The Effect of Diversification on the Dynamics of Mobile Genetic Elements in Prokaryotes: The Birth-Death-Diversification Model

Mobile genetic elements (MGEs) are ubiquitous among prokaryotes, and have important implications to many areas, such as the evolution of certain genes, bioengineering and the spread of antibiotic resistance. In order to understand the complex dynamics of MGEs, mathematical models are often used. One model that has been used to describe the dynamics of mobile promoters (a class of MGEs) is the birth-death-diversification model. This model is unique in that it allows MGEs to diversify to create new families. In this thesis, I analyze the dynamics of this model; in particular, I examine equilibrium distributions, extinction probabilities and mean time until extinction for MGE lineages. I find that diversification indirectly increases MGE propagation through increased horizontal gene transfer rates; therefore, diversification increases population growth rates and decreases extinction probability. Overall, this work indicates that diversification of elements should be considered in order to fully understand the dynamics of MGEs in prokaryotes

The Evolution of Dark Matter Haloes in Mergers

In the standard Λ-cold dark matter (ΛCDM) cosmological model, the present-day universe contains dominant components of dark energy (Λ) and cold dark matter (CDM). Fluctuations in the initial distribution of dark matter collapse to form dense, gravitationally bound dark matter haloes, which then evolve hierarchically through repeated mergers. Although the ΛCDM model is largely successful in describing our universe, the nature and identity of dark matter and dark energy remain unclear. ΛCDM may have problems describing structure on small scales, while on large scales, there are mild tensions between different estimates of the cosmological parameters. The structural properties of individual dark matter haloes, including their shape, spin, concentration, and substructure, are linked to halo growth history and thus reflect the cosmological model. The goal of this thesis is to understand how dark matter halo structural properties evolve in minor and major mergers, and to study how halo evolution can inform cosmology. Halo mergers can be classified as either major or minor based on the mass ratio of the merging systems. In minor mergers, smaller subhaloes fall into larger host haloes and evolve through tidal stripping. Predicting the evolution of subhaloes has important applications to studies of galaxy evolution and the nature of dark matter; in particular, the dense central regions of haloes dominate the signal from dark matter annihilation, so understanding how these central regions evolve is important for predicting the strength of the annihilation signal, and thus placing constraints on dark matter particle candidates. In the first part of this thesis (Chapters 2 and 3), we develop a simple, physically motivated model of tidal stripping that can be applied to any collisionless system to predict its structural evolution. In the second part of the thesis (Chapters 4 and 5), we perform a large suite of simulations of binary equal-mass mergers between isolated haloes with various density profiles to study the effects of major mergers on dark matter halo properties. We find that the axis ratios describing the 3D shapes of the merger remnants vary linearly with a scaled dimensionless energy parameter, κ, and an angular momentum (or spin) parameter, λ. The mass distribution is determined mainly by κ, where energetic (low-κ) encounters produce more extended remnants while mergers of strongly bound (high-κ) systems produce compact remnants. Surprisingly, major mergers seem to be relatively ineffective at changing the central densities of haloes, and thus unlikely to explain the mean trends in the concentration–mass–redshift relation. Overall, Chapters 2–5 present models for how haloes evolve in mergers, including the evolution of tidally stripped haloes in minor mergers, as well as a description for how halo spin, shape, mass distribution, and concentration evolve in major mergers. In the final chapter, we discuss a potential application of this work, to develop semi-analytic models of halo structural evolution and use these to predict how halo properties should vary with the cosmological model. Ultimately, the structural properties of haloes could provide powerful cosmological tests that will become feasible with the completion of next-generation surveys

Do assumptions about the central density of subhaloes affect dark matter annihilation and lensing calculations?

A growing body of evidence suggests that the central density of cuspy dark matter subhaloes is conserved in minor mergers. However, empirical models of subhalo evolution, calibrated from simulations, often assume a drop in the central density. Since empirical models of subhaloes are used in galaxy-galaxy lensing studies and dark matter annihilation calculations, we explore the consequences of assuming different subhalo models. We find that dark matter annihilation calculations are very sensitive to the assumed subhalo mass profile, and different models can give more than a magnitude difference in the J-factor and boost factor in individual haloes. On the other hand, the shear and convergence profiles used in galaxy-galaxy lensing are sensitive to the initial profile assumed (e.g., NFW versus Einato) but are otherwise well-approximated by a simple model in which the original profile is sharply truncated. We conclude that since the innermost parts of haloes are difficult to resolve in simulations, it is important to have a theoretical understanding of how subhaloes evolve to make accurate predictions of the dark matter annihilation signal.Comment: 15 pages, 13 figures. Submitted to MNRA

Cosmic Evolution Early Release Science (CEERS) survey: The colour evolution of galaxies in the distant Universe

