Significance of rare species in evaluating marine conservation effects on fish community using hill numbers

Abstract Marine protected areas (MPAs) have been established worldwide to protect biodiversity and enhance ecosystem services. Rare species play vital roles in marine conservation as they exhibit unique ecosystem functions and are vulnerable to extinction. However, determining their importance to conservation effects remains challenging due to the lack of feasible and standardized evaluation methods. The noninvasive environmental DNA (eDNA) method is increasingly used in marine biomonitoring because of its efficiency and sensitivity. Hill numbers provide a uniform evaluation scheme for assessing biodiversity. In this study, we calculated Hill numbers from eDNA data to determine marine fish diversity in MPAs. Traditional survey data and different bioinformatic clustering pipelines were also included to decide the impact of survey and analysis methods on ecological interpretation. The results showed that eDNA detected significantly more species than contemporaneous traditional survey data. We further found less significant inter-group differences for different seasons and pipelines when rare species diminished, indicating that excluding rare species in evaluations could affect the ecological interpretation of marine conservation effects. Protection time of MPAs demonstrated positive correlations with all diversity indices, albeit not statistically significant. In conclusion, we demonstrated the importance of rare species in marine biodiversity assessment and recommend appropriate usage of eDNA and downstream diversity indices to achieve a comprehensive evaluation of the marine conservation effect of MPAs.