153 research outputs found
Strategies for improving approximate Bayesian computation tests for synchronous diversification
Background: Estimating the variability in isolation times across co-distributed taxon pairs that may have experienced the same allopatric isolating mechanism is a core goal of comparative phylogeography. The use of hierarchical Approximate Bayesian Computation (ABC) and coalescent models to infer temporal dynamics of lineage co-diversification has been a contentious topic in recent years. Key issues that remain unresolved include the choice of an appropriate prior on the number of co-divergence events (Κ), as well as the optimal strategies for data summarization.
Methods: Through simulation-based cross validation we explore the impact of the strategy for sorting summary statistics and the choice of prior on Κ on the estimation of co-divergence variability. We also introduce a new setting (ÎČ) that can potentially improve estimation of Κ by enforcing a minimal temporal difference between pulses of co-divergence. We apply this new method to three empirical datasets: one dataset each of co-distributed taxon pairs of Panamanian frogs and freshwater fishes, and a large set of Neotropical butterfly sister-taxon pairs.
Results: We demonstrate that the choice of prior on Κ has little impact on inference, but that sorting summary statistics yields substantially more reliable estimates of co-divergence variability despite violations of assumptions about exchangeability. We find the implementation of ÎČ improves estimation of Κ, with improvement being most dramatic given larger numbers of taxon pairs. We find equivocal support for synchronous co-divergence for both of the Panamanian groups, but we find considerable support for asynchronous divergence among the Neotropical butterflies.
Conclusions: Our simulation experiments demonstrate that using sorted summary statistics results in improved estimates of the variability in divergence times, whereas the choice of hyperprior on Κ has negligible effect. Additionally, we demonstrate that estimating the number of pulses of co-divergence across co-distributed taxonpairs is improved by applying a flexible buffering regime over divergence times. This improves the correlation between Κ and the true variability in isolation times and allows for more meaningful interpretation of this hyperparameter. This will allow for more accurate identification of the number of temporally distinct pulses of codivergence that generated the diversification pattern of a given regional assemblage of sister-taxon-pairs
Phylogeny and divergence times of suckers (Cypriniformes: Catostomidae) inferred from Bayesian total-evidence analyses of molecules, morphology, and fossils
Catostomidae (âsuckersâ) is a diverse (76 species) and broadly distributed family of Holarctic freshwater fishes with a rich fossil record and a considerable number (âŒ35%) of threatened and imperiled species. We integrate DNA sequences (three mitochondrial genes, three nuclear genes), morphological data, and fossil information to infer sucker phylogenetic relationships and divergence times using Bayesian âtotal-evidenceâ methods, and then test hypotheses about the temporal diversification of the group. Our analyses resolved many nodes within subfamilies and clarified Catostominae relationships to be of the form ((Thoburniini, Moxostomatini), (Erimyzonini, Catostomini)). Patterns of subfamily relationships were incongruent, but mainly supported two placements of the Myxocyprininae; distinguishing these using Bayes factors lent strongest support to a model with Myxocyprininae sister to all remaining sucker lineages. We improved our Bayesian total-evidence dating analysis by excluding problematic characters, using a clock-partitioning scheme identified by Bayesian model selection, and employing a fossilized birth-death tree prior accommodating morphological data and fossils. The resulting chronogram showed that suckers evolved since the Late CretaceousâEocene, and that the Catostomini and Moxostomatini clades have accumulated species diversity since the early to mid-Miocene. These results agree with the fossil record and confirm previous hypotheses about dates for the origins of Catostomide and catostomine diversification, but reject previous molecular hypotheses about the timing of divergence of ictiobines, and between AsianâNorth American lineages. Overall, our findings from a synthesis of multiple data types enhance understanding of the phylogenetic relationships, taxonomic classification, and temporal diversification of suckers, while also highlighting practical methods for improving Bayesian divergence dating models by coupling phylogenetic informativeness profiling with relaxed-clock partitioning
A realistic meteorological assessment of perennial biofuel crop deployment: a Southern Great Plains perspective
Utility of perennial bioenergy crops (e.g., switchgrass and miscanthus) offers unique opportunities to transition
toward a more sustainable energy pathway due to their reduced carbon footprint, averted competition with food
crops, and ability to grow on abandoned and degraded farmlands. Studies that have examined biogeophysical
impacts of these crops noted a positive feedback between near-surface cooling and enhanced evapotranspiration
(ET), but also potential unintended consequences of soil moisture and groundwater depletion. To better understand
