Since the 1950s, fishery agencies on Lake Michigan have pursued Lake Trout Salvelinus namaycush rehabilitation through Sea Lamprey Petromyzon marinus control, harvest regulations, and stocking millions of fish annually. Stocking was prioritized at four historically important spawning locations beginning in 1985, and coded wire tags (CWTs) were used to help evaluate performance. We used data from coded-wire-tagged fish captured in fishery-independent surveys from 1998 to 2014 to evaluate relative postrelease survival of Lake Trout, estimated by CPUE and corrected for the number of fish stocked, across 173 CWT lots of the 1994-2003 year-classes stocked at the four locations. Boosted regression tree models were used to assess the relative influence of four variables on Lake Trout CPUE in two age-groups (ages 4-5 and ages 6-10) and were paired with ANOVAs to test for statistical significance. Genetic strain (29.1%), stocking location (27.8%), mortality at release (23.1%), and predator density (19.9%) had similar influences on the relative survival of younger fish, whereas the relative survival of older fish was heavily influenced by stocking location (79.8%). Survival of both age-groups was lowest for fish stocked in the Northern Refuge, where the age structure was truncated due to fishery harvest and Sea Lamprey predation. Survival of stocked fish was higher at the Southern Refuge, Clay Banks, and Julian's Reef, where mortality from Sea Lamprey and harvest was lower and where increases in wild Lake Trout have been observed in recent years. Stocked Lake Michigan remnant genetic strains also appeared to survive better than strains from other lakes at these three locations, but strain effects could not be fully disentangled from the effects of stocking location, and the continued stocking of multiple genetic strains may provide resiliency to future selection pressures. Continued progress toward rehabilitation will require reducing fishing and Sea Lamprey-induced mortality in northern Lake Michigan to build parental stocks of advanced ages as well as balancing efforts among competing management goals.

We compared the relative abundance of lake trout Salvelinus namaycush spawners in gill nets during fall 1999-2001 in Lake Michigan at 19 stocked spawning sites with that at 25 unstocked sites to evaluate how effective site-specific stocking was in recolonizing historically important spawning reefs. The abundance of adult fish was higher at stocked onshore and offshore sites than at unstocked sites. This suggests that site-specific stocking is more effective at establishing spawning aggregations than relying on the ability of hatchery-reared lake trout to find spawning reefs, especially those offshore. Spawner densities were generally too low and too young at most sites to expect significant natural reproduction. However, densities were sufficiently high at some sites for reproduction to occur and therefore the lack of recruitment was attributable to other factors. Less than 3% of all spawners could have been wild fish, which indicates that little natural reproduction occurred in past years. Wounding by sea lamprey Petromyzon marinus was generally lower for Seneca Lake strain fish and highest for strains from Lake Superior. Fish captured at offshore sites in southern Lake Michigan had the lowest probability of wounding, while fish at onshore sites in northern Lake Michigan had the highest probability. The relative survival of the Seneca Lake strain was higher than that of the Lewis Lake or the Marquette strains for the older year-classes examined. Survival differences among strains were less evident for younger year-classes. Recaptures of coded-wire-tagged fish of five strains indicated that most fish returned to their stocking site or to a nearby site and that dispersal from stocking sites during spawning was about 100 km. Restoration strategies should rely on site-specific stocking of lake trout strains with good survival at selected historically important offshore spawning sites to increase egg deposition and the probability of natural reproduction in Lake Michigan.