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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Elephant range and population, strontium isotopes, and genetics combine to give local-scale specificity to ivory hotspot tracking

We use Sr isotopes to increase the precision of DNA-based origin estimates of wildlife products. Population information is used to develop Sr isotope Elephant Polygons that are overlaid onto the region of origin identified by DNA assignment to determine the sources of seized ivory samples. Our approach is cognizant of isotope mixing due to isotope turnover within animals and also of the large home range of elephants or other mobile species. Genetic information from 3 different law enforcement ivory seizures suggests a region of origin confined to Kenya and Tanzania in eastern Africa. We determine characteristic 87 Sr/ 86 Sr ratios for each of 25 different Elephant Polygons within this region using analyses of more the 600 known-origin reference samples. Using both the 87 Sr/ 86 Sr ratios of the seized ivory samples and elephant population estimates from individual Elephant Polygons we find that at least 75 % of the samples likely came from a single Elephant Polygon which includes the Tsavo National Parks in Kenya and the Mkomazi National Park in Tanzania. A few samples may have come from other regions, most likely from Tanzania. This study illustrates the value of combining genetics, isotope geochemistry, and population surveys in wildlife forensics studies.

Africa↗
DOE OSTI2022

COMPILE: a GWAS computational pipeline for gene discovery in complex genomes

Abstract Background Genome-Wide Association Studies (GWAS) are used to identify genes and alleles that contribute to quantitative traits in large and genetically diverse populations. However, traits with complex genetic architectures create an enormous computational load for discovery of candidate genes with acceptable statistical certainty. We developed a streamlined computational pipeline for GWAS (COMPILE) to accelerate identification and annotation of candidate maize genes associated with a quantitative trait, and then matches maize genes to their closest rice and Arabidopsis homologs by sequence similarity. Results COMPILE executed GWAS using a Mixed Linear Model that incorporated, without compression, recent advancements in population structure control, then linked significant Quantitative Trait Loci (QTL) to candidate genes and RNA regulatory elements contained in any genome. COMPILE was validated using published data to identify QTL associated with the traits of α-tocopherol biosynthesis and flowering time, and identified published candidate genes as well as additional genes and non-coding RNAs. We then applied COMPILE to 274 genotypes of the maize Goodman Association Panel to identify candidate loci contributing to resistance of maize stems to penetration by larvae of the European Corn Borer ( Ostrinia nubilalis ). Candidate genes included those that encode a gene of unknown function, WRKY and MYB-like transcriptional factors, receptor-kinase signaling, riboflavin synthesis, nucleotide-sugar interconversion, and prolyl hydroxylation. Expression of the gene of unknown function has been associated with pathogen stress in maize and in rice homologs closest in sequence identity. Conclusions The relative speed of data analysis using COMPILE allowed comparison of population size and compression. Limitations in population size and diversity are major constraints for a trait and are not overcome by increasing marker density. COMPILE is customizable and is readily adaptable for application to species with robust genomic and proteome databases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

The Frequency of Sex: Population Genomics Reveals Differences in Recombination and Population Structure of the Aflatoxin-Producing Fungus Aspergillus flavus

The apparent rarity of sex in many fungal species has raised questions about how much sex is needed to purge deleterious mutations and how differences in frequency of sex impact fungal evolution. We sought to determine how differences in the extent of recombination between populations of Aspergillus flavus impact the evolution of genes associated with the synthesis of aflatoxin, a notoriously potent carcinogen. We sequenced the genomes of, and quantified aflatoxin production in, 94 isolates of A. flavus sampled from seven states in eastern and central latitudinal transects of the United States. The overall population is subdivided into three genetically differentiated populations (A, B, and C) that differ greatly in their extent of recombination, diversity, and aflatoxin-producing ability. Estimates of the number of recombination events and linkage disequilibrium decay suggest relatively frequent sex only in population A. Population B is sympatric with population A but produces significantly less aflatoxin and is the only population where the inability of nonaflatoxigenic isolates to produce aflatoxin was explained by multiple gene deletions. Population expansion evident in population B suggests a recent introduction or range expansion. Population C is largely nonaflatoxigenic and restricted mainly to northern sampling locations through restricted migration and/or selection. Despite differences in the number and type of mutations in the aflatoxin gene cluster, codon optimization and site frequency differences in synonymous and nonsynonymous mutations suggest that low levels of recombination in some A. flavus populations are sufficient to purge deleterious mutations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Correlational selection and genetic architecture shape the evolution of the leaf economics spectrum in a perennial grass

