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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Genetic diversity, population structure and anthracnose resistance response in a novel sweet sorghum diversity panel

Sweet sorghum is an attractive feedstock for the production of renewable chemicals and fuels due to the readily available fermentable sugars that can be extracted from the juice, and the additional stream of fermentable sugars that can be obtained from the cell wall polysaccharides in the bagasse. An important selection criterion for new sweet sorghum germplasm is resistance to anthracnose, a disease caused by the fungal pathogen Colletotrichum sublineolum. The identification of novel anthracnose-resistance sources present in sweet sorghum germplasm offers a fast track towards the development of new resistant sweet sorghum germplasm. We established a sweet sorghum diversity panel (SWDP) of 272 accessions from the USDA-ARS National Plant Germplasm (NPGS) collection that includes landraces from 22 countries and advanced breeding material, and that represents ~15% of the NPGS sweet sorghum collection. Genomic characterization of the SWDP identified 171,954 single nucleotide polymorphisms (SNPs) with an average of one SNP per 4,071 kb. Population structure analysis revealed that the SWDP could be stratified into four populations and one admixed group, and that this population structure could be aligned to sorghum’s racial classification. Results from a two-year replicated trial of the SWDP for anthracnose resistance response in Texas, Georgia, Florida, and Puerto Rico showed 27 accessions to be resistant across locations, while 145 accessions showed variable resistance response against local pathotypes. A genome-wide association study identified 16 novel genomic regions associated with anthracnose resistance. Four resistance loci on chromosomes 3, 6, 8 and 9 were identified against pathotypes from Puerto Rico, and two resistance loci on chromosomes 3 and 8 against pathotypes from Texas. In Georgia and Florida, three resistance loci were detected on chromosomes 4, 5, 6 and four on chromosomes 4, 5 (two loci) and 7, respectively. One resistance locus on chromosome 2 was effective against pathotypes from Texas and Puerto Rico and a genomic region of 41.6 kb at the tip of chromosome 8 was associated with resistance response observed in Georgia, Texas, and Puerto Rico. This publicly available SWDP and the extensive evaluation of anthracnose resistance represent a valuable genomic resource for the improvement of sorghum.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Exploring genetic diversity, population structure, and subgenome differences in the allopolyploid Camelina sativa : implications for future breeding and research studies

Abstract Camelina (Camelina sativa), an allohexaploid species, is an emerging aviation biofuel crop that has been the focus of resurgent interest in recent decades. To guide future breeding and crop improvement efforts, the community requires a deeper comprehension of subgenome dominance, often noted in allopolyploid species, “alongside an understanding of the genetic diversity” and population structure of material present within breeding programs. We conducted population genetic analyses of a C. sativa diversity panel, leveraging a new genome, to estimate nucleotide diversity and population structure, and analyzed for patterns of subgenome expression dominance among different organs. Our analyses confirm that C. sativa has relatively low genetic diversity and show that the SG3 subgenome has substantially lower genetic diversity compared to the other two subgenomes. Despite the low genetic diversity, our analyses identified 13 distinct subpopulations including two distinct wild populations and others putatively representing founders in existing breeding populations. When analyzing for subgenome composition of long non-coding RNAs, which are known to play important roles in (a)biotic stress tolerance, we found that the SG3 subgenome contained significantly more lincRNAs compared to other subgenomes. Similarly, transcriptome analyses revealed that expression dominance of SG3 is not as strong as previously reported and may not be universal across all organ types. From a global analysis, SG3 “was only significant higher expressed” in flower, flower bud, and fruit organs, which is an important discovery given that the crop yield is associated with these organs. Collectively, these results will be valuable for guiding future breeding efforts in camelina.

