Conservation Genetics of Inland Lake Trout in the Upper Mississippi River Basin: Stocked or Native Ancestry?

Although stocking for sport fishery enhancement has been practiced by resource managers for decades, the potential genetic effects of these stocking practices have remained largely unknown. We investigated the genetic contributions of stocking lake trout Salvelinus namaycush in two inland lakes in Wisconsin (Trout and Black Oak lakes in Vilas County), which represent the only known indigenous lake trout populations in the upper Mississippi River basin. Exogenous sources of lake trout (Lake Michigan and Lake Superior strains) have been stocked into each of these lakes for decades, although the long‐term effects of past stocking events on these populations are unknown. We used nine microsatellite loci and polymerase chain reaction– restriction fragment length polymorphism analysis of mitochondrial DNA to determine the distinctiveness and genetic ancestry of lake trout in Trout and Black Oak lakes. Measures of allelic variance indicated that Trout and Black Oak lakes were significantly different ( P < 0.05) from each other ( F ST = 0.162) and all other populations evaluated in this study ( F ST = 0.101 − 0.164). The combined microsatellite and mitochondrial DNA data indicate that upper Mississippi River basin lake trout have been minimally affected by past stocking practices. These populations should be managed as native gene pools, and interlake and interbasin stocking should be avoided.