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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Population Genetics of Sugar Kelp Throughout the Northeastern United States Using Genome-Wide Markers

An assessment of genetic diversity of marine populations is critical not only for the understanding and preserving natural biodiversity but also for its commercial potential. As commercial demand rises for marine resources, it is critical to generate baseline information for monitoring wild populations. Furthermore, anthropogenic stressors on the coastal environment, such as warming sea temperatures and overharvesting of wild populations, are leading to the destruction of keystone marine species such as kelps. In this study, we conducted a fine-scale genetic analysis using genome-wide high-density markers on Northwest Atlantic sugar kelp. The population structure for a total of 149 samples from the Gulf of Maine (GOM) and Southern New England (SNE) was investigated using AMOVA, FST, admixture, and PCoA. Genome-wide association analyses were conducted for six morphological traits, and the extended Lewontin and Krakauer (FLK) test was used to detect selection signatures. Our results indicate that the GOM region is more heterogeneous than SNE. These two regions have large genetic difference (between-location FST ranged from 0.21 to 0.32) and were separated by Cape Cod, which is known to be the biogeographic barrier for other taxa. We detected one significant SNP (P = 2.03 × 10 -7 ) associated with stipe length, and 248 SNPs with higher-than-neutral differentiation. The findings of this study provide baseline knowledge on sugar kelp population genetics for future monitoring, managing and potentially restoring wild populations, as well as assisting in selective breeding to improve desirable traits for future commercialization opportunities.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Range-wide population assessments for subalpine fir indicate widespread disturbance-driven decline

Subalpine forests in western North America are threatened by rapid climate change, increased activity by endemic and exotic insects and diseases, and changing wildfire regimes. The interactive effects of these stressors have resulted in pronounced population declines in many subalpine tree species; however, a systematic assessment of the status and trends of subalpine forests is lacking. Subalpine fir (Abies lasiocarpa) is a widespread species across the western United States, with documented population declines in many parts of its distribution. Here we use subalpine fir as an initial leverage point to build a more complete understanding of subalpine forest baseline conditions and responses to environmental change. Specifically, we leverage the USDA Forest Service Forest Inventory and Analysis (FIA) database to (1) ask how subalpine fir populations are changing across the species’ distribution in the western US, (2) assess the drivers of recent subalpine fir population trends, and (3) explore whether those changes imply generalized species-wide and/or system-wide decline. We found that subalpine fir abundance and basal area are declining concurrently across ~ 62% of the species’ distribution, and increasing across ~ 19%. Range-wide, we estimated 25.02 ± 2.74 % subalpine fir mortality between 2000 and 2009 and 2010–2019 FIA inventory periods, with higher mortality concentrated in the eastern Oregon Cascades, central Idaho, and parts of southern Colorado. High regeneration density did not predict positive population trajectories, which were instead associated with higher rates of adult recruitment. While the importance of different mortality agents varied substantially between ecoregions, 83.4% of total range-wide mortality was related to fire or biological disturbance. Declining subalpine fir basal area coincided with declines in the basal area of other co-occurring tree species in 39% of subalpine forest area, and with increases in conspecific basal area in 22% of forest area. Fire disturbance was the single largest cause of subalpine fir mortality; however, even where subalpine fir fire mortality was high, mortality among other species was primarily caused by insects. In conclusion, our results suggest that subalpine fir declines across large portions of the western United States are driven by forest disturbance, and that declines in subalpine fir populations may be indicative of negative change in subalpine forest systems broadly.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Dissecting the dominant hot spring microbial populations based on community-wide sampling at single-cell genomic resolution

