Great Smoky Mountains National Park (GRSM) is committed to monitoring ecological and evolutionary functions and processes of park ecosystems. Brook trout (Salvelinus fontinalis) is the only salmonid native to the Southern Appalachians and functions as a keystone species in some headwater streams. The historic use of hatchery-reared brook trout for supplemental and restorative stocking in GRSM underscores the need to recognize the evolutionary relationship among stream populations. A recent survey of microsatellite DNA variation in GRSM brook trout indicated the presence of highly significant differentiation at all hierarical levels which suggests that the individual stream should be considered the unit of management. Given that management resources are limited and that stream-specific management is often not practical, fisheries managers need to know whether the genetic divergence observed among GRSM brook trout reflect adaptive differences or is the variation due to stochastic processes like random genetic drift. DNA microarrays are a powerful method for the global analysis of steady-state intracellular mRNA levels, and thus identifying genes that are transcriptionally modulated as a consequence of metabolic or bioenergetic demands. The information gathered from these arrays of gene sequences can be used to characterize complex biological processes and interactions providing insight into the adaptive significance of observed genetic differentiation. This research objective, if funded, would represent the first attempt at determining whether GRSM fisheries managers should focus their resources on genetic relatedness or demographics.Brook trout (Salvelinus fontinalis) is the only trout native to the Southern Appalachians. Since the turn of the century, this native trout has lost approximately 75 percent of its range in Great Smoky Mountains National Park (GRSM) (Kelly et al. 1980). Initial range loss (about 50 percent) has been attributed to logging and resultant water quality degradation (King 1937). This activity virtually eliminated brook trout in streams below about 914 m (3,000 ft) in elevation. In turn, residents and loggers became concerned because they had nothing for which to fish. To meet the demand for recreational angling at the time (around 1910), logging companies began stocking both non-native rainbow trout and northern brook trout and continued this activity until the Park was established in 1934. The Park continued to allow the stocking of both species until 1974.Park staff in the 1930s and 1940s saw no harm in stocking rainbows and believed that as reforestation occurred, brook trout would reclaim lost range (King, personal communication). However, distribution surveys in the 1970s showed this not to be true and that 45 percent of the range exclusively occupied by brook trout had been lost since the mid-1930s (Kelly et al. 1980). The decline in allopatric brook trout range was the direct result of rainbow trout encroachment into previously unstocked brook trout streams (Larson and Moore 1985). Native brook trout had become restricted to marginal headwater streams above 1,067 m (3,500 ft), characterized by steep gradients and pH that is naturally slightly acidic. Based on the report by Kelly et al. (1980) it was determined that the only places brook trout could not be displaced are in streams above waterfalls where rainbows could not ascend.Historically, local residents were very vocal about introduced northern strains of brook trout being different from the native brook trout or "speckled trout." Studies in the 1950s showed that physical differences do exist between Southern Appalachian brook trout and hatchery fish. In 1993, a study conducted by the University of Tennessee provided conclusive evidence that Southern Appalachian brook trout are genetically distinct at the subspecies level from northern populations (McCracken et al. 1993). This effort collected brook trout from 47 streams across the Park and dem