Population genetics of Macrognathus siamensis (Synbranchiformes: Mastacembelidae): Implications for non-migratory fishery resources in the Mekong River basin

The spotted spiny eel, Macrognathus siamensis is an economically important freshwater fish in the Mekong River basin, which is undergoing dramatic biodiversity changes due to anthropogenic impacts. The species is non-migratory, with a moderate larval duration that facilitates downstream genetic connectivity. Restriction site-associated DNA sequence datasets that includes 3736 and 1244 single nucleotide polymorphisms representing putatively neutral loci, from all geographic sites and without the Tachileik site, indicate strong population structure in this sedentary fish, with a significant isolation-by-distance signature. This structure reflects isolation of tributary populations and downstream dispersal of these distinct populations to mix in the Mekong mainstem and contributes to increased genetic diversity in the lower reaches of the Mekong basin. Genetic data indicates that the dispersal of eggs and larvae downstream is not impeded by Khone Falls and that the falls prevent upstream dispersal of eggs and larvae. Despite this downstream connectivity, there is a strong population structure among above- and below-Khone Falls groups. An analysis of outlier loci putatively under selection provides evidence that the difference between connected metapopulations above and below the falls is due to the fundamental differences in environmental regimes. We hypothesize that instead of a physical barrier, the falls simply represents a demarcation between previously recognized upstream limited-floodplain environments and downstream extensive-floodplain environments. These findings emphasize the need to monitor genetic diversity of key sedentary fishery species to assess whether proposed dams along the river could affect genetic diversity downstream. This genetic diversity is particularly important for the resilience of downstream populations because of the many environmental impacts caused by dams, land use, and climate change. Early detection of reduced downstream genetic diversity could trigger remediation programs to ensure resilience and continued fisheries productivity of important non-migratory fish resources. [Display omitted] •Population genetic structure of Macrognathus siamensis was investigated using SNPs.•Isolation of the populations from UMB and tributary were detected.•Khone Falls appears as a physical barrier for the population structure in the LMB.•Larval dispersal may drive the high genetic diversity of downstream populations.•Stock management units s