The generality of the worldwide leaf economics spectrum (LES) has made it a pillar of trait-based ecological research. Yet, few studies have examined the processes shaping the evolution of the LES within species, in part, because most species occupy only a small portion of the LES. Here, to address this gap, we took advantage of the distinct leaf economics strategies present in different ecotypes of the phenotypically diverse perennial grass Panicum virgatum (switchgrass) to generate a genetic mapping population, which we planted in common gardens at three sites spanning 12 degrees of latitude in the central United States. With this genetic mapping population, we evaluated two potentially interacting causes of LES evolution: 1) genetic architecture, where multiple traits are influenced by either the same gene (pleiotropy) or by genes in close physical proximity (genetic linkage), and 2) correlational selection, where selection acts on traits in combination rather than in isolation. We found that shared genetic architecture influenced covariation between photosynthetic rate (A MASS ) and leaf nitrogen (N MASS ) and between A MASS and leaf mass per area (LMA). We also found that correlational selection favored the trait combinations predicted by the LES (e.g., high LMA with low N MASS or low LMA with high N MASS ) and disfavored other, mismatched trait combinations at two of the three sites. Together, these results demonstrate how the evolution of an integrated LES within species can arise from multiple evolutionary causes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A Pleiotropic Flowering Time QTL Exhibits Gene-by-Environment Interaction for Fitness in a Perennial Grass

Appropriate flowering time is a crucial adaptation impacting fitness in natural plant populations. Although the genetic basis of flowering variation has been extensively studied, its mechanisms in nonmodel organisms and its adaptive value in the field are still poorly understood. Here, we report new insights into the genetic basis of flowering time and its effect on fitness in Panicum hallii, a native perennial grass. Genetic mapping in populations derived from inland and coastal ecotypes identified flowering time quantitative trait loci (QTL) and many exhibited extensive QTL-by-environment interactions. Patterns of segregation within recombinant hybrids provide strong support for directional selection driving ecotypic divergence in flowering time. A major QTL on chromosome 5 (q-FT5) was detected in all experiments. Fine-mapping and expression studies identified a gene with orthology to a rice FLOWERING LOCUS T-like 9 (PhFTL9) as the candidate underlying q-FT5. We used a reciprocal transplant experiment to test for local adaptation and the specific impact of q-FT5 on performance. We did not observe local adaptation in terms of fitness tradeoffs when contrasting ecotypes in home versus away habitats. However, we observed that the coastal allele of q-FT5 conferred a fitness advantage only in its local habitat but not at the inland site. Sequence analyses identified an excess of low-frequency polymorphisms at the PhFTL9 promoter in the inland lineage, suggesting a role for either selection or population expansion on promoter evolution. Together, our findings demonstrate the genetic basis of flowering variation in a perennial grass and provide evidence for conditional neutrality underlying flowering time divergence.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Utilizing high-resolution genetic markers to track population-level exposure of migratory birds to renewable energy development

With new motivation to increase the proportion of energy demands met by zero-carbon sources, there is a greater focus on efforts to assess and mitigate the impacts of renewable energy development on sensitive ecosystems and wildlife, of which birds are of particular interest. One challenge for researchers, due in part to a lack of appropriate tools, has been estimating the effects from such development on individual breeding populations of migratory birds. To help address this, we utilize a newly developed, high-resolution genetic tagging method to rapidly identify the breeding population of origin of carcasses recovered from renewable energy facilities and combine them with maps of genetic variation across geographic space (called ‘genoscapes’) for five species of migratory birds known to be exposed to energy development, to assess the extent of population-level effects on migratory birds. We demonstrate that most avian remains collected were from the largest populations of a given species. In contrast, those remains from smaller, declining populations made up a smaller percentage of the total number of birds assayed. Results suggest that application of this genetic tagging method can successfully define population-level exposure to renewable energy development and may be a powerful tool to inform future siting and mitigation activities associated with renewable energy programs.

