A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements

Ray-finned fishes constitute the dominant radiation of vertebrates with over 30,000 species. Although molecular phylogenetics has begun to disentangle major evolutionary relationships within this vast section of the Tree of Life, there is no widely available approach for efficiently collecting phylogenomic data within fishes, leaving much of the enormous potential of massively parallel sequencing technologies for resolving major radiations in ray-finned fishes unrealized. Here, we provide a genomic perspective on longstanding questions regarding the diversification of major groups of ray-finned fishes through targeted enrichment of ultraconserved nuclear DNA elements (UCEs) and their flanking sequence. Our workflow efficiently and economically generates data sets that are orders of magnitude larger than those produced by traditional approaches and is well-suited to working with museum specimens. Analysis of the UCE data set recovers a well-supported phylogeny at both shallow and deep time-scales that supports a monophyletic relationship between Amia and Lepisosteus (Holostei) and reveals elopomorphs and then osteoglossomorphs to be the earliest diverging teleost lineages. Divergence time estimation based upon 14 fossil calibrations reveals that crown teleosts appeared ~270 Ma at the end of the Permian and that elopomorphs, osteoglossomorphs, ostarioclupeomorphs, and euteleosts diverged from one another by 205 Ma during the Triassic. Our approach additionally reveals that sequence capture of UCE regions and their flanking sequence offers enormous potential for resolving phylogenetic relationships within ray-finned fishes

Characterization of Neutron-Induced Defects in Isotopically Enriched Lithium Tetraborate

Lithium Tetraborate (LTB) is assessed for use as a material for neutron detection. LTB isotopically enriched in either Li-6 or B-10 provides a medium that efficiently captures and transmutes neutrons into more readily detected forms of material or energy. Neutron detection is desirable to detect elicit movement of special nuclear material or nuclear weapons. Single crystals of LTB, Li-6 or B-10 enriched, were neutron irradiated, and electron paramagnetic resonance was used to detect point defects induced by the neutrons. Multiple defects were noted in the irradiated crystals. Two particular defects, perturbed lithium vacancies and lithium clusters are proposed as induced by thermal neutrons. Parallel experiments on silver doped LTB indicated that fast neutrons induce interstitial defects including interstitial oxygen, lithium, and silver atoms in silver doped crystals. Electron paramagnetic resonance, electron-nuclear double resonance, pulsed anneal, and thermo luminescence studies prior to neutron irradiation concluded that silver doped LTB crystals contain silver point defects that trap both electrons and holes. Pulsed anneal and thermo luminescence studies of all crystal types prior to neutron irradiation suggest neutron induced defects are significantly more stable that as grown defects. Thermo luminescence may be a viable technique to detect neutron interactions in the crystals. Lastly, 511 keV gamma radiation observed after neutron irradiation of all crystals is attributed to positron annihilation in the crystals. The 6Li(7Li,2n)11C reaction is suggested as the responsible mechanism for positron production. The resulting C-11 nucleus radio actively decays via emission of a positron with a half life of 20.39 minutes

The Mean Ultraviolet Spectrum of a Representative Sample of Faint z~3 Lyman Alpha Emitters

We discuss the rest-frame ultraviolet emission line spectra of a large (~100) sample of low luminosity redshift z~3.1 Lyman alpha emitters (LAEs) drawn from a Subaru imaging survey in the SSA22 survey field. Our earlier work based on smaller samples indicated that such sources have high [OIII]/[OII] line ratios possibly arising from a hard ionising spectrum that may be typical of similar sources in the reionisation era. With optical spectra secured from VLT/VIMOS, we re-examine the nature of the ionising radiation in a larger sample using the strength of the high ionisation diagnostic emission lines of CIII]1909, CIV1549, HeII1640, and OIII]1661,1666 in various stacked subsets. Our analysis confirms earlier suggestions of a correlation between the strength of Ly-alpha and CIII] emission and we find similar trends with broad band UV luminosity and rest-frame UV colour. Using various diagnostic line ratios and our stellar photoionisation models, we determine both the gas phase metallicity and hardness of the ionisation spectrum characterised by xi_ion - the number of Lyman continuum photons per UV luminosity. We confirm our earlier suggestion that xi_ion is significantly larger for LAEs than for continuum-selected Lyman break galaxies, particularly for those LAEs with the faintest UV luminosities. We briefly discuss the implications for cosmic reionisation if the metal-poor intensely star-forming systems studied here are representative examples of those at much higher redshift.Comment: 15 pages, 9 figures. Accepted for publication in MNRA

