Red Fleet walleye

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Additional studies on the stock structure of walleye have revealed similar divergent haplotypes. In a DNA sequence analysis of walleyes throughout their range, Stepien and Faber (1998) found most haplotypes were consistent with Great Lakes haplotpyes, but also observed one particular haplotype, found in the Ohio River that was
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highly divergent from Great Lakes haplotypes. They suggested a time since separation of 1.5 million years from the Great Lakes haplotypes. A survey of walleye in the Ohio River using RFLPs, microsatellites, and allozymes (White et al. 2005) also found a divergent haplotype in the Upper Ohio River. It is likely that these haplotypes are similar to those observed by Billington (1996) and are possibly members of the same native population.
Mitochondrial DNA RFLP analysis of walleye in the New River and Claytor Lake, Virginia (Palmer et al. 2001) revealed unique haplotypes divergent from Great Lakes haplotypes, and suggested a unique New River stock. This haplotype could represent a relic strain of walleye that is native to this river system. White et al. (2005) found identical digest patterns exhibited by both the Ohio River and the New River walleye suggesting a close genetic relationship.
Stepien and Faber hypothesized a Teays River origin for the divergent walleye haplotype found in the Ohio River. The Teays River was a pre-Pleistocene river, dating to the Tertiary (Ver Steeg 1946), that originated in Virginia and flowed north across Ohio and Indiana and connected to the Mississippi River in Illinois (Figure 5, Ver Steeg 1936; Fidlar 1943, Hocutt et al. 1986). The lower two-thirds of the river was impounded by the Nebraskan glacial advance, leaving the upper third (present day Kanawha, New, Big Sandy, Gauley, and Little Kanawha Rivers) isolated (Hocutt et al. 1986). This region is a potential additional walleye refugium.

Sorry to keep quoting from the thesis, but it contradicts what you are saying. It specifically mentions planting walleyes into different drainages. It notes that there is hybridization. It delves in to the differences of habitats, but it consistently uses the Pleistocene as the benchmark for divergence of strains. It never suggests that there are new strains developing, only that there has been hybridization because of planting multiple strains in the same waters. It also suggests that if there is adequate habitat and differing forage and structure that some waters may hold more than one strain of walleye, and that the two different strains may not occupy the same area of a lake at the same time. And may therefore never hybridize. It never suggests that the development of new strains of walleye have been seen in modern times.
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