14 SOLAR ENERGY↗
DOE OSTI2022

MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations

Abstract Background Microbes and their viruses are hidden engines driving Earth’s ecosystems from the oceans and soils to humans and bioreactors. Though gene marker approaches can now be complemented by genome-resolved studies of inter-(macrodiversity) and intra-(microdiversity) population variation, analytical tools to do so remain scattered or under-developed. Results Here, we introduce MetaPop, an open-source bioinformatic pipeline that provides a single interface to analyze and visualize microbial and viral community metagenomes at both the macro - and microdiversity levels. Macrodiversity estimates include population abundances and α- and β-diversity. Microdiversity calculations include identification of single nucleotide polymorphisms, novel codon-constrained linkage of SNPs, nucleotide diversity ( π and θ ), and selective pressures (pN/pS and Tajima’s D ) within and fixation indices ( F ST ) between populations. MetaPop will also identify genes with distinct codon usage. Following rigorous validation, we applied MetaPop to the gut viromes of autistic children that underwent fecal microbiota transfers and their neurotypical peers. The macrodiversity results confirmed our prior findings for viral populations (microbial shotgun metagenomes were not available) that diversity did not significantly differ between autistic and neurotypical children. However, by also quantifying microdiversity, MetaPop revealed lower average viral nucleotide diversity ( π ) in autistic children. Analysis of the percentage of genomes detected under positive selection was also lower among autistic children, suggesting that higher viral π in neurotypical children may be beneficial because it allows populations to better “bet hedge” in changing environments. Further, comparisons of microdiversity pre- and post-FMT in autistic children revealed that the delivery FMT method (oral versus rectal) may influence viral activity and engraftment of microdiverse viral populations, with children who received their FMT rectally having higher microdiversity post-FMT. Overall, these results show that analyses at the macro level alone can miss important biological differences. Conclusions These findings suggest that standardized population and genetic variation analyses will be invaluable for maximizing biological inference, and MetaPop provides a convenient tool package to explore the dual impact of macro - and microdiversity across microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Population Subdivision in the Gopher Frog (Rana capito) across the Fragmented Longleaf Pine-Wiregrass Savanna of the Southeastern USA

Delineating genetically distinct population segments of threatened species and quantifying population connectivity are important steps in developing effective conservation and management strategies aimed at preventing extinction. The gopher frog (Rana capito) is a xeric-adapted, pond-breeding species endemic to the Gulf and Atlantic coastal plains of the southeastern United States. This species has experienced extensive habitat loss and fragmentation in the formerly widespread longleaf pine-wiregrass savanna where it lives, resulting in individual abundance declines and population extinctions throughout its range. We used individual-based clustering methods along with Bayesian inference of historical migration based on almost 1500 multilocus microsatellite genotypes to examine genetic structure in this taxon. Clustering analyses identified panhandle and peninsular populations in Florida as distinct genetic clusters separated by the Aucilla River, consistent with the division between the Coastal Plain and peninsular mitochondrial lineages, respectively. Analysis of historical migration indicated an east–west population divergence event followed by immigration to the east. Together, our results indicate that the genetically distinct Coastal Plain and peninsular Florida lineages should be considered separately for conservation and management purposes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Phylogeography of the blacklegged tick ( Ixodes scapularis ) throughout the USA identifies candidate loci for differences in vectorial capacity

Abstract The blacklegged tick ( Ixodes scapularis ( Journal of the Academy of Natural Sciences of Philadelphia , 1821, 2 , 59)) is a vector of Borrelia burgdorferi sensu stricto ( s.s .) ( International Journal of Systematic Bacteriology , 1984, 34 , 496), the causative bacterial agent of Lyme disease, part of a slow‐moving epidemic of Lyme borreliosis spreading across the northern hemisphere. Well‐known geographical differences in the vectorial capacity of these ticks are associated with genetic variation. Despite the need for detailed genetic information in this disease system, previous phylogeographical studies of these ticks have been restricted to relatively few populations or few genetic loci. Here we present the most comprehensive phylogeographical study of genome‐wide markers in I. scapularis , conducted by using 3RAD (triple‐enzyme restriction‐site associated sequencing) and surveying 353 ticks from 33 counties throughout the species' range. We found limited genetic variation among populations from the Northeast and Upper Midwest, where Lyme disease is most common, and higher genetic variation among populations from the South. We identify five spatially associated genetic clusters of I. scapularis . In regions where Lyme disease is increasing in frequency, the I. scapularis populations genetically group with ticks from historically highly Lyme‐endemic regions. Finally, we identify 10 variable DNA sites that contribute the most to population differentiation. These variable sites cluster on one of the chromosome‐scale scaffolds for I. scapularis and are within identified genes. Our findings illuminate the need for additional research to identify loci causing variation in the vectorial capacity of I. scapularis and where additional tick sampling would be most valuable to further understand disease trends caused by pathogens transmitted by I. scapularis .

