Ancient gene introgression promotes biodiversity of <i>Nymphaea nouchali</i> in Hainan under environmental changes

Abstract Hybridization is common in the plant kingdom. Under the influence of global climate change, an increasing number of hybrid species have experienced significant shifts from the geographical distribution of their parents, making it more difficult to detect ancient gene flows. Nymphaea nouchali is a rare aquatic flower native to Hainan Province. Owing to habitat destruction and human interference, the natural range of N. nouchali has gradually reduced to the point of extinction. To explore how hybrid populations form using RAD‐seq with population genetic analysis, it is shown that there are heterozygous deletions and inbreeding in N. nouchali and a number of ancestral components in Nymphaea lotus, low of genetic differentiation, and little gene flow between N. nouchali and N. lotus , and ancient introgression between ancestors may have been more frequent than gene exchange after the origin of the species. Accordingly, the ancient N. nouchali genotypes were gradually infiltrated by N. lotus genes and their forms changed in Hainan. Potential distribution pattern analysis also predicted the possible distribution of N. lotus in Hainan. This lays a foundation for exploring the natural genetic mechanisms of Nymphaea species formation and evolution.