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At least 1,297 records · Page 72
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

SDSS IV MaNGA: characteristics of edge-on galaxies with a counter-rotating gaseous disc

ABSTRACT Counter-rotating components in galaxies are one of the most direct forms of evidence for past gas accretion or merging. We discovered 10 edge-on disc gaseous counter-rotators in a sample of 523 edge-on galaxies identified in the final MaNGA (Mapping Nearby Galaxies at APO) IFU sample. The counter-rotators tend to located in small groups. The gaseous counter-rotators have intermediate stellar masses and and located in the green valley and red sequence of the colour–magnitude diagram. The average vertical extents of the stellar and ionized gas discs are the same as for the rest of the sample while their radial gas and stellar distributions are more centrally concentrated. This may point at angular momentum loss during the formation process of the counter-rotating discs. The counter-rotators have low gas and dust content, weak emission-line strengths, and low star formation rates. This suggests that the formation of counter-rotators may be an efficient way to quench galaxies. One counter-rotator, SDSS J080016.09+292817.1 (Galaxy F), has a post-starburst region and a possible AGN at the centre. Another counter-rotator, SDSS J131234.03+482159.8 (Galaxy H), is identified as a potential ongoing galaxy interaction with its companion satellite galaxy, a gas-rich spiral galaxy. This may be representative case of a gaseous counter-rotator forming through a merger origin. However, tidal distortions expected in mergers are only found in a few of the galaxies and we cannot rule out direct gas accretion as another formation mechanism.

Beom, Minje↗
DOE OSTI2022

A multiwavelength study of the flat-spectrum radio quasar NVSS J141922−083830 covering four flaring episodes

We present multiwavelength observations and a model for flat-spectrum radio quasar (FSRQ) NVSS J141922−083830, originally classified as a blazar candidate of unknown type (BCU II object) in the Third Fermi-LAT AGN Catalog. Relatively bright flares (>3 magnitudes) were observed on 2015 February 21 (MJD 57074) and 2018 September 8 (MJD 58369) in the optical band with the MASTER Global Robotic Net telescopes. Optical spectra obtained with the Southern African Large Telescope on 2015 March 1 (MJD 57082), during outburst, and on 2017 May 30 (MJD 57903), during quiescence, showed emission lines at 5325 Å and at ≈3630 Å that we identified as the Mg II III] 1909 Å lines, respectively, and hence derived a redshift z = 0.903. Analysis of Fermi-Large Area Telescope (LAT) data was performed in the quiescent regime (5 yr of data) and during four prominent flaring states in 2014 February–April, 2014 October–November, 2015 February–March, and 2018 September. We present spectral and timing analysis with Fermi-LAT . We report a hardening of the gamma-ray spectrum during the last three flaring periods, with a power-law spectral index Γ = 2.0–2.1. The maximum gamma-ray flux level was observed on 2014 October 24 (MJD 56954) at (7.57 ± 1.83) × 10 −7 ph cm −2 s −1 . The multiwavelength spectral energy distribution (SED) during the 2015 February–March flare supports the earlier evidence of this blazar to belong to the FSRQ class. The SED can be well represented with a single-zone leptonic model with parameters typical of FSRQs, but also a hadronic origin of the high-energy emission cannot be ruled out.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

The Zwicky Transient Facility phase I sample of hydrogen-rich superluminous supernovae without strong narrow emission lines

ABSTRACT We present a sample of 14 hydrogen-rich superluminous supernovae (SLSNe II) from the Zwicky Transient Facility (ZTF) between 2018 and 2020. We include all classified SLSNe with peaks Mg < −20 mag with observed broad but not narrow Balmer emission, corresponding to roughly 20 per cent of all hydrogen-rich SLSNe in ZTF phase I. We examine the light curves and spectra of SLSNe II and attempt to constrain their power source using light-curve models. The brightest events are photometrically and spectroscopically similar to the prototypical SN 2008es, while others are found spectroscopically more reminiscent of non-superluminous SNe II, especially SNe II-L. 56Ni decay as the primary power source is ruled out. Light-curve models generally cannot distinguish between circumstellar interaction (CSI) and a magnetar central engine, but an excess of ultraviolet (UV) emission signifying CSI is seen in most of the SNe with UV data, at a wide range of photometric properties. Simultaneously, the broad H α profiles of the brightest SLSNe II can be explained through electron scattering in a symmetric circumstellar medium (CSM). In other SLSNe II without narrow lines, the CSM may be confined and wholly overrun by the ejecta. CSI, possibly involving mass lost in recent eruptions, is implied to be the dominant power source in most SLSNe II, and the diversity in properties is likely the result of different mass loss histories. Based on their radiated energy, an additional power source may be required for the brightest SLSNe II, however – possibly a central engine combined with CSI.

