Multi-object spectroscopy of the field surrounding PKS 2126-158: Discovery of a z=0.66 galaxy group

The high-redshift radio-loud quasar PKS 2126-158 is found to have a large number of red galaxies in close apparent proximity. We use the Gemini Multi-Object Spectrograph (GMOS) on Gemini South to obtain optical spectra for a large fraction of these sources. We show that there is a group of galaxies at $z\sim0.66$, coincident with a metal-line absorption system seen in the quasar's optical spectrum. The multiplexing capabilities of GMOS also allow us to measure redshifts of many foreground galaxies in the field surrounding the quasar. The galaxy group has five confirmed members, and a further four fainter galaxies are possibly associated. All confirmed members exhibit early-type galaxy spectra, a rare situation for a Mg II absorbing system. We discuss the relationship of this group to the absorbing gas, and the possibility of gravitational lensing of the quasar due to the intervening galaxies.Comment: Monthly Notices of the Royal Astronomical Society, in press. 10 pages, 8 figure

The Optical/Near-IR Colours of Red Quasars

We present quasi-simultaneous multi-colour optical/near-IR photometry for 157 radio selected quasars, forming an unbiassed sub-sample of the Parkes Flat-Spectrum Sample. Data are also presented for 12 optically selected QSOs, drawn from the Large Bright QSO Survey. The spectral energy distributions of the radio- and optically-selected sources are quite different. The optically selected QSOs are all very similar: they have blue spectral energy distributions curving downwards at shorter wavelengths. Roughly 90% of the radio-selected quasars have roughly power-law spectral energy distributions, with slopes ranging from Fν ∝ ν0 to Fν, ∝ ν-2. The remaining 10% have spectral energy distributions showing sharp peaks: these are radio galaxies and highly reddened quasars. Four radio sources were not detected down to magnitude limits of H ∼ 19 · 6. These are probably high redshift (z > 3) galaxies or quasars. We show that the colours of our red quasars lie close to the stellar locus in the optical: they will be hard to identify in surveys such as the Sloan Digital Sky Survey. If near-IR photometry is added, however, the red power-law sources can be clearly separated from the stellar locus: IR surveys such as 2MASS should be capable of finding these sources on the basis of their excess flux in the K-band

The unique genomic properties of sex-biased genes: Insights from avian microarray data

In order to develop a framework for the analysis of sex-biased genes, we present a characterization of microarray data comparing male and female gene expression in 18 day chicken embryos for brain, gonad, and heart tissue

Hotspots of Biased Nucleotide Substitutions in Human Genes

Genes that have experienced accelerated evolutionary rates on the human lineage during recent evolution are candidates for involvement in human-specific adaptations. To determine the forces that cause increased evolutionary rates in certain genes, we analyzed alignments of 10,238 human genes to their orthologues in chimpanzee and macaque. Using a likelihood ratio test, we identified protein-coding sequences with an accelerated rate of base substitutions along the human lineage. Exons evolving at a fast rate in humans have a significant tendency to contain clusters of AT-to-GC (weak-to-strong) biased substitutions. This pattern is also observed in noncoding sequence flanking rapidly evolving exons. Accelerated exons occur in regions with elevated male recombination rates and exhibit an excess of nonsynonymous substitutions relative to the genomic average. We next analyzed genes with significantly elevated ratios of nonsynonymous to synonymous rates of base substitution (dN/dS) along the human lineage, and those with an excess of amino acid replacement substitutions relative to human polymorphism. These genes also show evidence of clusters of weak-to-strong biased substitutions. These findings indicate that a recombination-associated process, such as biased gene conversion (BGC), is driving fixation of GC alleles in the human genome. This process can lead to accelerated evolution in coding sequences and excess amino acid replacement substitutions, thereby generating significant results for tests of positive selection

Developing reduced SNP assays from whole-genome sequence data to estimate C-lineage introgression in the Iberian honeybee (Apis mellifera iberiensis)

The honeybee has been subject to a growing number of threats. In Western Europe one such threat is large-scale introductions of commercial strains (C-lineage), which is leading to introgressive hybridization and even the local extinction of native populations (M-lineage). Here, we developed reduced assays of highly informative SNPs from 176 whole genomes to estimate C-lineage introgression in ;M-lineage subspecies Apis mellifera iberiensis. We started by evaluating the effects of sample size and sampling a geographically restricted area on the number of highly informative SNPs. We demonstrated that a bias in the number of fixed SNPs (FST=1) is introduced when the sample size is small (N≤10) and when sampling only captures a small fraction of a population’s genetic diversity. These results underscore the importance of having a representative sample when developing reliable reduced SNP assays for organisms with complex genetic patterns. We used a training dataset to design four independent SNP assays selected from pairwise FST between the Iberian and C-lineage honeybees. The designed assays, which were validated in holdout and simulated hybrid datasets, proved to be highly accurate and can be readily used for monitoring populations not only in the native range of A. m. iberiensis in Iberia but also in the introduced range in the Balearic islands, Macaronesia, and South America, in a time- and cost-effective manner. While our approach used the Iberian honeybee as model system, it has a high value in a wide range of scenarios for the monitoring and conservation of potentially hybridized domestic and wildlife populations.info:eu-repo/semantics/publishedVersio

Função de genes associados à precipitação envolvidos na adaptação local da abelha ibérica

