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  • 1
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    Male size predicts extrapair paternity in a socially monogamous bird with extreme sexual size dimorphism (2015)
    Oxford University Press
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    Publication Date: 2015-01-30
    Description: Extrapair paternity (EPP) is purported to be an important contributor to the evolution of plumage dimorphism, and yet relatively few studies have demonstrated that EPP creates selection pressures on male traits. Sexual size dimorphism (SSD) is instead typically assumed to have evolved in association with polygyny rather than EPP. Yet, the New Zealand tui, Prosthemadera novaeseelandiae , is a socially monogamous passerine exhibiting extreme SSD and sexual plumage dimorphism. Here, we examine whether EPP has contributed to the evolution of SSD in body size and ornament size in the tui. We discovered one of the highest rates of EPP currently known, with extrapair young occurring in 72% of broods and accounting for 57% of all offspring. Both male body size and ornament size were strongly correlated to EPP, with within-pair paternity success positively related to both traits. Male ornament size, but not body size, was a significant predictor of a male’s success at siring extrapair offspring. Although these patterns may have arisen through either male–male competition or female choice, it is likely that these 2 mechanisms are not mutually exclusive in tui. This study provides evidence that EPP can both create selection pressures on male traits, and contribute to the evolution of SSD.
    Print ISSN: 1045-2249
    Electronic ISSN: 1465-7279
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Submegaparsec individual photometric redshift estimation from cosmic web constraints (2015)
    Oxford University Press
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    Publication Date: 2015-09-24
    Description: We present a method, PhotoWeb, for estimating photometric redshifts of individual galaxies , and their equivalent distance, with megaparsec and even submegaparsec accuracy using the cosmic web as a constraint over photo- z estimates. PhotoWeb redshift errors of individual galaxies are of the order of z ~= 0.0007, compared to errors of z ~= 0.02 for current photo- z techniques. The mean redshift error is of the order of z ~= 5  x  10 –5 –5  x  10 –4 compared to mean errors in the range z ~= 0.001–0.01 for the best available photo- z estimates in the literature. Current photo- z techniques produce redshift estimates with large errors due to the poor constraining power the galaxy's spectral energy distribution and projected clustering can provide. The cosmic web, on the other hand, provides the strongest constraints on the position of galaxies. The network of walls, filaments and voids occupy ~ 10 per centof the volume of the Universe, yet they contain ~ 95 per centof galaxies. The cosmic web, being a cellular system with well-defined boundaries, defines a restricted set of intermittent positions a galaxy can occupy along a given line of sight. Using the information in the density field computed from spectroscopic redshifts, we can narrow the possible locations of a given galaxy along the line of sight from a single broad probability distribution (from photo- z ) to one or a few narrow peaks. Our first results improve previous photo- z errors by more than one order of magnitude allowing submegaparsec errors in some cases. Such accurate estimates for tens of millions of galaxies will allow unprecedented galaxy-Large Scale Structure (LSS) studies. In this work, we apply our technique to the Sloan Digital Sky Survey photo- z galaxy sample and discuss its performance and future improvements.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 3
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    ANGES: reconstructing ANcestral GEnomeS maps (2012)
    Oxford University Press
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    Publication Date: 2012-09-08
    Description: : ANGES is a suite of Python programs that allows reconstructing ancestral genome maps from the comparison of the organization of extant-related genomes. ANGES can reconstruct ancestral genome maps for multichromosomal linear genomes and unichromosomal circular genomes. It implements methods inspired from techniques developed to compute physical maps of extant genomes. Examples of cereal, amniote, yeast or bacteria ancestral genomes are provided, computed with ANGES. Availability : ANGES is freely available for download at http://paleogenomics.irmacs.sfu.ca/ANGES/ . Documentation and examples are available together with the package. Contact: cedric.chauve@sfu.ca
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 4
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    Subhalo statistics of galactic haloes: beyond the resolution limit (2014)
    Oxford University Press
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    Publication Date: 2014-10-16
    Description: We study the substructure population of Milky Way (MW)-mass haloes in the cold dark matter (CDM) cosmology using a novel procedure to extrapolate subhalo number statistics beyond the resolution limit of N -body simulations. The technique recovers the mean and the variance of the subhalo abundance, but not its spatial distribution. It extends the dynamic range over which precise statistical predictions can be made by the equivalent of performing a simulation with 50 times higher resolution, at no additional computational cost. We apply this technique to MW-mass haloes, but it can easily be applied to haloes of any mass. We find up to 20 per cent more substructures in MW-mass haloes than found in previous studies. Our analysis lowers the mass of the MW halo required to accommodate the observation that the MW has only three satellites with a maximum circular velocity V max ≥ 30 km s – 1 in the CDM cosmology. The probability of having a subhalo population similar to that in the MW is 20 per cent for a virial mass, M 200  = 1 10 12 M and practically zero for haloes more massive than M 200  = 2 10 12 M .
