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      Diversity and structure of feather mite communities on seabirds from the north–east Atlantic and Mediterranean Sea

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          Abstract

          The richness and structure of symbiont assemblages are shaped by many factors acting at different spatial and temporal scales. Among them, host phylogeny and geographic distance play essential roles. To explore drivers of richness and structure of symbiont assemblages, feather mites and seabirds are an attractive model due to their peculiar traits. Feather mites are permanent ectosymbionts and considered highly host-specific with limited dispersal abilities. Seabirds harbour species-rich feather mite communities and their colonial breeding provides opportunities for symbionts to exploit several host species. To unravel the richness and test the influence of host phylogeny and geographic distance on mite communities, we collected feather mites from 11 seabird species breeding across the Atlantic Ocean and Mediterranean Sea. Using morphological criteria, we identified 33 mite species, of which 17 were new or recently described species. Based on community similarity analyses, mite communities were clearly structured by host genera, while the effect of geography within host genera or species was weak and sometimes negligible. We found a weak but significant effect of geographic distance on similarity patterns in mite communities for Cory’s shearwaters Calonectris borealis. Feather mite specificity mainly occurred at the host-genus rather than at host-species level, suggesting that previously inferred host species-specificity may have resulted from poorly sampling closely related host species. Overall, our results show that host phylogeny plays a greater role than geography in determining the composition and structure of mite assemblages and pinpoints the importance of sampling mites from closely-related host species before describing mite specificity patterns.

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          phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

          Background The analysis of microbial communities through DNA sequencing brings many challenges: the integration of different types of data with methods from ecology, genetics, phylogenetics, multivariate statistics, visualization and testing. With the increased breadth of experimental designs now being pursued, project-specific statistical analyses are often needed, and these analyses are often difficult (or impossible) for peer researchers to independently reproduce. The vast majority of the requisite tools for performing these analyses reproducibly are already implemented in R and its extensions (packages), but with limited support for high throughput microbiome census data. Results Here we describe a software project, phyloseq, dedicated to the object-oriented representation and analysis of microbiome census data in R. It supports importing data from a variety of common formats, as well as many analysis techniques. These include calibration, filtering, subsetting, agglomeration, multi-table comparisons, diversity analysis, parallelized Fast UniFrac, ordination methods, and production of publication-quality graphics; all in a manner that is easy to document, share, and modify. We show how to apply functions from other R packages to phyloseq-represented data, illustrating the availability of a large number of open source analysis techniques. We discuss the use of phyloseq with tools for reproducible research, a practice common in other fields but still rare in the analysis of highly parallel microbiome census data. We have made available all of the materials necessary to completely reproduce the analysis and figures included in this article, an example of best practices for reproducible research. Conclusions The phyloseq project for R is a new open-source software package, freely available on the web from both GitHub and Bioconductor.
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            TimeTree: A Resource for Timelines, Timetrees, and Divergence Times.

            Evolutionary information on species divergence times is fundamental to studies of biodiversity, development, and disease. Molecular dating has enhanced our understanding of the temporal patterns of species divergences over the last five decades, and the number of studies is increasing quickly due to an exponential growth in the available collection of molecular sequences from diverse species and large number of genes. Our TimeTree resource is a public knowledge-base with the primary focus to make available all species divergence times derived using molecular sequence data to scientists, educators, and the general public in a consistent and accessible format. Here, we report a major expansion of the TimeTree resource, which more than triples the number of species (>97,000) and more than triples the number of studies assembled (>3,000). Furthermore, scientists can access not only the divergence time between two species or higher taxa, but also a timetree of a group of species and a timeline that traces a species' evolution through time. The new timetree and timeline visualizations are integrated with display of events on earth and environmental history over geological time, which will lead to broader and better understanding of the interplay of the change in the biosphere with the diversity of species on Earth. The next generation TimeTree resource is publicly available online at http://www.timetree.org.
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              Host specificity in phylogenetic and geographic space.

