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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 811 records · Page 45
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Unveiling stimulation fluid-driven alterations in shale pore architecture through combined interpretation of TD-NMR and multi-component gas adsorption

The hydraulic fracturing stimulation process can alter petrophysical and flow properties of the shale matrix in unconventional reservoirs. These alterations can result from interactions with native and exogenous fluids, and can be detrimental to reservoir productivity. Different experimental procedures have been proposed to study reactive processes and thereby understand the aforementioned interactions. Most published works do not consider the rock initial saturation with formation fluid, or the effect of organic matter (OM). To gain insights into these effects, two reactive experimental sets, differing in experimental conditions, were conducted. In the first set, at 125°C and 45 MPa, a stimulation fluid surrogate was put in contact with Baxter Shale samples, previously saturated and equilibrated with synthetic formation fluid. A baseline consisted of exposure to formation fluid exclusively. In the second set, at 0.08 MPa and 25°C, contact with stimulation fluid took place as in the first set. Two additional assays in this second set either skipped the initial formation fluid saturation or removed the OM, respectively. Petrophysical properties analyses, focused on the pore architecture, relied on the combined interpretation of gas adsorption and Time-Domain Nuclear Magnetic Resonance (TD-NMR). Results show that the presence of the formation fluid significantly restricts pore space accessibility to the stimulation fluid and mitigates the pore-architecture alteration to the macro-pore region. Mineral dissolution and precipitation dominate over surface or wettability alteration. Next, results suggest that the OM restricts accessibility to some pores. Ultimately, the equilibration process with synthetic formation fluid drives mainly surface alteration, unhindered by OM.

58 GEOSCIENCES↗
DOE OSTI2024

Steady-state fuel performance analyses for the preliminary fuel concept of general atomics fast modular reactor

Here this manuscript presents the fuel performance analysis results of the General Atomics Fast Modular Reactor (FMR) based on an axi-symmetric (2D-RZ) geometry. Three fuel performance model sets that fit the FMR fuel specifications best, i.e., a BISON baseline model set, a BISON diffusion enhancement model set, and a BISON-FASTGRASS model set, were identified and evaluated against a series of relevant experimental cases featuring high burnup and low irradiation temperature conditions. The three BISON-based model sets were then utilized to conduct a comprehensive fuel performance analysis of the FMR fuel under normal operation including the shutdown/restarting periods for refueling. The evaluation of the fuel performance parameters, represented by temperature, internal pressure, stress, and strain, shows that the FMR fuel maintains its thermal and mechanical integrity during normal operation. Technology gaps and limitations are also discussed to guide future efforts for extending the performance analysis to transient scenarios as well as improving the fuel performance evaluation through experiments.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2022

Experimental study of the 34 m Cl beam production at intermediate energies

Here the isomeric content of a 34 Cl beam produced in the intermediate-energy projectile fragmentation of a 150 MeV/u 36 Ar beam on a 3 mm-thick Be target was studied. β-delayed γ-ray spectroscopy was used to measure the population of 34 Cl fragments in the ground vs. isomeric states at zero degrees relative to the incoming primary beam for four different momentum settings of the fragment separator near the predicted central velocity of these fragments, as well as, at two non-zero-degree settings for one momentum setting. Of the settings explored, which excluded rigidities within 0.5% of the value predicted to maximize total 34 Cl yield due to unreacted primary beam, the maximum rate for the production of Cl was found at a rigidity setting 0.75% below the predicted peak 34 Cl yield. The maximum population of the isomeric state relative to the ground state was observed at a rigidity 1.25% below the predicted maximum 34 Cl yield. Studies such as this are important in generating the understanding needed for producing isomer-enriched rare-isotope beams.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

The influence of thermochemistry on the reactivity of propane, the pentane isomers and $n$-heptane in the low temperature regime

