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 (Ψ), 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 Ψ on the estimation of co-divergence variability. We also introduce a new setting (β) that can potentially improve estimation of Ψ 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 Ψ 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 β improves estimation of Ψ, 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 Ψ 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 Ψ 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 (“suckers”) is a diverse (76 species) and broadly distributed family of Holarctic freshwater fishes with a rich fossil record and a considerable number (∼35%) 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 “total-evidence” 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 Cretaceous–Eocene, 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 Asian–North 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 (1–2 °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 long‐lived 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 top‐down inverse modeling. Here we present the first annual (2013–2014) statewide top‐down 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 1.5–2.5 times (at 95% confidence) the state inventory (41 Gg N_2O in 2014). Without mitigation, this estimate represents 4–7% 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 (0.15 µM). 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 (>100 µM). 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 μ{\mu}m PAH Star Formation Rate Calibration with JWST MIRI

We test the relationship between UV-derived star formation rates (SFRs) and the 7.7 ${\mu}$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 ${\mu}$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, $L_{FUV}$, and UV-derived SFRs. We then fit SED models to the JWST/MIRI 7.7 - 21 ${\mu}$m CEERS data to derive rest-frame 7.7 ${\mu}$m luminosities, $L_{770}$, using the average flux density in the rest-frame MIRI F770W bandpass. We observe a correlation between $L_{770}$ and $L_{FUV}$, where log $L_{770}$ is proportional to (1.27+/-0.04) log $L_{FUV}$. $L_{770}$ 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 $L_{770}$ which has a scatter from model estimated SFRs (${{\sigma}_{{\Delta}SFR}}$) 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 ${\mu}$m luminosity, which has a scatter of ${{\sigma}_{{\Delta}SFR}}$ = 0.21 dex. The relatively small decrease in ${\sigma}$ suggests this is near the systematic accuracy of the total SFRs using either calibration. These results demonstrate that the rest-frame 7.7 ${\mu}$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

Evidence for a Shallow Evolution in the Volume Densities of Massive Galaxies at z=4z=4 to 88 from CEERS

We analyze the evolution of massive (log$_{10}$ [$M_\star/M_\odot$] $>10$) galaxies at $z \sim$ 4--8 selected from the JWST Cosmic Evolution Early Release Science (CEERS) survey. We infer the physical properties of all galaxies in the CEERS NIRCam imaging through spectral energy distribution (SED) fitting with dense basis to select a sample of high redshift massive galaxies. Where available we include constraints from additional CEERS observing modes, including 18 sources with MIRI photometric coverage, and 28 sources with spectroscopic confirmations from NIRSpec or NIRCam wide-field slitless spectroscopy. We sample the recovered posteriors in stellar mass from SED fitting to infer the volume densities of massive galaxies across cosmic time, taking into consideration the potential for sample contamination by active galactic nuclei (AGN). We find that the evolving abundance of massive galaxies tracks expectations based on a constant baryon conversion efficiency in dark matter halos for $z \sim$ 1--4. At higher redshifts, we observe an excess abundance of massive galaxies relative to this simple model. These higher abundances can be explained by modest changes to star formation physics and/or the efficiencies with which star formation occurs in massive dark matter halos, and are not in tension with modern cosmology.Comment: 20 pages, 10 figure