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DOE OSTI2021

Impact of point spread function higher moments error on weak gravitational lensing

ABSTRACT Weak gravitational lensing is one of the most powerful tools for cosmology, while subject to challenges in quantifying subtle systematic biases. The point spread function (PSF) can cause biases in weak lensing shear inference when the PSF model does not match the true PSF that is convolved with the galaxy light profile. Although the effect of PSF size and shape errors – i.e. errors in second moments – is well studied, weak lensing systematics associated with errors in higher moments of the PSF model require further investigation. The goal of our study is to estimate their potential impact for LSST weak lensing analysis. We go beyond second moments of the PSF by using image simulations to relate multiplicative bias in shear to errors in the higher moments of the PSF model. We find that the current level of errors in higher moments of the PSF model in data from the Hyper Suprime-Cam survey can induce a ∼0.05 per cent shear bias, making this effect unimportant for ongoing surveys but relevant at the precision of upcoming surveys such as LSST.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2026

Operando Spectroscopic Analysis of Photovoltage Generation in Hematite Photoanodes

Solar-driven water splitting requires sufficient photovoltage to drive both water oxidation and proton reduction. Understanding the factors driving and limiting photovoltage generation is therefore crucial to optimizing photoelectrode design but has proven challenging to determine under operando conditions for photoanodes driving slow multiredox reactions such as water oxidation. In this work, operando optical spectroscopy is employed to measure the hole quasi-Fermi level (E F,p ) position in model hematite photoanodes as a function of applied bias and light intensity. The quasi-Fermi level splitting determined from these data are shown be in excellent agreement with the directly measured photovoltages, demonstrating the primarily electrochemical rather than primarily electrostatic origin of photovoltage in these photoelectrodes. E F,p pinning is observed at low light intensities and biases, indicative of hole trap states lying ∼0.2 eV above the valence band edge with a density of ∼1 nm −2 . Hole accumulation in these trap states is correlated with first order water oxidation. At higher light intensities and/or more anodic bias, E F,p becomes unpinned, assigned to saturation of these trap states, and correlated with the onset of third order water oxidation to molecular oxygen. Comparison with rate law analyses for other photoanodes indicates that such hole trap states may be a ubiquitous feature of metal oxides and suggests that materials processing strategies to suppress the density of such states would be a promising strategy to enhance photoanode performance.

Hematite↗

DOE OSTI2020

Initial Efforts Organizing WPNCS SG-8: Preservation of Expert Knowledge and Judgement Applied to Criticality Benchmarks

The Working Party on Nuclear Criticality Safety (WPNCS) under the guidance of the Organization for Economic Co-operation and Development (OECD) Nuclear Energy Agency (NEA) has over 20 years of experience addressing concerns related to static and transient configurations encountered within the nuclear fuel cycle: fuel fabrication, transportation, reprocessing, storage, and geological disposal. One of the cornerstone activities of the WPNCS is the International Criticality Safety Benchmark Evaluation Project (ICSBEP), which was established to identify a comprehensive set of criticality benchmark data, evaluate the data, including quantification of overall uncertainties; compile the data into a standardized format, perform sample calculations utilizing modern nuclear data sets and codes utilized in nuclear criticality safety, and formally document the work into a single source of verified benchmark data. Annually, members of the ICSBEP Technical Review Group (TRG) contribute evaluated benchmark data that undergoes comprehensive technical review prior to publication in the ICSBEP Handbook. In the years since the ICSBEP was established, there has been much work to prepare benchmark data to support validation activities in nuclear criticality safety. The 2020 edition of the ICSBEP Handbook contains acceptable benchmark specifications for 5,053 critical, subcritical, or near-critical configurations in 582 benchmark evaluations. Modern benchmark development benefits from decades of experienced international participants, a well-established handbook format, supplementary guides to deal with uncertainty quantification, and a comprehensive review process based upon independent reviews from international experts. The ICSBEP Handbook also contains 838 configurations deemed unacceptable to support criticality safety efforts. They are recorded, with the reasoning for their rejection, to preserve the experimental data, prevent reevaluation of data that are incomplete or contain known errors, and/or to potentially allow future reevaluation of the experiment pending the identification of sufficient data to resolve identified inconsistencies and errors. Users of the ICSBEP Handbook today might notice that the rigor and quality of modern criticality safety benchmarks is much greater than those prepared within the initial decade of the project. Benchmarks with 1s uncertainties in k eff greater than 1% were traditionally rejected unless they were identified as unique experiment types that encompassed materials, fuels, or designs not available from other benchmark experiments. However, benchmarks developed using modern experimental techniques and practices typically have uncertainties on the order of a few tenths of a percent. There have been ongoing efforts to improve the overall quality of previously published benchmark evaluations. Seventy-eight evaluations, containing approximately 600 configurations, have been revised just within the past decade. An additional eleven benchmarks are under revision for updated release in the 2020 edition of the ICSBEP Handbook. If some of the historic benchmarks were resubmitted in their current form to the TRG today, they would be rejected due to lack of data, missing components in the uncertainty analysis, or incomplete benchmark model development. The use of historic criticality safety benchmarks that underestimate the total uncertainty, lack properly quantified biases, or provide inadequate benchmark specifications do not sufficiently support modern criticality safety and nuclear data efforts. Although the ICSBEP Handbook is recognized by regulating bodies to support criticality safety, users are required to justify their reasons to ignore historic benchmark data and include additional safety margins within their designs. Discussions were held at the WPNCS 23rd Annual Meeting in September 2019 regarding the aforementioned issues. The resultant decision was to establish Subgroup 8 (SG-8): Preservation of Expert Knowledge and Judgement Applied to Criticality Benchmarks. The current activities of SG-8 are discussed herein.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Radio measurements of the depth of air-shower maximum at the Pierre Auger Observatory