The wavelength-coverage and sensitivity of JWST now enables us to probe the rest-frame UV - optical spectral energy distributions (SEDs) of galaxies at high-redshift ($z>4$). From these SEDs it is, in principle, through SED fitting possible to infer key physical properties, including stellar masses, star formation rates, and dust attenuation. These in turn can be compared with the predictions of galaxy formation simulations allowing us to validate and refine the incorporated physics. However, the inference of physical properties, particularly from photometry alone, can lead to large uncertainties and potential biases. Instead, it is now possible, and common, for simulations to be \emph{forward-modelled} to yield synthetic observations that can be compared directly to real observations. In this work, we measure the JWST broadband fluxes and colours of a robust sample of $5<z<10$ galaxies using the Cosmic Evolution Early Release Science (CEERS) Survey. We then analyse predictions from a variety of models using the same methodology and compare the NIRCam/F277W magnitude distribution and NIRCam colours with observations. We find that the predicted and observed magnitude distributions are similar, at least at $58$ the distributions differ somewhat, though our observed sample size is small and thus susceptible to statistical fluctuations. Likewise, the predicted and observed colour evolution show broad agreement, at least at $5<z<8$. There is however some disagreement between the observed and modelled strength of the strong line contribution. In particular all the models fails to reproduce the F410M-F444W colour at $z>8$, though, again, the sample size is small here.Comment: 11 pages, 10 figures, submitted to MNRA

Emericella quadrilineata as Cause of Invasive Aspergillosis

This opportunistic fungus is frequently misidentified because of its morphologic similarity to E. nidulans

The Web Epoch of Reionization Lyman-α\alpha Survey (WERLS) I. MOSFIRE Spectroscopy of z∼7−8\mathbf{z \sim 7-8} Lyman-α\alpha Emitters

We present the first results from the Web Epoch of Reionization Lyman-$\alpha$ Survey (WERLS), a spectroscopic survey of Lyman-$\alpha$ emission using Keck I/MOSFIRE and LRIS. WERLS targets bright ($J<26$) galaxy candidates with photometric redshifts of $5.5\lesssim z \lesssim 8$ selected from pre-JWST imaging embedded in the Epoch of Reionization (EoR) within three JWST deep fields: CEERS, PRIMER, and COSMOS-Web. Here, we report 11 $z\sim7-8$ Lyman-$\alpha$ emitters (LAEs; 3 secure and 8 tentative candidates) detected in the first five nights of WERLS MOSFIRE data. We estimate our observed LAE yield is $\sim13$%, broadly consistent with expectations assuming some loss from redshift uncertainty, contamination from sky OH lines, and that the Universe is approximately half-ionized at this epoch, whereby observable Lyman-$\alpha$ emission is unlikely for galaxies embedded in a neutral intergalactic medium. Our targets are selected to be UV-bright, and span a range of absolute UV magnitudes with $-23.1 < M_{\text{UV}} < -19.8$. With two LAEs detected at $z=7.68$, we also consider the possibility of an ionized bubble at this redshift. Future synergistic Keck+JWST efforts will provide a powerful tool for pinpointing beacons of reionization and mapping the large scale distribution of mass relative to the ionization state of the Universe.Comment: 27 pages, 8 figures; ApJ submitte

COSMOS-Web: Intrinsically Luminous z≳\gtrsim10 Galaxy Candidates Test Early Stellar Mass Assembly

We report the discovery of 15 exceptionally luminous $10\lesssim z\lesssim14$ candidate galaxies discovered in the first 0.28 deg$^2$ of JWST/NIRCam imaging from the COSMOS-Web Survey. These sources span rest-frame UV magnitudes of $-20.5>M_{\rm UV}>-22$, and thus constitute the most intrinsically luminous $z\gtrsim10$ candidates identified by JWST to-date. Selected via NIRCam imaging with Hubble ACS/F814W, deep ground-based observations corroborate their detection and help significantly constrain their photometric redshifts. We analyze their spectral energy distributions using multiple open-source codes and evaluate the probability of low-redshift solutions; we conclude that 12/15 (80%) are likely genuine $z\gtrsim10$ sources and 3/15 (20%) likely low-redshift contaminants. Three of our $z\sim12$ candidates push the limits of early stellar mass assembly: they have estimated stellar masses $\sim5\times10^{9}\,M_\odot$, implying an effective stellar baryon fraction of $\epsilon_{\star}\sim0.2-0.5$, where $\epsilon_{\star}\equiv M_{\star}/(f_{b}M_{halo})$. The assembly of such stellar reservoirs is made possible due to rapid, burst-driven star formation on timescales $<$100\,Myr where the star-formation rate may far outpace the growth of the underlying dark matter halos. This is supported by the similar volume densities inferred for $M_\star\sim10^{10}\,M_\odot$ galaxies relative to $M_\star\sim10^{9}\,M_\odot$ -- both about $10^{-6}$ Mpc$^{-3}$ -- implying they live in halos of comparable mass. At such high redshifts, the duty cycle for starbursts would be of order unity, which could cause the observed change in the shape of the UVLF from a double powerlaw to Schechter at $z\approx8$. Spectroscopic redshift confirmation and ensuing constraints of their masses will be critical to understanding how, and if, such early massive galaxies push the limits of galaxy formation in $\Lambda$CDM.Comment: 30 pages, 9 figures; ApJ submitte