O aparecimento de novas tecnologias em estudos genómicos permite-nos realizar análises mais aprofundadas e compreender de que modo as forças evolutivas atuam sobre o genoma dos organismos. Um scan genómico realizado previamente na abelha ibérica, revelou genes associados a imunidade, detoxificação e mecanismo da visão, estando alguns deles associados a variáveis ambientais (Chávez-Galarza et al. 2013). Na sequência deste estudo procurou se sinais de seleção em genomas completos de 84 indivíduos de abelha ibérica, integrando informação genética, geográfica e ambiental. Detetou-se a presença 315 genes associados à precipitação. O principal objetivo é caracterizar a função destes genes, e também tentar perceber que tipos de substituições nucleotídicas ocorrem nas sequências codificantes das proteínas. Para isso utilizaram se diversas bases genómicas, como o NCBI, BeeBase e Flybase, as quais mostraram que 51 das variações, presentes em 28 genes, são não-sinónimas, originando aminoácidos diferentes.info:eu-repo/semantics/publishedVersio

The Spectra of Red Quasars

We measure the spectral properties of a representative sub-sample of 187 quasars, drawn from the Parkes Half-Jansky, Flat-radio-spectrum Sample (PHFS). Quasars with a wide range of rest-frame optical/UV continuum slopes are included in the analysis: their colours range from 2 < B-K < 7. The median H-beta and [O III] emission-line equivalent widths of the red quasar sub-sample are a factor of ten weaker than those of the blue quasar sub-sample. Both the colours and the emission-line equivalent widths of the red quasars can be explained by the addition of a featureless red synchrotron continuum component to an otherwise normal blue quasar spectrum. The relative strengths of the blue and red components span two orders of magnitude at rest-frame 500nm. The blue component is weaker relative to the red component in low optical luminosity sources. This suggests that the fraction of accretion energy going into optical emission from the jet is greater in low luminosity quasars. This synchrotron model does not, however, fit around 10% of the quasars, which have both red colours and high equivalent width emission-lines. We hypothesise that these red, strong-lined quasars have intrinsically weak Big Blue Bumps. There is no discontinuity in spectral properties between the BL Lac objects in our sample and the other quasars. The synchrotron emission component only dominates the spectrum at longer wavelengths, so existing BL Lac surveys will be biassed against high redshift objects.Comment: 22 pages, 12 figures, accepted for publication in PASA. Data tables and composite spectra from the paper can be found at http://msowww.anu.edu.au/~pfrancis

Searching for signatures of selection in Iberian honey bee (Apis mellifera iberiensis) using whole genome sequences

The Iberian Peninsula comprises a diverse set of habitats. It was an important glacial refugium during the Pleistocene and has served as a bridge for populations migrating between Africa and Europe, resulting in a complex mix of ancestry and diversity. The Iberian honey bee (A. m. iberiensis) is no exception and has been the subject of numerous incongruent population genetic surveys. Recent mtDNA and SNP analyses indicate a steep northeastern-southwestern cline of African ancestry along the peninsula, which has been explained by selection. Advances in DNA sequencing technology and computational tools provide unprecedented opportunities to study demography, search for signatures of selection across the genome and illuminate its role in shaping genomic diversity. We used Illumina technology to sequence the whole genomes of 86 Iberian honeybees, collected across three longitudinal transects in the Iberian Peninsula and spanning semi-arid climates in the southeastern peninsula to oceanic in the North-West. The dataset was first analyzed for FST-outliers, CLR (composite-likelihood ratio) and EHH (Extended Haplotype Homozygosity) methods were further deployed to evaluate polymorphisms implicated in local adaptation and possibly in the response to human- mediated environmental changes, including known and novel variants in genes related to behavior, vision, xenobiotic detoxification and immune response.info:eu-repo/semantics/publishedVersio

Searching for signatures of selection in the Iberian honey bee (Apis mellifera iberiensis) using allele-environment association approaches

In the current context of a global human-mediated environmental crisis, understanding which genes and mechanisms are responsible for adaptation to different climates will enable predictions on how organisms will respond to a rapidly changing world. This is particularly important for the honey bee, a key-stone species for ecosystem functioning and economy, which is facing increasing pressures from the effects of intensified land use, climate change, and the spread of pests and pathogens. The aim of this work is searching for signatures of selection along the genome of 87 individuals using two different allele-environment association approaches.JC-G and DH are supported by Fundação para a Ciência e Tecnologia (FCT) through the scholarships SFRH/BD/68682/2010 and SFRH/BD/84195/2012, respectively. This research was funded by FCT and COMPETE/QREN/EU through the project PTDC/BIABEC/ 099640/2008 and BiodivERsA-FACCE2014-91. Bioinformatic analyses were performed using resources at the Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX)info:eu-repo/semantics/publishedVersio

Pyrotechnic Actuator for Retracting Tubes Between MSL Subsystems

An apparatus, denoted the "retractuator" (a contraction of "retracting actuator"), was designed to help ensure clean separation between the cruise stage and the entry-vehicle subsystem of the Mars Science Laboratory (MSL) mission. The retractuator or an equivalent mechanism is needed because of tubes that (1) transport a heat-transfer fluid between the stages during flight and (2) are cut immediately prior to separation of the stages retractuator. The role of the retractuator is to retract the tubes, after they are cut and before separation of the subsystem, so that cut ends of the tubes do not damage thermal-protection coats on the entry vehicle and do not contribute to uncertainty of drag and consequent uncertainty in separation velocity