In this study, the influence of thermochemistry on the reactivity of fuels at low temperatures (600–1000 K) is studied here. Specifically, the effect of different sets of thermochemistry on chemical model predictions is explored, where various sets are calculated at different levels of theory in addition to recently updated group additivity values. Experimentally measured ignition delay times for propane, the pentane isomers and n-heptane are simulated using NUIGMech1.2 and replacing the thermochemistry of the low-temperature species with the calculated values. For propane, three different thermochemistry sets were calculated, namely CCSD(T)-F12/TZ-F12//B2PLYP-D3/TZ//B2PLYP-D3/TZ (QM1), CCSD(T)-F12/TZ-F12//B2PLYP-D3/TZ//ωB97X-D/TZ (QM2) and B2PLYP-D3/TZ/ωB97X-D/6-31G*//ωB97X-D/6-31G* (QM3). The QM2 results provide parameters to optimize new group additivity (NGA) values which are used to calculate the fourth set of thermochemistry. The model predictions using these four sets are compared to those using NUIGMech1.2 for propane. As the QM1 and QM2 calculations are expensive, the thermochemistry calculated from the QM3 and NGA calculations are used in the pentane isomer and n-heptane models. For all of the models, it is found that the thermochemistry of the species involved in the low-temperature reaction sequence ($RH$, $\dot{R}$, $RO_2H$, $R\dot{O}_2$, $\dot{Q}OOH$ and $\dot{O}_2QOOH$ species) significantly affect fuel reactivity. The NGA values were developed based on all of these species except $\dot{O}_2QOOH$ radicals. The thermochemistry of $\dot{O}_2QOOH$ species cannot be accurately calculated with the NGA representations due to the importance of non-next-nearest neighbor interactions of –OOH substitution. Further development of the NGA method to capture such interactions is in progress. Overall, the model developed using the NGA thermochemistry shows better agreement with experimental data than the model using thermochemistry from affordable and prominent QM methods, such as QM3. Based on the results presented for propane, the pentane isomers and n-heptane, the thermochemistry calculated using the NGA method can be used to model the oxidation of higher order hydrocarbons at low temperatures.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2020

A Collection of More than 900 Gas Mixture Adsorption Experiments in Porous Materials from Literature Meta-Analysis

Information on mixture adsorption equilibrium is vital in developing adsorption-based separation processes. Because measuring mixture adsorption is more difficult than measuring single-component adsorption, far more data of the latter kind are available. Previous efforts to compile experimental mixture adsorption data for gases have given data sets with at most a few dozen examples. Here, we report the results of systematic literature meta-analysis that produced a data set of more than 900 gas mixture adsorption experiments. This collection includes data from 125 different binary mixtures including 60 different molecular species and information from 333 different adsorbents. We refer to this data set as the Binary adsorption ISOtherm ExperimeNtal 2020 (BISON-20) Database. Because the BISON-20 data set enormously expands the number and variety of experimental results for binary gas adsorption that are readily available, it will be a useful resource for future efforts in developing new materials or processes for gas separations. As initial applications of the BISON-20 data set, we show how identifying replicate measurements can be used to assess the reliability of binary adsorption data, how the accuracy of Ideal Adsorbed Solution Theory (IAST) can be systematically tested using experimental data, and how trends in selectivity for gas separations across many materials can be examined.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Pose Classification Using Three-Dimensional Atomic Structure-Based Neural Networks Applied to Ion Channel–Ligand Docking

The identification of promising lead compounds showing pharmacological activities toward a biological target is essential in early stage drug discovery. With the recent increase in available small-molecule databases, virtual high-throughput screening using physics-based molecular docking has emerged as an essential tool in assisting fast and cost-efficient lead discovery and optimization. However, the best scored docking poses are often suboptimal, resulting in incorrect screening and chemical property calculation. We address the pose classification problem by leveraging data-driven machine learning approaches to identify correct docking poses from AutoDock Vina and Glide screens. To enable effective classification of docking poses, we present two convolutional neural network approaches: a three-dimensional convolutional neural network (3D-CNN) and an attention-based point cloud network (PCN) trained on the PDBbind refined set. We demonstrate the effectiveness of our proposed classifiers on multiple evaluation data sets including the standard PDBbind CASF-2016 benchmark data set and various compound libraries with structurally different protein targets including an ion channel data set extracted from Protein Data Bank (PDB) and an in-house KCa3.1 inhibitor data set. Our experiments show that excluding false positive docking poses using the proposed classifiers improves virtual high-throughput screening to identify novel molecules against each target protein compared to the initial screen based on the docking scores.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Polishing the Gold Standard: The Role of Orbital Choice in CCSD(T) Vibrational Frequency Prediction

