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DOE OSTI2022

An overview of visualization and visual analytics applications in water resources management

Recent advances in information, communication, and environmental monitoring technologies have increased the availability, spatiotemporal resolution, and quality of water-related data, thereby leading to the emergence of many innovative big data applications. Among these applications, visualization and visual analytics, also known as the visual computing techniques, empower the synergy of computational methods (e.g., machine learning and statistical models) with human reasoning to improve the understanding and solution toward complex science and engineering problems. These approaches are frequently integrated with geographic information systems and cyberinfrastructure to provide new opportunities and methods for enhancing water resources management. Here, we present a comprehensive review of recent hydroinformatics applications that employ visual computing techniques to (1) support complex data-driven research problems, and (2) support the communication and decision-makings in the water resources management sector. Then, we conduct a technical review of the state-of-the-art web-based visualization technologies and libraries to share our experiences on developing shareable, adaptive, and interactive visualizations and visual interfaces for water resources management applications. We close with a vision that applies the emerging visual computing technologies and paradigms to develop the next generation of hydroinformatics applications.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Reactome and the Gene Ontology: digital convergence of data resources

Abstract Motivation Gene Ontology Causal Activity Models (GO-CAMs) assemble individual associations of gene products with cellular components, molecular functions and biological processes into causally linked activity flow models. Pathway databases such as the Reactome Knowledgebase create detailed molecular process descriptions of reactions and assemble them, based on sharing of entities between individual reactions into pathway descriptions. Results To convert the rich content of Reactome into GO-CAMs, we have developed a software tool, Pathways2GO, to convert the entire set of normal human Reactome pathways into GO-CAMs. This conversion yields standard GO annotations from Reactome content and supports enhanced quality control for both Reactome and GO, yielding a nearly seamless conversion between these two resources for the bioinformatics community. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Roles for Countercharge in the Voltage Sensor Domain of Ion Channels

Voltage-gated ion channels share a common structure typified by peripheral, voltage sensor domains. Their S4 segments respond to alteration in membrane potential with translocation coupled to ion permeation through a central pore domain. The mechanisms of gating in these channels have been intensely studied using pioneering methods such as measurement of charge displacement across a membrane, sequencing of genes coding for voltage-gated ion channels, and the development of all-atom molecular dynamics simulations using structural information from prokaryotic and eukaryotic channel proteins. One aspect of this work has been the description of the role of conserved negative countercharges in S1, S2, and S3 transmembrane segments to promote sequential salt-bridge formation with positively charged residues in S4 segments. These interactions facilitate S4 translocation through the lipid bilayer. In this review, we describe functional and computational work investigating the role of these countercharges in S4 translocation, voltage sensor domain hydration, and in diseases resulting from countercharge mutations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Systems and Implementation: Integrating Unmanned Aircraft Systems into Physical Protection Systems at Fixed Sites and During Transportation

Physical protection systems, and response forces in particular, are designed to prevent an adversary from successfully completing a malevolent act against a facility or transport operations. Timely detection and assessment of any potential adversary action against a target is an essential element of materials security. The timely detection and assessment must then be followed-up by a capable and timely response that might be enhanced with the additional situational awareness provided by unmanned aircraft systems (UAS). The United States Department of Energy’s National Nuclear Security Administration Office of International Nuclear Security has been exploring capabilities provided by UAS to support response force operations within the physical protection system. UAS have the potential to provide response force commanders and operators with situational awareness in assessing adversary locations and actions as well as the locations of responders. UAS may be utilized for area searches ahead of responder pathways to identify potential threats and to provide situational awareness of areas not normally covered by cameras (such as areas outside the fence line outside at fixed facilities). In addition, UAS can provide real-time information to transportation convoy teams that pass through constantly changing public access environments. This paper will provide operational recommendations to be addressed when integrating UAS into existing physical protection systems at fixed sites and during transport. Recommendations will include aspects of the following: needs analysis; tactics and techniques to support detection and assessment as well as response force deployment; remote pilot selection, qualifications, training, and currency; UAS selection criteria; UAS laws and regulations; possible cost sharing with other facility operations; and on-scene emergency management.

