Use of Genetic Markers to Evaluate the Effects of Fragmentation and Aid in Re-Establishing Migratory Connectivity in a Metapopulation of Bull Trout

Genetic markers were used to evaluate the impacts of three mainstem dams that have long fragmented an important migratory corridor for a large metapopulation of bull trout in the Lake Pend Oreille/Clark Fork River system, Idaho and Montana.  Populations were characterized by a low effective number of breeders (N_b<50 for 34 of 39 populations) and a significant degree of genetic variation among populations (F_ST = 0.132) at 12 microsatellite loci.  Population assignments of 290 adult bull trout collected below mainstem dams provided evidence that many of these fish (n = 197) originated in populations above the dams and were unable to complete their spawning migrations. A baseline genetic dataset was used to establish a real-time genotyping protocol to assist with trap-and-transport fish passage above these mainstem dams. Based on genetic assignments and transport criteria, 202 fish were passed upstream above one or more dams between 2004 and 2010.  This protocol has helped re-establish connectivity in a fragmented system providing increased numbers of spawning adults for numerically depressed populations above these mainstem dams a decade before the first upstream passage facility will become operational.  Other passage facilities are now in the planning/design phase justified in large part by this ongoing genetic analysis and it’s on the ground implementation.