Phylogenomics beyond the 'bag-of-genes' model.

Incorporating genomic position into phylogenomics reveals evolutionary signals missed by traditional 'bag-of-genes' models, advancing understanding of genome evolution.

• Why it matters: Ignoring the positional information of loci limits insights into complex evolutionary processes like demography, selection, and gene flow, which are encoded in correlated genealogies.
• What they did: The authors review recent developments in position-aware phylogenomic methods, including site-based approaches and coalescent hidden Markov models, to move beyond simplified models.
• The result: This approach uncovers new evolutionary signals and provides a more realistic framework for studying genome evolution, enabling deeper insights into the history of species.