"Ancient fish" and living fossil fish are regarded as windows to understand species evolution. Living fossil fish refer to species that have retained ancient morphological characteristics with remarkable stability throughout geological history. Their morphology, ecology and even genomic structure have changed slowly, exhibiting evolutionary rates far lower than most modern fish.

The lineages of these species have preserved a wealth of biological information from deep within geological history, which makes these ancient fish crucial subjects for exploring the diversification of fish, patterns of genomic evolution, and key evolutionary innovations in vertebrates, such as the transition from aquatic to terrestrial life.

In a study published in Genome Research, a research group led by CAS member Prof. HE Shunping from the Institute of Hydrobiology of the Chinese Academy of Sciences, along with Prof. Thomas J. Near's group from Yale University, revealed the genomic mechanisms underlying the slow morphological changes in fish from the order Lepisosteiformes.

The researchers assembled chromosome-level genomes for the alligator gar (Atractosteus spatula) and the longnose gar (Lepisosteus osseus). They systematically analyzed the sequence evolution, structural stability, and transposable element activity of the gar genome.

The researchers discovered chromosomal fusion events in the two gar genera. Despite diverging over 100 million years ago, these two genera still shared 83.35% genomic synteny. The differences in genome size primarily arose from single-nucleotide indels rather than large-scale structural changes.

Besides, the researchers found that microchromosomes were more stable than macrochromosomes and were enriched in genes related to DNA repair and apoptosis. The evolutionary rate of these microchromosomes was extremely slow with a chromosomal rearrangement rate of only about 0.5 events per million years.

Moreover, the researchers found that the gar's genomic similarity to tetrapods was even higher than that of closely related teleosts. The generation rate and activity of transposable elements were the lowest among vertebrates, suggesting that this low activity plays a crucial role in maintaining genomic stability.

Surprisingly, the two genera that diverged in the Cretaceous remained capable of intergeneric hybridization in contemporary environments, producing viable offspring. Population genomic analyses revealed that there was significant lineage differentiation between the two genera, but there had been limited gene flow events historically. This capacity for hybridization may stem from their long-term genomic structural conservation and low molecular incompatibility.

The findings of this study not only provide an important reference for comparative vertebrate genomics but also reveal a unique pattern of genomic evolution in living fossils.