Natural and anthropogenic drivers of genetic structure and low genetic variation in the endangered freshwater cod, Maccullochella mariensis

Abstract

Population genetic theory has identified several threats to small populations that have the potential to endanger species in the short and long term. Understanding these threats is particularly pertinent when management actions, such as stocking, have the potential to exacerbate them. In this study we explore existing genetic variation in the threatened Mary River Cod, Maccullochella mariensis, which has had a long stocking history in its endemic populations (Mary River and Tinana–Coondoo Creek) and has been translocated into other catchments in Southeast Queensland (SEQ). Using Bayesian clustering analysis, two genetically distinct sub-populations were detected (Mary and SEQ vs. Tinana–Coondoo), despite decades of stocking from one population (Tinana–Coondoo) into the other (Mary). Overall, genetic diversity (1–9 alleles per locus) and Ne (18–56) were low, but bigger in the Mary, relative to Tinana–Coondoo. Interestingly, evidence for historical unidirectional gene flow from Tinana–Coondoo into the Mary was detected, which was not as strongly reflected using contemporary estimators, suggesting stocking has not dramatically altered the existing genetic structure for this species. These results provide an opportunity for managers to strategically design stocking protocols and to improve the condition of this species in the wild.