Efficient species identification for Pacific salmon genetic monitoring programs.

Genetic monitoring of Pacific salmon in the Columbia River basin provides crucial information to fisheries managers that is otherwise challenging to obtain using traditional methods. Monitoring programs such as genetic stock identification (GSI) and parentage-based tagging (PBT) involve genotyping tens of thousands of individuals annually. Although rare, these large sample collections inevitably include misidentified species, which exhibit low genotyping success on species-specific Genotyping-in-Thousands by sequencing (GT-seq) panels. For laboratories involved in large-scale genotyping efforts, diagnosing non-target species and reassigning them to the appropriate monitoring program can be costly and time-consuming. To address this problem, we identified 19 primer pairs that exhibit consistent cross-species amplification among salmonids and contain 51 species informative variants. These genetic markers reliably discriminate among 11 salmonid species and two subspecies of Cutthroat Trout and have been included in species-specific GT-seq panels for Chinook Salmon, Coho Salmon, Sockeye Salmon, and Rainbow Trout commonly used for Pacific salmon genetic monitoring. The majority of species-informative amplicons (16) were newly identified from the four existing GT-seq panels, thus demonstrating a low-cost approach to species identification when using targeted sequencing methods. A species-calling script was developed that is tailored for routine GT-seq genotyping pipelines and automates the identification of non-target species. Following extensive testing with empirical and simulated data, we demonstrated that the genetic markers and accompanying script accurately identified species and are robust to missing genotypic data and low-frequency, shared polymorphisms among species. Finally, we used these tools to identify Coho Salmon incidentally caught in the Columbia River Chinook Salmon sport fishery and used PBT to determine their hatchery of origin. These molecular and computing resources provide a valuable tool for Pacific salmon conservation in the Columbia River basin and demonstrate a cost-effective approach to species identification for genetic monitoring programs.

A genomic region associated with iteroparous spawning phenology is linked with age-at-maturity in female steelhead trout.

Age-at-maturity and iteroparity are two life history variations of steelhead trout (Oncorhynchus mykiss) that are believed to increase population resilience and stability. While repeat-spawning individuals are thought to have historically made up a substantial portion of the reproductive population in the Columbia River and the majority of females still attempt outmigration as kelts, return rates of repeat-spawner are low throughout the basin and below 1% for the furthest migrating stocks. Notably, outmigrating adults exhibit variation in rematuration phenology, displaying either "consecutive" (reproduce immediately the following season) or "skip" (delay spawning for future seasons) spawning patterns. Here, we use low coverage whole genome sequencing of consecutive versus skip spawning female Columbia River steelhead from two populations to test for genomic differences between these two iteroparous phenotypes. We identified genomic regions on several chromosomes which were associated with the phenology of iteroparity, including a region on chromosome 25 containing two genes, estradiol receptor beta (ERß) and glycoprotein hormone beta-5 (GPHB5), which, in mammals, are estrogen-sensitive and expressed in reproductive tissues. Allele frequencies in this ERß/GPHB5 region differed among female steelhead of different age at maturity, but not males. These genes also shared an island of linkage disequilibrium with the SIX6 gene, 600Kbp away on the same chromosome, a region of known association with age-at-maturity. These observations contribute to growing evidence that age-at-maturity and the phenology of iteroparity are determined by overlapping physiological processes and genetic pathways.

Supportive breeding boosts natural population abundance with minimal negative impacts on fitness of a wild population of Chinook salmon.

While supportive breeding programmes strive to minimize negative genetic impacts to populations, case studies have found evidence for reduced fitness of artificially produced individuals when they reproduce in the wild. Pedigrees of two complete generations were tracked with molecular markers to investigate differences in reproductive success (RS) of wild and hatchery-reared Chinook salmon spawning in the natural environment to address questions regarding the demographic and genetic impacts of supplementation to a natural population. Results show a demographic boost to the population from supplementation. On average, fish taken into the hatchery produced 4.7 times more adult offspring, and 1.3 times more adult grand-offspring than naturally reproducing fish. Of the wild and hatchery fish that successfully reproduced, we found no significant differences in RS between any comparisons, but hatchery-reared males typically had lower RS values than wild males. Mean relative reproductive success (RRS) for hatchery F(1) females and males was 1.11 (P = 0.84) and 0.89 (P = 0.56), respectively. RRS of hatchery-reared fish (H) that mated in the wild with either hatchery or wild-origin (W) fish was generally equivalent to W × W matings. Mean RRS of H × W and H × H matings was 1.07 (P = 0.92) and 0.94 (P = 0.95), respectively. We conclude that fish chosen for hatchery rearing did not have a detectable negative impact on the fitness of wild fish by mating with them for a single generation. Results suggest that supplementation following similar management practices (e.g. 100% local, wild-origin brood stock) can successfully boost population size with minimal impacts on the fitness of salmon in the wild.

AcuteCare for Elders (ACE) tracker and e-Geriatrician: methods to disseminate ACE concepts to hospitals with no geriatricians on staff.

This article describes an innovative method to disseminate the Acute Care for Elders (ACE) model of care for hospitalized older patients implemented at 11 community hospitals in Wisconsin. The ACE Tracker is a computer-generated checklist of all older patients in a facility that takes information from multiple areas of the electronic medical record to identify the older patients' risk factors for functional decline and poor outcomes. The ACE Tracker report was validated against in-person observation of the older patients and found to be accurate. Interdisciplinary teams on medical-surgical units use this summary report to review each patient's plan of care and to efficiently assess the patients who are vulnerable to poor hospital outcomes. The ACE Tracker is also used during regular consultation provided through teleconferencing between an off-site geriatrician (e-Geriatrician) and the local ACE team. The effect of the ACE Tracker and e-Geriatrician models was assessed by measuring use of urinary catheters, physical restraints, high-risk medications, and social service evaluation at a single hospital for the 6 months before and after implementation of the models. There were significant improvements in urinary catheter and physical therapy referrals but no significant changes in the other outcomes. There was no change in the length of stay or in the rate of hospital readmission within 30 days.