Genetic diversity and population structure of Azolla inferred by trnL-trnF intergenic region and morphological data in Yogyakarta, Indonesia

Azolla, commonly known as fairy moss, is a floating aquatic fern found in both tropical and temperate regions. While it plays an important ecological and agricultural role—such as enhancing soil nutrients in rice paddies—it has also been identified as an invasive species in many freshwater ecosystems. Its spread is often associated with the aquarium plant trade and the interconnectedness of freshwater systems. Understanding the genetic variation and population structure of Azolla is essential for monitoring its spread and managing its ecological impact. This study aimed to analyze the distribution and population structure of Azolla species collected from both wild (rice fields) and cultivated (ponds) habitats in the Special Region of Yogyakarta, Indonesia. Morphological observations were conducted alongside molecular analyses using DNA sequences from the intergenic spacer region trnL-trnF. Phylogenetic analysis revealed that Azolla populations in Yogyakarta are grouped into two distinct clades, with genetic divergence values ranging from 0.00% to 0.74%. Each clade exhibited a unique haplotype with low nucleotide diversity. All samples were identified as Azolla cristata (conspecific with A. microphylla and A. mexicana) with 90% confidence. Clade groupings corresponded to habitat type, distinguishing wild from cultivated populations. Haplotype network analysis showed overlapping distribution patterns, likely influenced by the connectivity of regional freshwater systems. These findings contribute to the understanding of Azolla diversity in Indonesia and provide a foundation for future monitoring of its genetic structure. Broader population sampling is necessary to further evaluate potential invasiveness or the risk of biodiversity loss in freshwater environments.