Agriculture↗
DOE OSTI2024

Dosage optimization for reducing tumor burden using a phenotype-structured population model with a drug-resistance continuum

Abstract Drug resistance is a significant obstacle to effective cancer treatment. To gain insights into how drug resistance develops, we adopted a concept called fitness landscape and employed a phenotype-structured population model by fitting to a set of experimental data on a drug used for ovarian cancer, olaparib. Our modeling approach allowed us to understand how a drug affects the fitness landscape and track the evolution of a population of cancer cells structured with a spectrum of drug resistance. We also incorporated pharmacokinetic (PK) modeling to identify the optimal dosages of the drug that could lead to long-term tumor reduction. We derived a formula that indicates that maximizing variation in plasma drug concentration over a dosing interval could be important in reducing drug resistance. Our findings suggest that it may be possible to achieve better treatment outcomes with a drug dose lower than the levels recommended by the drug label. Acknowledging the current limitations of our work, we believe that our approach, which combines modeling of both PK and drug resistance evolution, could contribute to a new direction for better designing drug treatment regimens to improve cancer treatment.

Life Sciences & Biomedicine - Other Topics↗
DOE OSTI2023

Genome-Wide Informative Microsatellite Markers and Population Structure of Fusarium virguliforme from Argentina and the USA

Soybean sudden death syndrome (SDS) is a destructive disease that causes substantial yield losses in South and North America. Whereas four Fusarium species were identified as the causal agents, F. virguliforme is the primary SDS-causing pathogen in North America and it also contributes substantially to SDS in Argentina. In this study, we comparatively analyzed genome assemblies of four F. virguliforme strains and identified 29 informative microsatellite markers. Sixteen of the 29 markers were used to investigate the genetic diversity and population structure of this pathogen in a collection of 90 strains from Argentina and the USA. A total of 37 multilocus genotypes (MLGs) were identified, including 10 MLGs in Argentina and 26 in the USA. Only MLG2, the most dominant MLG, was found in both countries. Analyses with three different approaches showed that these MLGs could be grouped into three clusters. Cluster IA consisting of four MLGs exclusively from the USA has much higher genetic diversity than the other two clusters, suggesting that it may be the ancestral cluster although additional data are necessary to support this hypothesis. Clusters IB and II consisted of 13 and 21 MLGs, respectively. MLGs belonging to these two clusters were present in all four sampled states in Argentina and all five sampled states in the USA.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Population structure limits the use of genomic data for predicting phenotypes and managing genetic resources in forest trees

There is overwhelming evidence that forest trees are locally adapted to climate. Thus, genecological models based on population phenotypes have been used to measure local adaptation, infer genetic maladaptation to climate, and guide assisted migration. However, instead of phenotypes, there is increasing interest in using genomic data for gene resource management. We used whole-genome resequencing and common-garden experiments to understand the genetic architecture of adaptive traits in black cottonwood. We studied the potential of using genome-wide association studies (GWAS) and genomic prediction to detect causal loci, identify climate-adapted phenotypes, and inform gene resource management. We analyzed population structure by partitioning phenotypic and genomic (single-nucleotide polymorphism) variation among 840 genotypes collected from 91 stands along 16 rivers. Most phenotypic variation (60 to 81%) occurred among populations and was strongly associated with climate. Population phenotypes were predicted well using genomic data (e.g., predictive abilityr> 0.9) but almost as well using climate or geography (r> 0.8). In contrast, genomic prediction within populations was poor (r< 0.2). We identified many GWAS associations among populations, but most appeared to be spurious based on pooled within-population analyses. Hierarchical partitioning of linkage disequilibrium and haplotype sharing suggested that within-population genomic prediction and GWAS were poor because allele frequencies of causal loci and linked markers differed among populations. Given the urgent need to conserve natural populations and ecosystems, our results suggest that climate variables alone can be used to predict population phenotypes, delineate seed zones and deployment zones, and guide assisted migration.

Science & Technology - Other Topics↗
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 OSTI2026

Global population structures and demographic history of Suillus luteus, a pine co‐introduced ectomycorrhizal fungus associated with exotic forestry and invasion

Human colonization since the 19th century has resulted in the global spread of pines beyond their original northern boreal distribution. Although the introduction history of pines is documented through historical records, little is known about the introduction history of their ectomycorrhizal (ECM) fungi, which are critical symbionts for the survival and invasion of pines. Using Suillus luteus as an example, whole genomes of 208 individuals collected across native and introduced ranges were sequenced to reveal the introduction history of pine co-introduced ECM fungi. Population genomics analyses showed that all introductions originated from Europe. With the exception of North America, introduced populations were genetically differentiated from the European population, with varying magnitudes of population expansion in different introduced regions. Genetic variation within the native European population followed isolation by distance, but not in the introduced range, highlighting the disparity in the spatial-genetic patterns of native vs exotic habitats. The spread of S. luteus is mediated by human activities accompanying pine introductions, with its demographic history linked to forestry practices. The spatial, temporal, and demographic patterns observed in S. luteus offer insight into the population genetics of a widely introduced ECM fungus and are likely applicable to other pine co-introduced ECM fungi.

