogenetic approaches capable of exploiting allele-specific information. In this work, we propose a hierarchical distance model for genome-wide phylogenetic reconstruction based on allele-specific haplotypes. The model defines genetic distances through successive aggregation steps at the allele, genotype, chromosome, and genome levels, producing a unified distance matrix suitable for distance-based phylogenetic inference. Experiments on a population-scale Vitis vinifera dataset show that the proposed framework produces stable genome-wide phylogenies while preserving chromosome-specific evolutionary signals. Reconstructions obtained with Neighbor-Joining and Balanced Minimum Evolution are largely consistent, indicating that the proposed distance captures robust phylogenetic information. Our results suggest that hierarchical aggregation of haplotype-level information provides a promising framework for genome-wide phylogenetic analysis, and offers a promising foundation for future studies on large population-scale genomic datasets.