<![CDATA[Graphical Abstract Highlight Research 1. The first population genetic assessment of the Berau Archipelago (DKB and DKK) jellyfish populations. 2. Two lakes populations within Berau Archipelago exhibited low-to-moderate population genetic diversity level. 3. Retained connectivity yet distinct evolutionary history between DKB and DKK lakes population have been observed. 4. This research underscore vulnerability of the stingless jellyfish populations within Berau Archipelago that warrant effective conservation strategies. Abstract Kakaban Lake in East Kalimantan, Indonesia, is characterized by unique hydrographic conditions that support distinctive biodiversity. The stingless jellyfish Mastigias sp., one of the lake’s endemic faunas, is hypothesized to have evolved a loss of stinging capability due to prolonged isolation and adaptation within this enclosed ecosystem. Despite its uniqueness, there is no population genetic baseline data available for this species in Kakaban and nearby Lakes, which could threaten their survivability. This study aimed to provide baseline population genetic diversity and differentiation data for Mastigias sp. population in Berau Archipelago. Samples from individual jellyfish were collected from Kakaban Lake (DKB, N=20) and Kuku Lake, Maratua Island (DKK, N=19). Based on partial fragment of mtDNA 16S rRNA sequences, genetic diversity, genetic differentiation, and demographic history were estimated between two populations. Genetic analysis revealed moderate diversity across both populations (H=10; h=0.487 ± 0.099; π=0.00127 ± 0.00035). Weak and non-significant population differentiation (FST= 0.0012, p>0.05) was observed, alongside a high frequency of shared haplotypes, indicating retained connectivity between the two lakes. However, the presence of population-specific haplotypes in both DKB (6 haplotypes) and DKK (2 haplotypes) suggests evolutionary uniqueness, despite the overall weak genetic structure. Neutrality test consistent with pattern of demographic expansion following past bottleneck (Tajima’s D = -2.039, p<0.05). This study highlights evolutionary uniqueness of these populations, emphasizing the need for effective conservation strategies to ensure the long-term viability of this flagship species.]]>