Kangas, T. (ORCID:0000000254770217)↗
DOE OSTI2022

Hubble Space Telescope Captures UGC 12591: bulge/disc properties, star formation and ‘missing baryons’ census in a very massive and fast-spinning hybrid galaxy

We present Hubble Space Telescope (HST) observations of the nearby, massive, highly rotating hybrid galaxy UGC 12591, along with observations in the UV to FIRbands. HST data in V, I, and H bands is used to disentangle the structural components. Surface photometry shows a dominance of the bulge over the disc with an H-band B/D ratio of $69{{\,\rm per\,cent}}$. The spectral energy distribution (SED) fitting reveals an extremely low global star formation rate (SFR) of $\rm \sim 0.1\!-\!0.2\, M_\odot \, yr^{-1}$, exceptionally low for the galaxy’s huge stellar mass of $\rm 1.6\times 10^{11}M_\odot$, implying a strong quenching of its SFR with a star formation efficiency of 3–5 per cent. For at least the past $\rm 10^{8}$ yr, the galaxy has remained in a quiescent state as a sterile, ‘red and dead’ galaxy. UGC 12591 hosts a supermassive black hole (SMBH) of $\rm 6.18\times 10^{8} \, M_\odot$, which is possibly quiescent at present, i.e. we neither see large ($\rm \gt 1 kpc$) radio jets nor the SMBH contributing significantly to the mid-IR SED, ruling out strong radiative feedback of AGN. We obtained a detailed census of all observable baryons with a total mass of $\rm 6.46\times 10^{11} \, M_\odot$ within the virial radius, amounting to a baryonic deficiency of ${\sim }85{{\,\rm per\,cent}}$ relative to the cosmological mean. Only a small fraction of these baryons reside in a warm/hot circumgalactic X-ray halo, while the majority are still unobservable. We discussed various astrophysical scenarios to explain its unusual properties. Our work is a major step forward in understanding the assembly history of such extremely massive, isolated galaxies.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

The most probable host of CHIME FRB 190425A, associated with binary neutron star merger GW190425, and a late-time transient search

The identification and localization of fast radio bursts (FRBs) to their host galaxies have revealed important details about the progenitors of these mysterious, millisecond-long bursts of coherent radio emission. In this work, we study the most probable host galaxy of the apparently non-repeating CHIME/FRB event FRB 20190425A – a particularly high-luminosity, low-dispersion measure event that was demonstrated in a recent paper to be temporally and spatially coincident with the LIGO-Virgo-KAGRA binary neutron star merger GW190425, suggesting an astrophysical association ( p -value 0.0052). In this paper, we remain agnostic to this result, and we confirm UGC10667 as the most probable host galaxy of FRB 20190425A, demonstrating that the host galaxies of low-dispersion measure, one-off CHIME FRBs can be plausibly identified. We then perform multiwavelength observations to characterize the galaxy and search for any afterglow emission associated with the FRB and its putative GW counterpart. We find no radio or optical transient emission in our observations 2.5 yr post-burst. UGC10667 is a spiral galaxy at z ∼ 0.03, dominated by an old stellar population. We find no evidence of a large population of young stars, with nebular emission dominated by star formation at a rate of 1 -2 M $\odot$ yr -1 . While we cannot rule out a young magnetar as the origin of FRB 20190425A, our observations are consistent with an origin in a long delay-time neutron star binary merger.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

SN 2021fxy: mid-ultraviolet flux suppression is a common feature of Type Ia supernovae

