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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 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Divertor plasma detachment: roles of plasma momentum, energy, and particle balances

Abstract Contrary to statements from some recent papers, the bifurcation of the scrape-off layer and divertor plasma parameters, as described within a 1D model, does exist. The analysis of both numerical simulations and experimental data shows that the real physical reasons that can cause a strong reduction of the plasma particle flux to the target j d are impurity radiation loss and volumetric plasma recombination. Fitting the parameter describing the ‘plasma momentum removal’, based on the results of 2D numerical simulations, then using this fit in subsequent analytic expressions for j d , and finally interpreting the evolution of j d as the result of elastic plasma-neutral interactions break the causality principle and lead to a wrong physical picture of divertor plasma detachment.

Physics↗
DOE OSTI2022

Spectral transition of multiscale turbulence in the tokamak pedestal

The transition in the turbulence spectrum from ion-scale dominated regimes to multiscale transport regimes that couple ion and electron scales is studied with gyrokinetic simulations of turbulent transport. The simulations are based on DIII-D high-confinement mode (H-mode) plasma parameters in the tokamak pedestal. The transition is initiated by varying the ion temperature gradient. To our knowledge, no full multiscale simulations of pedestal-like transport have been done previously. The experimental parameters lie in a bifurcation region between the two regimes. At long wavelengths, a complex, ion-direction hybrid mode is the dominant linearly unstable drift wave, while an electron temperature gradient-driven mode is unstable at short wavelengths. In the transition from the multiscale branch to the ion-scale branch, the magnitude of the ion-scale poloidal wavenumber spectrum of the nonlinear turbulent energy flux increases and the magnitude of the high-wavenumber spectrum decreases. Here, the decrease in the electron-scale transport is due to nonlinear mixing with ion-scale fluctuations and the ion-scale-driven zonal flows. A shift in the total energy associated with the fluctuating electrostatic potential intensity from dominantly drift kinetic energy in the multiscale regime to dominantly potential intensity in the ion-scale regime is well-correlated with the trend in the total energy flux.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2026

Access and limits of RMP ELM suppression with n = 1 fields in DIII-D

This work reports on DIII-D experiments aimed at extending resonant magnetic perturbation (RMP) suppression of edge localized modes (ELMs) to n = 1 fields, where n is the toroidal mode number. Modeling of the 3D ideal MHD plasma response to the RMPs using the GPEC code is used to quantify edge and core resonant fluxes, guiding experimental strategies to increase plasma resilience against core error field penetration, optimize multicoil phasing, and explore higher q 95 operation. In DIII-D, ELM mitigation is regularly observed across a wide range of n = 1 RMP scenarios. A ∼100 ms phase of complete ELM suppression was achieved at q 95 ∼ 3.9 using an odd-parity coil configuration. The suppressed phase exhibited clear signatures of RMP ELM suppression, including the elimination of Dα spikes, increased pedestal rotation, enhanced magnetic response, and elevated broadband density turbulence. An optimized coil configuration for edge-to-core resonant flux did show increased edge resonance indicated by increased density pumpout, but did not yield RMP ELM suppression. At q 95 ∼ 5.1, a bifurcation to a grassy-like ELM regime occurred, while large type-I ELMs persisted. These results demonstrate progress in experimental access to n = 1 RMP ELM suppression in DIII-D, motivating further study for robust access. This work also highlights the potential role of 3D edge stability as well as rational surface alignment in RMP ELM suppression access, which has important implications for the use of low-n RMPs in future reactor-scale devices.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