With advances in DNA sequencing and miniaturized molecular biology workflows, rapid and affordable sequencing of single-cell genomes has become a reality. Compared to 16S rRNA gene surveys and shotgun metagenomics, large-scale application of single-cell genomics to whole microbial communities provides an integrated snapshot of community composition and function, directly links mobile elements to their hosts, and enables analysis of population heterogeneity of the dominant community members. To that end, we sequenced nearly 500 single-cell genomes from a low diversity hot spring sediment sample from Dewar Creek, British Columbia, and compared this approach to 16S rRNA gene amplicon and shotgun metagenomics applied to the same sample. We found that the broad taxonomic profiles were similar across the three sequencing approaches, though several lineages were missing from the 16S rRNA gene amplicon dataset, likely the result of primer mismatches. At the functional level, we detected a large array of mobile genetic elements present in the single-cell genomes but absent from the corresponding same species metagenome-assembled genomes. Moreover, we performed a single-cell population genomic analysis of the three most abundant community members, revealing differences in population structure based on mutation and recombination profiles. While the average pairwise nucleotide identities were similar across the dominant species-level lineages, we observed differences in the extent of recombination between these dominant populations. Most intriguingly, the creek's Hydrogenobacter sp. population appeared to be so recombinogenic that it more closely resembled a sexual species than a clonally evolving microbe. Together, this work demonstrates that a randomized single-cell approach can be useful for the exploration of previously uncultivated microbes from community composition to population structure.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Urban land patterns can moderate population exposures to climate extremes over the 21st century

Abstract Climate change and global urbanization have often been anticipated to increase future population exposure (frequency and intensity) to extreme weather over the coming decades. Here we examine how changes in urban land extent, population, and climate will respectively and collectively affect spatial patterns of future population exposures to climate extremes (including hot days, cold days, heavy rainfalls, and severe thunderstorm environments) across the continental U.S. at the end of the 21st century. Different from common impressions, we find that urban land patterns can sometimes reduce rather than increase population exposures to climate extremes, even heat extremes, and that spatial patterns instead of total quantities of urban land are more influential to population exposures. Our findings lead to preliminary suggestions for embedding long-term climate resilience in urban and regional land-use system designs, and strongly motivate searches for optimal spatial urban land patterns that can robustly moderate population exposures to climate extremes throughout the 21st century.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Population co-divergence in common cuttlefish (Sepia officinalis) and its dicyemid parasite in the Mediterranean Sea

Population structure and biogeography of marine organisms are formed by different drivers than in terrestrial organisms. Yet, very little information is available even for common marine organisms and even less for their associated parasites. Here we report the first analysis of population structure of both a cephalopod host ( Sepia officinalis ) and its dicyemid parasite, based on a homologous molecular marker (cytochrome oxidase I). We show that the population of common cuttlefish in the Mediterranean area is fragmented into subpopulations, with some areas featuring restricted level of gene flow. Amongst the studied areas, Sardinia was genetically the most diverse and Cyprus the most isolated. At a larger scale, across the Mediterranean, the population structure of the parasite shows co-diversification pattern with its host, but a slower rate of diversification. Differences between the two counterparts are more obvious at a finer scale, where parasite populations show increased level of fragmentation and lower local diversities. This discrepancy can be caused by local extinctions and replacements taking place more frequently in the dicyemid populations, due to their parasitic lifestyle.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Investigating the mixing between two black hole populations in LIGO-Virgo-KAGRA GWTC-3

Here, we introduce a population model to analyze the mixing between hypothesised power-law and ~ 35M ⊙ Gaussian bump black hole populations in the latest gravitational wave catalog, GWTC 3, estimating their co-location and separation. We find a relatively low level of mixing, $3.1^{+5.0}_{-3.1}$%, between the power-law and Gaussian populations, compared to the percentage of mergers containing two Gaussian bump black holes, $5.0^{+3.2}_{-1.7}$%. Our analysis indicates that black holes within the Gaussian bump are generally separate from the power-law population, with only a minor fraction engaging in mixing and contributing to the $\mathcal{M}$ ~ 14M ⊙ peak in the chirp mass. This leads us to identify a distinct population of Binary Gaussian Black Holes (BGBHs) that arise from mergers within the Gaussian bump. We suggest that current theories for the formation of the massive 35M ⊙ Gaussian bump population may need to reevaluate the underlying mechanisms that drive the preference for BGBHs.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Contrasting patterns of sequence variation in steelhead populations reflect distinct evolutionary processes