ABSTRACT We present ultraviolet (UV) to near-infrared (NIR) observations and analysis of the nearby Type Ia supernova SN 2021fxy. Our observations include UV photometry from Swift/UVOT, UV spectroscopy from HST/STIS, and high-cadence optical photometry with the Swope 1-m telescope capturing intranight rises during the early light curve. Early B − V colours show SN 2021fxy is the first ‘shallow-silicon’ (SS) SN Ia to follow a red-to-blue evolution, compared to other SS objects which show blue colours from the earliest observations. Comparisons to other spectroscopically normal SNe Ia with HST UV spectra reveal SN 2021fxy is one of several SNe Ia with flux suppression in the mid-UV. These SNe also show blueshifted mid-UV spectral features and strong high-velocity Ca ii features. One possible origin of this mid-UV suppression is the increased effective opacity in the UV due to increased line blanketing from high velocity material, but differences in the explosion mechanism cannot be ruled out. Among SNe Ia with mid-UV suppression, SNe 2021fxy and 2017erp show substantial similarities in their optical properties despite belonging to different Branch subgroups, and UV flux differences of the same order as those found between SNe 2011fe and 2011by. Differential comparisons to multiple sets of synthetic SN Ia UV spectra reveal this UV flux difference likely originates from a luminosity difference between SNe 2021fxy and 2017erp, and not differing progenitor metallicities as suggested for SNe 2011by and 2011fe. These comparisons illustrate the complicated nature of UV spectral formation, and the need for more UV spectra to determine the physical source of SNe Ia UV diversity.

Astronomy & Astrophysics↗
DOE OSTI2023

Spectroscopic survey of faint planetary-nebula nuclei – II. The subdwarf O central star of Fr 2-30

Fr 2-30 = PN? G126.8−15.5 is a faint emission nebula, hosting a 14th-mag central star that we identify here for the first time. Deep Hα and [O III ] images reveal a roughly elliptical nebula with dimensions of at least 22 arcmin × 14 arcmin, fading into a surrounding network of even fainter emission. Optical spectrograms of the central star show it to have a subdwarf O spectral type, with a Gaia parallax distance of 890 pc. A model-atmosphere analysis gives parameters of T eff = 60 000 K, log g = 6.0, and a low helium content of n He /n H = 0.0017. The location of the central star in the log g–T eff plane is inconsistent with a post-asymptotic-giant-branch evolutionary status. Two alternatives are that it is a helium-burning post-extreme-horizontal-branch object, or a hydrogen-burning post-red-giant-branch star. In either case, the evolutionary ages are so long that a detectable planetary nebula (PN) should not be present. We find evidence for a variable radial velocity (RV), suggesting that the star is a close binary. However, there are no photometric variations, and the spectral-energy distribution rules out a companion earlier than M2 V. The RVs of the star and surrounding nebula are discordant, and the nebula lacks typical PN morphology. We suggest that Fr 2-30 is a ‘PN mimic’ – the result of a chance encounter between the hot sdO star and an interstellar cloud. However, we note the puzzling fact that there are several nuclei of genuine PNe that are known to be in evolutionary states similar to that of the Fr 2-30 central star.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

An empirical approach to model selection: weak lensing and intrinsic alignments

ABSTRACT In cosmology, we routinely choose between models to describe our data, and can incur biases due to insufficient models or lose constraining power with overly complex models. In this paper, we propose an empirical approach to model selection that explicitly balances parameter bias against model complexity. Our method uses synthetic data to calibrate the relation between bias and the χ2 difference between models. This allows us to interpret χ2 values obtained from real data (even if catalogues are blinded) and choose a model accordingly. We apply our method to the problem of intrinsic alignments – one of the most significant weak lensing systematics, and a major contributor to the error budget in modern lensing surveys. Specifically, we consider the example of the Dark Energy Survey Year 3 (DES Y3), and compare the commonly used non-linear alignment (NLA) and tidal alignment and tidal torque (TATT) models. The models are calibrated against bias in the Ωm–S8 plane. Once noise is accounted for, we find that it is possible to set a threshold Δχ2 that guarantees an analysis using NLA is unbiased at some specified level Nσ and confidence level. By contrast, we find that theoretically defined thresholds (based on, e.g. p-values for χ2) tend to be overly optimistic, and do not reliably rule out cosmological biases up to ∼1–2σ. Considering the real DES Y3 cosmic shear results, based on the reported difference in χ2 from NLA and TATT analyses, we find a roughly $30{{\ \rm per\ cent}}$ chance that were NLA to be the fiducial model, the results would be biased (in the Ωm–S8 plane) by more than 0.3σ. More broadly, the method we propose here is simple and general, and requires a relatively low level of resources. We foresee applications to future analyses as a model selection tool in many contexts.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Search for subsolar-mass black hole binaries in the second part of Advanced LIGO’s and Advanced Virgo’s third observing run