The (AERA), part of the Pierre Auger Observatory, is currently the largest array of radio antenna stations deployed for the detection of cosmic rays, spanning an area of 17 km 2 with 153 radio stations. It detects the radio emission of extensive air showers produced by cosmic rays in the 30–80 MHz band. Here, we report the AERA measurements of the ( X max ), a probe for mass composition, at cosmic-ray energies between 10 17.5 and 10 18.8 eV , which show agreement with earlier measurements with the fluorescence technique at the Pierre Auger Observatory. We show advancements in the method for radio X max reconstruction by comparison to dedicated sets of / air-shower simulations, including steps of reconstruction-bias identification and correction, which is of particular importance for irregular or sparse radio arrays. Using the largest set of radio air-shower measurements to date, we show the radio X max resolution as a function of energy, reaching a resolution better than 15 g cm − 2 at the highest energies, demonstrating that radio X max measurements are competitive with the established high-precision fluorescence technique. In addition, we developed a procedure for performing an extensive data-driven study of systematic uncertainties, including the effects of acceptance bias, reconstruction bias, and the investigation of possible residual biases. These results have been cross-checked with air showers measured independently with both the radio and fluorescence techniques, a setup unique to the Pierre Auger Observatory. Published by the American Physical Society 2024

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2020

Measurement of space charge effects in the MicroBooNE LArTPC using cosmic muons

Large liquid argon time projection chambers (LArTPCs), especially those operating near the surface, are susceptible to space charge effects. In the context of LArTPCs, the space charge effect is the build-up of slow-moving positive ions in the detector primarily due to ionization from cosmic rays, leading to a distortion of the electric field within the detector. This effect leads to a displacement in the reconstructed position of signal ionization electrons in LArTPC detectors ("spatial distortions"), as well as to variations in the amount of electron-ion recombination experienced by ionization throughout the volume of the TPC. We present techniques that can be used to measure and correct for space charge effects in large LArTPCs by making use of cosmic muons, including the use of track pairs to unambiguously pin down spatial distortions in three dimensions. Finally, the performance of these calibration techniques are studied using both Monte Carlo simulation and MicroBooNE data, utilizing a UV laser system as a means to estimate the systematic bias associated with the calibration methodology.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Limitations of reanalysis data for wind power applications