High-energy ballistic electrons in low-pressure radio-frequency plasmas

This study demonstrates the presence of a small number of high-energy ballistic electrons (HEBEs) that originate from secondary electrons in low-pressure radio-frequency (rf) plasmas. The kinetic behaviors of the HEBEs are illustrated through electron energy probability functions from the fully kinetic particle-in-cell simulations, showing two wavy high-energy tails and two bifurcations during one rf cycle. Test-particle simulations and a semi-analytical method associated with nonlocal electron kinetics are performed to characterize the HEBE trajectories, which reveal the ballistic nature of the HEBEs and their typical bouncing features between the rf sheaths. Parameter dependence of the HEBEs on the discharge conditions (e.g., gas pressure, gap distance, and rf frequency) are identified, which is relevant to the plasma collisionality. With a pronounced presence of HEBEs, the overall impacts of the secondary electron emission on discharge parameters, such as electron power absorption and ionization rate, are also illustrated.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

The Auger Radioisotope Microscope: an instrument for characterization of Auger electron multiplicities and energy distributions

We describe a new instrument, the Argonne Auger Radioisotope Microscope (ARM), capable of characterizing the Auger electron (AE) emission of radionuclides, including candidates relevant in nuclear medicine. Our approach relies on event-by-event ion–electron coincidence, time-of-flight, and spatial readout measurement to determine correlated electron multiplicity and energy distributions of Auger decays. We present a proof-of-principle measurement with the ARM using x-ray photoionization of stable krypton beyond the K-edge and identify a bifurcation in the electron multiplicity distribution depending on the emission of K-LX electrons. Extension of the ARM to the characterization of radioactive sources of AE emissions is enabled by the combination of two recent developments: (1) cryogenic buffer gas beam technology to introduce Auger emitters into the detection region with well-defined initial conditions, and (2) large-area micro-channel plate detectors with multi-hit detection capabilities to simultaneously detect multiple electrons emitted in a single decay.

Auger emitters↗
DOE OSTI2020

Runaway electron beam dynamics at low plasma density in DIII-D: energy distribution, current profile, and internal instability

Parameters of the post-disruption runaway electron (RE) beam in the collisionless background plasma achieved after deuterium injection are investigated in DIII-D. The spatially resolved RE energy distribution function is measured for the first time during the RE plateau stage by inverting hard X-ray bremsstrahlung spectra. It has maximum energy up to 20 MeV and a non-monotonous feature at 5{6 MeV observed only in the core of the beam supporting the possibility of kinetic instabilities. The RE current profile is reconstructed for the first time using the spatially resolved RE energy distribution. It is found to be more peaked than the pre-disruption plasma current, with higher internal inductance, suggesting preferential formation of REs in the core plasma or potentially a radially inward motion of the REs. The accessed relatively low-current (180 kA) RE beam is found stable, likely due to its elevated q profile. From this base stable equilibrium, instability is accessed by ramping the solenoid current. Under a large applied accelerating loop voltage an internal kink mode is observed. The kink mode leads to sawtooth-like relaxation of the RE current profile, but drives no RE loss. Under conditions of a large decelerating voltage, chirping Alfvénic instabilities driven by REs during the RE plateau stage are observed for the first time. The low-frequency (0.1{7 MHz) Alfvénic instabilities, supposedly compressional Alfvén eigenmodes, are found to be correlated with a RE loss signal. Finally, this provides novel plasma conditions to study these instabilities and investigate opportunities to utilize them for RE control. Bifurcated electron cyclotron emission (ECE) spectrum is measured during the collisionless RE plateau, with a break point at ≈100 GHz suggesting resonant absorption of the ECE at low frequencies.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Nonlinear modeling of the scaling law for the m/n = 3/2 error field penetration threshold