Simulating High-Redshift Disk Galaxies: Applications to Long Duration Gamma-Ray Burst Hosts

The efficiency of star formation governs many observable properties of the cosmological galaxy population, yet many current models of galaxy formation largely ignore the important physics of star formation and the interstellar medium (ISM). Using hydrodynamical simulations of disk galaxies that include a treatment of the molecular ISM and star formation in molecular clouds (Robertson & Kravtsov 2008), we study the influence of star formation efficiency and molecular hydrogen abundance on the properties of high-redshift galaxy populations. In this work, we focus on a model of low-mass, star forming galaxies at 1<~z<~2 that may host long duration gamma-ray bursts (GRBs). Observations of GRB hosts have revealed a population of faint systems with star formation properties that often differ from Lyman-break galaxies (LBGs) and more luminous high-redshift field galaxies. Observed GRB sightlines are deficient in molecular hydrogen, but it is unclear to what degree this deficiency owes to intrinsic properties of the galaxy or the impact the GRB has on its environment. We find that hydrodynamical simulations of low-stellar mass systems at high-redshifts can reproduce the observed star formation rates and efficiencies of GRB host galaxies at redshifts 1<~z<~2. We show that the compact structure of low-mass high-redshift GRB hosts may lead to a molecular ISM fraction of a few tenths, well above that observed in individual GRB sightlines. However, the star formation rates of observed GRB host galaxies imply molecular gas masses of 10^8 - 10^9 M_sun similar to those produced in the simulations, and may therefore imply fairly large average H_2 fractions in their ISM.Comment: To appear in "The Galaxy Disk in Cosmological Context"; Proceedings of IAU254; Copenhagen; 9-13 June 2008; eds. J. Anderson, J. Bland-Hawthorn, B. Nordstrom; CU

The health and well-being of older adults with dual sensory impairment (DSI) in four countries

Objectives Dual sensory impairment (DSI) is a combination of vision and hearing impairments that represents a unique disability affecting all aspects of a person’s life. The rates of DSI are expected to increase due to population aging, yet little is known about DSI among older adults (65+). The prevalence of DSI and client characteristics were examined among two groups, namely, older adults receiving home care services or those residing in a long-term care (LTC) facility in four countries (Canada, US, Finland, Belgium). Methods Existing data, using an interRAI assessment, were analyzed to compare older adults with DSI to all others across demographic characteristics, functional and psychosocial outcomes. Results In home care, the prevalence of DSI across the four countries ranged from 13.4% to 24.6%; in LTC facilities, it ranged from 9.7% to 33.9%. Clients with DSI were more likely to be 85+, have moderate/severe cognitive impairment, impairments in activities of daily living, and have communication difficulties. Among residents of LTC facilities, individuals with DSI were more likely to be 85+ and more likely have a diagnosis of Alzheimer’s disease. Having DSI increased the likelihood of depression in both care settings, but after adjusting for other factors, it remained significant only in the home care sample. Conclusions While the prevalence of DSI cross nationally is similar to that of other illnesses such as diabetes, depression, and Alzheimer’s disease, we have a limited understanding of its affects among older adults. Raising awareness of this unique disability is imperative to insure that individuals receive the necessary rehabilitation and supportive services to improve their level of independence and quality of life