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All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Ecological connectivity and habitat loss shape patterns of genetic diversity in a threatened salamander

Context The maintenance of genetic diversity is essential for preserving adaptive potential in populations, yet it is increasingly threatened by landscape alteration. The field of landscape genetics offers a framework for assessing how patch-level landscape conditions, modeled at multiple scales, influence genetic diversity. Objectives We sought to assess how local environmental features and connectivity influence genetic diversity across 74 four-toed salamander (Hemidactylium scutatum) breeding wetlands in the southeastern United States. Methods Using next-generation sequencing data and hierarchical Bayesian models, we examined genome-wide heterozygosity in relation to local landscape features and ecological connectivity. We also assessed the scale of effect of landscape features and tested for temporal lag effects. Results Genetic diversity was lower in wetlands with higher levels of historic deforestation and lower connectivity. An interaction between deforestation and connectivity indicated that deforestation had stronger negative effects in isolated wetlands but weaker effects in well-connected wetlands. Accounting for scale of effect and temporal lags was critical for detecting these relationships. Conclusions Our analyses highlight the importance of assessing the spatial scale (scale of effect) and temporal lag of landscape features to detect key drivers of genetic diversity. In line with population genetic theory, our results indicate that the genetic consequences of habitat loss do not affect populations uniformly and are most severe in isolated populations where gene flow cannot buffer against loss of diversity. Altogether, we highlight the importance of considering the interaction of habitat loss and connectivity in conservation genetic management.

Hemidactylium scutatum↗
NASA NTRS2002

Atm heterozygous mice are more sensitive to radiation-induced cataracts than are their wild-type counterparts

It is important to know whether the human population includes genetically predisposed radiosensitive subsets. In vitro studies have shown that cells from individuals homozygous for ataxia telangiectasia (A-T) are much more radiosensitive than cells from unaffected individuals. Although cells heterozygous for the ATM gene (ATM(+/-)) may be slightly more radiosensitive in vitro, it remained to be determined whether the greater susceptibility of ATM(+/-) cells translates into an increased sensitivity for late effects in vivo, though there is a suggestion that radiotherapy patients that are heterozygous for the ATM gene may be more at risk of developing late normal tissue damage. We chose cataractogenesis in the lens as a means to assay for the effects of ATM deficiency in a late-responding tissue. One eye of wild-type, Atm heterozygous and homozygous knockout mice was exposed to 0.5-, 1.0-, 2.0-, or 4.0-Gy x rays. The animals were followed weekly for cataract development by conventional slit-lamp biomicroscopy. Cataract development in the animals of all three groups was strongly dependent on dose. The lenses of homozygous mice were the first to opacify at any given dose. Most important in the present context is that cataracts appeared earlier in the heterozygous versus wild-type animals. The data suggest that ATM heterozygotes in the human population may also be radiosensitive. This may influence the choice of individuals destined to be exposed to higher than normal doses of radiation, such as astronauts, and may also suggest that radiotherapy patients who are ATM heterozygotes could be predisposed to increased late normal tissue damage.

Non-NASA Center↗
DOE OSTI2026

Ornamental origins and genomic frontiers: a review of big-bracted dogwood research

The big-bracted (Benthamidia) dogwood clade consists of small- to medium-sized deciduous trees within the genus Cornus, known for their showy spring-time floral bract display. Cornus is within the family Cornaceae and order Cornales, and as Cornales is one of the earliest diverging asterids, these taxa have been important for phylogenetic research. Three species within the big-bracted clade, flowering (Cornus florida), kousa (C. kousa), and Pacific (C. nuttallii) dogwoods, are popular ornamental landscape plants in North America, with more than 130 cultivars released. Despite their commercial popularity, numerous research gaps have limited the expansion of fundamental research and dogwood breeding programs. In this present review, we aim to provide a thorough overview of our current understanding of 1) the phylogenetic and biogeographic context, 2) plant biology and major pests and pathogens impacting commercialization, 3) historical commercialization and propagation methods, and 4) genetic and genomic resources and how they have been implemented to understand these species. Research gaps and future directions to advance basic research and breeding of big-bracted ornamental dogwoods are discussed throughout.

