Removal of two dams in the Elwha River basin, Washington, started one of the largest river restoration projects ever attempted in the Pacific Northwest. These dams had eliminated Pacific Lamprey Entosphenus tridentatus populations upstream. After the dam removals, larval production increased in the upper watershed, but the sources and numbers of new adult spawners were unknown. We applied genetic stock identification (GSI), parentage assignment (PA), and sibship assignment (SA) methods to (1) determine the origins of Pacific Lamprey larvae and juveniles, (2) quantify the increase in numbers of successful Elwha River spawners (i.e., effective number of breeders [Nb]) and assess whether the current numbers of spawners have reached levels equivalent to those of neighboring undammed basins, and (3) determine the relative productivity of streams within the Elwha River and how overall productivity originating from this system may be distributed across the broader surrounding region. We utilized a highly accurate set of 263 single-nucleotide polymorphism (SNP) loci to perform PA and SA (>99% accuracy rate) and an additional set of 28 SNPs for GSI. Our results showed that a single stream (Indian Creek) was the source of 41% of larval and juvenile production in the Elwha River. Our Nb estimates for the Elwha River indicated a 12-fold increase in Nb during the 3 years after dam removal, with recent Nb estimates matching those of neighboring Olympic Peninsula basins. These results indicate rapid recolonization potential for this highly dispersive species, and high productivity within the Elwha River suggests that restoring passage to adequate habitat is a highly effective approach for re-establishing populations of Pacific Lamprey in coastal systems.

The Pacific Lamprey Entosphenus tridentatus is an anadromous fish that has severely declined in the Snake River basin. In 2007, the Nez Perce Tribe initiated translocation of adults to this region from the main‐stem Columbia River and has continued the translocations to this day. These actions are aimed at restoring larval abundance along with holistic habitat improvements. We performed parentage and sibship analyses with 260 single‐nucleotide polymorphism loci to monitor productivity of translocated lamprey over a decade (2007–2018). These results provide the first direct evidence that translocations boosted larval abundance, increased juvenile production in the interior Columbia River (~3% in 2017 and 2018), and demonstrated successful migration to the Pacific Ocean. Per capita juvenile production from Snake River adult lamprey translocations out‐performed that of their volitionally migrating counterparts in the interior Columbia River, demonstrating that translocating adults to suitable habitats increased overall productivity. We projected that the translocations may eventually return enough adult offspring to the Columbia River to replace the annual take of adults for translocations, despite many adults likely returning to other basins. These translocations are also restoring Pacific Lamprey to historical areas where they had been nearly extirpated, which has impactful benefits both culturally and ecologically. Further, this study provided an unprecedented volume of data that has redefined key biological attributes, including timing of life stage transformation (average of 6.7‐year‐old juveniles), larval growth rates (~22 mm/year for the first 4 years), ocean duration (average of 5.1 years), dispersal (~3% of Snake River‐origin adults that return to the Columbia River will divert to the Willamette River), and life span (median age of postspawn adults was 12.9 years). We even quantified a new biological phenomenon of delayed spawning, which occurs at low rates (~9%) in nature. These data provide an opportunity to monitor ongoing translocation efforts and inform adaptive management to aid species recovery.

Fish migrations are energetically costly, especially when moving between freshwater and saltwater, but are a viable strategy for Pacific salmon and trout (Oncorhynchus spp.) due to the advantageous resources available at various life stages. Anadromous steelhead (O. mykiss) migrate vast distances and exhibit variation for adult migration phenotypes that have a genetic basis at candidate genes known as greb1L and rock1. We examined the distribution of genetic variation at 13 candidate markers spanning greb1L, intergenic, and rock1 regions versus 226 neutral markers for 113 populations (n = 9,471) of steelhead from inland and coastal lineages in the Columbia River. Patterns of population structure with neutral markers reflected genetic similarity by geographic region as demonstrated in previous studies, but candidate markers clustered populations by genetic variation associated with adult migration timing. Mature alleles for late migration had the highest frequency overall in steelhead populations throughout the Columbia River, with only 9 of 113 populations that had a higher frequency of premature alleles for early migration. While a single haplotype block was evident for the coastal lineage, we identified multiple haplotype blocks for the inland lineage. The inland lineage had one haplotype block that corresponded to candidate markers within the greb1L gene and immediately upstream in the intergenic region, and the second block only contained candidate markers from the intergenic region. Haplotype frequencies had similar patterns of geographic distribution as single markers, but there were distinct differences in frequency between the two haplotype blocks for the inland lineage. This may represent multiple recombination events that differed between lineages where phenotypic differences exist between freshwater entry versus arrival timing as indicated by Micheletti et al. (2018a). Redundancy analyses were used to model environmental effects on allelic frequencies of candidate markers, and significant variables were migration distance, temperature, isothermality, and annual precipitation. This study improves our understanding of the spatial distribution of genetic variation underlying adult migration timing in steelhead as well as associated environmental factors and has direct conservation and management implications.

Parentage-based tagging (PBT) is a nonlethal, genetic tagging method that has been successfully applied in hatchery-supplemented populations to manage hatchery brood stock and monitor hatchery harvest and straying rates. We show that PBT can also improve the accuracy of escapement estimates by significantly reducing the number of hatchery-origin fish falsely classified as natural-origin. Unlike conventional abundance estimates, which use physical marks and tags to distinguish hatchery individuals from their wild counterparts, PBT identifies origin independent of physical form. We applied PBT to populations of Chinook salmon (Oncorhynchus tshawytscha) and steelhead (Oncorhynchus mykiss), which are classified as Threatened under the Endangered Species Act and subject to extensive hatchery supplementation efforts. For spawn years 2014–2018, 16 511 adipose-intact Chinook salmon and 21 953 adipose-intact steelhead were sampled, and PBT identified 19.6% of returning Chinook salmon and 8.3% of steelhead were of hatchery-origin, despite having no physical or mechanical marks. The 90% confidence intervals for escapement estimates of natural-origin Chinook salmon and steelhead made with and without corrections using PBT were nonoverlapping for nine of ten comparisons, indicating that failing to account for unmarked, untagged hatchery-origin fish would result in a significant overestimation of natural abundance.