              The measurement of host specificity goes well beyond counting how many host species can successfully be used by a parasite. In particular, specificity can be assessed with respect to how closely related the host species are, or whether a parasite exploits the same or different hosts across its entire geographic range. Recent developments in the measurement of biodiversity offer a new set of analytical tools that can be used to quantify the many aspects of host specificity. We describe here the multifaceted nature of host specificity, summarize the indices available to measure its different facets one at a time or in combination, and discuss their implications for parasite evolution and disease epidemiology. Copyright © 2011 Elsevier Ltd. All rights reserved.
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                Author and article information

                Contributors
                lauramihaelastefan@yahoo.com
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                23 March 2023
                23 March 2023
                2023
                : 13
                : 4793
                Affiliations
                [1 ]GRID grid.5841.8, ISNI 0000 0004 1937 0247, Institut de Recerca de La Biodiversitat (IRBio), Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, , Universitat de Barcelona, ; Av. Diagonal 643, 08028 Barcelona, Spain
                [2 ]GRID grid.435400.6, ISNI 0000 0004 0369 4845, Department of Cellular and Molecular Biology, , National Institute of Research and Development for Biological Sciences, ; Splaiul Independentei 296, 060031 Bucharest, Romania
                [3 ]GRID grid.121334.6, ISNI 0000 0001 2097 0141, Université de Montpellier- CNRS-IRD, UMR MIVEGEC, ; 900 Rue Jean-François Breton, 34090 Montpellier, France
                [4 ]GRID grid.5338.d, ISNI 0000 0001 2173 938X, Unidad de Zoología Marina, Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Parc Científic, , Universitat de València, ; PO Box 22085, 46071 Valencia, Spain
                [5 ]GRID grid.10894.34, ISNI 0000 0001 1033 7684, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, ; 27570 Bremerhaven, Germany
                [6 ]GRID grid.4711.3, ISNI 0000 0001 2183 4846, Instituto de Parasitología y Biomedicina López-Neyra, , Consejo Superior de Investigaciones Científicas (CSIC), ; Av. del Conocimiento 17, 18016 Granada, Spain
                [7 ]GRID grid.4886.2, ISNI 0000 0001 2192 9124, Zoological Institute, , Russian Academy of Sciences, ; Universitetskaya Embankment 1,, 199034 Saint Petersburg, Russia
                [8 ]GRID grid.35403.31, ISNI 0000 0004 1936 9991, Illinois Natural History Survey, Prairie Research Institute, , University of Illinois at Urbana-Champaign, ; 1816 S. Oak St., 61820 Champaign, IL USA
                [9 ]GRID grid.4489.1, ISNI 0000000121678994, Departamento de Biología Animal, , Univerdidad de Granada, ; Avenida de Fuente Nueva S/N, E-18071 Granada, Spain
                Article
                30858
                10.1038/s41598-023-30858-8
                10036324
                36959235
                0d8a13d5-31b1-442e-829e-c09d883f6b86
                © The Author(s) 2023

                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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 7 July 2022
                : 2 March 2023
                Funding
                Funded by: Romanian Ministry of Research, Innovation and Digitization
                Award ID: PN-III-P1-1.1-PD-2019-0611
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100005774, Universitat de Barcelona;
                Award ID: APIF fellowship
                Award Recipient :
                Funded by: Romanian Ministry of Research, Innovation and Digitization, Institutional Performance Project for Excellence Financing in RDI
                Award ID: 2PFE/2021
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100004837, Ministerio de Ciencia e Innovación;
                Award ID: REN2002-01164/GLO
                Award Recipient :
                Funded by: Fundación Banco Bilbao Vizcaya Argentaria
                Award ID: BIOCON04/099
                Award Recipient :
                Categories
                Article
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                © The Author(s) 2023

                Uncategorized
                ecology,zoology
                Uncategorized
                ecology, zoology

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