3RAD↗
DOE OSTI2021

The genetic basis of the root economics spectrum in a perennial grass

Significance Plants have evolved diverse root form and function across the Earth’s environment, yet only certain types of trait combinations have proved evolutionarily viable. Using a genetic mapping population of the native perennial switchgrass, our study demonstrates multiple genetic linkages among root morphology, growth, and turnover. Switching alleles derived from southern-origin ecotypes to alleles from northern-origin ecotypes increases root turnover but reduces tissue investment in root length construction. The genetic trade-off between construction and turnover likely facilitates the local adaptation of root strategy along the warm to cold climatic gradients of the species range. In practice, our study provides the genetic evidence that increasing switchgrass yield for bioenergy does not directly conflict with enhancing its root-derived carbon sequestration.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Genomic Diversity Evaluation of Populus trichocarpa Germplasm for Rare Variant Genetic Association Studies

Genome-wide association studies are powerful tools to elucidate the genome-to-phenome relationship. In order to explain most of the observed heritability of a phenotypic trait, a sufficient number of individuals and a large set of genetic variants must be examined. The development of high-throughput technologies and cost-efficient resequencing of complete genomes have enabled the genome-wide identification of genetic variation at large scale. As such, almost all existing genetic variation becomes available, and it is now possible to identify rare genetic variants in a population sample. Rare genetic variants that were usually filtered out in most genetic association studies are the most numerous genetic variations across genomes and hold great potential to explain a significant part of the missing heritability observed in association studies. Rare genetic variants must be identified with high confidence, as they can easily be confounded with sequencing errors. In this study, we used a pre-filtered data set of 1,014 pure Populus trichocarpa entire genomes to identify rare and common small genetic variants across individual genomes. We compared variant calls between Platypus and HaplotypeCaller pipelines, and we further applied strict quality filters for improved genetic variant identification. Finally, we only retained genetic variants that were identified by both variant callers increasing calling confidence. Based on these shared variants and after stringent quality filtering, we found high genomic diversity in P. trichocarpa germplasm, with 7.4 million small genetic variants. Importantly, 377k non-synonymous variants (5% of the total) were uncovered. We highlight the importance of genomic diversity and the potential of rare defective genetic variants in explaining a significant portion of P. trichocarpa's phenotypic variability in association genetics. The ultimate goal is to associate both rare and common alleles with poplar's wood quality traits to support selective breeding for an improved bioenergy feedstock.

Genetics & Heredity↗
DOE OSTI2021

Acoustic and Genetic Data Can Reduce Uncertainty Regarding Populations of Migratory Tree-Roosting Bats Impacted by Wind Energy

Wind turbine-related mortality may pose a population-level threat for migratory tree-roosting bats, such as the hoary bat (Lasiurus cinereus) in North America. These species are dispersed within their range, making it impractical to estimate census populations size using traditional survey methods. Nonetheless, understanding population size and trends is essential for evaluating and mitigating risk from wind turbine mortality. Using various sampling techniques, including systematic acoustic sampling and genetic analyses, we argue that building a weight of evidence regarding bat population status and trends is possible to (1) assess the sustainability of mortality associated with wind turbines; (2) determine the level of mitigation required; and (3) evaluate the effectiveness of mitigation measures to ensure population viability for these species. Long-term, systematic data collection remains the most viable option for reducing uncertainty regarding population trends for migratory tree-roosting bats. We recommend collecting acoustic data using the statistically robust North American Bat Monitoring Program (NABat) protocols and that genetic diversity is monitored at repeated time intervals to show species trends. There are no short-term actions to resolve these population-level questions; however, we discuss opportunities for relatively short-term investments that will lead to long-term success in reducing uncertainty.