While CCSD(T) with spin-restricted Hartree-Fock (RHF) orbitals has long been lauded for its ability to accurately describe closed-shell interactions, the performance of CCSD(T) on open-shell species is much more erratic, especially when using a spin-unrestricted HF (UHF) reference. Previous studies have shown improved treatment of open-shell systems when a non-HF set of molecular orbitals, like Brueckner or Kohn-Sham density functional theory (DFT) orbitals, is used as a reference. Inspired by the success of regularized orbital-optimized second-order Møller-Plesset perturbation theory (κ-OOMP2) orbitals as reference orbitals for MP3, we investigate the use of κ-OOMP2 orbitals and various DFT orbitals as reference orbitals for CCSD(T) calculations of the corrected ground-state harmonic vibrational frequencies of a set of 36 closed-shell (29 neutrals, 6 cations, 1 anion) and 59 open-shell diatomic species (38 neutrals, 15 cations, 6 anions). The aug-cc-pwCVTZ basis set is used for all calculations. The use of κ-OOMP2 orbitals in this context alleviates difficult cases observed for both UHF orbitals and OOMP2 orbitals. Removing two multireference systems and 12 systems with ambiguous experimental data leaves a pruned data set. Overall performance on the pruned data set highlights CCSD(T) with a B97 orbital reference (CCSD(T):B97), CCSD(T) with a κ-OOMP2 orbital reference (CCSD(T):κ-OOMP2), and CCSD(T) with a B97M-rV orbital reference (CCSD(T):B97M-rV) with RMSDs of 8.48 cm -1 , and 8.50 cm -1 , and 8.75 cm -1 respectively, outperforming CCSD(T):UHF by nearly a factor of 5. Moreover, the performance on the closed- and open-shell subsets shows these methods are able to treat open-shell and closed-shell systems with comparable accuracy and robustness. CCSD(T) with RHF orbitals is seen to improve upon UHF for the closed-shell species, while spatial symmetry breaking in a number of restricted open-shell HF (ROHF) references leads CCSD(T) with ROHF reference orbitals to exhibit the poorest statistical performance of all methods surveyed for open-shell species. The use of κ-OOMP2 orbitals has also proven useful in diagnosing multireference character that can hinder the reliability of CCSD(T).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Assessment of Performance of Density Functionals for Predicting Potential Energy Curves in Hydrogen Storage Applications

We report the availability of accurate computational tools for modeling and simulation is vital to accelerate the discovery of materials capable of storing hydrogen (H 2 ) under given parameters of pressure swing and temperature. Previously, we compiled the H2Bind275 data set consisting of equilibrium geometries and assessed the performance of 55 density functionals over this data set (Veccham, S. P.; Head-Gordon, M. J. Chem. Theory Comput. 2020, 16, 4963-4982). As it is crucial for computational tools to accurately model the entire potential energy curve (PEC), in addition to the equilibrium geometry, we extended this data set with 389 new data points to include two compressed and three elongated geometries along 78 PECs for H 2 binding, forming the H2Bind78 × 7 data set. By assessing the performance of 55 density functionals on this significantly larger and more comprehensive H2Bind78 × 7 data set, we identified the best performing density functionals for H 2 binding applications: PBE0-DH, ωB97X-V, ωB97M-V, and DSD-PBEPBE-D3(BJ). The addition of Hartree-Fock exchange improves the performance of density functionals, albeit not uniformly throughout the PEC. We recommend the usage of ωB97X-V and ωB97M-V density functionals as they offer good performance for both geometries and energies. In addition, we also identified B97M-V and B97M-rV as the best semilocal density functionals for predicting H 2 binding energy at its equilibrium geometry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

The Rise of Neural Networks for Materials and Chemical Dynamics

Machine learning (ML) is quickly becoming a premier tool for modeling chemical processes and materials. ML-based force fields, trained on large data sets of high-quality electron structure calculations, are particularly attractive due their unique combination of computational efficiency and physical accuracy. This Perspective summarizes some recent advances in the development of neural network-based interatomic potentials. Designing high-quality training data sets is crucial to overall model accuracy. One strategy is active learning, in which new data are automatically collected for atomic configurations that produce large ML uncertainties. Another strategy is to use the highest levels of quantum theory possible. Transfer learning allows training to a data set of mixed fidelity. A model initially trained to a large data set of density functional theory calculations can be significantly improved by retraining to a relatively small data set of expensive coupled cluster theory calculations. These advances are exemplified by applications to molecules and materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Large-Scale Interlaboratory DI-FT-ICR MS Comparability Study Employing Various Systems