Stockwell, Brandon↗

DOE OSTI2026

Developing a Process for Collaboration-Based Siting of a Federal Consolidated Interim Storage Facility in the United States: Learning from Communities Living with Legacy Waste

In June of 2023, the U.S. Department of Energy (DOE), Office of Nuclear Energy (NE) announced the selection of its Collaboration-Based Siting (CBS) Consortia, a group of 12 awardees, including the Consortium for Risk Evaluation with Stakeholder Participation (CRESP) (led by Vanderbilt University) to assist DOE-NE with the development of its process for siting a federal consolidated interim storage facility (FCISF) for spent nuclear fuel (SNF) storage. At this time, DOE NE is not soliciting interested host communities, rather the CBS Consortia are tasked with in-depth engagement, mutual learning, and capacity building to provide DOE NE with feedback on the CBS process. CRESP’s objective is to engage communities in two regions (the Pacific Northwest and the Southeast) with sites currently storing defense- and research-related SNF to foster learning concerning the best and worst practices in community participation in risk-informed decision making. This includes learning from existing structures for public input in radioactive waste management decision making [e.g. citizen advisory boards (CABs)] and other local parties about how to build and sustain trust among the parties. CRESP has been working to engage stakeholders and Tribes surrounding two DOE sites historically differing in receptiveness to engaging with DOE and trusting in DOE to accomplish its missions. CRESP’s approach to date has consisted of (1) engaging voluntarily members and former members of the DOE Office of Environmental Management’s CABs to develop a mutual understanding of their perspectives, values, and experiences related to risk and participatory decision making; (2) engaging members of those communities that would likely be part of any radioactive waste management discussions and who may provide valuable feedback for the development of the CBS process; and in the longer term, (3) engaging communities to foster knowledge sharing on understanding and definitions of risk and how risk is factored into community decision making. Our emphasis is to identify opportunities for improving risk communication frameworks, strategies, and decision making. The selection of a future FCISF site is likely to result in the creation of a structure similar to a CAB composed of members of the local community. We anticipate that these insights can help DOE NE learn from existing participatory risk communication structures in place at sites storing defenseor research-related SNF to understand best practices for fostering enduring and participatory relationships with future CABs. Within this paper, we (1) describe CRESP’s overall approach to assisting DOE NE with maturing the CBS process; (2) present a summary of preliminary phase 1 project results, including the development of a body of knowledge (describing available resources to support community engagement, risk communica tion, and participatory decision making) and community ecosystem information (leveraging demographic, social, economic, and environmental attribute mapping and advanced sentiment analysis of social media data); and (3) based on these results, provide observations for future research opportunities to support the development of CBS processes for radioactive waste management facilities, generally.

collaboration-based siting↗

DOE OSTI2023

Is land use producing robust signals in future projections from Earth system models, all else being equal?

Abstract We use six Earth system models (ESMs) run under SSP3-7.0, a scenario characterized by a relatively large land use change (LUC) over the 21st century, and under a variant of the same scenario where a significantly different pattern of LUC, taken from SSP1-2.6, was used, all else being equal. Our goal is to identify changes in climate extremes between the two scenarios that are statistically significant and robust across the ESMs. The motivation for this study is to test a long-held assumption of the shared socio-economic pathway-representative concentration pathway (SSP-RCP) scenario framework: that the signal from LUC can be safely disregarded when pairing different SSPs to the compatible RCPs, where compatibility only considers global radiative forcing, predominantly determined by well-mixed greenhouse gasses emissions. We analyze extremes of daily minimum and maximum temperatures and precipitation, after fitting non-stationary generalized extreme value distributions in a way that borrows strength along the length of the simulation (2015–2100) and across initial condition ensembles. We consider changes in the 20 year return levels (RL20s) of these metrics by 2100, and focus on eight locations where LUC is large within each scenario, and strongly differs between scenarios, averaging the RL20s over a neighborhood characterized by the same LUC to enhance the signal to noise. We find that precipitation extremes do not show significant differences attributable to LUC differences. For temperature extremes (cold and hot) results are mixed, with some location-index combination showing significant results for some of the ESMs but not all, and not many coherent changes appearing for indices across regions, or regions across indices. These ESMs are representative of what is typically adopted as the source of climate information for impact studies, when the SSP-RCP framework is put to use. Overall, our analysis suggests that the hypothesis to pair SSPs to RCPs in a flexible fashion is overall defensible. However, the appearance of some coherence in a few locations and for some indices invites further investigation.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

When do different scenarios of projected electricity demand start to meaningfully diverge?