Wind energy resource estimates commonly depend on simulated wind speed profiles generated by reanalysis or weather models due to the lack of long time series measurements with sufficient coverage at relevant heights (roughly 90 m above ground). However, modeled data, including reanalyses, can be noisy and display a wide range of biases and errors, variously attributed to terrain effects, poor coverage of assimilated inputs, and model resolution. Wind generation records, if available at high temporal and geographical resolution, can provide a proxy for wind measurements and allow for evaluation of reanalyses and weather model wind time series. We use a 7-year-long data set of hourly, plant-level generation records from over 100 wind plants across Texas to evaluate two commonly used reanalysis data sets (MERRA2 and ERA5). Additionally, we use 1-year of records (2019) to evaluate an operational, high-resolution regional weather modeling product (HRRR v3). We find that across the region, and across all modeling products, the modeled representation of wind generation (i.e., wind speeds at hub heights passed through a power curve) has relatively small mean errors when aggregated daily, but that accuracy and hourly correlation have a strong diurnal sensitivity. Accuracy and correlation systematically decline through the evening and markedly improve after sunrise. These diurnal patterns persist even in the highest resolution model tested (HRRR v3). We hypothesize the nighttime decline in accuracy is mostly due to poorly represented boundary layer conditions, perhaps related to model representation of stability, while other uncertainties (such as wake effects) play a secondary role.

17 WIND ENERGY↗

DOE OSTI2026

Low energy neutron light output characterization of EJ301D and deuterated stilbene with a comparison of light output characterization methods

The neutron-induced light yield of a 2.54 cm diameter by 2.54 cm long right circular cylinder of EJ301D and a (5.08 cm)3 custom made cube of deuterated trans-stilbene-d12 (d-stilbene) were measured over incident neutron energies from 300 keV to 2.2 MeV and 200 keV to 2.4 MeV, respectively. The measurements were performed using a time-of-flight experiment with a Cf-252 source and an approximately 1.5 m flight path. We compare three light output spectrum full energy deposition edge estimation methods: (1) simulating the neutron energy spectrum edge and fitting it to the light output spectrum, (2) using the inflection point of the light output spectrum edge (derivative method, a.k.a. Kornilov’s method), and (3) using an empirical model fit to the edge of the light output spectrum. Both the derivative and equation fit methods do not account for physical processes such as multiple neutron scattering in the detectors. They instead rely on assumptions about the linear shape continuum shape of the light output spectrum and the direct correlation between the location of the spectrum’s inflection point and maximum energy deposition. These assumptions were found to introduce bias into those methods when tested against simulated spectra with known edge locations. When tested against measured spectra the derivative method was found to differ from the simulation fit by greater than 30% at low energies with large discontinuities for adjacent data points above 800 keV incident neutron energy. The empirical equation fitting method was found to also exhibit bias of a similar magnitude, but with significantly more continuous behavior, especially with the lower count data of the smaller volumed EJ301D scintillator. Experimental light output yield for this neutron energy range is reported using the simulated spectrum fitting method because it includes physics neglected by the other methods, and did not exhibit the bias observed in the other methods

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2025

New H erwig7 underlying event tune: From RHIC to LHC energies

We present parameter sets corresponding to new underlying event tunes for the H erwig7.3 Monte Carlo event generator. The existing H erwig tunes are in good agreement with LHC data, however, they are not typically designed for center-of-mass energies below $\sqrt{𝑠}$ = 300 GeV. The tunes presented in this study can describe midrapidity data collected at the nominal RHIC energy of $\sqrt{𝑠}$ = 200 GeV as well as higher center-of-mass energies utilized by experiments at the LHC and Tevatron. The base “New Haven” tune is developed by fitting minimum-bias simulations of proton-proton ($𝑝⁢𝑝$) collisions to midrapidity identified hadron and jet data from the STAR experiment. The “Nashville” tune includes a separate set of parameters developed by tuning to Tevatron proton-antiproton ($𝑝\bar{⁢𝑝}$) data at $\sqrt{𝑠}$ = 300, 900 and 1960 GeV from CDF, and LHC $𝑝⁢𝑝$ measurements from CMS at $\sqrt{𝑠}$ =7 TeV, in addition to the STAR measurements. Both new tunes demonstrate significant improvements over the recommended default tune currently included in the latest version of H erwig for minimum bias production. As such, we advocate using these tunes for future simulation studies at midrapidity by experimental collaborations at RHIC (STAR and sPHENIX) and the LHC (ALICE, ATLAS, and CMS).