The scaling law for the m/n=3/2 error field (EF) penetration threshold is predicted numerically based on nonlinear single-fluid and two-fluid modeling using the TM1 code. The simulated penetration threshold of radial magnetic field b r at the plasma edge is scaled to the electron density n e , temperature T e , viscous time τ μ , toroidal field B t and the natural frequency ω in the form of b r /B t ∝n e αn T e αT τ μ αμ B t αB ω αω by scanning these parameters separately. Here, α n , α T , α μ , α B and α ω are the scaling coefficients on n e , T e , τ μ , B t and ω, respectively. Single-fluid modeling shows that the 3/2 EF threshold scales as b r /B t ∝n e 0.56 T e 0.6 τ μ -0.59 B t -1.15 ω, which is similar with the analytical scaling law in both the Rutherford and visco-resistive regimes. Yet, two-fluid modeling shows that the scaling law differs significantly in particular regarding the dependence on plasma rotation. In detail, the scaling coefficient α n on density decreases from 0.67 to 0.56 and α T on temperature decreases from 0.67 to 0.32, while α μ on viscous time is around -0.45 and α B on toroidal field decreases slightly from -1.15 to -1, when the ratio |ω E /ω *e | between plasma rotation frequency ω E and diamagnetic drift frequency ω *e varies from 0 to 10. Scans of the plasma rotation reveals that the penetration threshold linearly depends on the perpendicular rotation frequency (or natural frequency) ω ⊥e =ω E +ω *e , and there is a minimum in the required field amplitude when ω ⊥e 0. In addition, the enduring mystery of non-zero penetration threshold at zero plasma natural frequency in EF experiments is resolved by two-fluid simulations. We report that the very small island and smooth bifurcation in EF penetration near zero frequency is hard to detect in the experiment, leading to a finite penetration threshold within the capability of the experimental measurements.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Transport barrier and spinning blob dynamics in the tokamak edge

Abstract In this work, we investigate the dynamics of plasma blobs in the edge of magnetic confinement devices using a full-f gyrokinetic particle-in-cell code with X-point geometry. In simulations, the evolution of a seeded blob is followed as it approaches a naturally-forming zonal shear layer near the separatrix, where the blob is stabilized by a large spin induced by the self-consistent adiabatic electron response, and blob bifurcation and trapping are observed during the cross-field propagation of blobs. A new theoretical explanation in both the zonal free and zonal shear layer is constructed, where the dominant E × B spin motion is included. A theoretical condition for a transport barrier induced by the interaction between spinning blobs and the zonal shear layer is obtained, and its scaling is verified with simulations. The new theoretical framework, especially the transport barrier, is applicable to explain and predict various experimental phenomena. In particular, the transport barrier condition calculated with experimental parameters demonstrates that the blob radial transport for H mode is smaller than L mode in experiments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Geometric dependencies of the mean E × B shearing rate in negative triangularity tokamaks

Abstract This paper presents a comparative study of the poloidal distribution of the mean E × B shearing rate for positive triangularity (PT) and negative triangularity (NT) tokamaks. The effects of flux surface up–down asymmetry due to asymmetric upper and lower triangularities are also considered. Both direct eddy straining and the effects on Shafranov shift feedback loops are examined. Shafranov shift increases the shearing rate at all poloidal angles for all triangularities, due to flux surface compression. The maximum shearing rate bifurcates at a critical triangularity δ crit ( ≲ 0 ) . Thus, the shearing rate is maximal off the outboard midplane for NT, while it is maximal on the outboard midplane for PT. For up–down asymmetric triangularity, the usual up–down symmetry of the shearing rate is broken. The shearing rate at the outboard midplane is lower for NT than for PT, suggesting that the shearing efficiency in NT is reduced. Implications for turbulence stabilisation and confinement improvement in high- β p NT and internal transport barrier discharges are discussed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Evaluation of SPARC divertor conditions in H-mode operation using SOLPS-ITER

