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

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

Spectroscopic confirmation of CEERS NIRCam-selected galaxies at z≃8−10\boldsymbol{z \simeq 8-10}

We present JWST/NIRSpec prism spectroscopy of seven galaxies selected from the Cosmic Evolution Early Release Science Survey (CEERS) NIRCam imaging with photometric redshifts z_phot>8. We measure emission line redshifts of z=7.65 and 8.64 for two galaxies, and z=9.77(+0.37,-0.29) and 10.01(+0.14,-0.19) for two others via the detection of continuum breaks consistent with Lyman-alpha opacity from a mostly neutral intergalactic medium. The presence (absense) of strong breaks (strong emission lines) give high confidence that these two galaxies are at z>9.6, but the break-derived redshifts have large uncertainties given the low spectral resolution and relatively low signal-to-noise of the CEERS NIRSpec prism data. The two z~10 sources are relatively luminous (M_UV<-20), with blue continua (-2.3<beta<-1.9) and low dust attenuation (A_V=0.15(+0.3,-0.1)); and at least one of them has high stellar mass for a galaxy at that redshift (log(M_*/M_sol)=9.3(+0.2,-0.3)). Considered together with spectroscopic observations of other CEERS NIRCam-selected high-z galaxy candidates in the literature, we find a high rate of redshift confirmation and low rate of confirmed interlopers (8.3%). Ten out of 34 z>8 candidates with CEERS NIRSpec spectroscopy do not have secure redshifts, but the absence of emission lines in their spectra is consistent with redshifts z>9.6. We find that z>8 photometric redshifts are generally in agreement (within uncertainties) with the spectroscopic values. However, the photometric redshifts tend to be slightly overestimated (average Delta(z)=0.50+/-0.12), suggesting that current templates do not fully describe the spectra of very high-z sources. Overall, our results solidifies photometric evidence for a high space density of bright galaxies at z>8 compared to theoretical model predictions, and further disfavors an accelerated decline in the integrated UV luminosity density at z>8.Comment: Submitted to ApJL. 24 pages, 9 figures, 7 tables. File with Table 6 included in source .tar fil

The Physical Conditions of Emission-Line Galaxies at Cosmic Dawn from JWST/NIRSpec Spectroscopy in the SMACS 0723 Early Release Observations

We present rest-frame optical emission-line flux ratio measurements for five $z>5$ galaxies observed by the JWST Near-Infared Spectrograph (NIRSpec) in the SMACS 0723 Early Release Observations. We add several quality-control and post-processing steps to the NIRSpec pipeline reduction products in order to ensure reliable relative flux calibration of emission lines that are closely separated in wavelength, despite the uncertain \textit{absolute} spectrophotometry of the current version of the reductions. Compared to $z\sim3$ galaxies in the literature, the $z>5$ galaxies have similar [OIII]$\lambda$5008/H$\beta$ ratios, similar [OIII]$\lambda$4364/H$\gamma$ ratios, and higher ($\sim$0.5 dex) [NeIII]$\lambda$3870/[OII]$\lambda$3728 ratios. We compare the observations to MAPPINGS V photoionization models and find that the measured [NeIII]$\lambda$3870/[OII]$\lambda$3728, [OIII]$\lambda$4364/H$\gamma$, and [OIII]$\lambda$5008/H$\beta$ emission-line ratios are consistent with an interstellar medium that has very high ionization ($\log(Q) \simeq 8-9$, units of cm~s$^{-1}$), low metallicity ($Z/Z_\odot \lesssim 0.2$), and very high pressure ($\log(P/k) \simeq 8-9$, units of cm$^{-3}$). The combination of [OIII]$\lambda$4364/H$\gamma$ and [OIII]$\lambda$(4960+5008)/H$\beta$ line ratios indicate very high electron temperatures of $4.1<\log(T_e/{\rm K})<4.4$, further implying metallicities of $Z/Z_\odot \lesssim 0.2$ with the application of low-redshift calibrations for ``$T_e$-based'' metallicities. These observations represent a tantalizing new view of the physical conditions of the interstellar medium in galaxies at cosmic dawn.Comment: Accepted for publication in AAS Journals. 14 pages, 6 figures, 3 table

CEERS Key Paper. V. Galaxies at 4 &lt; z &lt; 9 Are Bluer than They Appear-Characterizing Galaxy Stellar Populations from Rest-frame ∼1 μm Imaging

We present results from the Cosmic Evolution Early Release Survey on the stellar population parameters for 28 galaxies with redshifts 4 &lt; z &lt; 9 using imaging data from the James Webb Space Telescope (JWST) Mid-Infrared Instrument (MIRI) combined with data from the Hubble Space Telescope and the Spitzer Space Telescope. The JWST/MIRI 5.6 and 7.7 μm data extend the coverage of the rest-frame spectral energy distribution to nearly 1 μm for galaxies in this redshift range. By modeling the galaxies’ SEDs the MIRI data show that the galaxies have, on average, rest-frame UV (1600 Å)—I-band colors 0.4 mag bluer than derived when using photometry that lacks MIRI. Therefore, the galaxies have lower ratios of stellar mass to light. The MIRI data reduce the stellar masses by 〈 Δ log M * 〉 = 0.25 dex at 4 &lt; z &lt; 6 and 0.37 dex at 6 &lt; z &lt; 9. This also reduces the star formation rates (SFRs) by 〈ΔlogSFR〉 = 0.14 dex at 4 &lt; z &lt; 6 and 0.27 dex at 6 &lt; z &lt; 9. The MIRI data also improve constraints on the allowable stellar mass formed in early star formation. We model this using a star formation history that includes both a “burst” at z f = 100 and a slowly varying (“delayed-τ”) model. The MIRI data reduce the allowable stellar mass by 0.6 dex at 4 &lt; z &lt; 6 and by ≈1 dex at 6 &lt; z &lt; 9. Applying these results globally, this reduces the cosmic stellar-mass density by an order of magnitude in the early Universe (z ≈ 9). Therefore, observations of rest-frame ≳1 μm are paramount for constraining the stellar-mass buildup in galaxies at very high redshifts.</p

