Phylogenomics beyond the 'bag-of-genes' model

Genome-scale data have transformed phylogenetics, yet most phylogenomic analyses disregard the genomic positions of the loci used to infer evolutionary histories. Although the role of deep coalescence is well studied, phylogenomics has paid far less attention to the fact that recombination generates correlated genealogies, with positional dependencies encoding rich information about demography, selection, and gene flow. Recent advances in genome assembly and computational modeling now make it feasible to move beyond long-standing simplifications that treat genomes as 'bags of genes'. Here, we synthesize the growing literature on position-aware phylogenomic approaches, from site-based methods to coalescent hidden Markov models. We argue that explicitly incorporating genomic position reveals evolutionary signals inaccessible to traditional approaches and represents a necessary step toward a more realistic framework for genome evolution.