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

Position-aware phylogenomics reveals evolutionary signals inaccessible to traditional 'bag-of-genes' models, advancing understanding of genome evolution.

• Why it matters: Most phylogenomic analyses ignore the influence of recombination and genomic positions, which encode important information about demography, selection, and gene flow, limiting insights into evolutionary history.
• What they did: The authors review recent developments in genome assembly and computational modeling, focusing on methods that incorporate genomic position, including site-based approaches and coalescent hidden Markov models.
• The result: Explicitly considering genomic position enables detection of evolutionary signals that traditional methods miss, marking a crucial step toward a more realistic framework for understanding genome evolution.