In evolutionary biology, “ancient fish” and the “living fossil” fish they represent have long been regarded as crucial windows for understanding species evolution. Living fossil fish refer to species that have retained extremely ancient morphological characteristics with remarkable stability throughout geological history, such as the coelacanth, lungfish, and gar. These lineages have typically undergone hundreds of millions of years of evolution; however, their morphology, ecology, and even genomic structure have changed slowly, exhibiting evolutionary rates far lower than most modern fish.

Because these species have remained so genetically and physically stagnant, these lineages preserve a wealth of biological information from deep within geological history. This preservation 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.

Based on previous work, a research group led by Prof. HE Shunping, a member of the Chinese Academy of Sciences, from the Institute of Hydrobiology (IHB) of the Chinese Academy of Sciences collaborated with Prof. Thomas J. Near's group at Yale University revealed the genomic mechanisms underlying the slow morphological changes in fish from the order Lepisosteiformes. This study was published in Genome Research.

In this study, researchers assembled chromosome-level genomes for the alligator gar (Atractosteus spatula) and the longnose gar (Lepisosteus osseus), and 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, revealing remarkable conservation. Despite diverging over 100 million years ago, these two genera still share 83.35% genomic synteny. The differences in genome size primarily arise from single-nucleotide indels rather than large-scale structural changes.

At the same time, microchromosomes are more stable than macrochromosomes and are significantly enriched in genes related to DNA repair and apoptosis. The evolutionary rate of these microchromosomes is extremely slow, with a chromosomal rearrangement rate of only about 0.5 events per million years. Moreover, the gar's genomic similarity to tetrapods is even higher than that of closely related teleosts. The generation rate and activity of transposable elements are 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 remain capable of intergeneric hybridization in contemporary environments, producing viable offspring. Population genomic analyses reveal that while there is significant lineage differentiation between the two genera, there have historically been limited gene flow events. This ongoing capacity for hybridization may stem from their long-term genomic structural conservation and low molecular incompatibility.

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

(Editor: MA Yun)

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