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  • 1
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    On the survival of resonant and non-resonant planetary systems in star clusters (2020)
    Oxford University Press
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    Publication Date: 2020-07-13
    Description: Despite the discovery of thousands of exoplanets in recent years, the number of known exoplanets in star clusters remains tiny. This may be a consequence of close stellar encounters perturbing the dynamical evolution of planetary systems in these clusters. Here, we present the results from direct N-body simulations of multiplanetary systems embedded in star clusters containing N = 8k, 16k, 32k, and 64k stars. The planetary systems, which consist of the four Solar system giant planets Jupiter, Saturn, Uranus, and Neptune, are initialized in different orbital configurations, to study the effect of the system architecture on the dynamical evolution of the entire planetary system, and on the escape rate of the individual planets. We find that the current orbital parameters of the Solar system giants (with initially circular orbits, as well as with present-day eccentricities) and a slightly more compact configuration, have a high resilience against stellar perturbations. A configuration with initial mean-motion resonances of 3:2, 3:2, and 5:4 between the planets, which is inspired by the Nice model, and for which the two outermost planets are usually ejected within the first 105 yr, is in many cases stabilized due to the removal of the resonances by external stellar perturbation and by the rapid ejection of at least one planet. Assigning all planets the same mass of 1 MJup almost equalizes the survival fractions. Our simulations reproduce the broad diversity amongst observed exoplanet systems. We find not only many very wide and/or eccentric orbits, but also a significant number of (stable) retrograde orbits.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
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  • 2
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    Sex-Chromosome Homomorphy in Palearctic Tree Frogs Results from Both Turnovers and X-Y Recombination (2015)
    Oxford University Press
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    Publication Date: 2015-08-20
    Description: Contrasting with birds and mammals, poikilothermic vertebrates often have homomorphic sex chromosomes, possibly resulting from high rates of sex-chromosome turnovers and/or occasional X–Y recombination. Strong support for the latter mechanism was provided by four species of European tree frogs, which inherited from a common ancestor (~5 Ma) the same pair of homomorphic sex chromosomes (linkage group 1, LG1), harboring the candidate sex-determining gene Dmrt1. Here, we test sex linkage of LG1 across six additional species of the Eurasian Hyla radiation with divergence times ranging from 6 to 40 Ma. LG1 turns out to be sex linked in six of nine resolved cases. Mapping the patterns of sex linkage to the Hyla phylogeny reveals several transitions in sex-determination systems within the last 10 My, including one switch in heterogamety. Phylogenetic trees of DNA sequences along LG1 are consistent with occasional X–Y recombination in all species where LG1 is sex linked. These patterns argue against one of the main potential causes for turnovers, namely the accumulation of deleterious mutations on nonrecombining chromosomes. Sibship analyses show that LG1 recombination is strongly reduced in males from most species investigated, including some in which it is autosomal. Intrinsically low male recombination might facilitate the evolution of male heterogamety, and the presence of important genes from the sex-determination cascade might predispose LG1 to become a sex chromosome.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Building confidence in projections of the responses of living marine resources to climate change (2016)
    Oxford University Press
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    Publication Date: 2016-06-24
    Description: The Fifth Assessment Report of the Intergovernmental Panel on Climate Change highlights that climate change and ocean acidification are challenging the sustainable management of living marine resources (LMRs). Formal and systematic treatment of uncertainty in existing LMR projections, however, is lacking. We synthesize knowledge of how to address different sources of uncertainty by drawing from climate model intercomparison efforts. We suggest an ensemble of available models and projections, informed by observations, as a starting point to quantify uncertainties. Such an ensemble must be paired with analysis of the dominant uncertainties over different spatial scales, time horizons, and metrics. We use two examples: (i) global and regional projections of Sea Surface Temperature and (ii) projection of changes in potential catch of sablefish ( Anoplopoma fimbria ) in the 21st century, to illustrate this ensemble model approach to explore different types of uncertainties. Further effort should prioritize understanding dominant, undersampled dimensions of uncertainty, as well as the strategic collection of observations to quantify, and ultimately reduce, uncertainties. Our proposed framework will improve our understanding of future changes in LMR and the resulting risk of impacts to ecosystems and the societies under changing ocean conditions.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press
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  • 4
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    The probability distribution functions of emission line flux measurements and their ratios (2016)
    Oxford University Press
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    Publication Date: 2016-05-12