Ke, Yi‐Hong↗
DOE OSTI2026

Sub-daily virus sampling at the Bermuda Atlantic Time Series reveals diel and depth-structured population dynamics without community-level shifts

Ocean microbes contribute to biogeochemical cycles and ecosystem function, but they do so under top-down pressure imposed by viruses. While viruses are increasingly understood spatially and beginning to be incorporated into predictive modeling, high-frequency ocean virus dynamics remain understudied due to methodological challenges. Here we sampled stratified Bermuda Atlantic Time Series (BATS) waters for 112 hours at sub-daily 4- (surface) or 12- (deep chlorophyll maximum) hour intervals, purified viral particles from these samples, sequenced their metagenomes, and used the resulting data to characterize high-frequency virus community dynamics. Aggregated community diversity metrics changed with depth, but were not statistically significant temporally at a fixed location. However, finer-scale population-level analyses revealed both depth and temporal change, including physicochemical depth-driven differences and, in surface waters, thousands of viral populations that exhibited statistically significant diel rhythms. Statistical analyses revealed three main archetypes of temporal dynamics that themselves differed in abundance patterns, host predictions, viral taxonomy, and gene functions. Among these, highlights include viruses resembling an archetype with a night peaking pattern in activity that include an over-representation of viruses that putatively infect Prochlorococcus, a phototrophic cyanobacteria. Together, these efforts provide baseline community- and population-scale short-time-frame observations relevant to future climate state modeling.

Carrillo, Alfonso [The Ohio State University, Colu↗
DOE OSTI2023

Structure-informed clustering for population stratification in association studies

Background: Identifying variants associated with complex traits is a challenging task in genetic association studies due to linkage disequilibrium (LD) between genetic variants and population stratification, unrelated to the disease risk. Existing methods of population structure correction use principal component analysis or linear mixed models with a random effect when modeling associations between a trait of interest and genetic markers. However, due to stringent significance thresholds and latent interactions between the markers, these methods often fail to detect genuinely associated variants. Results: To overcome this, we propose CluStrat, which corrects for complex arbitrarily structured populations while leveraging the linkage disequilibrium induced distances between genetic markers. It performs an agglomerative hierarchical clustering using the Mahalanobis distance covariance matrix of the markers. In simulation studies, we show that our method outperforms existing methods in detecting true causal variants. Applying CluStrat on WTCCC2 and UK Biobank cohorts, we found biologically relevant associations in Schizophrenia and Myocardial Infarction. CluStrat was also able to correct for population structure in polygenic adaptation of height in Europeans. Conclusions: CluStrat highlights the advantages of biologically relevant distance metrics, such as the Mahalanobis distance, which captures the cryptic interactions within populations in the presence of LD better than the Euclidean distance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Ultrafast population and structural dynamics of a Ni-bipyridine photoredox catalyst reveal a significant deactivation pathway

The ultrafast excited state pathways and dynamics of NiII-bipyridine complexes influence the yield of photochemical processes involved in their catalytic cross-coupling reactions. Here we present ultrafast Ni K x-ray emission spectroscopy (XES) and x-ray solution scattering (XSS) of a NiII-bipyridine aryl halide complex, [Ni(t-Bubpy)(o-tol)Br], to quantify the excited state population dynamics and structural changes of the pre-catalyst. Due to the local spin-sensitivity of XES, the population dynamics of metal-to-ligand charge transfer (MLCT) and metal-centered (MC) excited states is established. A rapid ground state recovery pathway is newly identified, representing a significant deactivation pathway during photocatalysis. Furthermore, the pseudotetrahedral structure of the long-lived MC excited state is unambiguously identified and refined by XSS. The results advance our understanding of the ultrafast relaxation mechanisms that impact the photocatalytic mechanism and yield for NiII-bipyridine aryl halide cross-coupling catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Exploring the Genetic Basis of Wild Boar ( Sus scrofa ) and Its Connection to Classical Swine Fever Spread