The predicted divertor conditions for the SPARC tokamak are calculated using SOLPS-ITER for a range of scrape-off-layer (SOL) heat flux widths λ q , input powers, and particle fueling locations. Under H-mode scenario conditions with an upstream separatrix density of 1 x 10 20 m -3 , the most conservative range of λ q extrapolations ( 0.15 mm) results in extremely high unmitigated particle and energy fluxes to the divertor, both under full field (12.2 T) and power (P SOL = 29 MW) conditions, and 2/3 field with P SOL = 10 MW. Increasing the cross-field SOL diffusivities by 2–10× reduces the magnitude of the mitigation challenge, however strategies such as impurity seeding or strike-point-sweeping will likely still be required. A combination of steady-state and time-dependent SOLPS-ITER simulations are used to map out phase space diagrams of upstream and divertor conditions. The simulations include parallel currents but neglect cross-field drifts. At low upstream density the inner and outer divertor conditions are highly asymmetric, with a large temperature difference and significant heat fluxes driven by parallel currents. The solution has sharp bifurcations with a region of hysteresis, depending on whether the initial state is at a low or high density. This behavior is observed even when the fueling location, cross-field diffusivity, and impurity level is changed, although the density window with asymmetry is reduced with increasing diffusivity. The addition of neon impurity seeding reduces the divertor heat fluxes, but also causes a drop in the upstream electron density with fixed particle throughput. This drop can be counteracted by increased main ion throughput, however too much neon results in a back transition into the asymmetric divertor regimes suggesting a need for control of both main ion and impurity seeding levels to achieve a desired divertor state.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Novel intrinsic helical cores and MHD dynamo flux pumping evidence in DIII-D

Evidence of a MHD dynamo brought about by intrinsic helical core structures in negative triangularity (NT) and ITER baseline scenario (IBS) plasmas demonstrates paths to operating tokamaks without seeds for deleterious global MHD modes. A stationary sawtooth- and edge localized mode-free state maintains high performance for long durations in a strong NT shape in the DIII-D tokamak. Disparity between minimum safety factor values predicted by magnetic flux diffusion theory and derived from experiment suggests anomalous flux diffusion by an MHD dynamo, driven by flows associated with quasi-interchange modes. Stability calculations with the GATO code find NT and IBS experimental equilibria unstable to quasi-interchange modes, in agreement with observed saturated activity. IBS discharges with similar magnetic winding structure occupy robust helical core states following a transition from sawtooth instabilities. These states agree with prior modeling of helical core bifurcation thresholds with the VMEC equilibrium code.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2026

On FIRE mode in KSTAR

We report on the status of Fast Ion Regulated Enhancement (FIRE) mode experiments in the Korea Superconducting Tokamak Advanced Research. This regime is being developed for high-performance, steady-state operation which features a stationary ion internal transport barrier, enabling a central ion temperature approaching 10 keV to be sustained for up to 50 s, without the need for delicate profile control and with no significant impurity accumulation. As its key novelty lies in the significant contribution of fast ions that stabilize core turbulence, the regime has been named FIRE mode. To achieve this regime, neutral beam injection is applied at moderate power levels near the L–H power threshold, while maintaining low plasma density to avoid the L–H transition. The scenario is typically established in diverted magnetic configurations. The core features of FIRE mode were investigated through power balance analysis and fluctuation measurements, revealing a clear transport bifurcation in the ion channel. At the plasma edge, FIRE mode occasionally exhibits I-mode characteristics, particularly in unfavorable magnetic null configurations with q 95 ∼ 4, including the presence of weakly coherent modes. In terms of MHD activity, sawtooth oscillations are observed but appear to be stabilized during the high-performance phase. Fast ion-driven Alfvénic eigenmodes (AEs), indicated by strong frequency chirping near 200 kHz, are also observed. Additionally, lower-frequency MHD activities, distinct from the fast ion-driven AEs, are present and have some influence on plasma performance. The enhancement of core confinement is primarily attributed to fast ion effects, which were evaluated with respect to dilution, alpha stabilization, and resonant interactions with turbulence using gyrokinetic analyses. Among these, the dilution effect was found to be the most dominant. The characteristics of FIRE mode were compared with those of other hot ion plasma scenarios, such as supershot and hot ion mode. While they share many similarities, FIRE mode is distinguished by the accessibility to conditions with T i ≈ T e , presence of I-mode edge features, and its long-duration sustainment. Predictive simulations of FIRE mode were performed using integrated transport modeling with TRIASSIC, employing the TGLF anomalous transport model. These simulations confirmed the critical role of fast ions in achieving this regime. The future prospect of FIRE mode for application in fusion reactors is discussed, with an emphasis on possibly extending the regime to higher density operation.

