Conserved genetic background but geographically differentiated DNA methylation patterns in invasive alligator weed (Alternanthera philoxeroides) populations of China and Japan

Alligator weed (Alternanthera philoxeroides) is a highly invasive species that has successfully established in numerous tropical and subtropical regions worldwide. Previous literature suggests that alligator weed was introduced to China in the 1930s as fodder for military horses by Japanese, while its presence in Japan only became apparent in the 1990s. Consequently, the introduction and genetic relationship between alligator weed populations in China and Japan remain uncertain, and the native source population is still unidentified. This study aimed to characterize the genetic diversity and structure of populations within the introduced range of China and Japan, as well as the native range of Argentina, using amplified fragment length polymorphism (AFLP) markers. Nine primer pairs were employed, resulting in a total of 573 distinct amplified bands for the China and Japan populations. However, none of these bands displayed polymorphism, indicating a uniform genetic background across all sampled populations in China and Japan. In contrast, the Argentine populations yielded 251 identifiable amplified bands using four well-performing primer pairs, of which 209 (80.69%) were found to be polymorphic. Genetic relationship and population structure analyses based on AFLP data revealed that the population from Jujuy, Argentina, exhibited the closest genetic affinity to the invasive populations in China and Japan, as indicated by Nei’s genetic identity value of 0.9281. Additionally, using methylation-sensitive amplified polymorphism (MSAP), we identified 258 epigenetic variation sites using five primer pairs in the Chinese and Japanese populations. Principal coordinate analysis (PCoA) based on the MSAP data revealed a geographic epigenetic structure within the alligator weed populations of China and Japan, with DNA methylation variation patterns exhibiting correlation with geographic distribution, thus implying their potential involvement in environmental adaptation. This research enhances our understanding of the invasion mechanisms of alligator weed and provides valuable insights into the roles of epigenetic factors in its successful spread.