Riverscape genetics of a limnophilic fish in a near-natural river system reveal implications for conservation management

Abstract River-floodplain systems are among the most impaired ecosystems globally, with severe impacts on associated biota. A key challenge in restoration is the limited understanding of natural metapopulation dynamics. The aim of the present study is to describe how a near-natural river network shapes the population structure of a limnophilic model fish species, the Southern-Balkan endemic Pelasgus thesproticus . Specifically, we aim to (I) infer population connectivity among floodplain habitats and (II) test environmental resistance driving metapopulation dynamics. Utilizing 30 anonymous nuclear markers and mitochondrial cytochrome b sequences, we genotyped 474 specimens from 13 sites in the Vjosa River system in southern Albania, one of the last free-flowing rivers in Europe. Population structure was inferred using clustering and distance-based approaches. The effects of riverscape properties on population connectivity were tested within a riverscape genetic framework. We found evidence for a strongly connected metapopulation linked to river network structure and flow. Gene flow was primarily directed downstream, and genetic differentiation increased with increasing distance to the mainstem. Restoring suitable habitats and hydrological connectivity are essential targets to re-establish functional metapopulations in impacted river-floodplain systems. Moreover, our study underscores the value of the few remaining near-natural rivers as reference conditions for studying natural ecological processes.