Abstract Multiple evolutionary processes influence genome‐wide allele frequencies and quantifying effects of genetic drift, and multiple forms of selection remain challenging in natural populations. Here, we investigate variation at major effect loci in contrast to patterns of neutral drift across a wide collection of steelhead ( Oncorhynchus mykiss ) populations that have declined in abundance due to anthropogenic impacts. Whole‐genome resequencing of 74 populations of steelhead revealed genome‐wide patterns (~8 million SNPs) consistent with expected neutral population structure. However, allelic variation at major effect loci associated with adult migration timing (chromosome 28: GREB1L / ROCK1 ) and age at maturity (chromosome 25: SIX6 ) reflected how selection has acted on phenotypic variation in contrast with neutral structure. Variation at major effect loci was influenced by evolutionary processes with differing signals between the strongly divergent Coastal and Inland lineages, while allele frequencies within and among populations within the Inland lineage have been driven by local natural selection as well as recent anthropogenic influences. Recent anthropogenic effects appeared to have influenced the frequency of major effect alleles including artificial selection for specific traits in hatchery stocks with subsequent gene flow into natural populations. Selection from environmental factors at various scales has also likely influenced variation for major effect alleles. These results reveal evolutionary mechanisms that influence allele frequencies at major effect loci that are critical for conservation of phenotypic traits and life history variation of this protected species.

Willis, Stuart↗
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 OSTI2025

Host population dynamics influence Leptospira spp. transmission patterns among Rattus norvegicus in Boston, Massachusetts, US

Leptospirosis (caused by pathogenic bacteria in the genus Leptospira ) is prevalent worldwide but more common in tropical and subtropical regions. Transmission can occur following direct exposure to infected urine from reservoir hosts, or a urine-contaminated environment, which then can serve as an infection source for additional rats and other mammals, including humans. The brown rat, Rattus norvegicus , is an important reservoir of Leptospira spp. in urban settings. We investigated the presence of Leptospira spp. among brown rats in Boston, Massachusetts and hypothesized that rat population dynamics in this urban setting influence the transportation, persistence, and diversity of Leptospira spp. We analyzed DNA from 328 rat kidney samples collected from 17 sites in Boston over a seven-year period (2016–2022); 59 rats representing 12 of 17 sites were positive for Leptospira spp. We used 21 neutral microsatellite loci to genotype 311 rats and utilized the resulting data to investigate genetic connectivity among sampling sites. We generated whole genome sequences for 28 Leptospira spp. isolates obtained from frozen and fresh tissue from some of the 59 positive rat kidneys. When isolates were not obtained, we attempted genomic DNA capture and enrichment, which yielded 14 additional Leptospira spp. genomes from rats. We also generated an enriched Leptospira spp. genome from a 2018 human case in Boston. We found evidence of high genetic structure among rat populations that is likely influenced by major roads and/or other dispersal barriers, resulting in distinct rat population groups within the city; at certain sites these groups persisted for multiple years. We identified multiple distinct phylogenetic clades of L. interrogans among rats that were tightly linked to distinct rat populations. This pattern suggests L. interrogans persists in local rat populations and its transportation is influenced by rat population dynamics. Finally, our genomic analyses of the Leptospira spp. detected in the 2018 human leptospirosis case in Boston suggests a link to rats as the source. These findings will be useful for guiding rat control and human leptospirosis mitigation efforts in this and other similar urban settings.