    Description: Many physical parameters in astrophysics are derived using the ratios of two observed quantities. If the relative uncertainties on measurements are small enough, uncertainties can be propagated analytically using simplifying assumptions, but for large normally distributed uncertainties, the probability distribution of the ratio become skewed, with a modal value offset from that expected in Gaussian uncertainty propagation. Furthermore, the most likely value of a ratio A/B is not equal to the reciprocal of the most likely value of B/A. The effect is most pronounced when the uncertainty on the denominator is larger than that on the numerator. We show that this effect is seen in an analysis of 12 126 spectra from the Sloan Digital Sky Survey (SDSS). The intrinsically fixed ratio of the [O iii ] lines at 4959 and 5007 Å is conventionally expressed as the ratio of the stronger line to the weaker line. Thus, the uncertainty on the denominator is larger, and non-Gaussian probability distributions result. By taking this effect into account, we derive an improved estimate of the intrinsic 5007/4959 ratio. We obtain a value of 3.012 ± 0.008, which is slightly but statistically significantly higher than the theoretical value of 2.98. We further investigate the suggestion that fluxes measured from emission lines in noisy spectra are strongly biased upwards. We were unable to detect this effect in the SDSS line flux measurements, and we could not reproduce the results of Rola and Pelat who first described this bias. We suggest that the magnitude of this effect may depend strongly on the specific fitting algorithm used.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 5
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    Projected ocean warming creates a conservation challenge for river herring populations (2015)
    Oxford University Press
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    Publication Date: 2015-01-20
    Description: The term river herring collectively refers to alewife ( Alosa pseudoharengus ) and blueback herring ( A. aestivalis ), two anadromous fishes distributed along the east coast of North America. Historically, river herring spawning migrations supported important fisheries, and their spawning runs continue to be of cultural significance to many coastal communities. Recently, substantial declines in spawning run size prompted a petition to consider river herring for listing under the Endangered Species Act (ESA). The ESA status review process requires an evaluation of a species' response to multiple stressors, including climate change. For anadromous species that utilize a range of habitats throughout their life cycle, the response to a changing global climate is inherently complex and likely varies regionally. River herring occupy marine habitat for most of their lives, and we demonstrate that their relative abundance in the ocean has been increasing in recent years. We project potential effects of ocean warming along the US Atlantic coast on river herring in two seasons (spring and fall), and two future periods (2020–2060 and 2060–2100) by linking species distribution models to projected temperature changes from global climate models. Our analyses indicate that climate change will likely result in reductions in total suitable habitat across the study region, which will alter the marine distribution of river herring. We also project that density will likely decrease for both species in fall, but may increase in spring. Finally, we demonstrate that river herring may have increased sensitivity to climate change under a low abundance scenario. This result could be an important consideration for resource managers when planning for climate change because establishing effective conservation efforts in the near term may improve population resiliency and provide lasting benefits to river herring populations.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press
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  • 6
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    Cusk (Brosme brosme) and climate change: assessing the threat to a candidate marine fish species under the US Endangered Species Act (2012)
    Oxford University Press
    Details
    Publication Date: 2012-10-13
    Description: Hare, J.A., Manderson, J.P., Nye, J.A., Alexander, M.A., Auster, P.J., Borggaard, D.L., Capotondi, A.M., Damon-Randall, K.B., Heupel, E., Mateo, I., O'Brien, L., Richardson, D.E., Stock, C.A., and Biege, S.T. 2012. Cusk ( Brosme brosme ) and climate change: assessing the threat to a candidate marine fish species under the US Endangered Species Act. – ICES Journal of Marine Science, 69: 1753–1768. In the Northwest Atlantic Ocean cusk ( Brosme brosme ) has declined dramatically, primarily as a result of fishing activities. These declines have led to concern about its status, which has prompted reviews under the US Endangered Species Act and the Canadian Species at Risk Act. Changes in distribution and abundance of a number of marine fish in the Northwest Atlantic have been linked to climate variability and change, suggesting that both fishing and climate may affect the status of cusk. Our goal was to evaluate potential effects of climate change on Northwest Atlantic cusk distribution. Coupling a species niche model with the output from an ensemble of climate models, we projected cusk distribution in the future. Our results indicate cusk habitat in the region will shrink and fragment, which is a result of a spatial mismatch between high complexity seafloor habitat and suitable temperature. The importance of habitat patch connectivity for cusk is poorly understood, so the population-level consequences of climate-related habitat fragmentation are uncertain. More broadly, climate change may reduce appropriate thermal habitat and increase habitat fragmentation for other cold-water species in the region; thereby, increasing the potential for regional overexploitation and extirpation.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press
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  • 7
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    Placing Environmental Next-Generation Sequencing Amplicons from Microbial Eukaryotes into a Phylogenetic Context (2014)
    Oxford University Press
    Details
    Publication Date: 2014-03-22
