Next-generation sequencing data can be mined for highly informative single nucleotide polymorphisms (SNPs) to develop high-throughput genomic assays for nonmodel organisms. However, choosing a set of SNPs to address a variety of objectives can be difficult because SNPs are often not equally informative. We developed an optimal combination of 96 high-throughput SNP assays from a total of 4439 SNPs identified in a previous study of Pacific lamprey (Entosphenus tridentatus) and used them to address four disparate objectives: parentage analysis, species identification and characterization of neutral and adaptive variation. Nine of these SNPs are FST outliers, and five of these outliers are localized within genes and significantly associated with geography, run-timing and dwarf life history. Two of the 96 SNPs were diagnostic for two other lamprey species that were morphologically indistinguishable at early larval stages and were sympatric in the Pacific Northwest. The majority (85) of SNPs in the panel were highly informative for parentage analysis, that is, putatively neutral with high minor allele frequency across the species' range. Results from three case studies are presented to demonstrate the broad utility of this panel of SNP markers in this species. As Pacific lamprey populations are undergoing rapid decline, these SNPs provide an important resource to address critical uncertainties associated with the conservation and recovery of this imperiled species.

The Pacific Lamprey Entosphenus tridentatus, an anadromous fish native to the northern Pacific Ocean and bordering freshwater habitats, has recently experienced steep declines in abundance and range contractions along the West Coast of North America. During the early 1990s, Native American tribes recognized the declining numbers of lamprey and championed their importance. In 2012, 26 entities signed a conservation agreement to coordinate and implement restoration and research for Pacific Lamprey. Regional plans have identified numerous threats, monitoring needs, and strategies to conserve and restore Pacific Lamprey during their freshwater life stages. Prime among these are needs to improve lamprey passage, restore freshwater habitats, educate stakeholders, and implement lamprey‐specific research and management protocols. Key unknowns include range‐wide trends in status, population dynamics, population delineation, limiting factors, and marine influences. We synthesize these key unknowns, with a focus on the freshwater life stages of lamprey in the Columbia River basin.

Elucidation of genetic mechanisms underpinning migratory behavior could help predict how changes in genetic diversity may affect future spatiotemporal distribution of a migratory species. This ability would benefit conservation of one such declining species, anadromous Pacific lamprey (Entosphenus tridentatus). Nonphilopatric migration of adult Pacific lamprey has homogenized population-level neutral variation but has maintained adaptive variation that differentiates groups based on geography, run-timing and adult body form. To investigate causes for this adaptive divergence, we examined 647 adult lamprey sampled at a fixed location on the Columbia River and radiotracked during their subsequent upstream migration. We tested whether genetic variation [94 neutral and adaptive single nucleotide polymorphisms (SNPs) previously identified from a genomewide association study] was associated with phenotypes of migration distance, migration timing, or morphology. Three adaptive markers were strongly associated with morphology, and one marker also correlated with upstream migration distance and timing. Genes physically linked with these markers plausibly influence differences in body size, which is also consistently associated with migration distance in Pacific lamprey. Pacific lamprey conservation implications include the potential to predict an individual's upstream destination based on its genotype. More broadly, the results suggest a genetic basis for intrapopulation variation in migration distance in migratory species.

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Complex life histories render anadromous fishes particularly susceptible to environmental and anthropogenic change. Adult Pacific Lampreys Entosphenus tridentatus migrating in the Columbia River and its tributaries must ascend a series of dams to reach interior spawning sites. While considerable research has focused on improving dam passage for lampreys, little is known about adult Pacific Lamprey behavior and distribution patterns within free‐flowing environments, particularly within the interior portions of their distribution. In this 3‐year study, we monitored the movements of 146 adult Pacific Lampreys in the Snake River and its tributaries upstream from Lower Granite Dam, the eighth dam from the Pacific Ocean. Our objectives were to characterize migration and test several hypotheses about adult upstream movement after dam passage. A majority of radio‐tagged adults, released above Lower Granite Dam, migrated upstream after release and many moved hundreds of kilometers upstream into Snake River tributaries. Of those with telemetry records after release, 59–70% were recorded in the Clearwater River, 16–25% were in the Snake River, and 13–16% were in the Salmon River. Lampreys that passed the Snake River–Clearwater River confluence were significantly more likely, in most years, to enter the lower‐discharge Clearwater River. Adults moved primarily at night during the summer–fall migration and did not exhibit a consistent response to changes in water temperature or discharge. These findings highlight the importance of the Clearwater River to Pacific Lampreys in the lower Snake River basin and indicate that adults that successfully pass through the Columbia–Snake hydrosystem can continue upstream migration into many Snake River subbasins. This distribution suggests that improved passage efficiency at dams may increase the number of adult Pacific Lampreys available for spawning within the interior portions of their distribution.Received May 12, 2014; accepted November 5, 2014