Cornus florida↗
DOE OSTI2023

Lower viral evolutionary pressure under stable versus fluctuating conditions in subzero Arctic brines

Climate change threatens Earth’s ice-based ecosystems which currently offer archives and eco-evolutionary experiments in the extreme. Arctic cryopeg brine (marine-derived, within permafrost) and sea ice brine, similar in subzero temperature and high salinity but different in temporal stability, are inhabited by microbes adapted to these extreme conditions. However, little is known about their viruses (community composition, diversity, interaction with hosts, or evolution) or how they might respond to geologically stable cryopeg versus fluctuating sea ice conditions. We used long- and short-read viromics and metatranscriptomics to study viruses in Arctic cryopeg brine, sea ice brine, and underlying seawater, recovering 11,088 vOTUs (~species-level taxonomic unit), a 4.4-fold increase of known viruses in these brines. More specifically, the long-read-powered viromes doubled the number of longer (≥25 kb) vOTUs generated and recovered more hypervariable regions by >5-fold compared to short-read viromes. Distribution assessment, by comparing to known viruses in public databases, supported that cryopeg brine viruses were of marine origin yet distinct from either sea ice brine or seawater viruses, while 94% of sea ice brine viruses were also present in seawater. A virus-encoded, ecologically important exopolysaccharide biosynthesis gene was identified, and many viruses (~half of metatranscriptome-inferred “active” vOTUs) were predicted as actively infecting the dominant microbial genera Marinobacter and Polaribacter in cryopeg and sea ice brines, respectively. Evolutionarily, microdiversity (intra-species genetic variations) analyses suggested that viruses within the stable cryopeg brine were under significantly lower evolutionary pressures than those in the fluctuating sea ice environment, while many sea ice brine virus-tail genes were under positive selection, indicating virus-host co-evolutionary arms races. Our results confirmed the benefits of long-read-powered viromics in understanding the environmental virosphere through significantly improved genomic recovery, expanding viral discovery and the potential for biological inference. Evidence of viruses actively infecting the dominant microbes in subzero brines and modulating host metabolism underscored the potential impact of viruses on these remote and underexplored extreme ecosystems. Microdiversity results shed light on different strategies viruses use to evolve and adapt when extreme conditions are stable versus fluctuating. Together, these findings verify the value of long-read-powered viromics and provide foundational data on viral evolution and virus-microbe interactions in Earth’s destabilized and rapidly disappearing cryosphere.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Abundance and Migration Success of Overshoot Steelhead in the Upper Columbia River

Abstract Summer steelhead Oncorhynchus mykiss may enter freshwater almost a year before spawning and potentially make long migrations (>1,000 km) to interior headwater habitats. However, in response to suboptimal freshwater habitat conditions (e.g., warmer water temperatures), adult summer steelhead may exhibit complex behaviors during upstream migration in the Columbia River basin. Steelhead may migrate upstream of their natal tributary (hereafter, referred to as “overshoot”) and spend days to several months before subsequently migrating downstream (hereafter, referred to as “fallback”) to their natal tributary to spawn. An expansion of an existing Bayesian patch occupancy model, derived from observations of adult steelhead that were PIT-tagged to estimate population-specific abundance upstream of the tagging location, incorporated downstream detection locations to estimate the abundance of overshoot fallbacks. Overshoot steelhead abundance at the tagging location was estimated based on the relationship between the number of known overshoot fallbacks (i.e., the number of steelhead that overshot and successfully migrated downstream to their natal tributary) and their model-estimated abundance. During the study period (2010–2017), the annual mean proportion of overshoot steelhead that successfully migrated downstream of the tagging location (Priest Rapids Dam) was 0.59 (SD = 0.14). The number of dams encountered by overshoot steelhead during their downstream migration was negatively correlated with their downstream migration success probability. Improved downstream passage survival for adult steelhead will increase the abundance of affected populations while reducing potential genetic introgression of upstream populations (i.e., strays). This is the first study to estimate the abundance of overshoot and fallback steelhead, providing the data necessary for scientists to estimate potential conservation benefits of improved downstream survival. For example, surface flow passage routes (e.g., sluiceways and temporary spillway weirs) are very effective in guiding and passing adult steelhead downstream of Columbia River hydroelectric projects and data from this assessment show that changes in dam operations throughout the downstream migration period may maximize conservation benefits.

