Analyses of Genetic Variation in Populations of Oregon Chub, a Threatened Floodplain Minnow in a Highly Altered Environment

The Oregon chub (Oregonichthys crameri) is a small floodplain minnow endemic to the Willamette River basin of western Oregon. Historically the species was widely abundant and relied on periodic floods for dispersal and genetic exchange among populations. The species has declined substantially in the past 100 years due to habitat alterations and the introductions of nonnative species and is currently listed as threatened under the U.S. Endangered Species Act. Information on the level of genetic variation within and among populations did not exist when the species was listed or when a recovery plan was being developed. In this study we used a suite of nine microsatellite loci to characterize genetic variation within and among 16 populations of Oregon chub and provide information to help guide future recovery efforts. Despite the fact that most populations are presently isolated from one another, we observed relatively high levels of genetic variation within populations. Temporal population samples revealed that levels of genetic variation were stable over time despite fluctuations in population size. Estimates of effective population size (N_e) for three populations ranged from approximately 120 to approximately 220 and suggest no immediate threat from inbreeding or genetic drift. We observed a significant level of genetic variation among populations (global F_ST = 0.078) and significant differences in allele frequencies among all population pairs. Genetic distance based and Bayesian methods suggested a hierarchical genetic structure among populations and that the different subbasins of the Willamette River represent different evolutionary groups which could form the basis for recovery areas. Information presented in this study will help guide Oregon chub recovery implementation including future population introduction efforts and help address the challenge of managing populations largely in isolation from one another in order to minimize threats from nonnative species.