Genetic assessment of complex dynamics in an interior salmonid metapopulation

Habitat destruction and fragmentation are the most prevalent threats endangering species. As a result, metapopulation theory has become a popular tool for predicting the impact of habitat structure on population dynamics and species persistence. However, a key problem in applying the metapopulation concept to real-world conservation issues is the need to identify population structure a priori, as application of the metapopulation concept requires identifying the scale at which interactions are localized and for which parameters such as dispersal, extinction and colonization rates apply.; The metapopulation concept has been invoked extensively in the salmonid literature despite little empirical evidence for true metapopulation dynamics in salmonids. Defining salmonid population structure can be difficult. River habitat may have few boundaries to dispersal, but can be highly structured by tributaries. Resident and migratory life histories as observed in many salmonids also have the potential induce complex patterns of dispersal and population structure. I used microstatellite markers to examine the influences of landscape structure and population processes on the genetic structure of a putative metapopulation of Lahontan cutthroat trout (LCT; Oncorhynchus clarki henshawi). F-statistics demonstrated that populations were highly differentiated within this small watershed. To some extent, population structure mirrored habitat structure (i.e., tributary branching). Additional differentiation within streams was observed, and was congruent with genetic assignment test results showing significant differences in movement between fish found in headwater versus confluence habitats. These results suggested that life-history variability might influence dispersal behavior and genetic structure within this system. Findings of extremely small local effective population sizes and severe population bottlenecks suggested that local populations are at-risk of extinction. Inference from a combination of genetic analyses that reflect contemporary movement (assignment tests) and long-term dispersal patterns (coalescent simulations) suggested that population turnover has occurred in at least one site in this system. I concluded that metapopulation processes are relevant to the persistence of this LCT population network, and that these processes occur at a smaller geographic scale than generally recognized in salmonids. Additionally, genetic structure can be complex in this species, and is likely shaped by life-history variability and habitat quality in addition to habitat structure.