Murdoch, Andrew R. (ORCID:0000000324827689)↗
DOE OSTI2021

Genomic variation within the maize stiff-stalk heterotic germplasm pool

The stiff-stalk heterotic group in Maize (Zea mays L.) is an important source of inbreds used in U.S. commercial hybrid production. Founder inbreds B14, B37, B73, and, to a lesser extent, B84, are found in the pedigrees of a majority of commercial seed parent inbred lines. We created high-quality genome assemblies of B84 and four expired Plant Variety Protection (ex-PVP) lines LH145 representing B14, NKH8431 of mixed descent, PHB47 representing B37, and PHJ40, which is a Pioneer Hi-Bred International (PHI) early stiff-stalk type. Sequence was generated using long-read sequencing achieving highly contiguous assemblies of 2.13-2.18 Gbp with N50 scaffold lengths >200 Mbp. Inbred-specific gene annotations were generated using a core five-tissue gene expression atlas, whereas transposable element (TE) annotation was conducted using de novo and homology-directed methodologies. Compared with the reference inbred B73, synteny analyses revealed extensive collinearity across the five stiff-stalk genomes, although unique components of the maize pangenome were detected. Comparison of this set of stiff-stalk inbreds with the original Iowa Stiff Stalk Synthetic breeding population revealed that these inbreds represent only a proportion of variation in the original stiff-stalk pool and there are highly conserved haplotypes in released public and ex-Plant Variety Protection inbreds. Despite the reduction in variation from the original stiff-stalk population, substantial genetic and genomic variation was identified supporting the potential for continued breeding success in this pool. The assemblies described here represent stiff-stalk inbreds that have historical and commercial relevance and provide further insight into the emerging maize pangenome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Assembly and comparative genome analysis of a Patagonian Aureobasidium pullulans isolate reveals unexpected intraspecific variation

Aureobasidium pullulans is a yeast-like fungus with remarkable phenotypic plasticity widely studied for its importance for the pharmaceutical and food industries. So far, genomic studies with strains from all over the world suggest they constitute a genetically unstructured population, with no association by habitat. However, the mechanisms by which this genome supports so many phenotypic permutations are still poorly understood. Recent works have shown the importance of sequencing yeast genomes from extreme environments to increase the repertoire of phenotypic diversity of unconventional yeasts. In this study, we present the genomic draft of A. pullulans strain from a Patagonian yeast diversity hotspot, re-evaluate its taxonomic classification based on taxogenomic approaches, and annotate its genome with high-depth transcriptomic data. Here, our analysis suggests this isolate could be considered a novel variant at an early stage of the speciation process. The discovery of divergent strains in a genomically homogeneous group, such as A. pullulans, can be valuable in understanding the evolution of the species. The identification and characterization of new variants will not only allow finding unique traits of biotechnological importance, but also optimize the choice of strains whose phenotypes will be characterized, providing new elements to explore questions about plasticity and adaptation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Experimental evolution reveals nitrate tolerance mechanisms in Desulfovibrio vulgaris