Stone, Nathan E.↗
DOE OSTI2022

Population Structure of White Sturgeon (Acipenser transmontanus) in the Columbia River Inferred from Single-Nucleotide Polymorphisms

White sturgeon (Acipenser transmontanus) are the largest freshwater fish in North America, with reproducing populations in the Sacramento-San Joaquin, Fraser, and Columbia River Basins. Of these, the Columbia River is the largest, but it is also highly fragmented by hydroelectric dams, and many segments are characterized by declining abundance and persistent recruitment failure. Efforts to conserve and supplement these fish requires an understanding of their spatial genetic structure. Here, we assembled a large set of samples from throughout the Columbia River Basin, along with representative collections from adjacent basins, and genotyped them using a panel of 325 single-nucleotide markers. Results from individual- and group-based analyses of these data indicate that white sturgeon in the uppermost Columbia River Basin, in the Kootenai and upper Snake Rivers, are the most distinct, while the remaining populations downstream in the basin can be described as a genetic gradient consistent with an isolation-by-distance effect. Notably, the population in the lowest reaches of the Columbia River is more distinct from the middle or upper reaches than from outside basins, and suggests historically a higher or more recent gene exchange through coastal routes than with populations in the interior Columbia Basin. Nonetheless, proximal reaches were generally only marginally or non-significantly divergent, suggesting that transplanting larvae or juveniles from nearby sources poses relatively little risk of outbreeding depression. Indeed, we inferred examples of dispersal between reaches via close-kin mark-recapture and genetic mark-recapture that indicate movement between nearby reaches is not unusual. Samples from the Kootenai and upper Snake Rivers exhibited notably lower genetic diversity than the remaining samples as a result of population bottlenecks, genetic drift, and/or historical divergence. Conservation actions, such as supplementation, are underway to maintain population viability and will require balanced efforts to increase demographic abundance while maintaining genetic diversity.

Willis, Stuart C.↗
DOE OSTI2025

Popnet : computer vision based deep learning model for forecasting gridded population

Here, this study introduces Popnet, a deep learning model for forecasting 1 km-gridded populations, integrating U-Net, ConvLSTM, a Spatial Autocorrelation module and deep ensemble methods. Using spatial variables and population data from 2000 to 2020, Popnet predicts South Korea’s population trends by age groups (under 14, 15-64 and over 65) up to 2040. In validation, it outperforms traditional machine learning and state-of-the-art computer vision models. The output of this model discovered significant polarisation: population growth in urban areas, especially the capital region, and severe depopulation in rural areas. Popnet is a robust tool for offering significant insights to policymakers and related stakeholders about the detailed future population, which allows them to establish detailed, localised planning and resource allocations.

computer vision↗
DOE OSTI2023

Climatic factors and human population changes in Eurasia between the Last Glacial Maximum and the early Holocene

Archaeological records document a significant expansion of populations from the Last Glacial Maximum (LGM, ~23–19 ka) to the early Holocene (EH, ~9 ka) in Eurasia, which is often attributed to the influence of orbital-scale climate changes. Yet, information remains limited concerning the climatic factor(s) which were responsible for conditioning demographic patterns. Here, in this work, we present results from an improved Minimalist Terrestrial Resource Model (MTRM), forced by a transient climate simulation from the LGM to the EH. Simulated potential hunter-gatherer population densities and spatial distributions across Eurasia are supported by observed archaeological sites in Europe and China. In the low latitudes, potential population size change was predominantly controlled by precipitation and its strong influence on plant and animal resources. In the middle-high latitudes, temperature was the dominant driver in influencing potential population size change and animal resource availability. Different regional responses of potential populations to climate change across Eurasia - owing to variations in available food resources between the LGM and EH - provide a better understanding of human dispersal during the Late Pleistocene.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Genetic characterization of a Sorghum bicolor multiparent mapping population emphasizing carbon-partitioning dynamics