We report ultra-high resolution mass spectrometry (UHR-MS) coupled with direct infusion (DI) electrospray ionization offers a fast solution for accurate untargeted profiling. Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometers have been shown to produce a wealth of insights into complex chemical systems because they enable unambiguous molecular formula assignment even if the vast majority of signals is of unknown identity. Inter-laboratory comparisons are required to apply this type of instrumentation in quality control (for food industry or pharmaceutics), large-scale environmental studies or clinical diagnostics. Extended comparisons employing different FT-ICR MS instruments with qualitative direct infusion analysis are scarce since the majority of detected compounds cannot be quantified. The extent to which observations can be reproduced by different laboratories remains unknown. We set up a preliminary study which encompassed a set of seventeen laboratories around the globe, diverse in instrumental characteristics and applications, to analyze the same sets of extracts from commercially available standard human blood plasma and Standard Reference Material (SRM) for blood plasma (SRM1950), which were delivered at different dilutions or spiked with different concentrations of pesticides. The aim of this study was to assess the extent to which the outputs of differently tuned FTICR mass spectrometers, with different technical specifications, are comparable for setting the frames of a future DI-FT-ICR MS ring trial. We concluded that a cluster of five laboratories, with diverse instrumental characteristics showed comparable and representative performance across all experiments, setting a reference to be used in a future ring trial on blood plasma.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

Long‐Term Large‐Scale Atmospheric Forcing Data From Three‐Dimensional Constrained Variational Analysis for the ARM SGP Site

Here, this study presents a long‐term three‐dimensional large‐scale forcing data set (VARANAL3D) derived from the three‐dimensional constrained variational analysis (3DCVA) method at the Atmospheric Radiation Measurement (ARM) program Southern Great Plains (SGP) site from 2004 to 2018. Building on the same input data sets as the conventional continuous forcing data set (VARANAL), VARANAL3D maintains overall consistency in domain‐averaged fields while introducing spatial variability, offering critical insights into the influence of mesoscale synoptic systems on cloud‐related processes. Evaluations are conducted across four cloud and precipitation regimes: Clear‐sky, Shallow‐clouds, Afternoon‐precipitation, and Nocturnal‐precipitation, presenting high consistency of the domain‐mean forcing data sets while emphasizing the role of subdomain forcing variability particularly in precipitating regimes. Single column model (SCM) simulations demonstrate that subdomain VARANAL3D forcing improves cloud and precipitation representation, with the ensemble outperforming domain‐mean forcing in three cloudy and precipitating regimes. Overall, these results highlight VARANAL3D's value for investigating the impacts of spatial variability of large‐scale forcing on atmospheric processes. The VARANAL3D data set provides new opportunities for evaluating model physics, advancing the development of scale‐aware parameterizations and deepening our understanding of cloud and precipitation dynamics.

Environmental sciences↗
DOE OSTI2024

Non-linear relationships between daily temperature extremes and US agricultural yields uncovered by global gridded meteorological datasets

Global agricultural commodity markets are highly integrated among major producers. Prices are driven by aggregate supply rather than what happens in individual countries in isolation. Furthermore, estimating the effects of weather-induced shocks on production, trade patterns and prices hence requires a globally representative weather data set. Recently, two data sets that provide daily or hourly records, GMFD and ERA5-Land, became available. Starting with the US, a data rich region, we formally test whether these global data sets are as good as more fine-scaled country-specific data in explaining yields and whether they estimate similar response functions. While GMFD and ERA5-Land have lower predictive skill for US corn and soybeans yields than the fine-scaled PRISM data, they still correctly uncover the underlying non-linear temperature relationship. All specifications using daily temperature extremes under any of the weather data sets outperform models that use a quadratic in average temperature. Correctly capturing the effect of daily extremes has a larger effect than the choice of weather data. In a second step, focusing on Sub Saharan Africa, a data sparse region, we confirm that GMFD and ERA5-Land have superior predictive power to CRU, a global weather data set previously employed for modeling climate effects in the region.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Substructure in the stellar halo near the Sun: I. Data-driven clustering in integrals-of-motion space