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Large Scale Caching and Streaming of Training Data for Online Deep Learning

The training of deep neural network models on large data remains a difficult problem, despite progress towards scalable techniques. In particular, there is a mismatch between the random but predetermined order in which AI flows select training samples and the streaming I/O patterns for which traditional HPC data storage (e.g., parallel file systems) are designed. In addition, as more data are obtained, it is feasible neither simply to train learning models incrementally, due to catastrophic forgetting (i.e., bias towards new samples), nor to train frequently from scratch, due to prohibitive time and/or resource constraints. In this paper, we study data management techniques that combine caching and streaming with rehearsal support in order to enable efficient access to training samples in both offline training and continual learning. We revisit state-of-art streaming approaches based on data pipelines that transparently handle prefetching, caching, shuffling, and data augmentation, and discuss the challenges and opportunities that arise when combining these methods with data-parallel training techniques. We also report on preliminary experiments that evaluate the I/O overheads involved in accessing the training samples from a parallel file system (PFS) under several concurrency scenarios, highlighting the impact of the PFS on the design of the data pipelines.

data pipelines↗

DOE OSTI2021

New, improved analysis of correlation ECE data to accurately determine turbulent electron temperature spectra and magnitudes (invited)

Turbulent electron temperature fluctuation measurement using a correlation electron cyclotron emission (CECE) radiometer has become an important diagnostic for studying energy transport in fusion plasmas, and its use is widespread in tokamaks (DIII-D, ASDEX Upgrade, Alcator C-Mod, Tore Supra, EAST, TCV, HL-2A, etc.). The CECE diagnostic typically performs correlation analysis between two closely spaced (within the turbulent correlation length) ECE channels that are dominated by uncorrelated thermal noise emission. This allows electron temperature fluctuations embedded in the thermal noise to be revealed and fluctuation level and spectra determined. We have demonstrated a new, improved CECE coherency-based analysis for calculating the temperature fluctuation frequency spectrum and level, which has been verified both numerically through the simulation of synthetic ECE radiometer data and through analysis of experimental data from the CECE system on DIII-D. The new formulation places coherency-based analysis on a firm foundational footing and corrects some currently published methodologies. This new method accurately accounts for bias error in the coherence function and correctly calculates noise levels for a fixed data record length. It provides excellent accuracy in determining temperature fluctuation level (e.g., <10% error) even for a small realization number in the ensemble average. The method also has a smaller uncertainty (i.e., error bar) in the power spectrum when compared to the more standard cross-power method when evaluated at low coherency. Direct calculation of system noise level using correlation between randomized intermediate frequency signals is recommended.

Wang, G. (ORCID:0000000225739827)↗

DOE OSTI2026

Beyond interpolation: Physics-inspired gating transformers for extrapolating irradiation conditions to novel nuclear fuels

The qualification of advanced nuclear fuels relies on irradiation experiments in test reactors that emulate commercial conditions. Designing these tests requires accurate prediction of key irradiation quantities, particularly heat generation rate and burnup, yet obtaining them typically involves computationally expensive multi-step simulation workflows. We propose a physics-inspired gating transformer (PIGT) that integrates an inverse-square, distance-based attenuation into the encoder representation to bias attention toward physically relevant spatial relationships while retaining data-driven flexibility. Using MiniFuel irradiation data from the High Flux Isotope Reactor at Oak Ridge National Laboratory, we benchmark against ensemble methods, feedforward and recurrent networks, convolutional models, and standard transformers. While baseline models perform well under interpolation, they exhibit a pronounced generalization gap when evaluated on fuels not included in the training set. The proposed model consistently improves extrapolative accuracy and stability, yielding the strongest performance on unseen fuel configurations. These results indicate that a lightweight physics structure embedded within attention mechanisms can substantially improve robustness, enabling more reliable surrogate predictions to accelerate the design of nuclear fuel irradiation experiments.

Fuel qualification↗

DOE OSTI2022

Energy dependence of prompt fissions neutron multiplicity in the 239 Pu(n, ƒ) reaction

Accurate multiplicities of prompt fission neutrons emitted in neutron-induced fission on a large energy range are essential for fundamental and applied nuclear physics. Measuring them to high precision for radioactive fissioning nuclides remains, however, an experimental challenge. In this work, the average prompt-neutron multiplicity emitted in the 239 Pu(n, ƒ) reaction was extracted as a function of the incident-neutron energy, over the range 1-700 MeV, with a novel technique, which allowed to minimize and correct for the main sources of bias and thus achieve unprecedented precision. At low energies, our data validate for the first time the ENDF/B-VIII.0 nuclear data evaluation with an independent measurement and reduce the evaluated uncertainty by up to 60%. This work opens up the possibility of precisely measuring prompt fission neutron multiplicities on highly radioactive nuclei relevant for an essential component of energy production world-wide.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

Characterization of wind speed and directional shear at the AWAKEN field campaign site