Resource adequacy studies look at balancing electricity supply and demand on 10- to 15-year time horizons while asset investment planning typically evaluates returns on 20- to 40-year time horizons. Projections of electricity demand are factored into the decision-making in both cases. Climate, energy policy, and socioeconomic changes are key uncertainties known to influence electricity demands, but their relative importance for demands over the next 10-40 years is unclear. The power sector would benefit from a better understanding of the need to characterize these uncertainties for resource adequacy and investment planning. In this study, we quantify when projected United States (U.S.) electricity demands start to meaningfully diverge in response to a range of climate, energy policy, and socioeconomic drivers. Here we use a wide yet plausible range of 21st century scenarios for the U.S. The projections span two population/economic growth scenarios (Shared Socioeconomic Pathways 3 and 5) and two climate/energy policy scenarios, one including climate mitigation policies and one without (Representative Concentration Pathways 4.5 and 8.5). Each climate/energy policy scenario has two warming levels to reflect a range of climate model uncertainty. We show that the socioeconomic scenario matters almost immediately – within the next 10 years, the climate/policy scenario matters within 25-30 years, and the climate model uncertainty matters only after 50+ years. This work can inform the power sector working to integrate climate change uncertainties into their decision-making.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2021

Turn-key constrained parameter space exploration for particle accelerators using Bayesian active learning

Abstract Particle accelerators are invaluable discovery engines in the chemical, biological and physical sciences. Characterization of the accelerated beam response to accelerator input parameters is often the first step when conducting accelerator-based experiments. Currently used techniques for characterization, such as grid-like parameter sampling scans, become impractical when extended to higher dimensional input spaces, when complicated measurement constraints are present, or prior information known about the beam response is scarce. Here in this work, we describe an adaptation of the popular Bayesian optimization algorithm, which enables a turn-key exploration of input parameter spaces. Our algorithm replaces the need for parameter scans while minimizing prior information needed about the measurement’s behavior and associated measurement constraints. We experimentally demonstrate that our algorithm autonomously conducts an adaptive, multi-parameter exploration of input parameter space, potentially orders of magnitude faster than conventional grid-like parameter scans, while making highly constrained, single-shot beam phase-space measurements and accounts for costs associated with changing input parameters. In addition to applications in accelerator-based scientific experiments, this algorithm addresses challenges shared by many scientific disciplines, and is thus applicable to autonomously conducting experiments over a broad range of research topics.

43 PARTICLE ACCELERATORS↗

DOE OSTI2022

EXCESS workshop: Descriptions of rising low-energy spectra

Many low-threshold experiments observe sharply rising event rates of yet unknown origins below a few hundred eV, and larger than expected from known backgrounds. Due to the significant impact of this excess on the dark matter or neutrino sensitivity of these experiments, a collective effort has been started to share the knowledge about the individual observations. For this, the EXCESS Workshop was initiated. In its first iteration in June 2021, ten rare event search collaborations contributed to this initiative via talks and discussions. The contributing collaborations were CONNIE, CRESST, DAMIC, EDELWEISS, MINER, NEWS-G, NUCLEUS, RICOCHET, SENSEI and SuperCDMS. They presented data about their observed energy spectra and known backgrounds together with details about the respective measurements. In this paper, we summarize the presented information and give a comprehensive overview of the similarities and differences between the distinct measurements. The provided data is furthermore publicly available on the workshop's data repository together with a plotting tool for visualization.

