Metal Lines in Cosmological Models of Lyman-Alpha Absorbers

The metal absorption lines found in association with \lya absorbers of moderate to high HI column density contain valuable information about the metallicity and ionization conditions within the absorbers and offer a stronger test of models of the intergalactic medium at \sim 3 than HI absorption lines alone. We have developed a method to predict the strengths of metal absorption lines within the framework of cosmological models for the \lya forest. The method consists of evaluating a quantity, the Line Observability Index, for a database of hundreds of candidate metal lines, allowing a comprehensive identification of the lines the model predicts to be detectable associated with a \lya absorber of a given HI column density and metallicity. Applying this technique to a particular class of models at \sim 2-4, we predict that the OVI(1032 \AA, 1038 \AA) doublet is the only practical probe of the metallicity of low column density absorbers (HI \simlt 10^{14.5} cm^{-2}$), that CIV (1548 \AA) is the strongest line with rest wavelength$\lambda_r > 1216$\AA{} regardless of HI$, and that the strongest metal lines should be CIII(977 \AA) and SiIII(1206.5 \AA), which peak at HI \sim 10^{17} cm^{-2}$.Comment: To appear in the proceedings from the 13th IAP Workshop (1-5 July 1997) "Evolution of the Intergalactic Medium From QSO Absorption Line Systems

The Observability of Metal Lines Associated with the Lyman-alpha Forest

We develop a prescription for characterizing the strengths of metal lines associated with Lyman-alpha forest absorbers (LYFAs) of a given neutral hydrogen column density N_HI and metallicity [Fe/H]. This Line Observability Index (LOX) is line-specific and translates, for weak lines, into a measure of the equivalent width. It can be evaluated quickly for thousands of transitions within the framework of a given model of the Lyman-alpha forest, providing a ranking of the lines in terms of their strengths and enabling model builders to select the lines that should be detectable in observed spectra of a given resolution and signal-to-noise ratio. We compute the LOX for a large number of elements and transitions in two cosmological models of the Lyman-alpha forest at z=3 derived from a hydrodynamic simulation of structure formation, and we discuss how the LOX depends on redshift and on model parameters such as the mean baryonic density and radiation field. We find that the OVI (1032,1038) doublet is the best probe of the metallicity in low column density LYFAs N_{HI} \approx 10^{14.5} cm^{-2}). Metallicities down to [O/H] \sim -3 ([Fe/H] \sim -3.5 with the assumed [O/Fe] ratio) yield OVI absorption features that should be detectable in current high-quality spectra, provided that the expected position of the OVI feature is not contaminated by HI absorption. The strongest transitions in lower ionisation states of oxygen are OV(630), OIV(788), and OIII(833), and are likely to be detected with next generation UV instruments. Of the lines with rest wavelengths \lambda_r > 1216, which can potentially be observed redwards of the \lya forest, the CIV(1548,1551) doublet is expected to dominate in all LYFAs, regardless of the value of N_HI.Comment: Substantially revised version: larger line database, additional cosmological model analyzed. Accepted for Ap

Constraining the Metallicity of the Low Density Lyman-alpha Forest Using OVI Absorption

We search for OVI absorption in a Keck HIRES spectrum of the z=3.62 quasar Q1422+231. Comparison of CIV measurements to cosmological simulations shows that \lya forest absorbers with N_HI > 10^{14.5} have [C/H]~=-2.5, for the UV background spectrum of Haardt & Madau (HM). Lower column density absorption arises in lower density gas, where OVI is the most sensitive metal tracer. Since OVI lines lie at wavelengths contaminated by Lyman series absorption, we interpret our Q1422 results by comparing to artificial spectra drawn from an SPH simulation of a Lambda-dominated CDM model. A search for deep, narrow features in Q1422 yields only a few candidate OVI lines, statistically consistent with the number in artificial spectra with no metals; spectra generated with the HM background and [O/H] >= -2.5 predict too many narrow lines. However, applying the optical depth ratio technique of Songaila (1998), we DO find significant OVI associated with CIV systems; matching Q1422 requires [O/C]~=+0.5, implying [O/H]~=-2.0. Taken together these results imply that (a) the metallicity in the low density IGM is at least a factor of three below that in the overdense regions where CIV absorption is detectable, and (b) oxygen is overabundant in these regions, consistent with the enrichment pattern of old halo stars. If the UV background is heavily truncated above 4 Ry, an implausibly high oxygen overabundance ([O/C]>+2) is required by the data; thus a majority of the volume of the universe must have undergone helium reionization by z=3.(Abridged)Comment: Submitted to ApJ, 48 pp including 14 ps figures, uses aaspp4.st

Accelerated gene evolution and subfunctionalization in the pseudotetraploid frog Xenopus laevis

Ancient whole genome duplications have been implicated in the vertebrate and teleost radiations, and in the emergence of diverse angiosperm lineages, but the evolutionary response to such a perturbation is still poorly understood. The African clawed frog Xenopus laevis experienced a relatively recent tetraploidization {approx} 40 million years ago. Analysis of the considerable amount of EST sequence available for this species together with the genome sequence of the related diploid Xenopus tropicalis provides a unique opportunity to study the genomic response to whole genome duplication

