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© 2025. This work is published under http://creativecommons.org/licenses/by/4.0/ (the "License"). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.

Abstract

ABSTRACT

While acquiring age information is crucial for efficient stock management and biodiversity conservation, traditional aging methods fail to offer a universal, non‐invasive, and precise way of estimating a wild animal's age. DNA methylation from tissue DNA (tDNA) was recently proposed as a method to overcome these issues and showed more accurate results than telomere‐length‐based age assessments. Here, we used environmental DNA (eDNA) for the first time as a template for age estimation, focusing on the larval phase (10–24 days post‐hatch) of cultured Dicentrarchus labrax (seabass), a species of major economic and conservation interest. Using third‐generation sequencing, we were able to directly detect various modification types (e.g., cytosine and adenosine methylation in all contexts) across the whole genome using amplification‐free nanopore sequencing. However, aging sites were only present in the mitogenome, which could be a specific feature of eDNA methylation or the consequence of better DNA protection within mitochondria. By considering qualitative and quantitative information about aging sites according to an objective model selection framework, our epigenetic clock reached a cross‐validated accuracy of 2.6 days (Median Absolute Error). Such performances are higher than those of previous clocks, notably for adult seabass even when scaling MAE to the age range, which could be linked to a more dynamic epigenome during early life stages. Overall, our pilot study proposes new methods to determine the potential of eDNA for simultaneous age and biodiversity assessments, although robust validation of our preliminary results along with methodological developments are needed before field applications can be envisaged.

Details

Title
Environmental DNA Epigenetics Accurately Predicts the Age of Cultured Fish Larvae
Author
Ruiz, Eliot 1   VIAFID ORCID Logo  ; Leprieur, Fabien 1 ; Sposito, Gérard 2 ; Lüthi, Martina 3 ; Schmidlin, Michel 3 ; Panfili, Jacques 1 ; Pellissier, Loïc 3   VIAFID ORCID Logo  ; Albouy, Camille 3 

 MARBEC, Univ Montpellier, IRD, IFREMER, CNRS, Montpellier, France 
 Mediterranean Coastal Environment Station, University of Montpellier, Sète, France 
 Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zürich, Zürich, Switzerland, Land Change Science Research Unit, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland 
Section
RESEARCH ARTICLE
Publication year
2025
Publication date
Feb 1, 2025
Publisher
John Wiley & Sons, Inc.
e-ISSN
20457758
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
3171479412
Copyright
© 2025. This work is published under http://creativecommons.org/licenses/by/4.0/ (the "License"). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.