Classical swine fever (CSF) is the one of the most devastating contagious diseases in domestic swine and wild boar/pigs (Sus scrofa). Population genetics is often used to estimate animal dispersal and can also help evaluate host population connectivity, which is crucial for understanding pathogen dispersal. We surveyed genetic population structure of boars using MIG-seq analysis to clarify the geographic barriers that influence boar dispersal in north-central Japan and to demonstrate the relationship between the spread of CSF infection among boars and their population structure. We obtained 382 single-nucleotide polymorphisms from 348 wild boar samples, and the results of STRUCTURE analysis indicated that the highest ΔK value was at K = 2, followed by K = 4. Based on these results, it is evident that the Abukuma river, a major river within north-central Japan, does not act as a barrier to the gene flow of boars, but rather that human infrastructure hinders their dispersal. Further, according to the time series change in the capture site of CSF-infected wild boar and the sum of the probability of belonging to each of the four clades in individual CSF-infected wild boar, our results indicated that the genetic structure of boar populations was correlated with the outbreak pathway of CSF across our study region. Our study suggests that predictions of disease spread, especially for widely distributed host species, is challenging because of the risk of cryptic breaks and changes in wide range connectivity; however, understanding the genetic population structure of wild boar can be a useful tool for predicting the spread of CSF. We concluded that genetic analysis of host population structure may have the possibility to improve predictions of the future dynamics of disease spread.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

An integrated integral projection model ( IPM 2 ) to disentangle size‐structured harvest and natural mortality

Abstract Body size is one of the most important traits governing individual‐level demographic rates and modulating population‐level processes. Multiple size‐dependent demographic rates can simultaneously change population structure, so distinguishing their individual contributions to overall population dynamics remains a challenge. Disentangling size‐dependent harvest rates from other demographic rates is critical for assessing the impact of removal on populations of invasive species. Inference about invasive populations can be difficult, however, as observations are often collected opportunistically as part of removal programs, rather than experimentally designed. Yet accurate inference is essential for understanding the feasibility of population suppression and optimising management decisions. We develop an integrated integral projection model (IPM 2 ) that leverages the strengths of the integrated population model and integral projection model to enable inference about complex, size‐structured demographic rates from imperfect observations. We apply the IPM 2 in the context of invasive European green crab ( Carcinus maenas ), a species for which individual body size strongly regulates both the observation‐generating process and latent, population dynamics. The IPM 2 facilitates the distinct estimation of green crab size‐structured harvest and natural mortality rates, parameters for which no explicit data is collected and that are unidentifiable in component datasets of the integrated population model. The model represents how the green crab population changes over time, providing the first estimates of size‐structured abundance of this high‐priority species. By forecasting the stable size distribution and equilibrium population size under varying removal efforts, we demonstrate that extremely high levels of removal effort can reduce the equilibrium green crab population size. Yet these high mortality rates also shift the stable size distribution and increase the equilibrium abundance of smaller crabs, since size‐selective removal alters intraspecific interactions. The ecological outcome of this shift in size structure will be variable, as green crab size modulates only some of its interactions with other species. These results highlight the value of the IPM 2 framework for inferring complex population dynamics with information needs that outpace information in individual observational datasets, providing a path forward for accurate assessment of conservation programs.

Keller, Abigail G. [Department of Environment Scie↗
DOE OSTI2025

Virulence and Genetic Diversity of Puccinia spp., Causal Agents of Rust on Switchgrass (Panicum virgatum L.) in the USA

Switchgrass (Panicum virgatum L.) is an important cellulosic biofuel grass native to North America. Rust, caused by Puccinia spp. is the most predominant disease of switchgrass and has the potential to impact biomass conversion. In this study, virulence patterns were determined on a set of 38 switchgrass genotypes for 14 single-spore rust isolates from 14 field samples collected in seven states. Single nucleotide polymorphism (SNP) variation was also assessed in 720 sequenced cloned amplicons representing 654 base pairs of the elongation factor 1-α gene from the field samples. Five major haplotypes were identified differing by 11 out of the 39 SNP positions identified. STRUCTURE, Principal Coordinate Analysis, and phylogenetic analyses divided the rust population into two genetic clusters. Virginia and Georgia had the highest and lowest rust genetic diversity, respectively. Only nine accessions showed a differential disease response between the 14 isolates, allowing the identification of eight races, differing by 1–3 virulence factors. Overall, the results suggested clonal reproduction of the pathogen and a North–South differentiation via local adaptation. However, similar haplotypes and races were also recovered from several states, suggesting migration events, and highlighting the need to further investigate the switchgrass rust population structure and evolution in the USA.

