Francis et al. (2025) investigate the relationship between genomic rearrangement, specifically macro- and micro-synteny, and speciation across a broad range of animal phyla. Using chromosome-level genome assemblies, they generated 1:1 ortholog pairs and analyzed synteny conservation using custom bioinformatics pipelines to quantify microsynteny. The study is well written, methodologically sound, and offers valuable insights beyond comparative genomics.

The authors show that while most congeneric species pairs exhibit disruptions in micro-synteny, they retain high levels of protein sequence identity. They also find that macro- and micro-synteny decay with speciation but are often decoupled, indicating no universal genomic trajectory during divergence. Their conclusion, that synteny patterns alone are insufficient to define species boundaries (Steenwyk and King 2024), is well supported by their data.

The discussion effectively situates the work within the broader context of speciation research. It thoughtfully addresses study limitations, such as challenges in synteny block quantification, chromosomal rearrangement rates, and the scarcity of high-quality genome assemblies. The manuscript also outlines clear directions for future research, including the need for more accurate divergence time estimates and expanded taxonomic sampling (Formenti et al. 2022).

              
References

Formenti G, Theissinger K, Fernandes C, Bista I, Bombarely A, Bleidorn C, et al. (2022) The era of reference genomes in conservation genomics. Trends in Ecology & Evolution, 37, 197–202. https://doi.org/10.1016/j.tree.2021.11.008

Francis WR, Vargas S, Wörheide G (2025) Genomic changes are varied across congeneric species pairs of animals. bioRxiv, ver. 4 peer-reviewed and recommended by PCI Genomics https://doi.org/10.1101/2024.09.05.611358

Steenwyk JL, King N (2024) The promise and pitfalls of synteny in phylogenomics. PLOS Biology, 22, e3002632. https://doi.org/10.1371/journal.pbio.3002632