Evaluation of biodiversity metrics through environmental DNA metabarcoding outperforms visual and capturing surveys

Abstract

Information on alpha (local), beta (between habitats), and gamma (regional) diversity is fundamental to conserving biodiversity and the functions and stability of ecosystem processes. Robust methods like environmental DNA (eDNA) metabarcoding are currently considered useful to investigate biodiversity. However, the performance of eDNA methods in evaluating diversity has not been tested quantitatively. We compared the performance of eDNA metabarcoding and visual and capturing surveys in estimating alpha, beta, and gamma diversity in river fish communities, particularly considering community nestedness and turnover. In five rivers across west Japan, when compared with visual and capturing surveys, eDNA metabarcoding detected higher alpha and gamma diversity in local habitats, and indicated differences in beta diversity more clearly; this suggests the superiority of eDNA metabarcoding over visual/capturing surveys in estimating diversity. The statistical frameworks, particularly nestedness and turnover, can provide quantitative evidences needed to assess diversity component estimation by new survey methods.