Adari, Prakruth↗

DOE OSTI2022

EXCESS workshop: Descriptions of rising low-energy spectra

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2020

D and D Research on KM-IT Platform - 20494

The Knowledge Management Information Tool (KM-IT) is a web-based system developed to maintain and preserve the Department of Energy's (DoE's) knowledge base. The system was developed by Florida International University's Applied Research Center (FIU-ARC) with the support of the D and D community including the DOE Office of Environmental Management, and with the collaboration and support of the DoE's Energy Facility Contractors Group (EFCOG) and the former ALARA Centers at Hanford and Savannah. The KM-IT system is a community driven system tailored to serve the technical issues faced by the workforce across the DOE Complex. This KM-IT web-based interactive system is operational and available for use at www.dndkm.org and is currently comprised of the following modules: Web Crawler, Hotline, Technology, Hanford's ALARA Center Reports, Specialist Directory, Lessons Learned, Best Practices, Video/Picture Library, Vendors and Industry News. The Web Crawler dynamically searches through the KM-IT repository as well as the web and displays search results based on the search criteria. The Hotline allows registered users to post questions/problems related to D and D and to receive solutions from a subject-matter specialist. The Technology module serves as repository of D and D technologies and contains technology/ demonstration fact sheets and vendor information. D and D community members can add Lessons Learned, Best Practices, and Pictures/Videos to the D and D repository, after a formal approval process. The Vendor module provides a directory of commercial vendors who provide D and D related technologies, supplies, and services. KM-IT makes an excellent use of the knowledge that exists within the D and D community by allowing D and D project managers around the DOE complex to collaborate by sharing innovative ideas, past experiences, and practices and by maintaining a directory of subject matter specialists. FIU has developed the dedicated module on KM-IT platform to publish D and D research being performed at FIU. This module highlights current EM research efforts and activities in support of D and D being performed at FIU/SRNL associated with fixatives and intumescent products. FIU will expand this module to include the recent and current D and D research being performed across multiple DOE EM sites, national labs and universities. FIU will collaborate with SRNL, INL, ANL and other universities to explore and publish D and D research activities on KM-IT. As a result, the user community will have a centralized location to review new D and D related research across the DOE EM complex. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2025

Footprints of Worldwide Adaptation in Structured Populations of Drosophila melanogaster Through the Expanded DEST 2.0 Genomic Resource

Abstract Large-scale genomic resources can place genetic variation into an ecologically informed context. To advance our understanding of the population genetics of the fruit fly Drosophila melanogaster, we present an expanded release of the community-generated population genomics resource Drosophila Evolution over Space and Time (DEST 2.0; https://dest.bio/). This release includes 530 high-quality pooled libraries from flies collected across six continents over more than a decade (2009 to 2021), most at multiple time points per year; 211 of these libraries are sequenced and shared here for the first time. We used this enhanced resource to elucidate several aspects of the species' demographic history and identify novel signs of adaptation across spatial and temporal dimensions. For example, we showed that the spatial genetic structure of populations is stable over time, but that drift due to seasonal contractions of population size causes populations to diverge over time. We identified signals of adaptation that vary between continents in genomic regions associated with xenobiotic resistance, consistent with independent adaptation to common pesticides. Moreover, by analyzing samples collected during spring and fall across Europe, we provide new evidence for seasonal adaptation related to loci associated with pathogen response. Furthermore, we have also released an updated version of the DEST genome browser. This is a useful tool for studying spatiotemporal patterns of genetic variation in this classic model system.

Biochemistry & Molecular Biology↗

DOE OSTI2021

History of Ethanol Fuel Adoption in the United States: Policy, Economics, and Logistics