Sorghum bicolor, a photosynthetically efficient C4 grass, represents an important source of grain, forage, fermentable sugars, and cellulosic fibers that can be utilized in myriad applications ranging from bioenergy to bioindustrial feedstocks. Sorghum’s efficient fixation of carbon per unit time per unit area per unit input has led to its classification as a preferred biomass crop highlighted by its designation as an advanced biofuel by the U.S. Department of Energy. Due to its extensive genetic diversity and worldwide colonization, sorghum has considerable diversity for a range of phenotypes influencing productivity, composition, and sink/source dynamics. To dissect the genetic basis of these key traits, we present a sorghum carbon-partitioning nested association mapping (NAM) population generated by crossing 11 diverse founder lines with Grassl as the single recurrent female. By exploiting existing variation among cellulosic, forage, sweet, and grain sorghum carbon partitioning regimes, the sorghum carbon-partitioning NAM population will allow the identification of important biomass-associated traits, elucidate the genetic architecture underlying carbon partitioning and improve our understanding of the genetic determinants affecting unique phenotypes within Poaceae. We contrast this NAM population with an existing grain population generated using Tx430 as the recurrent female. Genotypic data are assessed for quality by examining variant density, nucleotide diversity, linkage decay, and are validated using pericarp and testa phenotypes to map known genes affecting these phenotypes. We release the 11-family NAM population along with corresponding genomic data for use in genetic, genomic, and agronomic studies with a focus on carbon-partitioning regimes.

multiparental populations↗
DOE OSTI2023

Developing an Evolutionary Baseline Model for Humans: Jointly Inferring Purifying Selection with Population History

Building evolutionarily appropriate baseline models for natural populations is not only important for answering fundamental questions in population genetics—including quantifying the relative contributions of adaptive versus nonadaptive processes—but also essential for identifying candidate loci experiencing relatively rare and episodic forms of selection (e.g., positive or balancing selection). Here, a baseline model was developed for a human population of West African ancestry, the Yoruba, comprising processes constantly operating on the genome (i.e., purifying and background selection, population size changes, recombination rate heterogeneity, and gene conversion). Specifically, to perform joint inference of selective effects with demography, an approximate Bayesian approach was employed that utilizes the decay of background selection effects around functional elements, taking into account genomic architecture. This approach inferred a recent 6-fold population growth together with a distribution of fitness effects that is skewed towards effectively neutral mutations. Importantly, these results further suggest that, although strong and/or frequent recurrent positive selection is inconsistent with observed data, weak to moderate positive selection is consistent but unidentifiable if rare.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Population Count on Intel® CPU, GPU, and FPGA

Population count is a primitive used in many applications. Commodity processors have dedicated instructions for achieving high-performance population count. Motivated by the productivity of high-level synthesis and the importance of population count, in this paper we investigated the OpenCL implementations of population count algorithms, and evaluated their performance and resource utilizations on an FPGA. Based on the results, we select the most efficient implementation. Then we derived a reduction pattern from a representative application of population count. We parallelized the reduction with atomic functions, and optimized it with vectorized memory accesses, tree reduction, and compute-unit duplication. We evaluated the performance of the reduction kernel on an Intel (R) Xeon (R) CPU and an Intel (R) IrisT Pro integrated GPU, and an FPGA card that features an Intel (R) Arria (R) 10 FPGA. When DRAM memory bandwidth is comparable on the three computing platforms, the FPGA can achieve the highest kernel performance for large workload. On the other hand, we described performance bottlenecks on the FPGA. To make FPGAs more competitive in raw performance compared to high-performant CPU and GPU platforms, it is important to increase external memory bandwidth, minimize data movement between a host and a device, and reduce OpenCL runtime overhead on an FPGA.

heterogeneous computing↗
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 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 OSTI2021

Effect of Image Classification Accuracy on Dasymetric Population Estimation

Dasymetric mapping involves the disaggregation of count data, usually relating to population/demographics, from census enumeration areas to smaller target zones with the aid of an ancillary layer related to population density. The ancillary layer is often a binary classification such as developed versus undeveloped, building versus non-building, and residential versus non-residential, in which one class is treated as populated and the other as unpopulated. While dasymetric mapping relies heavily on ancillary data, little research has been done to address the error in ancillary data and its effects on dasymetric mapping accuracy. This chapter reports our research effort to investigate the effect of image classification accuracy on dasymetric population estimates by developing a binomial classification of buildings from high-resolution remote sensor imagery. The classifier was systematically and iteratively manipulated to generate a series of outputs with variegated accuracy characteristics. Lastly, we generated a corresponding series of population estimates based on the mapped building area from each iteration to investigate the relationship between the accuracy of classification and population estimation.

McKee, Jacob↗