ABSTRACT We describe a search for gravitational waves from compact binaries with at least one component with mass $0.2$–$1.0 \, \mathrm{M}_\odot$ and mass ratio q ≥ 0.1 in Advanced Laser Interferometer Gravitational-Wave Observatory (LIGO) and Advanced Virgo data collected between 2019 November 1, 15:00 utc and 2020 March 27, 17:00 utc. No signals were detected. The most significant candidate has a false alarm rate of $0.2 \, \rm {yr}^{-1}$. We estimate the sensitivity of our search over the entirety of Advanced LIGO’s and Advanced Virgo’s third observing run, and present the most stringent limits to date on the merger rate of binary black holes with at least one subsolar-mass component. We use the upper limits to constrain two fiducial scenarios that could produce subsolar-mass black holes: primordial black holes (PBH) and a model of dissipative dark matter. The PBH model uses recent prescriptions for the merger rate of PBH binaries that include a rate suppression factor to effectively account for PBH early binary disruptions. If the PBHs are monochromatically distributed, we can exclude a dark matter fraction in PBHs $f_\mathrm{PBH} \gtrsim \, 0.6$ (at 90 per cent confidence) in the probed subsolar-mass range. However, if we allow for broad PBH mass distributions, we are unable to rule out fPBH = 1. For the dissipative model, where the dark matter has chemistry that allows a small fraction to cool and collapse into black holes, we find an upper bound fDBH < 10−5 on the fraction of atomic dark matter collapsed into black holes.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

The Dark Energy Survey Supernova Program: slow supernovae show cosmological time dilation out to z ~ 1.

ABSTRACT We present a precise measurement of cosmological time dilation using the light curves of 1504 Type Ia supernovae from the Dark Energy Survey spanning a redshift range $0.1\lesssim z\lesssim 1.2$. We find that the width of supernova light curves is proportional to $(1+z)$, as expected for time dilation due to the expansion of the Universe. Assuming Type Ia supernovae light curves are emitted with a consistent duration $\Delta t_{\rm em}$, and parametrizing the observed duration as $\Delta t_{\rm obs}=\Delta t_{\rm em}(1+z)^b$, we fit for the form of time dilation using two methods. First, we find that a power of $b \approx 1$ minimizes the flux scatter in stacked subsamples of light curves across different redshifts. Secondly, we fit each target supernova to a stacked light curve (stacking all supernovae with observed bandpasses matching that of the target light curve) and find $b=1.003\pm 0.005$ (stat) $\pm \, 0.010$ (sys). Thanks to the large number of supernovae and large redshift-range of the sample, this analysis gives the most precise measurement of cosmological time dilation to date, ruling out any non-time-dilating cosmological models at very high significance.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

The variability structure function of the highest luminosity quasars on short time-scales

ABSTRACT The stochastic photometric variability of quasars is known to follow a random-walk phenomenology on emission time-scales of months to years. Some high-cadence rest-frame optical monitoring in the past has hinted at a suppression of variability amplitudes on shorter time-scales of a few days or weeks, opening the question of what drives the suppression and how it might scale with quasar properties. Here, we study a few thousand of the highest luminosity quasars in the sky, mostly in the luminosity range of $L_{\rm bol}$$=[46.4, 47.3]$ and redshift range of $z=[0.7, 2.4]$. We use a data set from the NASA/Asteroid Terrestrial-impact Last Alert System facility with nightly cadence, weather permitting, which has been used before to quantify strong regularity in longer term rest-frame-UV variability. As we focus on a careful treatment of short time-scales across the sample, we find that a linear function is sufficient to describe the UV variability structure function. Although the result can not rule out the existence of breaks in some groups completely, a simpler model is usually favoured under this circumstance. In conclusion, the data are consistent with a single-slope random walk across rest-frame time-scales of $\Delta t=[10, 250]$ d.

Tang, Ji-Jia (ORCID:0000000218600886)↗
DOE OSTI2024

A VLBA-uGMRT search for candidate binary black holes: study of six X-shaped radio galaxies with double-peaked emission lines

ABSTRACT Identifying methods to discover dual active galactic nucleus (AGN) has proven to be challenging. Several indirect tracers have been explored in the literature, including X/S-shaped radio morphologies and double-peaked (DP) emission lines in the optical spectra. However, the detection rates of confirmed dual AGN candidates from the individual methods remain extremely small. We search for binary black holes (BBH) in a sample of six sources that exhibit both X-shaped radio morphology and DP emission lines using the Very Long Baseline Array (VLBA). Three out of the six sources show dual VLBA compact components, making them strong candidates for BBH sources. In addition, we present deep uGMRT images revealing the exquisite details of the X-shaped wings in three sources. We present a detailed precession modeling analysis of these sources. The black hole separations estimated from the simplistic geodetic precession model are incompatible with those estimated from emission line offsets and the VLBA separations. However, precession induced by a non-coplanar secondary black hole is a feasible mechanism for explaining the observed X-shaped radio morphologies and the black hole separations estimated from other methods. The black hole separations estimated from the double-peaked emission lines agree well with the VLBA compact component separations. Future multifrequency VLBA observations will be critical in ruling out or confirming the BBH scenario in the three galaxies with dual component detections.