Elevated nitrate in the environment inhibits sulfate reduction by important microorganisms of sulfate-reducing bacteria (SRB). Several SRB may respire nitrate to survive under elevated nitrate, but how SRB that lack nitrate reductase survive to elevated nitrate remains elusive. To understand nitrate adaptation mechanisms, we evolved 12 populations of a model SRB (i.e., Desulfovibrio vulgaris Hildenborough, DvH) under elevated NaNO 3 for 1000 generations, analyzed growth and acquired mutations, and linked their genotypes with phenotypes. Nitrate-evolved (EN) populations significantly (p < 0.05) increased nitrate tolerance, and whole-genome resequencing identified 119 new mutations in 44 genes of 12 EN populations, among which six functional gene groups were discovered with high mutation frequencies at the population level. In this work, we observed a high frequency of nonsense or frameshift mutations in nitrosative stress response genes (NSR: DVU2543, DVU2547, and DVU2548), nitrogen regulatory protein C family genes (NRC: DVU2394-2396, DVU2402, and DVU2405), and nitrate cluster (DVU0246-0249 and DVU0251). Mutagenesis analysis confirmed that loss-of-functions of NRC and NSR increased nitrate tolerance. Also, functional gene groups involved in fatty acid synthesis, iron regulation, and two-component system (LytR/LytS) known to be responsive to multiple stresses, had a high frequency of missense mutations. Additionally, mutations in those gene groups could increase nitrate tolerance through regulating energy metabolism, barring entry of nitrate into cells, altering cell membrane characteristics, or conferring growth advantages at the stationary phase. This study advances our understanding of nitrate tolerance mechanisms and has important implications for linking genotypes with phenotypes in DvH.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Synergistic epistasis enhances the co-operativity of mutualistic interspecies interactions

Abstract Early evolution of mutualism is characterized by big and predictable adaptive changes, including the specialization of interacting partners, such as through deleterious mutations in genes not required for metabolic cross-feeding. We sought to investigate whether these early mutations improve cooperativity by manifesting in synergistic epistasis between genomes of the mutually interacting species. Specifically, we have characterized evolutionary trajectories of syntrophic interactions of Desulfovibrio vulgaris (Dv) with Methanococcus maripaludis (Mm) by longitudinally monitoring mutations accumulated over 1000 generations of nine independently evolved communities with analysis of the genotypic structure of one community down to the single-cell level. We discovered extensive parallelism across communities despite considerable variance in their evolutionary trajectories and the perseverance within many evolution lines of a rare lineage of Dv that retained sulfate-respiration (SR+) capability, which is not required for metabolic cross-feeding. An in-depth investigation revealed that synergistic epistasis across pairings of Dv and Mm genotypes had enhanced cooperativity within SR− and SR+ assemblages, enabling their coexistence within the same community. Thus, our findings demonstrate that cooperativity of a mutualism can improve through synergistic epistasis between genomes of the interacting species, enabling the coexistence of mutualistic assemblages of generalists and their specialized variants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Estimating the strength of selection for new SARS-CoV-2 variants

Abstract Controlling the SARS-CoV-2 pandemic becomes increasingly challenging as the virus adapts to human hosts through the continual emergence of more transmissible variants. Simply observing that a variant is increasing in frequency is relatively straightforward, but more sophisticated methodology is needed to determine whether a new variant is a global threat and the magnitude of its selective advantage. We present two models for quantifying the strength of selection for new and emerging variants of SARS-CoV-2 relative to the background of contemporaneous variants. These methods range from a detailed model of dynamics within one country to a broad analysis across all countries, and they include alternative explanations such as migration and drift. We find evidence for strong selection favoring the D614G spike mutation and B.1.1.7 (Alpha), weaker selection favoring B.1.351 (Beta), and no advantage of R.1 after it spreads beyond Japan. Cutting back data to earlier time horizons reveals that uncertainty is large very soon after emergence, but that estimates of selection stabilize after several weeks. Our results also show substantial heterogeneity among countries, demonstrating the need for a truly global perspective on the molecular epidemiology of SARS-CoV-2.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina)