Ethanol has the achieved the greatest market share of all the alternative transportation fuels that have been researched, developed, and deployed in the US. There are multiple lessons to be learned from the history of ethanol adoption that can be applied to future fuels and products. Ethanol has replaced portions of gasoline in three main blend levels, with corresponding vehicles, equipment, benefits, and policies. The first is E10, which has replaced nearly all pure gasoline (E0) sold in the United States today (U.S. Energy Information Administration 2015). This was brought about through generations of policies that were motivated by multiple factors related to engine performance, energy security, health, air quality, and climate protection. Ethanol's high octane has been a consistent driver of the fuel because this enables higher performance engines. Early policies (1973-1979) were largely motivated by the desire to reduce dependence on petroleum sourced from members of the Organization of the Petroleum Exporting Countries, or OPEC. Fuel policy in the 1980s was largely in pursuit of promoting octane number enhancers that could replace lead. Criteria pollutant reduction was the overarching goal of actions taken from 1990 to 2005. From 2005 to the present, fuel policy has been largely motivated by energy security and climate protection goals. These policies were usually technology-agnostic and promoted multiple fuels and additives during each period. However, ethanol is the only fuel identified that is cost effective with qualities that enabled it to prosper in the policy environments of all four of these periods.The second market for ethanol is via 85% ethanol (E85). This fuel has the advantage of a greater concentration of ethanol but the disadvantage of not being compatible with regular gasoline vehicles. Instead, it can only be used in flexible-fuel vehicle (FFVs), which can use every blend level from E0 to E85. Therefore, much of the effort to increase E85 consumption has been aimed at incentivizing automakers to manufacture FFVs, drivers to purchase FFVs, and fueling stations to equip themselves to sell E85.The third, and newest, market through which ethanol is consumed is 15% ethanol (E15), which builds upon the E10 market to increase ethanol consumption by common gasoline vehicles. Efforts to create the E15 market consisted largely of testing vehicles and refueling equipment for compatibility, creating waivers to allow the use of E15, placing requirements on E15 retailers, and incentivizing retailers to equip themselves to purchase E15.

09 BIOMASS FUELS↗

DOE OSTI2022

Licensing, Regulations and Developing Guidance for Nuclear Technology Deployment for Embarking countries in Africa

The African region is witnessing an increased number of countries at different stages of implementing or considering the introduction of peaceful nuclear power programs to meet the demand of their rapidly growing economies as well as clean energy needs. Grid size, cost, licensing, and regulations will be some of the challenges to deploying larger power reactors. A key element of the regulatory framework will be the inclusion of nuclear security information and assurance that security is integrated into the license review process.As each country continue to implement and consider different reactor designs from several vendors, the significance of customer knowledge of licensing, Regulations, and guidance document to facilitate the deployment and operational needs for nuclear technology cannot be over-emphasized. This special session will bring together a selected panel of key stakeholders and policymakers from embarking countries in Africa to participate in a panel discussion to share their experience in the licensing, regulations, and development of guidance for power plant deployment. The session will also consider and identify potential gaps that may affect the licensing and regulatory applications for the future nuclear infrastructure. As well, the panel will promote regional networking and communication to increase capacities in readiness for the potential deployment of additional technology, such as Small Modular Reactors.

Dahunsi, Stephen↗

DOE OSTI2021

The CanBikeCO Mini Pilot: Preliminary Results and Lessons Learned

In fall 2020, the Colorado Energy Office, as part of the State of Colorado’s “Can Do Colorado” initiative, initiated a project aimed at encouraging energy-efficient transportation during the COVID-19 pandemic. The initial mini-pilot provided e-bikes to 13 low-income households under an individual ownership model. This report assesses the impact of providing this additional mobility option on the travel behavior of participants. It also outlines the lessons learned from deploying a continuous monitoring platform to track the travel behavior. These lessons will influence the evaluation component for the full pilot, which will cover multiple geographic regions, starting in summer 2021, and run for 2 years. The continuous data collection was enabled by a customized version of the open-source e-mission platform, called CanBikeCO, configured with a behavioral gamification feature. The Colorado Energy Office used this system to collect a unique data set consisting of 3 months of partially automated travel diaries, combining sensed and surveyed data and linked with demographic information, from 12 participants. The data collection process worked well overall: users generally liked the app, appreciated the game, and did not complain about battery life. The long tracking period introduced behavioral challenges in user engagement, which we plan to address using repeated patterns and automated status checks for the full pilot. The analysis results, based on the subset of trips with user-reported labels (68%), indicate that the e-bike was the dominant commute mode share (31%), in sharp contrast to the census bicycle commute mode share (<1%). E-bike trips primarily replaced single-occupancy vehicle (SOV) trips (28%), followed closely by walking (24%) and regular bike (20%). The nonmotorized mode replacement corresponds to lower travel time and increased productivity enabled by the program. The emissions impact analysis of the program, computed using trip-level energy intensity factors, indicates savings of 1,367 lbs. of CO 2 . Although the results are strongly positive, the narrow demographic profile of study participants, their limited mobility alternatives, and nonuniform labeling indicate caution in broader interpretation. These preliminary results do suggest that such programs, supported by real-time education and support from program managers, can simultaneously meet equity and sustainability goals. The planned full pilot, addressing the data collection challenges and broadening the geographic scope, will provide additional insights into the generality of this approach.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2021