CEERS Key Paper IV: Galaxies at 4<z<94 < z < 9 are Bluer than They Appear -- Characterizing Galaxy Stellar Populations from Rest-Frame ∼1\sim 1 micron Imaging

We present results from the Cosmic Evolution Early Release Survey (CEERS) on the stellar-population parameters for 28 galaxies with redshifts $4<z<9$ using imaging data from the James Webb Space Telescope (JWST) Mid-Infrared Instrument (MIRI) combined with data from the Hubble Space Telescope and the Spitzer Space Telescope. The JWST/MIRI 5.6 and 7.7 $\mu$m data extend the coverage of the rest-frame spectral-energy distribution (SED) to nearly 1 micron for galaxies in this redshift range. By modeling the galaxies' SEDs the MIRI data show that the galaxies have, on average, rest-frame UV (1600 \r{A}) $-$ $I$-band colors 0.4 mag bluer than derived when using photometry that lacks MIRI. Therefore, the galaxies have lower (stellar)-mass-to-light ratios. The MIRI data reduce the stellar masses by $\langle \Delta\log M_\ast\rangle=0.25$ dex at $4<z<6$ (a factor of 1.8) and 0.37 dex at $6<z<9$ (a factor of 2.3). This also reduces the star-formation rates (SFRs) by $\langle \Delta\log\mathrm{SFR} \rangle=0.14$ dex at $4<z<6$ and 0.27 dex at $6<z<9$. The MIRI data also improve constraints on the allowable stellar mass formed in early star-formation. We model this using a star-formation history that includes both a "burst' at $z_f=100$ and a slowly varying ("delayed-$\tau$") model. The MIRI data reduce the allowable stellar mass by 0.6 dex at $4<z< 6$ and by $\approx$1 dex at $6<z<9$. Applying these results globally, this reduces the cosmic stellar-mass density by an order of magnitude in the early universe ($z\approx9$). Therefore, observations of rest-frame $\gtrsim$1 $\mu$m are paramount for constraining the stellar-mass build-up in galaxies at very high-redshifts.Comment: Updated with accepted ApJ version. Part of the CEERS Focus Issue. 27 pages, many figures (4 Figure Sets, available upon reasonable request

Correction for Johansson et al., An open challenge to advance probabilistic forecasting for dengue epidemics.

Correction for “An open challenge to advance probabilistic forecasting for dengue epidemics,” by Michael A. Johansson, Karyn M. Apfeldorf, Scott Dobson, Jason Devita, Anna L. Buczak, Benjamin Baugher, Linda J. Moniz, Thomas Bagley, Steven M. Babin, Erhan Guven, Teresa K. Yamana, Jeffrey Shaman, Terry Moschou, Nick Lothian, Aaron Lane, Grant Osborne, Gao Jiang, Logan C. Brooks, David C. Farrow, Sangwon Hyun, Ryan J. Tibshirani, Roni Rosenfeld, Justin Lessler, Nicholas G. Reich, Derek A. T. Cummings, Stephen A. Lauer, Sean M. Moore, Hannah E. Clapham, Rachel Lowe, Trevor C. Bailey, Markel García-Díez, Marilia Sá Carvalho, Xavier Rodó, Tridip Sardar, Richard Paul, Evan L. Ray, Krzysztof Sakrejda, Alexandria C. Brown, Xi Meng, Osonde Osoba, Raffaele Vardavas, David Manheim, Melinda Moore, Dhananjai M. Rao, Travis C. Porco, Sarah Ackley, Fengchen Liu, Lee Worden, Matteo Convertino, Yang Liu, Abraham Reddy, Eloy Ortiz, Jorge Rivero, Humberto Brito, Alicia Juarrero, Leah R. Johnson, Robert B. Gramacy, Jeremy M. Cohen, Erin A. Mordecai, Courtney C. Murdock, Jason R. Rohr, Sadie J. Ryan, Anna M. Stewart-Ibarra, Daniel P. Weikel, Antarpreet Jutla, Rakibul Khan, Marissa Poultney, Rita R. Colwell, Brenda Rivera-García, Christopher M. Barker, Jesse E. Bell, Matthew Biggerstaff, David Swerdlow, Luis Mier-y-Teran-Romero, Brett M. Forshey, Juli Trtanj, Jason Asher, Matt Clay, Harold S. Margolis, Andrew M. Hebbeler, Dylan George, and Jean-Paul Chretien, which was first published November 11, 2019; 10.1073/pnas.1909865116. The authors note that the affiliation for Xavier Rodó should instead appear as Catalan Institution for Research and Advanced Studies (ICREA) and Climate and Health Program, Barcelona Institute for Global Health (ISGlobal). The corrected author and affiliation lines appear below. The online version has been corrected