Genome‐Wide Population Structure of Lake Whitefish ( <i>Coregonus clupeaformis</i> ) in a Subarctic Great Lake

ABSTRACT Advances in genomics have facilitated the delineation of fisheries management units, which can be challenging in systems such as large lakes, in which high gene flow tends to limit genetic structure. In Great Slave Lake, Lake Whitefish populations have supported an important commercial fishery since the mid‐1940s. The genetic structure of Lake Whitefish, however, has never been assessed, preventing the implementation of population‐specific monitoring. Using low‐coverage whole‐genome resequencing of 305 samples from 10 sampling locations, we identified eight genetically differentiated populations of Lake Whitefish in Great Slave Lake and its main tributary, the Slave River. In the lake, we observed elevated levels of genetic differentiation among putative spawning locations in environmentally heterogeneous sections of the Main Basin despite small geographic distances among sites. In contrast, we observed weak genetic structure between populations in the comparatively homogeneous East Arm despite large geographic distances. Our observations suggest that mechanisms such as spawning site fidelity, adfluvial migratory behaviour, or local adaptation might shape population structure in this system. Using genome‐wide scans, we found multiple genomic regions of elevated differentiation, with some displaying patterns coherent with chromosomal inversions. These results highlight the potential role of chromosomal rearrangements in maintaining local adaptation in the face of gene flow in environmentally heterogeneous lakes. Overall, our study provides novel insights into the genetic structure of fish populations in vast, recently deglaciated lakes. Furthermore, our results highlight the power of genomic data for population delineation in systems with high gene flow. Lastly, our precise assessment of genetic structure will provide a baseline for the genetic monitoring of culturally and socio‐economically important Lake Whitefish commercial fisheries in this subarctic Great Lake.