hydrometeorological effects of perennial bioenergy crop expansion, this study conducted high-resolution
(2-km grid spacing) simulations with a state-of-the-art atmospheric model (Weather Research and Forecasting
system) dynamically coupled to a land surface model. We applied the modeling system over the Southern Plains
of the United States during a normal precipitation year (2007) and a drought year (2011). By focusing the
deployment of bioenergy cropping systems on marginal and abandoned farmland areas (to reduce the potential
conflict with food systems), the research presented here is the first realistic examination of hydrometeorological
impacts associated with perennial bioenergy crop expansion. Our results illustrate that the deployment of perennial
bioenergy crops leads to widespread cooling (1â2 °C) that is largely driven by an enhanced reflection of
shortwave radiation and, secondarily, due to an enhanced ET. Bioenergy crop deployment was shown to reduce
the impacts of drought through simultaneous moistening and cooling of the near-surface environment. However,
simulated impacts on near-surface cooling and ET were reduced during the drought relative to a normal
precipitation year, revealing differential effects based on background environmental conditions. This study
serves as a key step toward the assessment of hydroclimatic sustainability associated with perennial bioenergy
crop expansion under diverse hydrometeorological conditions by highlighting the driving mechanisms and processes
associated with this energy pathway.This work was funded by NSF Grant EAR-1204774S
Inverse Estimation of an Annual Cycle of California's Nitrous Oxide Emissions
Nitrous oxide (N_2O) is a potent longâlived greenhouse gas (GHG) and the strongest current emissions of global anthropogenic stratospheric ozone depletion weighted by its ozone depletion potential. In California, N_2O is the third largest contributor to the state's anthropogenic GHG emission inventory, though no study has quantified its statewide annual emissions through topâdown inverse modeling. Here we present the first annual (2013â2014) statewide topâdown estimates of anthropogenic N_2O emissions. Utilizing continuous N_2O observations from six sites across California in a hierarchical Bayesian inversion, we estimate that annual anthropogenic emissions are 1.5â2.5 times (at 95% confidence) the state inventory (41 Gg N_2O in 2014). Without mitigation, this estimate represents 4â7% of total GHG emissions assuming that other reported GHG emissions are reasonably correct. This suggests that control of N_2O could be an important component in meeting California's emission reduction goals of 40% and 80% below 1990 levels of the total GHG emissions (in CO_2 equivalent) by 2030 and 2050, respectively. Our seasonality analysis suggests that emissions are similar across seasons within posterior uncertainties. Future work is needed to provide source attribution for subregions and further characterization of seasonal variability
Thermoelastic Properties of Ringwoodite [Fe_x,Mg_(1-x)]_2SiO_4: Its Relationship to the 520 km Seismic Discontinuity
We combine density functional theory (DFT) within the local density
approximation (LDA), the quasiharmonic approximation (QHA), and a model
vibrational density of states (VDoS) to calculate elastic moduli and sound
velocities of gamma-[Fe_x,Mg_(1-x)]_2SiO_4 (ringwoodite), the most abundant
mineral of the lower Earth's transition zone (TZ). Comparison with experimental
values at room-temperature and high pressure or ambient-pressure and high
temperature shows good agreement with our first-principles findings. Then, we
investigate the contrasts associated with the
beta-to-gamma-[Fe_x,Mg_(1-x)]_2SiO_4 transformation at pressures and
temperatures relevant to the TZ. This information offers clearly defined
reference values to advance the understanding of the nature of the 520 km
seismic discontinuity.Comment: 29 pages, 6 figures, 2 tables. Under Revie
Thiostrepton inhibits stable 70S ribosome binding and ribosome-dependent GTPase activation of elongation factor G and elongation factor 4
Thiostrepton, a macrocyclic thiopeptide antibiotic, inhibits prokaryotic translation by interfering with the function of elongation factor G (EF-G). Here, we have used 70S ribosome binding and GTP hydrolysis assays to study the effects of thiostrepton on EF-G and a newly described translation factor, elongation factor 4 (EF4). In the presence of thiostrepton, ribosome-dependent GTP hydrolysis is inhibited for both EF-G and EF4, with IC(50) values equivalent to the 70S ribosome concentration (0.15â”M). Further studies indicate the mode of thiostrepton inhibition is to abrogate the stable binding of EF-G and EF4 to the 70S ribosome. In support of this model, an EF-G truncation variant that does not possess domains IV and V was shown to possess ribosome-dependent GTP hydrolysis activity that was not affected by the presence of thiostrepton (>100â”M). Lastly, chemical footprinting was employed to examine the nature of ribosome interaction and tRNA movements associated with EF4. In the presence of non-hydrolyzable GTP, EF4 showed chemical protections similar to EF-G and stabilized a ratcheted state of the 70S ribosome. These data support the model that thiostrepton inhibits stable GTPase binding to 70S ribosomal complexes, and a model for the first step of EF4-catalyzed reverse-translocation is presented
