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      Environmental DNA can act as a biodiversity barometer of anthropogenic pressures in coastal ecosystems

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          Abstract

          Loss of biodiversity from lower to upper trophic levels reduces overall productivity and stability of coastal ecosystems in our oceans, but rarely are these changes documented across both time and space. The characterisation of environmental DNA (eDNA) from sediment and seawater using metabarcoding offers a powerful molecular lens to observe marine biota and provides a series of ‘snapshots’ across a broad spectrum of eukaryotic organisms. Using these next-generation tools and downstream analytical innovations including machine learning sequence assignment algorithms and co-occurrence network analyses, we examined how anthropogenic pressures may have impacted marine biodiversity on subtropical coral reefs in Okinawa, Japan. Based on 18 S ribosomal RNA, but not ITS2 sequence data due to inconsistent amplification for this marker, as well as proxies for anthropogenic disturbance, we show that eukaryotic richness at the family level significantly increases with medium and high levels of disturbance. This change in richness coincides with compositional changes, a decrease in connectedness among taxa, an increase in fragmentation of taxon co-occurrence networks, and a shift in indicator taxa. Taken together, these findings demonstrate the ability of eDNA to act as a barometer of disturbance and provide an exemplar of how biotic networks and coral reefs may be impacted by anthropogenic activities.

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          Ror2 signaling regulates Golgi structure and transport through IFT20 for tumor invasiveness

          Signaling through the Ror2 receptor tyrosine kinase promotes invadopodia formation for tumor invasion. Here, we identify intraflagellar transport 20 (IFT20) as a new target of this signaling in tumors that lack primary cilia, and find that IFT20 mediates the ability of Ror2 signaling to induce the invasiveness of these tumors. We also find that IFT20 regulates the nucleation of Golgi-derived microtubules by affecting the GM130-AKAP450 complex, which promotes Golgi ribbon formation in achieving polarized secretion for cell migration and invasion. Furthermore, IFT20 promotes the efficiency of transport through the Golgi complex. These findings shed new insights into how Ror2 signaling promotes tumor invasiveness, and also advance the understanding of how Golgi structure and transport can be regulated.
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            Search and clustering orders of magnitude faster than BLAST.

            Biological sequence data is accumulating rapidly, motivating the development of improved high-throughput methods for sequence classification. UBLAST and USEARCH are new algorithms enabling sensitive local and global search of large sequence databases at exceptionally high speeds. They are often orders of magnitude faster than BLAST in practical applications, though sensitivity to distant protein relationships is lower. UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters. UCLUST offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets. Binaries are available at no charge for non-commercial use at http://www.drive5.com/usearch.
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              Diversity in tropical rain forests and coral reefs.

              The commonly observed high diversity of trees in tropical rain forests and corals on tropical reefs is a nonequilibrium state which, if not disturbed further, will progress toward a low-diversity equilibrium community. This may not happen if gradual changes in climate favor different species. If equilibrium is reached, a lesser degree of diversity may be sustained by niche diversification or by a compensatory mortality that favors inferior competitors. However, tropical forests and reefs are subject to severe disturbances often enough that equilibrium may never be attained.
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                Author and article information

                Contributors
                josephdibattista@gmail.com
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                20 May 2020
                20 May 2020
                2020
                : 10
                Affiliations
                [1 ]ISNI 0000 0004 0375 4078, GRID grid.1032.0, Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, ; Perth, WA 6102 Australia
                [2 ]ISNI 0000 0004 0470 8815, GRID grid.438303.f, Australian Museum Research Institute, Australian Museum, ; 1 William St, Sydney, NSW 2010 Australia
                [3 ]ISNI 0000 0001 0685 5104, GRID grid.267625.2, Molecular Invertebrate and Systematics Ecology Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, ; 1 Senbaru, Nishihara Okinawa, 903-0213 Japan
                [4 ]ISNI 0000 0001 0685 5104, GRID grid.267625.2, Tropical Biosphere Research Center, University of the Ryukyus, ; 1 Senbaru, Nishihara Okinawa, 903-0213 Japan
                [5 ]ISNI 0000 0000 8831 109X, GRID grid.266842.c, School of Environmental and Life Sciences, The University of Newcastle, ; Callaghan, NSW 2308 Australia
                [6 ]ISNI 0000 0001 2292 3111, GRID grid.267827.e, School of Biological Sciences, Victoria University of Wellington, ; PO Box 600, Wellington, 6140 New Zealand
                [7 ]ISNI 0000 0004 1936 8403, GRID grid.9909.9, School of Biology, Faculty of Biological Sciences, University of Leeds, ; Leeds, LS2 9JT United Kingdom
                [8 ]ISNI 0000 0001 2158 5405, GRID grid.1004.5, Department of Biological Sciences, Macquarie University, ; North Ryde, 2113 Australia
                [9 ]Environmental Protection Authority, 215 Lambton Quay, Wellington, 6011 New Zealand
                Article
                64858
                10.1038/s41598-020-64858-9
                7239923
                32433472
                27df07b4-7bfe-4103-a7cc-15910ad87fdb
                © The Author(s) 2020

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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                © The Author(s) 2020

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                biodiversity,ecological genetics,molecular ecology,marine biology,environmental impact

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