The CanBikeCO Mini Pilot: Procedure and Preliminary Results

In fall 2020, the Colorado Energy Office, as part of the State of Colorado's "Can Do Colorado" initiative, initiated a project aimed at encouraging energy-efficient transportation during the COVID-19 pandemic. The initial mini-pilot provided e-bikes to 13 low-income households under an individual ownership model. This report assesses the impact of providing this additional mobility option on the travel behavior of participants. It also outlines the lessons learned from deploying a continuous monitoring platform to track the travel behavior. These lessons will influence the evaluation component for the full pilot, which will cover multiple geographic regions, start in summer 2021, and run for 2 years. The continuous data collection was enabled by a customized version of the open-source e-mission platform, called CanBikeCO, configured with a behavioral gamification feature. The Colorado Energy Office used this system to collect a unique data set consisting of 3 months of partially automated travel diaries, combining sensed and surveyed data and linked with demographic information, from 12 participants. The data collection process worked well overall: users generally liked the app, appreciated the game, and did not complain about battery life. The long tracking period introduced behavioral challenges in user engagement, which we plan to address using repeated patterns and automated status checks for the full pilot. The analysis results, based on the subset of trips with user-reported labels (68%), indicate that the e-bike was the dominant commute mode share (31%), in sharp contrast to the census bicycle commute mode share (<1%). E-bike trips primarily replaced single-occupancy vehicle (SOV) trips (28%), followed closely by walking (24%) and regular bike (20%). The non-motorized mode replacement corresponds to lower travel time and increased productivity enabled by the program. The emissions impact analysis of the program, computed using trip-level energy intensity factors, indicates savings of 1,367 lbs. of CO2. Although the results are strongly positive, the narrow demographic profile of study participants, their limited mobility alternatives, and nonuniform labeling indicate caution in broader interpretation. These preliminary results do suggest that such programs, supported by real-time education and support from program managers, can simultaneously meet equity and sustainability goals. The planned full pilot, addressing the data collection challenges and broadening the geographic scope, will provide additional insights into the generality of this approach.

ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2020

The chemical properties of the Milky Way’s on-bar and off-bar regions: evidence for inhomogeneous star formation history in the bulge

ABSTRACT Numerous studies of integrated starlight, stellar counts, and kinematics have confirmed that the Milky Way is a barred galaxy. However, far fewer studies have investigated the bar’s stellar population properties, which carry valuable independent information regarding the bar’s formation history. Here, we conduct a detailed analysis of chemical abundance distributions ([Fe/H] and [Mg/Fe]) in the on-bar and off-bar regions to study the azimuthal variation of star formation history (SFH) in the inner Galaxy. We find that the on-bar and off-bar stars at Galactocentric radii 3 kpc < rGC < 5 kpc have remarkably consistent [Fe/H] and [Mg/Fe] distribution functions and [Mg/Fe]–[Fe/H] relation, suggesting a common SFH shared by the long bar and the disc. In contrast, the bar and disc at smaller radii (2 kpc < rGC < 3 kpc) show noticeable differences, with relatively more very metal-rich ($\rm [Fe/H] \sim 0.4$) stars but fewer solar abundance stars in the bar. Given the three-phase star formation history proposed for the inner Galaxy in Lian et al., these differences could be explained by the off-bar disc having experienced either a faster early quenching process or recent metal-poor gas accretion. Vertical variations of the abundance distributions at small rGC suggest a wider vertical distribution of low-α stars in the bar, which may serve as chemical evidence for vertical heating through the bar buckling process. The lack of such vertical variations outside the bulge may then suggest a lack of vertical heating in the long bar.

Lian, Jianhui↗

DOE OSTI2024

Efficient species identification for Pacific salmon genetic monitoring programs

Abstract 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.

Robinson, Zachary L.↗