FIRE mode↗
DOE OSTI2026

Overview of ST40 results and future: expanding the physics basis of high-field spherical tokamaks

The goal of the ST40 programme is to explore the physics of high-field spherical tokamaks (STs), to validate empirical and theoretical models and, hence, to build confidence in predictions required to support the design of future generations of STs. ST40 is a compact high-field ST that has achieved the following parameters: R 0 = 0.4–0.55 m, I p = 0.20–0.85 MA, B t (R= 0.4 m) = 0.7–2.1 T, κ ⩽ 1.9, and A = 1.6–1.9. Highlights of recent experimental results include (i) H-mode and confinement studies at B t ⩽ 2.1 T, (ii) observation of bifurcation of the scrape-off-layer power fall-off width, λ q , into a ‘wide’ branch that follows existing H-mode scalings and a ‘narrow’ branch that exhibits λ q values that are up to 10 times lower than the predictions of established scalings, (iii) development of high-performance scenarios with plasma current, I p , up to 0.85 MA, (iv) development of highly non-inductive scenarios with high β p , and (v) the first ST40 experiments utilising the newly commissioned impurity powder dropper. The work on all these topics has been supported by a number of advancements in ST40 hardware and software, from plasma control to data analysis and interpretation. At the end of 2025, ST40 embarked on a major upgrade to further expand its capabilities by introducing, among other improvements, all-metal plasma-facing components, 1 MW of electron cyclotron heating, a pellet injector, and a pair of lithium evaporators for wall conditioning.

confinement↗
DOE OSTI2022

3-regular three-XORSAT planted solutions benchmark of classical and quantum heuristic optimizers

With current semiconductor technology reaching its physical limits, special-purpose hardware has emerged as an option to tackle specific computing-intensive challenges. Optimization in the form of solving quadratic unconstrained binary optimization problems, or equivalently Ising spin glasses, has been the focus of several new dedicated hardware platforms. These platforms come in many different flavors, from highly-efficient hardware implementations on digital-logic of established algorithms to proposals of analog hardware implementing new algorithms. In this work, we use a mapping of a specific class of linear equations whose solutions can be found efficiently, to a hard constraint satisfaction problem (three-regular three-XORSAT, or an Ising spin glass) with a 'golf-course' shaped energy landscape, to benchmark several of these different approaches. We perform a scaling and prefactor analysis of the performance of Fujitsu's digital annealer unit (DAU), the D-Wave advantage quantum annealer, a virtual MemComputing machine, Toshiba's simulated bifurcation machine (SBM), the SATonGPU algorithm from Bernaschi et al, and our implementation of parallel tempering. We identify the SATonGPU and DAU as currently having the smallest scaling exponent for this benchmark, with SATonGPU having a small scaling advantage and in addition having by far the smallest prefactor thanks to its use of massive parallelism. Furthermore, our work provides an objective assessment and a snapshot of the promise and limitations of dedicated optimization hardware relative to a particular class of optimization problems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Models of bars − II. Exponential profiles

