Estimating fish population abundance by integrating quantitative data on environmental DNA and hydrodynamic modelling

Keiichi Fukaya, Hiroaki Murakami, Seokjin Yoon, Kenji Minami, Yutaka Osada, Satoshi Yamamoto, Reiji Masuda, Akihide Kasai, Kazushi Miyashita, Toshifumi Minamoto, Michio Kondoh

Research output: Contribution to journalArticlepeer-review

42 Citations (Scopus)


Molecular analysis of DNA left in the environment, known as environmental DNA (eDNA), has proven to be a powerful and cost-effective approach to infer occurrence of species. Nonetheless, relating measurements of eDNA concentration to population abundance remains difficult because detailed knowledge on the processes that govern spatial and temporal distribution of eDNA should be integrated to reconstruct the underlying distribution and abundance of a target species. In this study, we propose a general framework of abundance estimation for aquatic systems on the basis of spatially replicated measurements of eDNA. The proposed method explicitly accounts for production, transport and degradation of eDNA by utilizing numerical hydrodynamic models that can simulate the distribution of eDNA concentrations within an aquatic area. It turns out that, under certain assumptions, population abundance can be estimated via a Bayesian inference of a generalized linear model. Application to a Japanese jack mackerel (Trachurus japonicus) population in Maizuru Bay revealed that the proposed method gives an estimate of population abundance comparable to that of a quantitative echo sounder method. Furthermore, the method successfully identified a source of exogenous input of eDNA (a fish market), which may render a quantitative application of eDNA difficult to interpret unless its effect is taken into account. These findings indicate the ability of eDNA to reliably reflect population abundance of aquatic macroorganisms; when the “ecology of eDNA” is adequately accounted for, population abundance can be quantified on the basis of measurements of eDNA concentration.

Original languageEnglish
Pages (from-to)3057-3067
Number of pages11
JournalMolecular Ecology
Issue number13
Publication statusPublished - 2021 Jul


  • Abundance estimation
  • Environmental DNA
  • Japanese jack mackerel (Trachurus japonicus)
  • Quantitative echo sounder
  • Quantitative PCR
  • Tracer model


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