Julien April | Search USGS

USGS2026

Epigenetics in captivity: Restoring wild phenotypes in captive-reared salmonids

Captive rearing is a common practice for the stocking, conservation, and supplementation of fish species worldwide, but captive-reared fish can exhibit altered phenotypes leading to reduced fitness in nature compared to wild conspecifics. In salmonids, certain studies have found limited genetic differentiation between wild and captive-reared fish. However, documented changes in gene expression in hatchery fish have led scientists to investigate epigenetic mechanisms, such as DNA methylation, as a source of these differences. In this binational collaborative piece, we synthesize the knowledge and efforts of academics and government scientists to highlight how interactions between captive rearing and the epigenome elicit parallel phenotypic changes across salmonid species. We examine the known and potential links between DNA methylation and the phenotypic effects of captive rearing including changes in behavior, color, gut microbiomes, and developmental abnormalities. We review efforts to minimize these phenotypic and epigenetic effects including attempts to modify the hatchery environment and rearing protocols. We provide a framework to integrate epigenetic considerations into hatchery rearing protocols by weighing the heritable nature of DNA methylation with the goals of different captive rearing programs and explore whether minimizing the phenotypic and epigenetic effects of captive rearing is worthwhile. We examine heritability and persistence of epigenetic effects, and we propose the exploitation of heritable bet-hedging as an epigenetic buffer to increase post-release survival. We also suggest novel applications of epigenomic biomarkers as a non-lethal method for post-release monitoring. Ultimately, collaborative multi-disciplinary research across species is needed to understand the comprehensive effects of captive rearing, reduce the ecological impacts of captive fish in the wild, and increase population resilience. Integrating epigenetics into fish hatchery management will provide new opportunities for optimizing and improving captive rearing.

Evolutionary Applications↗

USGS2026

Working group on American Eel (WGAMEEL; outputs from 2024 meeting)

The Working Group on American Eel (WGAMEEL) met virtually three times in 2022-2024 to address the five Terms of Reference (ToRs) of its three-year term. The first two ToRs tasked WGAMEEL with listing and evaluating data on American eel landings, abundance indices, and spatial and habitat data and also to describe assessment methods used in Canada and the US. Canada-wide American eel trajectory was estimated using 12 fishery-independent datasets. Generally, longer datasets had more negative trends than shorter ones. Limiting data to the post-2000 years produced fewer negative trends that did not differ from zero, suggesting the observed declines occurred pre-2000. Spatial modelling for American eel requires knowledge and mapping that covers the breadth of habitat types occupied by the species, including freshwater, estuarine, and marine environments. In recent years there has been an expansion of online databases with data from the aquatic environment, particularly in freshwater, with estuarine and marine data less consistently documented. This report broadly compiles abiotic data series of relevance to American eel. A larger challenge for spatial modelling will be acquiring enough high quality, georeferenced biological data sets with suitable observations to assess occurrence, abundance, and trends over time in a spatial framework. The third ToR considered Indigenous Knowledge Systems for American eel. A survey reaching First Nations representatives from four Canadian provinces confirmed the cultural importance of eels in Indigenous communities, and that Indigenous knowledge possessed by the participant groups are place-based and contextual, especially regarding threats impacting eels. The final two ToRs focused on identifying stock assessment modelling approaches applicable to American and European eel, and assessing whether any of these approaches might be appropriate for American eel management moving forward. WGAMEEL evaluated the various approaches for assessing American eel or providing management advice. Two approaches that could be completed in the next few years because of their minimal data needs are index-based methods and catch-only method. A suite of approaches considered by WGAMEEL that would take more time and data were spatial or habitat models, management strategy evaluation, and spawner-per-recruit (SPR) models potentially paired with meta-population models.

ICES Scientific Reports↗