Bahri, Bochra A. (ORCID:0000000159055880)↗
DOE OSTI2026

Global divergence in urban demographic change and migration patterns

Cities are central to economic development, climate adaptation and social stability, yet globally consistent evidence on how city populations are changing remains limited. Here we analyze annual age- and sex-structured population estimates for more than 10,000 cities worldwide from 2000 to 2020 and show that urban demographic change was highly uneven. Globally, the ratio of children and older adults to working-age adults declined from 0.87 to 0.59, but smaller cities remained consistently younger than larger cities, especially in Africa. We also find pronounced spatial variation in urban sex ratios, including strong male surpluses in parts of the Middle East and North Africa, consistent with patterns of labor migration. Finally, we estimate that 45% of urban population growth was attributable to net migration and 55% to natural increase. These results show that national averages can obscure substantial differences between cities, and highlight the value of globally consistent city-level demographic estimates for understanding regional demographic change and informing locally tailored urban planning.

development studies↗
DOE OSTI2023

The first two chromosome‐scale genome assemblies of American hazelnut enable comparative genomic analysis of the genus Corylus

Summary The native, perennial shrub American hazelnut ( Corylus americana ) is cultivated in the Midwestern United States for its significant ecological benefits, as well as its high‐value nut crop. Implementation of modern breeding methods and quantitative genetic analyses of C. americana requires high‐quality reference genomes, a resource that is currently lacking. We therefore developed the first chromosome‐scale assemblies for this species using the accessions ‘Rush’ and ‘Winkler’. Genomes were assembled using HiFi PacBio reads and Arima Hi‐C data, and Oxford Nanopore reads and a high‐density genetic map were used to perform error correction. N50 scores are 31.9 Mb and 35.3 Mb, with 90.2% and 97.1% of the total genome assembled into the 11 pseudomolecules, for ‘Rush’ and ‘Winkler’, respectively. Gene prediction was performed using custom RNAseq libraries and protein homology data. ‘Rush’ has a BUSCO score of 99.0 for its assembly and 99.0 for its annotation, while ‘Winkler’ had corresponding scores of 96.9 and 96.5, indicating high‐quality assemblies. These two independent assemblies enable unbiased assessment of structural variation within C. americana , as well as patterns of syntenic relationships across the Corylus genus. Furthermore, we identified high‐density SNP marker sets from genotyping‐by‐sequencing data using 1343 C. americana , C. avellana and C. americana × C. avellana hybrids, in order to assess population structure in natural and breeding populations. Finally, the transcriptomes of these assemblies, as well as several other recently published Corylus genomes, were utilized to perform phylogenetic analysis of sporophytic self‐incompatibility (SSI) in hazelnut, providing evidence of unique molecular pathways governing self‐incompatibility in Corylus .

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Population assignment of migratory Westslope Cutthroat Trout (WCT) in the Clark Fork–Pend Oreille River basin

