Kopack, C. J. | Search bioRxiv

bioRxiv2025

The effect of environmental enrichment on whole-brain gene expression in an imperiled fish

When hatchery-reared fish are used to augment wild populations, phenotypic mismatch caused by differences between hatchery and wild environments can limit efforts to conserve fish species at risk of extinction. Some phenotypes adapted to or induced by hatchery environments are thought to be maladapted for life in the wild. Thus, enriching the hatchery environment (abiotically and biotically) to make it more similar to the wild may induce phenotypes, including gene expression profiles, that are better suited to the environments fish will experience after release. Here, we took a molecular approach (TagSeq) to elucidate how abiotic and biotic (predator training) enrichment impacts the whole-brain gene expression of a species of conservation concern, the Arkansas darter (Etheostoma cragini), comparing the effects in two hatchery populations to a wild reference population. While we found no effect of biotic enrichment, we found that numerous genes were differentially expressed between populations and abiotic enrichment treatments. Notably, we found that expression profiles of hatchery fish more closely resembled those of wild fish when reared with abiotic enrichment. Functional analysis revealed that many differentially expressed genes were related to feeding behavior, development, and reproduction. These results have implications for conservation, supporting the management of darters at the level of the population and the use of abiotic enrichment to reduce phenotypic mismatch between hatchery and wild fish.

molecular biology↗

bioRxiv2020

Rapture-ready darters: sequence capture outperforms whole genome data regardless of reference genome in Etheostoma

Researchers studying non-model organisms have an increasing number of methods available for generating genomic data. However, the applicability of different methods across species, as well as the effect of reference genome choice on population genomic inference, are still difficult to predict in many cases. We evaluated the impact of data type (whole-genome vs. reduced representation) and reference genome choice on data quality and on population genomic and phylogenomic inference across several species of darters (subfamily Etheostomatinae), a highly diverse radiation of freshwater fish. We generated a high-quality reference genome and developed a hybrid RADseq/sequence capture (Rapture) protocol for the Arkansas darter (Etheostoma cragini). Rapture data from 1900 individuals spanning four darter species showed recovery of most loci across darter species at high depth and consistent estimates of heterozygosity regardless of reference genome choice. Loci with baits spanning both sides of the restriction enzyme cut site performed especially well across species. For low-coverage whole-genome data, choice of reference genome affected read depth and inferred heterozygosity. For similar amounts of sequence data, Rapture performed better at identifying fine-scale genetic structure compared to whole-genome sequencing. Rapture loci also recovered an accurate phylogeny for the study species and demonstrated high phylogenetic informativeness across the evolutionary history of the genus Etheostoma. Low cost and high cross-species effectiveness regardless of reference genome suggest that Rapture and similar sequence capture methods may be worthwhile choices for studies of diverse species radiations.

genomics↗