A Latent Variable Approach to Multivariate Quantitative Trait Loci

A novel approach based on latent variable modelling is presented for the analysis of multivariate quantitative and qualitative trait loci. The approach is general in the sense that it enables the joint analysis of many kinds of quantitative and qualitative traits (including count data and censored traits) in a single modelling framework. In the framework, the observations are modelled as functions of latent variables, which are then affected by quantitative trait loci. Separating the analysis in this way means that measurement errors in the phenotypic observations can be included easily in the model, providing robust inferences. The performance of the method is illustrated using two real multivariate datasets, from barley and Scots pine

The Genome of the "Great Speciator" Provides Insights into Bird Diversification

Among birds, white-eyes (genus Zosterops) have diversified so extensively that Jared Diamond and Ernst Mayr referred to them as the “great speciator.” The Zosterops lineage exhibits some of the fastest rates of species diversification among vertebrates, and its members are the most prolific passerine island colonizers. We present a high-quality genome assembly for the silvereye (Zosterops lateralis), a white-eye species consisting of several subspecies distributed across multiple islands. We investigate the genetic basis of rapid diversification in white-eyes by conducting genomic analyses at varying taxonomic levels. First, we compare the silvereye genome with those of birds from different families and searched for genomic features that may be unique to Zosterops. Second, we compare the genomes of different species of white-eyes from Lifou island (South Pacific), using whole genome resequencing and restriction site associated DNA. Third, we contrast the genomes of two subspecies of silvereye that differ in plumage color. In accordance with theory, we show that white-eyes have high rates of substitutions, gene duplication, and positive selection relative to other birds. Below genus level, we find that genomic differentiation accumulates rapidly and reveals contrasting demographic histories between sympatric species on Lifou, indicative of past interspecific interactions. Finally, we highlight genes possibly involved in color polymorphism between the subspecies of silvereye. By providing the first whole-genome sequence resources for white-eyes and by conducting analyses at different taxonomic levels, we provide genomic evidence underpinning this extraordinary bird radiation

Multi-frequency VLBA study of the blazar S5 0716+714 during the active state in 2004: I. Inner jet kinematics

We observed the blazar \object{0716+714} with the VLBA during its active state in 2003-2004. In this paper we discuss multi-frequency analysis of the inner jet (first 1 mas) kinematics. The unprecedentedly dense time sampling allows us to trace jet components without misidentification and to calculate the component speeds with good accuracy. In the smooth superluminal jet we were able to identify and track three components over time moving outwards with relatively high apparent superluminal speeds (8.5-19.4 $c$), which contradicts the hypothesis of a stationary oscillating jet in this source. Component ejections occur at a relatively high rate (once in two months), and they are accompanied by mm-continuum outbursts. Superluminal jet components move along wiggling trajectories, which is an indication of actual helical motion. Fast proper motion and rapid decay of the components suggest that this source should be observed with the VLBI at a rate of at least once in one or two months in order to trace superluminal jet components without confusion.Comment: 4 pages, 3 figures, Astronomy & Astrophysics Letter, language corrections adde

Chloroplast microsatellites: measures of genetic diversity and the effect of homoplasy

Chloroplast microsatellites have been widely used in population genetic studies of conifers in recent years. However, their haplotype configurations suggest that they could have high levels of homoplasy, thus limiting the power of these molecular markers. A coalescent-based computer simulation was used to explore the influence of homoplasy on measures of genetic diversity based on chloroplast microsatellites. The conditions of the simulation were defined to fit isolated populations originating from the colonization of one single haplotype into an area left available after a glacial retreat. Simulated data were compared with empirical data available from the literature for a species of Pinus that has expanded north after the Last Glacial Maximum. In the evaluation of genetic diversity, homoplasy was found to have little influence on Nei's unbiased haplotype diversity (H(E)) while Goldstein's genetic distance estimates (D2sh) were much more affected. The effect of the number of chloroplast microsatellite loci for evaluation of genetic diversity is also discussed

Information seeking behavioural paths of physicians for diabetes mellitus care: a qualitative comparative analysis of information needs, sources, and barriers

This study addresses diabetes physicians’ information seeking behavioural paths (digital, conventional, interpersonal) which lead to information needs satisfaction and the barriers encountered in this process. The study was based on empirical evidence from a survey of 159 physicians. Theoretical analysis was informed by Wilson’s model of information seeking behaviour. The data were analysed using fuzzy set qualitative comparative analysis method. The method was successful in identifying five behavioural paths leading to physicians’ information needs satisfaction (professional/health coaching) which demonstrate different relationships between information sources (conventional/interpersonal/digital) and information barriers (personal/digital illiteracy) and five behavioural paths that are not leading to satisfaction

Coalbed Methane Development in Indonesia: Design and Economic Analysis of Upstream Petroleum Fiscal Policy

Due to increasing demand for natural gas in Indonesia, the Government now promotes exploration for coalbed methane (CBM). Currently, Indonesia has 453 trillion cubic feet (TCF) of CBM reserves. However, CBM development in the country is still in the exploration phase, with significant under-investment. To attract investors, a tailored Production Sharing Contracts (PSC) regime is required. Based on a combination of Factor Analysis (FA), Discounted Cash Flows (DCF) and Parameter Sensitivity Analysis, the research explores an optimal scenario of a company’s share of revenue that optimised CBM development contracts. We find that a combination of 5 years straight line depreciation (SLD), 5% First Tranche Petroleum (FTP), 78% Contractor Share (CS) and 35% income tax best spreads the risk of CBM development and exploitation between the government and the contractor. This combination is a more suitable PSC regime for developing CBM in an early stage of the industry. Therefore, the Government must cede some taxes during exploration to incentivise CBM development. Three PSCs regimes are thus required to fully develop and exploit CBM, including exploration, transitional and exploitation phase PSCs which better match contractor risks and returns and ensure reasonable certainty of contractor cost recovery