Sebastian, Biny (ORCID:0000000184286525)↗
DOE OSTI2025

Strange quark matter as dark matter: 40 yr later, a reappraisal

ABSTRACT Forty years ago Witten suggested that dark matter could be composed of macroscopic clusters of strange quark matter. This idea was very popular for several years, but it dropped out of fashion once lattice quantum chromodynamics calculations indicated that the confinement/deconfinement transition, at small baryonic chemical potential, is not first order, which seemed to be a crucial requirement in order to produce large clusters of quarks. Here, we revisit the conditions under which strangelets can be produced in the Early Universe. We discuss the impact of an instability in the hadronic phase separating a low density, positive-strange-charge phase from a high-density phase with a negative strange charge. This second phase can rapidly stabilize by forming colour-superconducting gaps. The strangelets then undergo partial evaporation. In this way, we obtain distributions of their sizes in agreement with the observational constraints and we discuss the many astrophysical and cosmological implications of these objects. Finally, we examine the most promising techniques to detect this type of strangelets. We also show that strangelets can exist with masses $\lesssim $1017 g, while primordial black holes are ruled out in that mass range, allowing us to distinguish between these two dark matter candidates.

Clemente, Francesco Di (ORCID:0000000282573819)↗
DOE OSTI2025

The luminous, slow-rising orphan afterglow AT2019pim as a candidate moderately relativistic outflow

ABSTRACT Classical gamma-ray bursts (GRBs) have two distinct emission episodes: prompt emission from ultrarelativistic ejecta and afterglow from shocked circumstellar material. While both components are extremely luminous in known GRBs, a variety of scenarios predict the existence of luminous afterglow emission with little or no associated high-energy prompt emission. We present AT 2019pim, the first spectroscopically confirmed afterglow with no observed high-energy emission to be identified. Serendipitously discovered during follow-up observations of a gravitational-wave trigger and located in a contemporaneous TESS sector, it is hallmarked by a fast-rising ($t \approx 2$ h), luminous ($M_{\rm UV,peak} \approx -24.4$ mag) optical transient with accompanying luminous X-ray and radio emission. No gamma-ray emission consistent with the time and location of the transient was detected by Fermi-GBM or by Konus, placing constraining limits on an accompanying GRB. We investigate several independent observational aspects of the afterglow in the context of constraints on relativistic motion and find all of them are consistent with an initial Lorentz factor of $\Gamma _0 \approx$ 10–30 for the on-axis material, significantly lower than in any well-observed GRB and consistent with the theoretically predicted ‘dirty fireball’ scenario in which the high-energy prompt emission is stifled by pair production. However, we cannot rule out a structured jet model in which only the line-of-sight material was ejected at low-$\Gamma$, off-axis from a classical high-$\Gamma$ jet core, and an on-axis GRB with below-average gamma-ray efficiency also remains a possibility. This event represents a milestone in orphan afterglow searches, demonstrating that luminous optical afterglows lacking detected GRB counterparts can be identified and spectroscopically confirmed in real time.

Perley, Daniel A. (ORCID:0000000184721996)↗
DOE OSTI2025

Forecasting constraints on the high-z IGM thermal state from the Lyman-α forest flux autocorrelation function

ABSTRACT The autocorrelation function of the Lyman-$\alpha$ (Ly $\alpha$) forest flux from high-z quasars probes the small-scale structure of the intergalactic medium (IGM). The thermal state of the IGM, determined by the physics of reionization, sets the small-scale power observed in the Ly $\alpha$ forest. To explore the sensitivity of the autocorrelation function to the IGM’s thermal state, we compute the autocorrelation function from a cosmological hydrodynamical simulation with an instantaneous reionization model and 135 post-processed thermal states. Using mock data sets of 20 quasars, we forecast constraints on $T_0$ and $\gamma$, which characterize the post-processed IGM thermal state, at $5.4 \le z \le 6$. While this model simplifies the IGM’s thermal state, it serves as a key first step in assessing future observational prospects. We also perform an inference test on mocks and re-weight out posterior distributions to guarantee that they exhibit statistically correct behaviour. At $z = 5.4$, we find that an idealized data set constrains $T_0$ to 59 per cent and $\gamma$ to 16 per cent at the 1$\sigma$ equivalent confidence level. To explore more realistic, non-instantaneous reionization scenarios, we analyse four models combining temperature and ultraviolet background (UVB) fluctuations at $z = 5.8$. We find that mock data generated from a model with both temperature and UVB fluctuations can rule out a model with only temperature fluctuations at the $> 1\sigma$ level 73.9 per cent of the time.