17 WIND ENERGY↗
DOE OSTI2026

Higher_wood_density_lowers_feedstock_cost_and_has_minimal_impact_on_biomass_conversion_to_biofuels

Poplar and other woody feedstocks have the potential to provide up to 200 million tons of biomass per year that could be converted to liquid fuels. Most forestry strategies that aim at increasing biomass productivity per hectare rely on short rotation plantations of fast-growing varieties. The improvement of wood density as a key trait itself has largely been overlooked. We evaluated natural variation in wood density across a population of genetically diversePopulus trichocarpatrees grown in a common garden. Wood density varies greatly within this population but is heritable higher wood density was not systematically associated with reduced growth, challenging assumptions of a trade-off between wood density and biomass accumulation. Furthermore, denser wood led to significant improvements throughout the supply chain, including, lowering biomass production and transportation costs. Higher density not correlate to changes in biomass composition. Density did not impact bioconversion in the two feedstock-to-fuel pipelines tested (pretreatment by ionic liquids or soaking in aqueous ammonia, and fermentation to ethanol) on a representative subset of poplars. These findings highlight wood density as a promising breeding target for accelerating the development of high-yielding, conversion-efficient bioenergy crops and as an avenue for increasing land-use efficiency and reducing biomass transportation cost. This data set contain three datasets.

CBI↗
DOE OSTI2026

Higher Wood Density Lowers Feedstock Cost and Has Minimal Impact on Biomass Conversion to Biofuels

Poplar and other woody feedstocks have the potential to provide up to 200 million tons of biomass per year that can be converted to liquid fuels. Most forestry strategies that aim to increase biomass productivity per hectare rely on short rotation plantations of fast-growing varieties. The improvement of the wood density as a key trait itself has largely been overlooked. We evaluated natural variation in wood density across a population of genetically diverse Populus trichocarpa trees grown in a common garden. Wood density varies greatly within this population but is heritable; higher wood density was not systematically associated with reduced growth, challenging assumptions of a trade-off between wood density and biomass accumulation. Furthermore, denser wood led to significant improvements throughout the supply chain including lowering biomass production and transportation costs. Higher density did not correlate with changes in biomass composition. Density did not impact bioconversion in the two feedstock-to-fuel pipelines tested (pretreatment by ionic liquids and fermentation to bisabolene or soaking in aqueous ammonia and fermentation to ethanol) on a representative subset of poplars. These findings highlight wood density as a promising breeding target for accelerating the development of high-yielding, conversion-efficient bioenergy crops and as an avenue for increasing landuse efficiency and reducing biomass transportation cost.

09 BIOMASS FUELS↗
DOE OSTI2022

Dose-finding studies in drug development for rare genetic diseases

The small patient populations inherent to rare genetic diseases present many challenges to the traditional drug development paradigm. One major challenge is generating sufficient data in early phase studies to inform dose selection for later phase studies and dose optimization for clinical use of the drug. However, optimizing the benefit-risk profile of drugs through appropriate dose selection during drug development is critical for all drugs, including those being developed to treat rare diseases. Recognizing the challenges of conducting dose finding studies in rare disease populations and the importance of dose selection and optimization for successful drug development, we assessed the dose-finding studies and analyses conducted for drugs recently approved for rare genetic diseases. Of the 40 marketing applications for new molecular entity (NME) drugs and biologics approved by the United States Food and Drug Administration for rare genetic diseases from 2015 to 2020, 21 (53%) of the development programs conducted at least one dedicated dose-finding study. In addition, the majority of drug development programs conducted clinical studies in healthy subjects and included population pharmacokinetic and exposure–response analyses; some programs also conducted clinical studies in patient populations other than the disease for which the drug was initially approved. The majority of primary endpoints utilized in dedicated dose-finding studies were biomarkers, and the primary endpoint of the safety and efficacy study matched the primary endpoint used in the dose finding study in 9 of 13 (69%) drug development programs where primary study endpoints were assessed. Our study showed that NME drug development programs for rare genetic diseases utilize multiple data sources for dosing information, including studies in healthy subjects, population pharmacokinetic analyses, and exposure–response analyses. In addition, our results indicate that biomarkers play a key role in dose-finding studies for rare genetic disease drug development programs. Our findings highlight the need to develop study designs and methods to allow adequate dose-finding efforts within rare disease drug development programs that help overcome the challenges presented by low patient prevalence and other factors. Furthermore, the frequent reliance on biomarkers as endpoints for dose-finding studies underscores the importance of biomarker development in rare diseases.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Multigeneration Pedigrees to Monitor Hatchery Broodstock Composition and Genetic Variation of Spring/Summer Chinook Salmon in the Columbia River Basin