    Description: Nucleotide positions in the hypervariable V4 and V9 regions of the small subunit (SSU)-rDNA locus are normally difficult to align and are usually removed before standard phylogenetic analyses. Yet, with next-generation sequencing data, amplicons of these regions are all that are available to answer ecological and evolutionary questions that rely on phylogenetic inferences. With ciliates, we asked how inclusion of the V4 or V9 regions, regardless of alignment quality, affects tree topologies using distinct phylogenetic methods (including PairDist that is introduced here). Results show that the best approach is to place V4 amplicons into an alignment of full-length Sanger SSU-rDNA sequences and to infer the phylogenetic tree with RAxML. A sliding window algorithm as implemented in RAxML shows, though, that not all nucleotide positions in the V4 region are better than V9 at inferring the ciliate tree. With this approach and an ancestral-state reconstruction, we use V4 amplicons from European nearshore sampling sites to infer that rather than being primarily terrestrial and freshwater, colpodean ciliates may have repeatedly transitioned from terrestrial/freshwater to marine environments.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    Herschel-PACS measurements of nitrogen enrichment in nebulae around Wolf-Rayet stars (2014)
    Oxford University Press
    Details
    Publication Date: 2014-05-31
    Description: For three nebulae that have early-WN Wolf–Rayet exciting stars, NGC 6888, WR 8 and Abell 48, we have obtained Herschel -PACS line scans of the [N iii ] 57-μm and [O iii ] 88-μm lines, along with the 122- and 205-μm lines of [N ii ]. From the former two lines we have derived N 2+ /O 2+ abundance ratios, equal to the overall N/O ratio under a wide range of nebular conditions. We find that all of the nebulae observed possess significant nitrogen enrichment, with derived N/O ratios greater than solar. The two nebulae with massive Wolf–Rayet exciting stars, NGC 6888 and WR 8 are found to have N/O ratios that are enhanced by factors of 7 – 10 relative to the solar N/O ratio, consistent with an origin as material ejected just before the onset of the Wolf–Rayet phase. The other nebula, Abell 48, has recently been reclassified as a member of the rare class of three planetary nebulae that have early-WN central stars and are not of Peimbert type I. We derive a nebular N/O ratio for it that is a factor of 4 enhanced relative to solar and slightly above the range of N/O values that have been measured for the other three members of its [WN] planetary nebula class.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 9
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    Active Pacific North America Plate boundary tectonics as evidenced by seismicity in the oceanic lithosphere offshore Baja California, Mexico (2014)
    Oxford University Press
    Details
    Publication Date: 2014-02-13
    Description: Pacific Ocean crust west of southwest North America was formed by Cenozoic seafloor spreading between the large Pacific Plate and smaller microplates. The eastern limit of this seafloor, the continent–ocean boundary, is the fossil trench along which the microplates subducted and were mostly destroyed in Miocene time. The Pacific–North America Plate boundary motion today is concentrated on continental fault systems well to the east, and this region of oceanic crust is generally thought to be within the rigid Pacific Plate. Yet, the 2012 December 14 M w 6.3 earthquake that occurred about 275 km west of Ensenada, Baja California, Mexico, is evidence for continued tectonism in this oceanic part of the Pacific Plate. The preferred main shock centroid depth of 20 km was located close to the bottom of the seismogenic thickness of the young oceanic lithosphere. The focal mechanism, derived from both teleseismic P -wave inversion and W -phase analysis of the main shock waveforms, and the 12 aftershocks of M  ~3–4 are consistent with normal faulting on northeast striking nodal planes, which align with surface mapped extensional tectonic trends such as volcanic features in the region. Previous Global Positioning System (GPS) measurements on offshore islands in the California Continental Borderland had detected some distributed Pacific and North America relative plate motion strain that could extend into the epicentral region. The release of this lithospheric strain along existing zones of weakness is a more likely cause of this seismicity than current thermal contraction of the oceanic lithosphere or volcanism. The main shock caused weak to moderate ground shaking in the coastal zones of southern California, USA, and Baja California, Mexico, but the tsunami was negligible.
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 10
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    R-type bacteriocins in related strains of Xenorhabdus bovienii: Xenorhabdicin tail fiber modularity and contribution to competitiveness (2017)
    Oxford University Press
    Details
    Publication Date: 2017-01-19
    Description: R-type bacteriocins are contractile phage tail-like structures that are bactericidal towards related bacterial species. The C-terminal region of the phage tail fiber protein determines target-binding specificity. The mutualistic bacteria Xenorhabdus nematophila and X. bovienii produce R-type bacteriocins (xenorhabdicins) that are selectively active against different Xenorhabdus species. We analyzed the P2-type remnant prophage clusters in draft sequences of nine strains of X. bovienii . The C-terminal tail fiber region in each of the respective strains was unique and consisted of mosaics of modular units. The region between the main tail fiber gene ( xbpH1 ) and the sheath gene ( xbpS1 ) contained a variable number of modules encoding tail fiber fragments. DNA inversion and module exchange between strains was involved in generating tail fiber diversity. Xenorhabdicin-enriched fractions from three different X. bovienii strains isolated from the same nematode species displayed distinct activities against each other. In one set of strains, the strain that produced highly active xenorhabdicin was able to eliminate a sensitive strain. In contrast, xenorhabdicin activity was not a determining factor in the competitive fitness of a second set of strains. These findings suggest that related strains of X. bovienii use xenorhabdicin and additional antagonistic molecules to compete against each other.
    Keywords: Environmental Microbiology
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
    Published by Oxford University Press
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