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 5
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    Milky Way mass constraints from the Galactic satellite gap (2014)
    Oxford University Press
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    Publication Date: 2014-10-16
    Description: We use the distribution of maximum circular velocities, V max , of satellites in the Milky Way (MW) to constrain the virial mass, M 200 , of the Galactic halo under an assumed prior of a cold dark matter universe. This is done by analysing the subhalo populations of a large sample of haloes found in the Millennium II cosmological simulation. The observation that the MW has at most three subhaloes with V max  ≥ 30 km s –1 requires a halo mass M 200  ≤ 1.4 10 12 M , while the existence of the Magellanic Clouds (assumed to have V max  ≥ 60 km s –1 ) requires M 200  ≥ 1.0 10 12 M . The first of these conditions is necessary to avoid the ‘too-big-to-fail’ problem highlighted by Boylan-Kolchin et al., while the second stems from the observation that massive satellites like the Magellanic Clouds are rare. When combining both requirements, we find that the MW halo mass must lie in the range 0.25 ≤  M 200 /(10 12 M ) ≤ 1.4 at 90 per cent confidence. The gap in the abundance of Galactic satellites between 30 km s –1  ≤  V max  ≤ 60 km s –1 places our galaxy in the tail of the expected satellite distribution.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 6
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    Governing 'dual-use' research in Canada: A policy review (2014)
    Oxford University Press
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    Publication Date: 2014-02-15
    Description: National and international organisations have implemented governance mechanisms to address a diversity of ethical, security and policy challenges raised by advances in research and innovation. These challenges become particularly complex when research or innovations are considered ‘dual-use’, i.e. can lead to both beneficial and harmful uses, and in particular, civilian (peaceful) and military (hostile) applications. While many countries have mechanisms (i.e. export controls) to govern the transfer of dual-use technology (e.g. nuclear, cryptography), it is much less clear how dual-use research from across the range of academic disciplines can or should be governed. Using the Canadian research and policy context as case study, this paper will first, examine the governance mechanisms currently in place to mitigate the negative implications of dual-use research and innovation; second, compare these with other relevant international governance contexts; and finally, propose some ways forward (i.e. a risk analysis approach) for developing more robust governance mechanisms.
    Print ISSN: 0302-3427
    Electronic ISSN: 1471-5430
    Topics: Nature of Science, Research, Systems of Higher Education, Museum Science
    Published by Oxford University Press
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  • 7
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    Evolution of a Catalytic Mechanism (2016)
    Oxford University Press
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    Publication Date: 2016-03-04
    Description: The means by which superfamilies of specialized enzymes arise by gene duplication and functional divergence are poorly understood. The escape from adaptive conflict hypothesis, which posits multiple copies of a gene encoding a primitive inefficient and highly promiscuous generalist ancestor, receives support from experiments showing that resurrected ancestral enzymes are indeed more substrate-promiscuous than their modern descendants. Here, we provide evidence in support of an alternative model, the innovation–amplification–divergence hypothesis, which posits a single-copied ancestor as efficient and specific as any modern enzyme. We argue that the catalytic mechanisms of plant esterases and descendent acetone cyanohydrin lyases are incompatible with each other (e.g., the reactive substrate carbonyl must bind in opposite orientations in the active site). We then show that resurrected ancestral plant esterases are as catalytically specific as modern esterases, that the ancestor of modern acetone cyanohydrin lyases was itself only very weakly promiscuous, and that improvements in lyase activity came at the expense of esterase activity. These observations support the innovation–amplification–divergence hypothesis, in which an ancestor gains a weak promiscuous activity that is improved by selection at the expense of the ancestral activity, and not the escape from adaptive conflict in which an inefficient generalist ancestral enzyme steadily loses promiscuity throughout the transition to a highly active specialized modern enzyme.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    Biodiversity patterns of plankton assemblages at the extremes of the Red Sea (2016)
    Oxford University Press
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    Publication Date: 2016-02-13