Abstract Hatchery production of Chinook Salmon Oncorhynchus tshawytscha in the Columbia River basin comprises most of the anadromous salmonid production in this region. Hatchery facilities and programs serve to mitigate for impacts to salmonids due to the construction and operation of hydropower dams and habitat impacts from development in addition to the conservation and restoration of natural populations. A genetic method referred to as parentage-based tagging (PBT) enables highly reliable detection of hatchery-origin fish and inference of multigeneration pedigrees. This study compiles 11 years of PBT data from nearly 125,000 interior stream-type Chinook Salmon from 24 spawning hatcheries located on tributaries of the mid- and upper Columbia River and in the Salmon, Clearwater, and Grande Ronde River subbasins. Multigenerational pedigrees allowed for investigation of the proportions of natural- and hatchery-origin broodstock (pNOB and pHOB, respectively) for each hatchery and enumeration of the scale of production between segregated and integrated programs. We then compared how pHOB and the scale of production influenced the number of stray fish observed, genetic diversity, relatedness, and age-class compositions within broodstocks. Over 91.0% of hatchery broodstock could be assigned back to their parents, and overall less than 1.0% of broodstock consisted of fish that were unintentionally incorporated into nonnatal hatchery programs. We evaluated 11 segregated programs with 0.0–10.0% pNOB, 9 intermediate programs (10.1–50.0% pNOB), and 3 integrated programs (>50.0% pNOB). There was no correlation between the scale of production or pNOB with the level of genetic diversity, but as production size increased, so did the effective number of breeders. This study demonstrates the utility of PBT as a monitoring tool for hatchery broodstocks, and results suggest that segregated and integrated programs have tradeoffs that generally align with their intended broodstock management purpose of providing fish for harvest and/or fish for supplementation or reintroduction.

Horn, Rebekah L.↗
DOE OSTI2022

Retracted: Monitoring Hatchery Broodstock Composition and Genetic Variation of Spring/Summer Chinook Salmon in the Columbia River Basin with Multigeneration Pedigrees

Abstract Hatchery production of Chinook Salmon Oncorhynchus tshawytscha in the Columbia River basin comprises most of the anadromous salmonid production in this region. Hatchery facilities and programs serve to mitigate for impacts to salmonids due to the construction and operation of hydropower dams and habitat impacts from development in addition to the conservation and restoration of natural populations. A genetic method referred to as parentage-based tagging (PBT) enables highly reliable detection of hatchery-origin fish and inference of multigeneration pedigrees. This study compiles 11 years of PBT data from nearly 125,000 interior stream-type Chinook Salmon from 24 spawning hatcheries located in tributaries of the mid- and upper Columbia River as well as the Salmon, Clearwater, and Grande Ronde River subbasins. Multigenerational pedigrees allowed investigation of the proportion of natural- and hatchery-origin broodstock (pNOB and pHOB, respectively) for each hatchery and enumeration of the scale of production between segregated and integrated programs. We then compared how pHOB and the scale of production influenced the number of stray fish observed, genetic diversity, relatedness, and age-class compositions within broodstocks. Over 91.0% of hatchery broodstock could be assigned back to their parents, and there was an overall rate of less than 1.0% of broodstock that were unintentionally incorporated into nonnatal hatchery programs. We evaluated 14 segregated programs with 0.0–10.0% pNOB, 7 intermediate programs (10.1–50.0% pNOB), and 3 integrated programs (>50.0% pNOB). There was no correlation between the scale of production or pNOB with the level of genetic diversity, but as production size increased, so did the effective number of breeders. This study demonstrates the utility of PBT as a monitoring tool for hatchery broodstocks, and results suggest that segregated and integrated programs have tradeoffs that generally align with their intended broodstock management purpose of providing fish for harvest and/or fish for supplementation or reintroduction.

Horn, Rebekah L.↗