The American wake experiment (AWAKEN) is taking place in northern Oklahoma, USA, close to the Atmospheric Radiation Measurement Southern Great Plains (ARM SGP) atmospheric observatory. The planning for the deployment of the instruments in this observational field campaign required an assessment of the wind characteristics of the site. This paper analyzes long-term data collected by instruments at the ARM SGP observatory to characterize the winds near the AWAKEN site. The analysis shows that this site experiences high wind shear and veer events with a large number of nocturnal low-level jets. A total of 7086 low-level jet wind profiles over 6 years are examined and found to be dominant from the south and southeast. Significant nocturnal wind veer is observed, which causes southerly wind near the surface to become westerly wind aloft. By identifying a strong relationship between atmospheric stability and wind shear, the wind shear at the site is predicted using the Monin–Obukhov similarity theory (MOST) and validated with the observational data collected by a scanning Doppler lidar. The results show that wind speed at a height of 91 m, a proxy hub height for wind turbines in this area, can be predicted from data collected at a height of 10 m with a bias of −0.35 and 0.65 m s−1 in unstable and stable atmospheric boundary layers, respectively. The bias of the predicted wind speed is mostly in the region of low wind speed, and wind speed above 5 m s−1 at a height of 91 m can be predicted with a bias of less than 0.2 m s−1, and the limitations of the MOST in predicting winds during the stably stratified boundary layer is well-observed.

17 WIND ENERGY↗

DOE OSTI2022

Determining the bubble nucleation efficiency of low-energy nuclear recoils in superheated C 3 F 8 dark matter detectors

The bubble nucleation efficiency of low-energy nuclear recoils in superheated liquids plays a crucial role in interpreting results from direct searches for weakly interacting massive particle (WIMP) dark matter. Here, the PICO collaboration presents the results of the efficiencies for bubble nucleation from carbon and fluorine recoils in superheated C 3 F 8 from calibration data taken with five distinct neutron spectra at various thermodynamic thresholds ranging from 2.1 to 3.9 keV. Instead of assuming any particular functional forms for the nuclear recoil efficiency, a generalized piecewise linear model is proposed with systematic errors included as nuisance parameters to minimize model-introduced uncertainties. A Markov chain Monte Carlo routine is applied to sample the nuclear recoil efficiency for fluorine and carbon at 2.45 and 3.29 keV thermodynamic thresholds simultaneously. The nucleation efficiency for fluorine was found to be ≥ 50% for nuclear recoils of 3.3 keV (3.7 keV) at a thermodynamic Seitz threshold of 2.45 keV (3.29 keV), and for carbon the efficiency was found to be ≥ 50% for recoils of 10.6 keV (11.1 keV) at a threshold of 2.45 keV (3.29 keV). Simulated datasets are used to calculate a p value for the fit, confirming that the model used is compatible with the data. The fit paradigm is also assessed for potential systematic biases, which although small, are corrected for. Additional steps are performed to calculate the expected interaction rates of WIMPs in the PICO-60 detector, a requirement for calculating WIMP exclusion limits.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

First Direct-Detection Results on Sub-GeV Dark Matter Using the SENSEI Detector at SNOLAB

Here, we present the first results from a dark matter search using six Skipper-CCDs in the SENSEI detector operating at SNOLAB. We employ a bias-mitigation technique of hiding approximately 46% of our total data and aggressively mask images to remove backgrounds. Given a total exposure after masking of 100.72 gram-days from well-performing sensors, we observe 55 two-electron events, 4 three-electron events, and no events containing 4–10 electrons. The two-electron events are consistent with pileup from one-electron events. Among the 4 three-electron events, 2 appear in pixels that are likely impacted by detector defects, although not strongly enough to trigger our “hot-pixel” mask. We use these data to set world-leading constraints on sub-GeV dark matter interacting with electrons and nuclei.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2022

Radiation testing of 2.4 micron wavelength extended InGaAs photodiodes for 100 MeV/n carbon ions