    Description: The diversity of microbial plankton has received limited attention in the main basin of the Red Sea. This study investigates changes in the community composition and structure of prokaryotes and eukaryotes at the extremes of the Red Sea along cross-shelf gradients and between the surface and deep chlorophyll maximum. Using molecular methods to target both the 16S and 18S rRNA genes, it was observed that the dominant prokaryotic classes were Acidimicrobiia, Alphaproteobacteria and Cyanobacteria, regardless of the region and depth. The eukaryotes Syndiniophyceae and Dinophyceae between them dominated in the north, with Bacillariophyceae and Mamiellophyceae more prominent in the southern region. Significant differences were observed for prokaryotes and eukaryotes for region, depth and distance from shore. Similarly, it was noticed that communities became less similar with increasing distance from the shore. Canonical correspondence analysis at the class level showed that Mamiellophyceae and Bacillariophyceae correlated with increased nutrients and chlorophyll a found in the southern region, which is influenced by the input of Gulf of Aden Intermediate Water.
    Print ISSN: 0168-6496
    Electronic ISSN: 1574-6941
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    The topology of the cosmic web in terms of persistent Betti numbers (2016)
    Oxford University Press
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    Publication Date: 2016-12-28
    Description: We introduce a multiscale topological description of the Megaparsec web-like cosmic matter distribution. Betti numbers and topological persistence offer a powerful means of describing the rich connectivity structure of the cosmic web and of its multiscale arrangement of matter and galaxies. Emanating from algebraic topology and Morse theory, Betti numbers and persistence diagrams represent an extension and deepening of the cosmologically familiar topological genus measure and the related geometric Minkowski functionals. In addition to a description of the mathematical background, this study presents the computational procedure for computing Betti numbers and persistence diagrams for density field filtrations. The field may be computed starting from a discrete spatial distribution of galaxies or simulation particles. The main emphasis of this study concerns an extensive and systematic exploration of the imprint of different web-like morphologies and different levels of multiscale clustering in the corresponding computed Betti numbers and persistence diagrams. To this end, we use Voronoi clustering models as templates for a rich variety of web-like configurations and the fractal-like Soneira–Peebles models exemplify a range of multiscale configurations. We have identified the clear imprint of cluster nodes, filaments, walls, and voids in persistence diagrams, along with that of the nested hierarchy of structures in multiscale point distributions. We conclude by outlining the potential of persistent topology for understanding the connectivity structure of the cosmic web, in large simulations of cosmic structure formation and in the challenging context of the observed galaxy distribution in large galaxy surveys.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 10
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    Evolution of the cosmic web (2014)
    Oxford University Press
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    Publication Date: 2014-05-30
    Description: The cosmic web is the largest scale manifestation of the anisotropic gravitational collapse of matter. It represents the transitional stage between linear and non-linear structures and contains easily accessible information about the early phases of structure formation processes. Here we investigate the characteristics and the time evolution of morphological components. Our analysis involves the application of the NEXUS Multiscale Morphology Filter technique, predominantly its NEXUS+ version, to high resolution and large volume cosmological simulations. We quantify the cosmic web components in terms of their mass and volume content, their density distribution and halo populations. We employ new analysis techniques to determine the spatial extent of filaments and sheets, like their total length and local width. This analysis identifies clusters and filaments as the most prominent components of the web. In contrast, while voids and sheets take most of the volume, they correspond to underdense environments and are devoid of group-sized and more massive haloes. At early times the cosmos is dominated by tenuous filaments and sheets, which, during subsequent evolution, merge together, such that the present-day web is dominated by fewer, but much more massive, structures. The analysis of the mass transport between environments clearly shows how matter flows from voids into walls, and then via filaments into cluster regions, which form the nodes of the cosmic web. We also study the properties of individual filamentary branches, to find long, almost straight, filaments extending to distances larger than 100 h –1 Mpc. These constitute the bridges between massive clusters, which seem to form along approximatively straight lines.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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