Currents are unique drivers of oceanic phylogeography and thus determine the distribution of marine coastal species, along with past glaciations and sea-level changes. Here we reconstruct the worldwide colonization history of eelgrass (Zostera marina L.), the most widely distributed marine flowering plant or seagrass from its origin in the Northwest Pacific, based on nuclear and chloroplast genomes. We identified two divergent Pacific clades with evidence for admixture along the East Pacific coast. Two west-to-east (trans-Pacific) colonization events support the key role of the North Pacific Current. Time-calibrated nuclear and chloroplast phylogenies yielded concordant estimates of the arrival of Z. marina in the Atlantic through the Canadian Arctic, suggesting that eelgrass-based ecosystems, hotspots of biodiversity and carbon sequestration, have only been present there for ~243 ky (thousand years). Mediterranean populations were founded ~44 kya, while extant distributions along western and eastern Atlantic shores were founded at the end of the Last Glacial Maximum (~19 kya), with at least one major refuge being the North Carolina region. The recent colonization and five- to sevenfold lower genomic diversity of the Atlantic compared to the Pacific populations raises concern and opportunity about how Atlantic eelgrass might respond to rapidly warming coastal oceans.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

The Number and Pattern of Viral Genomic Reassortments are not Necessarily Identifiable from Segment Trees

Reassortment is an evolutionary process common in viruses with segmented genomes. These viruses can swap whole genomic segments during cellular co-infection, giving rise to novel progeny formed from the mixture of parental segments. Since large-scale genome rearrangements have the potential to generate new phenotypes, reassortment is important to both evolutionary biology and public health research. However, statistical inference of the pattern of reassortment events from phylogenetic data is exceptionally difficult, potentially involving inference of general graphs in which individual segment trees are embedded. In this paper, we argue that, in general, the number and pattern of reassortment events are not identifiable from segment trees alone, even with theoretically ideal data. We call this fact the fundamental problem of reassortment, which we illustrate using the concept of the “first-infection tree,” a potentially counterfactual genealogy that would have been observed in the segment trees had no reassortment occurred. Further, we illustrate four additional problems that can arise logically in the inference of reassortment events and show, using simulated data, that these problems are not rare and can potentially distort our observation of reassortment even in small data sets. Finally, we discuss how existing methods can be augmented or adapted to account for not only the fundamental problem of reassortment, but also the four additional situations that can complicate the inference of reassortment.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1982

Cloning higher plants from aseptically cultured tissues and cells

A review of aseptic culture methods for higher plants is presented, which focuses on the existing problems that limit or prevent the full realization of cloning plants from free cells. It is shown that substantial progress in clonal multiplication has been made with explanted stem tips or lateral buds which can be stimulated to produce numerous precocious axillary branches. These branches can then be separated or subdivided and induced to root in order to yield populations of genetically and phenotypically uniorm plantlets. Similarly, undifferentiated calluses can sometimes be induced to form shoots and/or roots adventitiously. Although the cell culture techniques required to produce somatic embryos are presently rudimentary, steady advances are being made in learning how to stimulate formation of somatic or adventive embryos from totipotent cells grown in suspension cultures. It is concluded that many problems exist in the producing and growing of totipotent or morphogenetically competent cell suspensions, but the potential benefits are great.

Krikorian, A. D.↗
NASA NTRS1993

Chromite-rich mafic silicate chondrules in ordinary chondrites: Formation by impact melting