The X-Ray Forest: A New Prediction of Hierarchical Structure Formation Models

We use numerical simulations of structure formation in a Cold Dark Matter model to predict the absorption lines in the soft X-rays produced by heavy elements in the shock-heated intergalactic medium at low redshift. The simulation incorporates a model for metal production in galaxies and the subsequent dispersion of the metals to the intergalactic medium. We analyze in particular absorption lines produced by oxygen, and calculate the ionization stage taking into account the observed X-ray background at the present time. We find that oxygen is fully ionized by the X-ray background in low-density voids, and is mostly in the form of OVII and OVIII in the sheets and filamentary regions. Strong absorption lines of OVII and OVIII with equivalent widths W ~ 100 km/s are produced in filamentary regions of overdensities ~ 100 and temperatures ~ 10^6 K, located in the outskirts of groups and clusters of galaxies. The OVII line at E = 574 eV is generally the strongest one in these systems. Our model predicts that any X-ray source (such as a quasar) should typically show about one OVII absorption line with W > 100 km/s in the interval from z=0 to z=0.3. These lines could be detected with the upcoming generation of X-ray telescopes, and their origin in intervening systems could be confirmed by the association with groups of galaxies and X-ray emitting halos near the line-of-sight at the same redshift. The hot intergalactic medium may be one of the main reservoirs of baryons in the present universe, and the heavy element X-ray absorption lines offer a promising possibility of detecting this new component in the near future.Comment: Accepted by ApJ. The full resolution color GIF version of Fig.2 is include

The Structure of Isothermal, Self-gravitating Gas Spheres for Softened Gravity

A theory for the structure of isothermal, self-gravitating gas spheres in pressure equilibrium in a softened gravitational field is developed. The one parameter spline softening proposed by Hernquist & Katz (1989) is used. We show that the addition of this extra scale parameter implies that the set of equilibrium solutions constitute a one-parameter family, rather than the one and only one isothermal sphere solution for Newtonian gravity. We demonstrate the perhaps somewhat surprising result that for any finite choice of softening length and temperature, it is possible to deposit an arbitrarily large mass of gas in pressure equilibrium and with a non-singular density distribution inside of r_0 for any r_0 > 0. The theoretical predictions of our models are compared with the properties of the small, massive, quasi-isothermal gas clumps which typically form in numerical Tree-SPH simulations of 'passive' galaxy formation of Milky Way sized galaxies. We find reasonable agreement despite the neglect of rotational support in the models. We comment on whether the hydrodynamical resolution in our numerical simulation of galaxy formation is sufficient, and finally we conclude that one should be cautious, when comparing results of numerical simulations involving gravitational softening and hydrodynamical smoothing, with reality.Comment: 22 pages Latex + 12 figure

Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa

This is the publisher’s final pdf. The article is copyrighted by the New Phytologist Trust and published by John Wiley & Sons, Inc. It can be found at: http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291469-8137. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work.•Plant population genomics informs evolutionary biology, breeding, conservation and bioenergy feedstock development. For example, the detection of reliable phenotype–genotype associations and molecular signatures of selection requires a detailed knowledge about genome-wide patterns of allele frequency variation, linkage disequilibrium and recombination.\ud •We resequenced 16 genomes of the model tree Populus trichocarpa and genotyped 120 trees from 10 subpopulations using 29 213 single-nucleotide polymorphisms.\ud •Significant geographic differentiation was present at multiple spatial scales, and range-wide latitudinal allele frequency gradients were strikingly common across the genome. The decay of linkage disequilibrium with physical distance was slower than expected from previous studies in Populus, with r² dropping below 0.2 within 3–6 kb. Consistent with this, estimates of recent effective population size from linkage disequilibrium (N[subscript e] ≈ 4000–6000) were remarkably low relative to the large census sizes of P. trichocarpa stands. Fine-scale rates of recombination varied widely across the genome, but were largely predictable on the basis of DNA sequence and methylation features.\ud •Our results suggest that genetic drift has played a significant role in the recent evolutionary history of P. trichocarpa. Most importantly, the extensive linkage disequilibrium detected suggests that genome-wide association studies and genomic selection in undomesticated populations may be more feasible in Populus than previously assumed

The amphioxus genome and the evolution of the chordate karyotype

Lancelets ('amphioxus') are the modern survivors of an ancient chordate lineage, with a fossil record dating back to the Cambrian period. Here we describe the structure and gene content of the highly polymorphic approx520-megabase genome of the Florida lancelet Branchiostoma floridae, and analyse it in the context of chordate evolution. Whole-genome comparisons illuminate the murky relationships among the three chordate groups (tunicates, lancelets and vertebrates), and allow not only reconstruction of the gene complement of the last common chordate ancestor but also partial reconstruction of its genomic organization, as well as a description of two genome-wide duplications and subsequent reorganizations in the vertebrate lineage. These genome-scale events shaped the vertebrate genome and provided additional genetic variation for exploitation during vertebrate evolution