ABSTRACT We present a new model for galactic bars with exponentially falling major axis luminosity profiles and Gaussian cross-sections. This is based on the linear superposition of Gaussian potential–density pairs with an exponential weight function, using an extension of the method originally introduced by Long & Murali. We compute the density, potential, and forces, using Gaussian quadrature. These quantities are given as explicit functions of position. There are three independent scaled bar parameters that can be varied continuously to produce bespoke bars of a given mass and shape. We categorize the effective potential by splitting a reduced parameter space into six regions. Unusually, we find bars with three stable Lagrange points on the major axis are possible. Our model reveals a variety of unexpected orbital structure, including a bifurcating x1 orbit coexisting with a stable x4 orbit. Propeller orbits are found to play a dominant role in the orbital structure, and we find striking similarities between our bar configuration and the model of Kaufmann & Contopoulos. We find a candidate orbital family, sired from the propeller orbits, that may be responsible for the observed high-velocity peaks in the Milky Way’s bar. As a cross-check, we inspect, for the first time, the proper motions of stars in the high-velocity peaks, which also match our suggested orbital family well. This work adds to the increasing body of evidence that real galactic bars may be supported at least partly by propeller orbits rather than solely by elliptical-like orbits of the x1 family.

McGough, D. P.↗
DOE OSTI2023

Shedding far-ultraviolet light on the donor star and evolutionary state of the neutron-star LMXB Swift J1858.6−0814

ABSTRACT The evolution of accreting X-ray binary systems is closely coupled to the properties of their donor stars. Consequently, we can constrain the evolutionary track a system is by establishing the nature of its donor. Here, we present far-ultraviolet (far-UV) spectroscopy of the transient neutron-star low-mass X-ray binary J1858 in different accretion states (low-hard, high-hard, and soft). All of these spectra exhibit anomalous N v, C iv, Si iv, and He ii lines, suggesting that its donor star has undergone CNO processing. We also determine the donor’s effective temperature, Td ≃ 5700 K, and radius, Rd ≃ 1.7 R⊙, based on photometric observations obtained during quiescence. Lastly, we leverage the transient nature of the system to set an upper limit of $\dot{M}_{\rm acc} \lesssim 10^{-8.5}~{\rm M}_{\odot }~\mathrm{ yr}^{-1}$ on the present-day mass-transfer rate. Combining these with the orbital period of the system, Porb = 21.3 h, we search for viable evolution paths. The initial donor masses in the allowed solutions span the range 1 M⊙ ≲ Md,i ≲ 3.5 M⊙. All but the lowest masses in this range are consistent with the strong CNO-processing signature in the UV line ratios. The present-day donor mass in the permitted tracks are 0.5 M⊙ ≲ Md,obs ≲ 1.3 M⊙, higher than suggested by eclipse modelling. Since Porb is close to the so-called bifurcation period, both converging and diverging binary tracks are permitted. If the former is confirmed, J1858 will end its life as an ultracompact system with a substellar donor.

Castro Segura, N. (ORCID:0000000258700443)↗
DOE OSTI2025

Mutation-driven RRE stem-loop II conformational change induces HIV-1 nuclear export dysfunction

Abstract The Rev response element (RRE) forms an oligomeric complex with the viral protein Rev to facilitate the nuclear export of intron-retaining viral RNAs during the late phase of HIV-1 (human immunodeficiency virus type 1) infection. However, the structures and mechanisms underlying this process remain largely unknown. Here, we determined the crystal structure of the HIV-1 RRE stem-loop II (SLII), revealing a unique three-way junction architecture in which the base stem (IIa) bifurcates into the stem-loops (IIb and IIc) to compose Rev binding sites. The crystal structures of various SLII mutants demonstrated that while some mutants retain the same “compact” fold as the wild type, other single-nucleotide mutants induce drastic conformational changes, forming an “extended” SLII structure. Through in vitro Rev binding assays and Rev activity measurements in HIV-1-infected cells using structure-guided SLII mutants designed to favor specific conformers, we showed that while the compact fold represents a functional SLII, the alternative extended conformation inhibits Rev binding and oligomerization and consequently stimulates HIV-1 RNA nuclear export dysfunction. The propensity of SLII to adopt multiple conformations as captured in crystal structures and their influence on Rev oligomerization illuminate emerging perspectives on RRE structural plasticity-based regulation of HIV-1 nuclear export and provide opportunities for developing anti-HIV drugs targeting specific RRE conformations.

Biochemistry & Molecular Biology↗
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↗