Abstract Objective The Clark Fork–Pend Oreille River basin of northeastern Washington and the Idaho Panhandle historically supported a robust metapopulation of the Westslope Cutthroat Trout (WCT) Oncorhynchus lewisi, a western native salmonid of high cultural and economic value. The construction of impassible hydroelectric dams and smaller instream barriers has prevented the return of migratory WCT to spawning tributaries, leading to the fragmentation of this metapopulation over the past 100 years. One such impassible barrier is Albeni Falls Dam (AFD) near Newport, Washington, which was completed without fish passage capabilities in 1955. We sought to examine large-scale genetic patterns in the study area and determine the most likely spawning tributary of origin for migratory WCT captured below AFD. Methods We created a genetic baseline representative of populations within the Clark Fork–Pend Oreille River basin from upstream and downstream of the dam using 191 biallelic single-nucleotide polymorphism genetic markers. Our data set included 124 collections, which allowed for an examination of population structure and hatchery influence across the study area and provided a robust tool for population assignment. Population assignment tests were conducted using the program RUBIAS. Result Population assignment tests were successful for all pure WCT of unknown origin despite potential influence from hatchery lineages across the study area. Of 83 migratory WCT captured below AFD, approximately 80% were assigned to tributaries upstream of AFD with a posterior assignment probability of at least 90%. Only one fish was assigned to a tributary downstream of AFD. Conclusion Our results indicate that AFD disrupts the natural metapopulation dynamics of WCT populations in the basin. Passage for WCT at this barrier would reestablish metapopulation connectivity within the basin by allowing migratory individuals to make genetic contributions to populations upstream of the dam.

Wells, Craig D. (ORCID:0000000258513250)↗
DOE OSTI2023

A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera)

Abstract Macrocystis pyrifera (giant kelp), is a brown macroalga of great ecological importance as a primary producer and structure-forming foundational species that provides habitat for hundreds of species. It has many commercial uses (e.g. source of alginate, fertilizer, cosmetics, feedstock). One of the limitations to exploiting giant kelp’s economic potential and assisting in giant kelp conservation efforts is a lack of genomic tools like a high quality, contiguous reference genome with accurate gene annotations. Reference genomes attempt to capture the complete genomic sequence of an individual or species, and importantly provide a universal structure for comparison across a multitude of genetic experiments, both within and between species. We assembled the giant kelp genome of a haploid female gametophyte de novo using PacBio reads, then ordered contigs into chromosome level scaffolds using Hi-C. We found the giant kelp genome to be 537 MB, with a total of 35 scaffolds and 188 contigs. The assembly N50 is 13,669,674 with GC content of 50.37%. We assessed the genome completeness using BUSCO, and found giant kelp contained 94% of the BUSCO genes from the stramenopile clade. Annotation of the giant kelp genome revealed 25,919 genes. Additionally, we present genetic variation data based on 48 diploid giant kelp sporophytes from three different Southern California populations that confirms the population structure found in other studies of these populations. This work resulted in a high-quality giant kelp genome that greatly increases the genetic knowledge of this ecologically and economically vital species.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Demographic and genetic consequences of a steelhead supplementation program

Abstract Objective Supplementation of naturally spawning populations by the addition of hatchery-spawned individuals is commonly conducted for recovery of threatened and endangered populations and to support harvest opportunities. Our objective was to evaluate whether the use of a juvenile captive broodstock and an integrated paradigm could increase returns of steelhead, the anadromous form of Rainbow Trout Oncorhynchus mykiss, while avoiding negative genetic impacts commonly associated with hatchery propagation. Methods We analyzed 291 genetic markers in adult steelhead returning to an integrated population in southwest Washington over the course of 15 years. Reproductive success (RS) of fish spawning in the natural environment was evaluated by origin (hatchery versus natural) and return year. Data were then pooled over years to maximize sample sizes for comparing RS estimates among groups (i.e., estimation of relative reproductive success [RRS]). Result We observed a weak relationship between RS and origin (male p = 0.347; female p = 0.066), but a significant relationship between RS and return year (male p < 0.001, η2 = 0.896; female p ⟨ 0.001, η2 = 0.867) (i.e., hatchery- and natural-origin fish did well or poorly together each year). Estimates of RRS for fish spawned in the hatchery ranged from 2.4 to 6.4, indicating that fish spawned in the hatchery produced more returning adult progeny than did fish allowed to spawn in the natural environment. Estimates of RRS were ⟨1.0 for hatchery-origin fish spawning in the natural environment, but the difference was nonsignificant for males and marginally significant for females. Hatchery-origin fish exhibited reduced genetic diversity as well as evidence of increased temporal population structure. Conclusion We conclude that the program was successful in achieving an increase in adult returns but not in avoiding negative genetic effects on the population and that any lasting impacts of supplementation remain to be determined.

Smith, Christian T. (ORCID:0000000240522669)↗