{"paper_id":"dabce09f-aa14-47f9-9d96-e0ac19d00de2","body_text":"Abstract\nVertebrate immune systems exhibit striking evolutionary diversity, yet our understanding remains biased toward mammalian models. Here, we generate a single-cell atlas of immune cells from the ecologically and economically important salmonid Salmo trutta (brown trout), a lineage characterized by an ancestral whole-genome duplication (WGD). Profiling over 83,000 kidney-derived immune cells, we resolved 34 transcriptionally distinct populations, identified core immune lineages, and uncovered novel markers in neutrophils, macrophages, T- and B-cells. We detected pervasive transcriptional divergence between WGD-derived ohnologue pairs, indicating putative sub- and neofunctionalization in immune gene regulation. We further show that the transcriptional identity of immune cells is shaped by rearing history: fish raised in hatcheries—whether for one or multiple generations—showed shifts in immune gene expression across cell types. These included genes involved in G protein-coupled receptor signalling, a process which has previously been implicated in domestication. Our findings provide insight into the evolution of vertebrate immunity and raise concerns about the immunological fitness of hatchery-reared fish released into the wild.\nCompeting Interest Statement\nThe authors have declared no competing interest.\nFootnotes\n- Readability and flow of the text, namely the abstract and aspects of the introduction and discussion have been streamlined. - Correction to analysis of ohnologue pairs to account for three previously missing pairs. - Added statement in the acknowledgements regarding use of AI. - Additional citations.","source_license":"CC-BY-4.0","license_restricted":false}