Context. Merger debris is expected to populate the stellar haloes of galaxies. In the case of the Milky Way, this debris should be apparent as clumps in a space defined by the orbital integrals of motion of the stars. Aims. Our aim is to develop a data-driven and statistics-based method for finding these clumps in integrals-of-motion space for nearby halo stars and to evaluate their significance robustly. Methods. We used data from Gaia EDR3, extended with radial velocities from ground-based spectroscopic surveys, to construct a sample of halo stars within 2.5 kpc from the Sun. We applied a hierarchical clustering method that makes exhaustive use of the single linkage algorithm in three-dimensional space defined by the commonly used integrals of motion energy E, together with two components of the angular momentum, L z and L ⊥ . To evaluate the statistical significance of the clusters, we compared the density within an ellipsoidal region centred on the cluster to that of random sets with similar global dynamical properties. By selecting the signal at the location of their maximum statistical significance in the hierarchical tree, we extracted a set of significant unique clusters. By describing these clusters with ellipsoids, we estimated the proximity of a star to the cluster centre using the Mahalanobis distance. Additionally, we applied the HDBSCAN clustering algorithm in velocity space to each cluster to extract subgroups representing debris with different orbital phases. Results. Our procedure identifies 67 highly significant clusters (> 3σ), containing 12% of the sources in our halo set, and 232 subgroups or individual streams in velocity space. In total, 13.8% of the stars in our data set can be confidently associated with a significant cluster based on their Mahalanobis distance. Inspection of the hierarchical tree describing our data set reveals a complex web of relations between the significant clusters, suggesting that they can be tentatively grouped into at least six main large structures, many of which can be associated with previously identified halo substructures, and a number of independent substructures. This preliminary conclusion is further explored in a companion paper, in which we also characterise the substructures in terms of their stellar populations. Conclusions. Our method allows us to systematically detect kinematic substructures in the Galactic stellar halo with a data-driven and interpretable algorithm. The list of the clusters and the associated star catalogue are provided in two tables available at the CDS.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Performance of the spin-component-scaled methods for energy bands

The performance of various spin-component-scaled parameterisations is examined for the second-order many-body Green's-function [MBGF(2)] calculations of valence energy bands, taking three of the experimentally well-characterised polymers as examples: polyethylene, polytetrafluoroethylene, and polyacetylene. The parameterisations considered are Grimme's original SCS parameter set, Jung et al.'s original SOS set (retaining the opposite-spin component only), Śmiga et al.'s SCS(IP) set (calibrated specifically for ionization energies), and Śmiga et al.'s SOS(IP) set (calibrated for ionization energies with the opposite-spin component only; implicit in the os-D2 model of Opoku et al.). The SCS(IP) and SOS(IP) parameterisations are found to shift both outer and inner valence bands by up to a few electronvolts away from the experimental data. The original SCS and SOS parameter sets do not improve upon, but largely maintain the accuracy of the unscaled MBGF(2) methods. Given that the SOS-MBGF(2) method can be implemented in a quartic-scaling algorithm (for all roots), it is most promising for solid-state applications. Furthermore this observation is consistent with the success of the quartic-scaling GW methods without the vertex correction based on a density-functional theory reference.

Green’s-function theory↗
DOE OSTI2022

Polarization angle requirements for CMB B-mode experiments. Application to the LiteBIRD satellite

A methodology to provide the polarization angle requirements for different sets of detectors, at a given frequency of a CMB polarization experiment, is presented. The uncertainties in the polarization angle of each detector set are related to a given bias on the tensor-to-scalar ratio r parameter. The approach is grounded in using a linear combination of the detector sets to obtain the CMB polarization signal. In addition, assuming that the uncertainties on the polarization angle are in the small angle limit (lower than a few degrees), it is possible to derive analytic expressions to establish the requirements. The methodology also accounts for possible correlations among detectors, that may originate from the optics, wafers, etc. The approach is applied to the LiteBIRD space mission. We show that, for the most restrictive case (i.e., full correlation of the polarization angle systematics among detector sets), the requirements on the polarization angle uncertainties are of around 1 arcmin at the most sensitive frequency bands (i.e., ≈ 150 GHz) and of few tens of arcmin at the lowest (i.e., ≈ 40 GHz) and highest (i.e., ≈ 400 GHz) observational bands. Conversely, for the least restrictive case (i.e., no correlation of the polarization angle systematics among detector sets), the requirements are ≈ 5 times less restrictive than for the previous scenario. At the global and the telescope levels, polarization angle knowledge of a few arcmins is sufficient for correlated global systematic errors and can be relaxed by a factor of two for fully uncorrelated errors in detector polarization angle. The reported uncertainty levels are needed in order to have the bias on r due to systematics below the limit established by the LiteBIRD collaboration.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Data-centric machine learning in quantum information science

