Strong bidirectional gene flow between fish lineages separated for over 100,000 years

Abstract Restoring levels of genetic diversity in small and declining populations is increasingly being considered biodiversity conservation. Evidence-based management requires assessment risks benefits crossing populations. Because are challenging to assess experimentally, e.g. through multi-generational crosses, decision-support approaches utilize proxy risk factors such as time since separation lineages. However, the paucity empirical datasets on fitness consequences longer times tends favour lineages with conservatively short separations, restricting wildlife managers’ options. Here, we assessed outcomes interbreeding wild between a threatened Australian freshwater fish (Macquarie perch) separated by an estimated 119,000–385,000 years evolution distinct environments. Fish belonging Murray-Darling Basin (MDB) lineage escaped from Cataract Dam—into which they were translocated ~ 1915—into River, where interbred local Hawkesbury-Nepean (HNB) lineage. Analyses reduced-representation genomic data revealed no evidence incompatibilities during two River: assignment genotypic clusters indicated spectrum hybrid types including second generation hybrids backcrosses both parental Thus, adverse effects detected mixing > 100,000 years. We not advocating purposely for purposes under present cost–benefit considerations, because there currently sufficient intra-lineage source beneficially mix. Instead, this study presents useful calibration point: morphologically different evolved habitats can successfully interbreed.