Chromium-rich chondrules constitute less than 0.1 percent of all ordinary chondrite (OC) chondrules and comprise three groups: chromian-spinel chondrules, chromian-spinel inclusions, and chromite-rich mafic silicate (CRMS) chondrules. Chromian-spinel chondrules (typically 100-300 microns in apparent diameter) exhibit granular, porphyritic and unusual textures and occur mainly in H chondrites. Their morphologies are distinct from the irregularly shaped chromian-spinel inclusions of similar mineralogy. Chromian-spinel chondrules and inclusions consist of grains of chromian-spinel embedded in plagioclase (Pl) or mesostasis of Pl composition. Many also contain accessory ilmenite (Ilm), high-Ca pyroxene (Px), merrillite (Mer), and rare olivine (Ol); some exhibit concentric mineral and chemical zoning. CRMS chondrules (300-1100 microns in apparent diameter) are generally larger than chromian-spinel chondrules and occur in all metamorphosed OC groups. Most CRMS chondrules are nearly spherical although a few are ellipsoidal with a/b aspect ratios ranging up to 1.7. Textures include cryptocrystalline, granular, radial, barred, and porphyritic varieties; some contain apparently relict grains. The chondrules consist of chromite (Chr), Ol and Pl, along with accessory Mer, troilite (Tr), metallic Fe-Ni (Met), Px and Ilm. The mesostasis in CRMS chondrules is nearly opaque in transmitted light; thus, they can be easily recognized in the optical microscope. Based on the similarity of mineralogy and chemistry between CRMS chondrules of different textures (opaque chromite-rich mesostasis, skeletal morphology of Ol grains, similar bulk compositions) we suggest that these chondrules form a genetically related population.

Krot, Alexander N.↗
NASA NTRS2002

Supercomputing 2002: NAS Demo Abstracts

The hyperwall is a new concept in visual supercomputing, conceived and developed by the NAS Exploratory Computing Group. The hyperwall will allow simultaneous and coordinated visualization and interaction of an array of processes, such as a the computations of a parameter study or the parallel evolutions of a genetic algorithm population. Making over 65 million pixels available to the user, the hyperwall will enable and elicit qualitatively new ways of leveraging computers to accomplish science. It is currently still unclear whether we will be able to transport the hyperwall to SC02. The crucial display frame still has not been completed by the metal fabrication shop, although they promised an August delivery. Also, we are still working the fragile node issue, which may require transplantation of the compute nodes from the present 2U cases into 3U cases. This modification will increase the present 3-rack configuration to 5 racks.

Parks, John↗
DOE OSTI2021

Population genomics provides insights into the genetic basis of adaptive evolution in the mushroom-forming fungus Lentinula edodes

Introduction: Mushroom-forming fungi comprise diverse species that develop complex multicellular structures. In cultivated species, both ecological adaptation and artificial selection have driven genome evolution. However, little is known about the connections among genotype, phenotype and adaptation in mushroom-forming fungi. Objectives: This study aimed to (1) uncover the population structure and demographic history of Lentinula edodes, (2) dissect the genetic basis of adaptive evolution in L. edodes, and (3) determine if genes related to fruiting body development are involved in adaptive evolution. Methods: We analyzed genomes and fruiting body-related traits (FBRTs) in 133 L. edodes strains and conducted RNA-seq analysis of fruiting body development in the YS69 strain. Combined methods of genomic scan for divergence, genome-wide association studies (GWAS), and RNA-seq were used to dissect the genetic basis of adaptive evolution. Results: We detected three distinct subgroups of L. edodes via single nucleotide polymorphisms, which showed robust phenotypic and temperature response differentiation and correlation with geographical distribution. Demographic history inference suggests that the subgroups diverged 36,871 generations ago. Moreover, L. edodes cultivars in China may have originated from the vicinity of Northeast China. A total of 942 genes were found to be related to genetic divergence by genomic scan, and 719 genes were identified to be candidates underlying FBRTs by GWAS. Integrating results of genomic scan and GWAS, 80 genes were detected to be related to phenotypic differentiation. A total of 364 genes related to fruiting body development were involved in genetic divergence and phenotypic differentiation. Conclusion: Adaptation to the local environment, especially temperature, triggered genetic divergence and phenotypic differentiation of L. edodes. A general model for genetic divergence and phenotypic differentiation during adaptive evolution in L. edodes, which involves in signal perception and transduction, transcriptional regulation, and fruiting body morphogenesis, was also integrated here.

59 BASIC BIOLOGICAL SCIENCES↗