We have successfully tested simultaneously 2.4 Micron Wavelength, Extended InGaAs Photodiodes having diameters of 20, 30, 40, 50, 100, 150, 200, 250, and 290 Micron, coupled with a Single Mode Fiber using 100 MeV/n Carbon (C) Ions up to a cumulative dose of ~40 krad. During irradiation, the devices were maintained at dry ice temperature, reverse biased at 100 mV, and their leakage current was continuously monitored in-situ during the run. After the exposure was completed, all nine devices were monitored for any change in their leakage current at 100 mV and room temperature for several weeks to monitor any annealing effects that may occur. Nine Photodiodes with the above varying diameters were radiated with 100 MeV/n Carbon Ions with a fluence of 10 6 , 10 7 , 10 8 , 10 9 , and 10 10 ions/cm 2 at each fluence level. At 100 MeV/n the Linear Energy Transfer (LET) of Carbon Ion is ~0.156 MeV-cm 2 /mg in Extended InGaAs, which is an order magnitude more than Proton (H) and Helium (He) Ions of 100 MeV/n energy. Thus, significant displacement damage is anticipated in the Extended InGaAs Photodiode with 100 MeV/n Carbon Ions with a total fluence of 1 × 1010 ions/cm 2 . Pre- and Post- radiation results were also measured for: (1) Leakage Current Vs. Voltage for the Extended InGaAs Photodiodes; (2) Responsivity (Quantum Efficiency) in A/W for Photodiodes; and (3) Bandwidth of the Photodiodes. All devices were found to be fully functional at the normal operating conditions and at both dry ice and room temperature. The leakage current increased up to a factor of ~2X at lower bias of 100 mV at the highest fluence of 10 10 ions/cm 2 , but not significantly at higher bias of 2 V. Finally, we did not observe any post radiation annealing effect for leakage current at room temperature and 100 mV bias for any of the devices after several weeks of data logging.

2.4 micron wavelength↗

DOE OSTI2021

Five-day track forecast skills of WRF model for the western North Pacific tropical cyclones

In this study, the characteristics of simulated tropical cyclones (TCs) over the western North Pacific by a regional model (the WRF Model) are verified. We utilize 12-km horizontal grid spacing, and simulations are integrated for 5 days from model initialization. A total of 125 forecasts are divided into five clusters through the k-means clustering method. The TCs in the cluster 1 and 2 (group 1), which includes many TCs moving northward in the subtropical region, generally have larger track errors than for TCs in cluster 3 and 4 (group 2). The optimal steering vector is used to examine the difference in the track forecast skill between these two groups. The bias in the steering vector between the model and analysis data is found to be more substantial for group 1 TCs than group 2 TCs. The larger steering vector difference for group 1 TCs indicates that environmental fields tend to be poorly simulated in group 1 TC cases. Furthermore, the residual terms, including the storm-scale process, asymmetric convection distribution, or beta-related effect, are also larger for group 1 TCs than group 2 TCs. Therefore, it is probable that the large track forecast error for group 1 TCs is a result of unreasonable simulations of environmental wind fields and residual processes in the midlatitudes.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Major Revisions in Arthropod Phylogeny Through Improved Supermatrix, With Support for Two Possible Waves of Land Invasion by Chelicerates

Deep phylogeny involving arthropod lineages is difficult to recover because the erosion of phylogenetic signals over time leads to unreliable multiple sequence alignment (MSA) and subsequent phylogenetic reconstruction. One way to alleviate the problem is to assemble a large number of gene sequences to compensate for the weakness in each individual gene. Such an approach has led to many robustly supported but contradictory phylogenies. A close examination shows that the supermatrix approach often suffers from two shortcomings. The first is that MSA is rarely checked for reliability and, as will be illustrated, can be poor. The second is that, to alleviate the problem of homoplasy at the third codon position of protein-coding genes due to convergent evolution of nucleotide frequencies, phylogeneticists may remove or degenerate the third codon position but may do it improperly and introduce new biases. We performed extensive reanalysis of one of such “big data” sets to highlight these two problems, and demonstrated the power and benefits of correcting or alleviating these problems. Our results support a new group with Xiphosura and Arachnopulmonata (Tetrapulmonata + Scorpiones) as sister taxa. This favors a new hypothesis in which the ancestor of Xiphosura and the extinct Eurypterida (sea scorpions, of which many later forms lived in brackish or freshwater) returned to the sea after the initial chelicerate invasion of land. Our phylogeny is supported even with the original data but processed with a new “principled” codon degeneration. We also show that removing the 1673 codon sites with both AGN and UCN codons (encoding serine) in our alignment can partially reconcile discrepancies between nucleotide-based and AA-based tree, partly because two sequences, one with AGN and the other with UCN, would be identical at the amino acid level but quite different at the nucleotide level.

59 BASIC BIOLOGICAL SCIENCES↗