Timing of Population Fragmentation in a Vulnerable Minnow, the Umpqua Chub, and the Role of Nonnative Predators

We examined the distribution of Umpqua Chub Oregonichthys kalawatseti, an endemic, vulnerable minnow in western Oregon, and whether six ecological populations (based on distribution patterns) had sufficient genetic cohesion to be considered evolutionary populations. We also evaluated the influence of Holocene geological events and recent nonnative predator introductions on the timing of population formation or fragmentation. Based on data from 10 microsatellite loci, we found evidence for four evolutionary populations of Umpqua Chub. One population, in the Smith River, is isolated by the Umpqua estuary and is more than 100 river kilometers from the other three populations: Elk Creek, Calapooya CreekOlalla Creek, and Cow CreekSouth Umpqua River. Quantile regression was used to examine the timing of genetic divergence among evolutionary populations assuming a genetic isolation-by-distance model. The quantile regression suggested that the genetic differentiation index (F [subscript ST]) should change by at least 0.0002/km; most fragmentation was recent and with similar timing, but the Smith River isolation event may have been about 2-4times older. We could not distinguish whether the timing of the Smith River isolation corresponded to the last major tsunami event or the introduction of Striped Bass Morone saxatilis, a likely predator. All population fragmentation appears to be relatively recent, with the three upstream populations restricted to third- and fourth-order streams, most likely fragmented by either nonnative Smallmouth Bass Micropterus dolomieu, which now dominate sixth-order streams, or in the case of Elk Creek, a dam. The mid-drainage CalapooyaOlalla population was the most genetically diverse and appeared to be a mix of the other populations, which showed a significant isolation-by-distance relationship to this population. We hypothesize that Umpqua Chub populations have formed and fragmented by peripheral isolation from a larger population, the remnant of which is the mid-drainage CalapooyaOlalla population. Received April 20, 2012; accepted August 25, 2012Keywords: Conservation, Regression quantiles, River, Program, Oregon Chub, Genetic

Testing advances in molecular discrimination among Chinook salmon life histories: evidence from a blind test

The application of DNA-based markers toward the task of discriminating among alternate salmon runs has evolved in accordance with ongoing genomic developments and increasingly has enabled resolution of which genetic markers associate with important life-history differences. Accurate and efficient identification of the most likely origin for salmon encountered during ocean fisheries, or at salvage from fresh water diversion and monitoring facilities, has far-reaching consequences for improving measures for management, restoration and conservation. Near-real-time provision of high-resolution identity information enables prompt response to changes in encounter rates. We thus continue to develop new tools to provide the greatest statistical power for run identification. As a proof of concept for genetic identification improvements, we conducted simulation and blind tests for 623 known-origin Chinook salmon (Oncorhynchus tshawytscha) to compare and contrast the accuracy of different population sampling baselines and microsatellite loci panels. This test included 35 microsatellite loci (1266 alleles), some known to be associated with specific coding regions of functional significance, such as the circadian rhythm cryptochrome genes, and others not known to be associated with any functional importance. The identification of fall run with unprecedented accuracy was demonstrated. Overall, the top performing panel and baseline (HMSC21) were predicted to have a success rate of 98%, but the blind-test success rate was 84%. Findings for bias or non-bias are discussed to target primary areas for further research and resolution.Keywords: Microsatellites, Oncorhynchus tshawytscha, Individual-identificationKeywords: Microsatellites, Oncorhynchus tshawytscha, Individual-identificatio

Minor shifts towards more natural conditions in captivity improve long-term survival among reintroduced Atlantic salmon

Elevating winter water temperatures is a common practice when rearing salmonids for supplementation or reintroduction. Doing so elevates developmental rates, producing larger juveniles with greater smolt-to-adult survival, but does not guarantee improved adult returns to stocked tributaries. To test whether more natural developmental conditions improve adult returns to stocked tributaries, three consecutive cohorts of yearling (age 1+) landlocked Atlantic salmon (Salmo salar) were released into two tributaries of Lake Champlain. Cohorts were reared under two winter thermal conditions (seasonal surface water and above-seasonal groundwater) and (or) two release times (early and normal). Relative to standard hatchery practices, modelled returns to experimental tributaries increased over replicate cohorts by 286% on average following exposure to seasonal rearing temperatures, but decreased by 89% on average when release dates were advanced. By utilizing cost-effective shifts towards hatchery rearing techniques that more closely resemble natural growth conditions, we demonstrate how hatchery programs may improve long-term survival and returns for fish species with complex life histories involved in supplementation and reintroduction programs.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Nonanadromous and anadromous Atlantic salmon differ in orientation responses to magnetic displacements

Many animals undertaking long-distance migrations use Earth’s magnetic field as a “map” to assess their position for orientation. This phenomenon been particularly well-studied in salmonids using “magnetic displacement” experiments, in which animals are presented with magnetic field conditions that are characteristic of other geographic locations. However, whether use of magnetic map cues differs among populations of salmon has not been investigated. Here we show that nonanadromous and anadromous populations of Atlantic salmon (Salmo salar) raised under the same conditions within their native range differ in their response to magnetic displacements in the North Atlantic. The directions adopted by anadromous salmon juveniles to each of the magnetic displacements would support their migration from the eastern US to western Greenland, had the fish actually been at those locations. In contrast, nonanadromous salmon did not appear to respond to the magnetic displacements. The findings are consistent with the hypothesis that the innate magnetic map of anadromous salmon is adapted to guide their marine migration.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Data from: Gene flow among Modoc sucker and Sacramento sucker populations in the upper Pit River

The Modoc sucker (Catostomus microps) is a species that received legal protection in the United States based partially on concerns that anthropogenic environmental changes had restricted migration among populations and catalyzed hybridization with a congener, the Sacramento sucker (C. occidentalis). We applied eight microsatellite markers to samples of both species collected from throughout the range of Modoc suckers: two tributaries in the Pit River sub-basin and one tributary in the Goose Lake sub-basin. Modoc sucker populations in these three tributaries appeared to be largely isolated from one another: migration among Pit River tributaries appeared no greater than migration among sub-basins. Sacramento sucker populations appeared relatively more connected with one another, especially within the sub-basins. Interspecific hybrids were detected in all three tributaries. Tributaries in the Pit River sub-basin, which have retained typical habitats for both species, yielded relatively low proportions of hybrids (1.6% - 2.3%). The tributary in the Goose Lake sub-basin, which has undergone multiple cycles of hydrological change over the past two centuries, yielded a higher proportion of hybrids (10.9%). We conclude that hybridization between Modoc suckers and Sacramento suckers is not an active threat, but may be of conservation concern in situations where the habitat of one or both of these species has been eliminated or modified