Exploring the spreading layer of GX 9+9 using RXTE and INTEGRAL

We have fitted ~200 RXTE and INTEGRAL spectra of the neutron star LMXB GX 9+9 from 2002-2007 with a model consisting of a disc blackbody and another blackbody representing the spreading layer (SL), i.e. an extended accretion zone on the NS surface as opposed to the more traditional disc-like boundary layer. Contrary to theory, the SL temperature was seen to increase towards low SL luminosities, while the approximate angular extent had a nearly linear luminosity dependency. Comptonization was not required to adequately fit these spectra. Together with the ~70 degree upper bound of inclination implied by the lack of eclipses, the best-fitting normalization of the accretion disc blackbody component implies a distance of ~10 kpc, instead of the usually quoted 5 kpc.Comment: 14 pages, 10 figures, accepted for publication in MNRA

Multi-Epoch Multiwavelength Spectra and Models for Blazar 3C~279

Of the blazars detected by EGRET in GeV gamma rays, 3C 279 is not only the best-observed by EGRET, but also one of the best-monitored at lower frequencies. We have assembled eleven spectra, from GHz radio through GeV gamma rays, from the time intervals of EGRET observations. Although some of the data have appeared in previous publications, most are new, including data taken during the high states in early 1999 and early 2000. All of the spectra show substantial gamma-ray contribution to the total luminosity of the object; in a high state, the gamma-ray luminosity dominates over that at all other frequencies by a factor of more than 10. There is no clear pattern of time correlation; different bands do not always rise and fall together, even in the optical, X-ray, and gamma-ray bands. The spectra are modeled using a leptonic jet, with combined synchrotron self-Compton + external Compton gamma-ray production. Spectral variability of 3C 279 is consistent with variations of the bulk Lorentz factor of the jet, accompanied by changes in the spectral shape of the electron distribution. Our modeling results are consistent with the UV spectrum of 3C 279 being dominated by accretion disk radiation during times of low gamma-ray intensity.Comment: 39 pages including 13 figures; data tables not included (see ApJ web version or contact author

The unprecedented optical outburst of the quasar 3C 454.3. The WEBT campaign of 2004-2005

The radio quasar 3C 454.3 underwent an exceptional optical outburst lasting more than 1 year and culminating in spring 2005. The maximum brightness detected was R = 12.0, which represents the most luminous quasar state thus far observed (M_B ~ -31.4). In order to follow the emission behaviour of the source in detail, a large multiwavelength campaign was organized by the Whole Earth Blazar Telescope (WEBT). Continuous optical, near-IR and radio monitoring was performed in several bands. ToO pointings by the Chandra and INTEGRAL satellites provided additional information at high energies in May 2005. The historical radio and optical light curves show different behaviours. Until about 2001.0 only moderate variability was present in the optical regime, while prominent and long-lasting radio outbursts were visible at the various radio frequencies, with higher-frequency variations preceding the lower-frequency ones. After that date, the optical activity increased and the radio flux is less variable. This suggests that the optical and radio emissions come from two separate and misaligned jet regions, with the inner optical one acquiring a smaller viewing angle during the 2004-2005 outburst. Moreover, the colour-index behaviour (generally redder-when-brighter) during the outburst suggests the presence of a luminous accretion disc. A huge mm outburst followed the optical one, peaking in June-July 2005. The high-frequency (37-43 GHz) radio flux started to increase in early 2005 and reached a maximum at the end of our observing period (end of September 2005). VLBA observations at 43 GHz during the summer confirm theComment: 7 pages, 4 figures, to be published in A&

High genetic diversity at the extreme range edge: nucleotide variation at nuclear loci in Scots pine (Pinus sylvestris L.) in Scotland

Nucleotide polymorphism at 12 nuclear loci was studied in Scots pine populations across an environmental gradient in Scotland, to evaluate the impacts of demographic history and selection on genetic diversity. At eight loci, diversity patterns were compared between Scottish and continental European populations. At these loci, a similar level of diversity (θsil=~0.01) was found in Scottish vs mainland European populations, contrary to expectations for recent colonization, however, less rapid decay of linkage disequilibrium was observed in the former (ρ=0.0086±0.0009, ρ=0.0245±0.0022, respectively). Scottish populations also showed a deficit of rare nucleotide variants (multi-locus Tajima's D=0.316 vs D=−0.379) and differed significantly from mainland populations in allelic frequency and/or haplotype structure at several loci. Within Scotland, western populations showed slightly reduced nucleotide diversity (πtot=0.0068) compared with those from the south and east (0.0079 and 0.0083, respectively) and about three times higher recombination to diversity ratio (ρ/θ=0.71 vs 0.15 and 0.18, respectively). By comparison with results from coalescent simulations, the observed allelic frequency spectrum in the western populations was compatible with a relatively recent bottleneck (0.00175 × 4Ne generations) that reduced the population to about 2% of the present size. However, heterogeneity in the allelic frequency distribution among geographical regions in Scotland suggests that subsequent admixture of populations with different demographic histories may also have played a role