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  • 1
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 352, No. 6283 ( 2016-04-15), p. 345-349
    Abstract: Brazil has experienced an unprecedented epidemic of Zika virus (ZIKV), with ~30,000 cases reported to date. ZIKV was first detected in Brazil in May 2015, and cases of microcephaly potentially associated with ZIKV infection were identified in November 2015. We performed next-generation sequencing to generate seven Brazilian ZIKV genomes sampled from four self-limited cases, one blood donor, one fatal adult case, and one newborn with microcephaly and congenital malformations. Results of phylogenetic and molecular clock analyses show a single introduction of ZIKV into the Americas, which we estimated to have occurred between May and December 2013, more than 12 months before the detection of ZIKV in Brazil. The estimated date of origin coincides with an increase in air passengers to Brazil from ZIKV-endemic areas, as well as with reported outbreaks in the Pacific Islands. ZIKV genomes from Brazil are phylogenetically interspersed with those from other South American and Caribbean countries. Mapping mutations onto existing structural models revealed the context of viral amino acid changes present in the outbreak lineage; however, no shared amino acid changes were found among the three currently available virus genomes from microcephaly cases. Municipality-level incidence data indicate that reports of suspected microcephaly in Brazil best correlate with ZIKV incidence around week 17 of pregnancy, although this correlation does not demonstrate causation. Our genetic description and analysis of ZIKV isolates in Brazil provide a baseline for future studies of the evolution and molecular epidemiology of this emerging virus in the Americas.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2016
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  • 2
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2010
    In:  ICES Journal of Marine Science Vol. 67, No. 4 ( 2010-05-01), p. 787-795
    In: ICES Journal of Marine Science, Oxford University Press (OUP), Vol. 67, No. 4 ( 2010-05-01), p. 787-795
    Abstract: Link, J. S., Yemane, D., Shannon, L. J., Coll, M., Shin, Y-J., Hill, L., and Borges, M. F. 2010. Relating marine ecosystem indicators to fishing and environmental drivers: an elucidation of contrasting responses. – ICES Journal of Marine Science, 67: 787–795. The usefulness of indicators in detecting ecosystem change depends on three main criteria: the availability of data to estimate the indicator (measurability), the ability to detect change in an ecosystem (sensitivity), and the ability to link the said change in an indicator as a response to a known intervention or pressure (specificity). Here, we specifically examine the third aspect of indicator change, with an emphasis on multiple methods to explore the “relativity” of major ecosystem drivers. We use a suite of multivariate methods to explore the relationships between a pre-established set of fisheries-orientated ecosystem status indicators and the key drivers for those ecosystems (particularly emphasizing proxy indicators for fishing and the environment). The results show the relative importance among fishing and environmental factors, which differed notably across the major types of ecosystems. Yet, they also demonstrated common patterns in which most ecosystems, and indicators of ecosystem dynamics are largely driven by fisheries (landings) or human (human development index) factors, and secondarily by environmental drivers (e.g. AMO, PDO, SST). How one might utilize this empirical evidence in future efforts for ecosystem approaches to fisheries is discussed, highlighting the need to manage fisheries in the context of environmental and other human (e.g. economic) drivers.
    Type of Medium: Online Resource
    ISSN: 1095-9289 , 1054-3139
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2010
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  • 3
    In: ICES Journal of Marine Science, Oxford University Press (OUP), Vol. 67, No. 4 ( 2010-05-01), p. 692-716
    Abstract: Shin, Y-J., Shannon, L. J., Bundy, A., Coll, M., Aydin, K., Bez, N., Blanchard, J. L., Borges, M. F., Diallo, I., Diaz, E., Heymans, J. J., Hill, L., Johannesen, E., Jouffre, D., Kifani, S., Labrosse, P., Link, J. S., Mackinson, S., Masski, H., Möllmann, C., Neira, S., Ojaveer, H., ould Mohammed Abdallahi, K., Perry, I., Thiao, D., Yemane, D., and Cury, P. M. 2010. Using indicators for evaluating, comparing, and communicating the ecological status of exploited marine ecosystems. 2. Setting the scene. – ICES Journal of Marine Science, 67: 692–716. Background is provided to the selection of ecological indicators by the IndiSeas Working Group, and the methodology adopted for analysis and comparison of indicators across exploited marine ecosystems is documented. The selected indicators are presented, how they are calculated is explained, and the philosophy behind the comparative approach is given. The combination of selected indicators is intended to reflect different dynamics, tracking processes that display differential responses to fishing, and is meant to provide a complementary means of assessing marine ecosystem trends and states. IndiSeas relied on inputs and insights provided by the local experts from participating ecosystems, helping to understand state and trend indicators and to disentangle the effect of other potential ecosystem drivers, such as climate variability. This project showed that the use of simple and available indicators under an ecosystem approach can achieve a real, wide-reaching evaluation of marine ecosystem status caused by fishing. This is important because the socio-economics of areas where fishing activities develop differs significantly around the globe, and in many countries, insufficient data are available for complex and exhaustive analyses.
    Type of Medium: Online Resource
    ISSN: 1095-9289 , 1054-3139
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2010
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  • 4
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2010
    In:  Nature Vol. 467, No. 7315 ( 2010-9), p. 531-531
    In: Nature, Springer Science and Business Media LLC, Vol. 467, No. 7315 ( 2010-9), p. 531-531
    Type of Medium: Online Resource
    ISSN: 0028-0836 , 1476-4687
    RVK:
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    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2010
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  • 5
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2010
    In:  ICES Journal of Marine Science Vol. 67, No. 4 ( 2010-05-01), p. 745-768
    In: ICES Journal of Marine Science, Oxford University Press (OUP), Vol. 67, No. 4 ( 2010-05-01), p. 745-768
    Abstract: Bundy, A., Shannon, L. J., Rochet, M-J., Neira, S., Shin, Y-J., Hill, L., and Aydin, K. 2010. The good(ish), the bad, and the ugly: a tripartite classification of ecosystem trends. – ICES Journal of Marine Science, 67: 745–768. Marine ecosystems have been exploited for a long time, growing increasingly vulnerable to collapse and irreversible change. How do we know when an ecosystem may be in danger? A measure of the status of individual stocks is only a partial gauge of its status, and does not include changes at the broader ecosystem level, to non-commercial species or to its structure or functioning. Six ecosystem indicators measuring trends over time were collated for 19 ecosystems, corresponding to four ecological attributes: resource potential, ecosystem structure and functioning, conservation of functional biodiversity, and ecosystem stability and resistance to perturbations. We explored the use of a decision-tree approach, a definition of initial ecosystem state (impacted or non-impacted), and the trends in the ecosystem indicators to classify the ecosystems into improving, stationary, and deteriorating. Ecosystem experts classified all ecosystems as impacted at the time of their initial state. Of these, 15 were diagnosed as “ugly”, because they had deteriorated from an already impacted state. Several also exhibited specific combinations of trends indicating “fishing down the foodweb”, reduction in size structure, reduction in diversity and stability, and changed productivity. The classification provides an initial evaluation for scientists, resource managers, stakeholders, and the general public of the concerning status of ecosystems globally.
    Type of Medium: Online Resource
    ISSN: 1095-9289 , 1054-3139
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2010
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