Wolfson, Molly↗
DOE OSTI2020

From hydrogen to helium: the spectral evolution of white dwarfs as evidence for convective mixing

ABSTRACT We present a study of the hypothesis that white dwarfs undergo a spectral change from hydrogen- to helium-dominated atmospheres using a volume-limited photometric sample drawn from the Gaia-DR2 catalogue, the Sloan Digital Sky Survey (SDSS), and the Galaxy Evolution Explorer (GALEX). We exploit the strength of the Balmer jump in hydrogen-atmosphere DA white dwarfs to separate them from helium-dominated objects in SDSS colour space. Across the effective temperature range from 20 000 to 9000 K, we find that 22 per cent of white dwarfs will undergo a spectral change, with no spectral evolution being ruled out at 5σ. The most likely explanation is that the increase in He-rich objects is caused by the convective mixing of DA stars with thin hydrogen layers, in which helium is dredged up from deeper layers by a surface hydrogen convection zone. The rate of change in the fraction of He-rich objects as a function of temperature, coupled with a recent grid of 3D radiation-hydrodynamic simulations of convective DA white dwarfs – which include the full overshoot region – lead to a discussion on the distribution of total hydrogen mass in white dwarfs. We find that 60 per cent of white dwarfs must have a hydrogen mass larger than MH/MWD = 10−10, another 25 per cent have masses in the range MH/MWD = 10−14–10−10, and 15 per cent have less hydrogen than MH/MWD = 10−14. These results have implications for white dwarf asteroseismology, stellar evolution through the asymptotic giant branch and accretion of planetesimals on to white dwarfs.

Cunningham, Tim↗
DOE OSTI2023

Inferring Viral Transmission Time from Phylogenies for Known Transmission Pairs

When the time of an HIV transmission event is unknown, methods to identify it from virus genetic data can reveal the circumstances that enable transmission. We developed a single-parameter Markov model to infer transmission time from an HIV phylogeny constructed of multiple virus sequences from people in a transmission pair. Our method finds the statistical support for transmission occurring in different possible time slices. We compared our time-slice model results to previously described methods: a tree-based logical transmission interval, a simple parsimony-like rules-based method, and a more complex coalescent model. Across simulations with multiple transmitted lineages, different transmission times relative to the source’s infection, and different sampling times relative to transmission, we found that overall our time-slice model provided accurate and narrower estimates of the time of transmission. We also identified situations when transmission time or direction was difficult to estimate by any method, particularly when transmission occurred long after the source was infected and when sampling occurred long after transmission. Applying our model to real HIV transmission pairs showed some agreement with facts known from the case investigations. We also found, however, that uncertainty on the inferred transmission time was driven more by uncertainty from time calibration of the phylogeny than from the model inference itself. Encouragingly, comparable performance of the Markov time-slice model and the coalescent model—which make use of different information within a tree—suggests that a new method remains to be described that will make full use of the topology and node times for improved transmission time inference.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

DRAM for distilling microbial metabolism to automate the curation of microbiome function

Abstract Microbial and viral communities transform the chemistry of Earth's ecosystems, yet the specific reactions catalyzed by these biological engines are hard to decode due to the absence of a scalable, metabolically resolved, annotation software. Here, we present DRAM (Distilled and Refined Annotation of Metabolism), a framework to translate the deluge of microbiome-based genomic information into a catalog of microbial traits. To demonstrate the applicability of DRAM across metabolically diverse genomes, we evaluated DRAM performance on a defined, in silico soil community and previously published human gut metagenomes. We show that DRAM accurately assigned microbial contributions to geochemical cycles and automated the partitioning of gut microbial carbohydrate metabolism at substrate levels. DRAM-v, the viral mode of DRAM, established rules to identify virally-encoded auxiliary metabolic genes (AMGs), resulting in the metabolic categorization of thousands of putative AMGs from soils and guts. Together DRAM and DRAM-v provide critical metabolic profiling capabilities that decipher mechanisms underpinning microbiome function.

59 BASIC BIOLOGICAL SCIENCES↗