Single nucleotide polymorphisms reveal the population genetics and evolutionary history of the Asian swamp eel across Asia

The Asian swamp eel (putatively Monopterus albus ) is recognized as one of the most economically significant specialty freshwater fishes in China. Nonetheless, there is a lack of systematic research on eel population genetics utilizing genome-wide analyses. This study sequenced the genomes of 559 eel samples from 37 regions in Asia, identifying 82.71 million single nucleotide polymorphisms and revealing the existence of multiple genetic structure breaks in the eel population. Combining phylogenetic and population structure analyses with genetic differentiation and kinship heat maps, we classified Asian swamp eel populations into three clusters at the macroscopic level and hypothesized that they each belonged to different species within the genus Monopterus . These findings reveal cryptic and complex diversification, attributed to geographical isolation and both artificial and natural selection. Furthermore, we analyzed the evolutionary origins of the eel based on the available data and hypothesized that it originated in the South Asian subcontinent of Bangladesh. This work determined the evolutionary history and genetic diversity of eel populations, alongside the selection mechanisms potentially influencing their adaptations. These findings will provide new insights into the genetic structure of the species, aimed at establishing a foundation for the conservation and management of eel genetic diversity and the selection of high-quality germplasm in the future.