Molecular analyses confirm genetically distinct populations of two indigenous estuarine fish species in an isolated coastal lake: implications for the management of introduced ichthyofauna

Groenvlei is a coastal, near-freshwater lake in the Garden Route region of South Africa, which became isolated from the ocean about 4,000 years ago due to sea level regression. It contains only two native fish species—Atherina breviceps and Gilchristella aestuaria—and several non-native species, including the illegally introduced common carp (Cyprinus carpio). Options for controlling this highly invasive species in Groenvlei are presently being considered and as such, it is pertinent that the conservation status of native species be assessed. Mitochondrial DNA analyses support significant divergence of both native fish species inhabiting Groenvlei from nearby populations. Additionally, genetic structuring of A. breviceps populations inhabiting other sampling localities was also detected. In Groenvlei, populations of both species displayed slightly lower haplotype diversity and much lower nucleotide diversity than those inhabiting nearby estuaries. Given the level of genetic divergence, native fish populations in Groenvlei should be recognised as a distinct management unit. It is acknowledged that invasive species, such as carp, pose a serious threat to the Groenvlei ecosystem. However, the divergence of the Groenvlei populations—as evidenced by this study—implies that any large-scale actions aimed at removing invasive ichthyofauna should not impact the native species because the unique evolutionary signals of both populations could be destroyed. Our results highlight the importance of incorporating a genetic approach to understanding the evolutionary history of southern African estuarine species and decision-making processes supporting conservation of biodiversity in the region.