Comparison of the 12S rRNA and COI Regions of Mitochondrial DNA for eDNA Detection of Alligator Gar (Atractosteus spatula)

Alligator gar (Atractosteus spatula) has been introduced to many places outside its native range. The fish is considered as an invasive alien species that needs to be eradicated upon encounter in Indonesia due to its aggressive behavior. Despite existing regulations in Indonesia, the fish is still bred and widely distributed as a pet fish which increases the potential of being released into native waters. Non-invasive early detection of alligator gar is important as part of management efforts. This experiment was conducted to compare the 12S rRNA and COI regions of mitochondrial DNA for detection and estimation of alligator gar. Water samples (250 mL) were obtained from mesocosms containing one and three fish. The environmental DNA (eDNA) was filtered and extracted from the samples before amplified using quantitative PCR (qPCR). The eDNA concentrations amplified using 12S primers were higher than COI primers with 49.2×106–14.2×109 average copies/sample. There was negligible correlation between fish biomass and eDNA copy numbers amplified using 12S primers, but there was significant correlation (y = 330.6x − 1175, R2 = 0.3356, p < 0.05) between fish biomass and eDNA copy numbers amplified using COI primers. Thus, targeted qPCR using specific primers is more effective for detection and estimation of alligator gar in nature.