Abstract We propose a series of data-centric heuristics for improving the performance of machine learning systems when applied to problems in quantum information science. In particular, we consider how systematic engineering of training sets can significantly enhance the accuracy of pre-trained neural networks used for quantum state reconstruction without altering the underlying architecture. We find that it is not always optimal to engineer training sets to exactly match the expected distribution of a target scenario, and instead, performance can be further improved by biasing the training set to be slightly more mixed than the target. This is due to the heterogeneity in the number of free variables required to describe states of different purity, and as a result, overall accuracy of the network improves when training sets of a fixed size focus on states with the least constrained free variables. For further clarity, we also include a ‘toy model’ demonstration of how spurious correlations can inadvertently enter synthetic data sets used for training, how the performance of systems trained with these correlations can degrade dramatically, and how the inclusion of even relatively few counterexamples can effectively remedy such problems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Cosmological cross-correlations and nearest neighbour distributions

ABSTRACT Cross-correlations between data sets are used in many different contexts in cosmological analyses. Recently, k-nearest neighbour cumulative distribution functions (kNN-CDF) were shown to be sensitive probes of cosmological (auto) clustering. In this paper, we extend the framework of NN measurements to describe joint distributions of, and correlations between, two data sets. We describe the measurement of joint kNN-CDFs, and show that these measurements are sensitive to all possible connected N-point functions that can be defined in terms of the two data sets. We describe how the cross-correlations can be isolated by combining measurements of the joint kNN-CDFs and those measured from individual data sets. We demonstrate the application of these measurements in the context of Gaussian density fields, as well as for fully non-linear cosmological data sets. Using a Fisher analysis, we show that measurements of the halo-matter cross-correlations, as measured through NN measurements are more sensitive to the underlying cosmological parameters, compared to traditional two-point cross-correlation measurements over the same range of scales. Finally, we demonstrate how the NN cross-correlations can robustly detect cross-correlations between sparse samples – the same regime where the two-point cross-correlation measurements are dominated by noise.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria

Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due to widespread horizontal gene transfers (HGTs). Consequently, representing evolutionary relationships of prokaryotes as bifurcating trees has long been controversial. However, studies reporting conflicts among gene trees derived from phylogenomic data sets have shown that these conflicts can be the result of artifacts or evolutionary processes other than HGT, such as incomplete lineage sorting, low phylogenetic signal, and systematic errors due to substitution model misspecification. Here, we present the results of an extensive exploration of phylogenetic conflicts in the cyanobacterial order Nostocales, for which previous studies have inferred strongly supported conflicting relationships when using different concatenated phylogenomic data sets. We found that most of these conflicts are concentrated in deep clusters of short internodes of the Nostocales phylogeny, where the great majority of individual genes have low resolving power. We then inferred phylogenetic networks to detect HGT events while also accounting for incomplete lineage sorting. Our results indicate that most conflicts among gene trees are likely due to incomplete lineage sorting linked to an ancient rapid radiation, rather than to HGTs. Moreover, the short internodes of this radiation fit the expectations of the anomaly zone, i.e., a region of the tree parameter space where a species tree is discordant with its most likely gene tree. In this work, we demonstrated that concatenation of different sets of loci can recover up to 17 distinct and well-supported relationships within the putative anomaly zone of Nostocales, corresponding to the observed conflicts among well-supported trees based on concatenated data sets from previous studies. Our findings highlight the important role of rapid radiations as a potential cause of strongly conflicting phylogenetic relationships when using phylogenomic data sets of bacteria. We propose that polytomies may be the most appropriate phylogenetic representation of these rapid radiations that are part of anomaly zones, especially when all possible genomic markers have been considered to infer these phylogenies.

59 BASIC BIOLOGICAL SCIENCES↗