A strong relationship between environmental DNA metabarcoding and rank-based abundance of fish

Littlefair, J. E.; Hayhurst, L. D.; Yates, M. C.; Rennie, M. D.; Cristescu, M. E.

doi:10.1101/2025.01.22.634322

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bioRxiv · 10.1101/2025.01.22.634322

A strong relationship between environmental DNA metabarcoding and rank-based abundance of fish

Littlefair, J. E.·Hayhurst, L. D.·Yates, M. C.·Rennie, M. D.·Cristescu, M. E.

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Abstract

O_LIIncreasingly, molecular methods of species monitoring are integrated into freshwater biodiversity surveys and fisheries management. Inferring organism abundance or biomass from sequence counts derived from metabarcoding data has been an exciting but contentious concept in the biomonitoring community for some time. Although demonstrating a strong correlation with abundance has proven difficult, many researchers have assumed that quantitative metabarcoding data can at least provide broad-scale ranking of abundance. However, robust field validations of this widely-held assumption remain scarce. C_LIO_LIHere, we analyse metabarcoding read counts of fish eDNA data derived from 20 lakes and use betabinomial mixed effects models to compare this to rank abundance generated from long-term fish survey data. Rank abundance data for 18 species was generated within-species across-sites, meaning that ranks compare the abundance of the same species in different lakes. We also investigated a possible allometric effect on eDNA production by analysing a subset of data for effects of fish body mass on the amount of eDNA sequences. C_LIO_LIWe found a good relationship between species-specific eDNA sequences and within-species rank abundance categories for fishes, with rare fish producing 3% of sequences in a library, moderately abundant producing 7% and abundant fish producing 29%, according to model predictions. C_LIO_LIWe found a small negative effect of body mass on the amount of eDNA sequences, where the proportion of reads recovered significantly decreased with increased mean body mass of the population. C_LIO_LISynthesis and applications: The benefit of this approach is the potential for rapid assessment of rank abundance for multiple species, including smaller species which are often missed by conventional methods such as gillnetting, with relatively low amounts of additional effort. This approach will assist practitioners taking a species-based approach to freshwater habitat management in lakes worldwide. C_LI

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Littlefair, J. E., Hayhurst, L. D., Yates, M. C., Rennie, M. D., Cristescu, M. E.. 2025-01-24. A strong relationship between environmental DNA metabarcoding and rank-based abundance of fish. https://doi.org/10.1101/2025.01.22.634322

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