CEERS: 7.7 m PAH Star Formation Rate Calibration with JWST MIRI
We test the relationship between UV-derived star formation rates (SFRs) and
the 7.7 m polycyclic aromatic hydrocarbon (PAH) luminosities from the
integrated emission of galaxies at z ~ 0 - 2. We utilize multi-band photometry
covering 0.2 - 160 m from HST, CFHT, JWST, Spitzer, and Herschel for
galaxies in the Cosmic Evolution Early Release Science (CEERS) Survey. We
perform spectral energy distribution (SED) modeling of these data to measure
dust-corrected far-UV (FUV) luminosities, , and UV-derived SFRs. We
then fit SED models to the JWST/MIRI 7.7 - 21 m CEERS data to derive
rest-frame 7.7 m luminosities, , using the average flux density
in the rest-frame MIRI F770W bandpass. We observe a correlation between
and , where log is proportional to (1.27+/-0.04)
log . diverges from this relation for galaxies at lower
metallicities, lower dust obscuration, and for galaxies dominated by evolved
stellar populations. We derive a "single-wavelength" SFR calibration for
which has a scatter from model estimated SFRs
() of 0.24 dex. We derive a "multi-wavelength"
calibration for the linear combination of the observed FUV luminosity
(uncorrected for dust) and the rest-frame 7.7 m luminosity, which has a
scatter of = 0.21 dex. The relatively small decrease
in suggests this is near the systematic accuracy of the total SFRs
using either calibration. These results demonstrate that the rest-frame 7.7
m emission constrained by JWST/MIRI is a tracer of the SFR for distant
galaxies to this accuracy, provided the galaxies are dominated by
star-formation with moderate-to-high levels of attenuation and metallicity.Comment: 20 pages, 11 figures, 2 tables, submitted to Ap
Structure in phase space associated with spiral and bar density waves in an N-body galactic disk
An N-body hybrid simulation, integrating both massive and tracer particles,
of a Galactic disk is used to study the stellar phase space distribution or
velocity distributions in different local neighborhoods. Pattern speeds
identified in Fourier spectrograms suggest that two-armed and three-armed
spiral density waves, a bar and a lopsided motion are coupled in this
simulation, with resonances of one pattern lying near resonances of other
patterns. We construct radial and tangential (uv) velocity distributions from
particles in different local neighborhoods. More than one clump is common in
these local velocity distributions regardless of the position in the disk.
Features in the velocity distribution observed at one galactic radius are also
seen in nearby neighborhoods (at larger and smaller radii) but with shifted
mean v values. This is expected if the v velocity component of a clump sets the
mean orbital galactic radius of its stars. We find that gaps in the velocity
distribution are associated with the radii of kinks or discontinuities in the
spiral arms. These gaps also seem to be associated with Lindblad resonances
with spiral density waves and so denote boundaries between different dominant
patterns in the disk. We discuss implications for interpretations of the Milky
Way disk based on local velocity distributions. Velocity distributions created
from regions just outside the bar's Outer Lindblad resonance and with the bar
oriented at 45 degrees from the Sun-Galactic center line more closely resemble
that seen in the solar neighborhood (triangular in shape at lower uv and with a
Hercules like stream) when there is a strong nearby spiral arm, consistent with
the observed Centaurus Arm tangent, just interior to the solar neighborhood.Comment: accepted for publication in MNRA
Characterizing the Average Interstellar Medium Conditions of Galaxies at 5.6-9 with UV and Optical Nebular Lines
Ultraviolet (UV; rest-frame A) spectra provide a wealth of
diagnostics to characterize fundamental galaxy properties, such as their
chemical enrichment, the nature of their stellar populations, and their amount
of Lyman-continuum (LyC) radiation. In this work, we leverage publicly released
JWST data to construct the rest-frame UV-to-optical composite spectrum of a
sample of 63 galaxies at , spanning the wavelength range from 1500 to
5200 A. Based on the composite spectrum, we derive an average dust attenuation
from \hb/\hg, electron density cm from the [O II] doublet ratio, electron
temperature K from the [O III] / [O
III] ratio, and an ionization parameter
from the [O III]/[O II] ratio. Using a direct
method, we calculate an oxygen abundance
and the carbon-to-oxygen (C/O) abundance
ratio . This C/O ratio is smaller
than compared to and - 4 star-forming galaxies, albeit with
moderate significance. This indicates the reionization-era galaxies might be
undergoing a rapid build-up of stellar mass with high specific star-formation
rates. A UV diagnostic based on the ratios of C III]
/He II versus O III] /He II
suggests that the star formation is the dominant source of
ionization, similar to the local extreme dwarf galaxies and - 4 He
II-detected galaxies. The [O III]/[O II] and C IV/C III] ratios of the
composite spectrum are marginally larger than the criteria used to select
galaxies as LyC leakers, suggesting that some of the galaxies in our sample are
strong contributors to the reionizing radiation.Comment: 21 pages, 7 figures, 4 tables. Submitted. Comments are welcom
- âŠ