The pangenome: a statistical model, not a fixed biological property

Abstract The pangenome, representing the complete genetic repertoire of a species, has become a central concept in modern prokaryotic genomics, moving the field beyond the limitations of a single reference genome. This review provides a comprehensive overview of the pangenomic landscape, from its conceptual foundations to its diverse applications. We critically examine the methodological and statistical underpinnings of pangenome analysis, emphasizing that the pangenome is not a fixed biological entity but a statistical model whose outputs are fundamentally dependent on dataset quality, curation, and taxonomic resolution. We discuss the transition from the simple open/closed dichotomy to more nuanced, ecologically-driven models like pangenome fluidity and the ecogenome, which better explain the evolutionary dynamics of prokaryotic genomes. With a special focus on the archaeal pangenome, we highlight the unique challenges and novel evolutionary insights emerging from this under-explored domain. As the field moves towards graph-based representations, AI-driven analysis, the expansion into metapangenomics integrated with functional multi-omics (transcriptomics and metabolomics) to bridge the genotype-phenotype gap, we argue that a rigorous and critical approach to data interpretation will be paramount to unlocking a true understanding of microbial evolution and function.