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 (FST 5 0.162) and all other populations evaluated in this study (FST 5 0.101 2 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. The conservation and management of exploited or declining fishery stocks requires a fundamental understanding of the genetic population structure of the species involved. For many years, stocking hatchery-reared fish was the most common way to restore declining fishery stocks, with little regard to the ecological or genetic consequences for native stocks (Nielsen 1993). Although a growing number of empirical studies have shown that the introduction of exogenous strains may have negative genetic impacts on native fish stocks through * Corresponding author: [email protected] 1 Present address: Department of Biological Sciences, Southeastern Louisiana University, Box 10736, Hammond, Louisiana 70402, USA. Received March 2, 2004; accepted November 16, 2004 Published online June 13, 2005 hybridization and introgression (Allendorf 1991; Hindar et al. 1991; Krueger and May 1991; Philipp 1991), other studies have been unsuccessful in documenting considerable stocking effects on native fish populations (Wishard et al. 1984; Vuorinen and Berg 1989; Hansen et al. 2000). In the last half century, the lake trout Salvelinus namaycush has been one of the most heavily cultured and stocked species in North America. Catastrophic declines of lake trout in the Laurentian Great Lakes during the mid-20th century triggered massive stocking and restoration efforts (Selgeby et al. 1995 and references therein). Although most management efforts have focused on rehabilitating Great Lakes populations, introductions and stocking of lake trout have also been widespread in inland lakes (Crossman 1995; Powell and Carl 2003). Only recently has significant attention been