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      Imperial trophy or island relict? A new extinction paradigm for Père David's deer: a Chinese conservation icon

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          Abstract

          Determining the ‘dynamic biogeography’ of range collapse in threatened species is essential for effective conservation, but reconstruction of spatio-temporal patterns of population vulnerability and resilience can require use of non-standard ecological data such as historical archives. Père David's deer or milu, one of the few living mammal species that has become extinct in the wild, is historically known only from a small captive herd of unknown provenance that survived until 1900 in the Imperial Hunting Park near Beijing, from which all living individuals are descended. Using ancient DNA analysis, we demonstrate that two fawns collected in 1868 from Hainan Island, off the southern Chinese mainland, represent the only known wild milu specimens and were sampled from probably the last wild population. The Hainan milu population shows extremely low genetic differentiation from descendants of the Beijing herd, suggesting that this now-extinct population may have been the source of the captive herd. This revised extinction model refutes the supposed long-term survival of a captive milu herd for centuries or millennia after final extinction of wild populations, highlighting the vulnerability of remnant mammal populations in the absence of proactive management and the importance of historical museum collections for providing unique new insights on evolution, biogeography and conservation. Milu experienced a pattern of final population persistence on an island at the periphery of their former range, consistent with the ‘range eclipse’ or ‘contagion’ model of range collapse, and matching the spatial extinction dynamics of other extinct mammals such as the thylacine and woolly mammoth.

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          The status of the world's land and marine mammals: diversity, threat, and knowledge.

          Knowledge of mammalian diversity is still surprisingly disparate, both regionally and taxonomically. Here, we present a comprehensive assessment of the conservation status and distribution of the world's mammals. Data, compiled by 1700+ experts, cover all 5487 species, including marine mammals. Global macroecological patterns are very different for land and marine species but suggest common mechanisms driving diversity and endemism across systems. Compared with land species, threat levels are higher among marine mammals, driven by different processes (accidental mortality and pollution, rather than habitat loss), and are spatially distinct (peaking in northern oceans, rather than in Southeast Asia). Marine mammals are also disproportionately poorly known. These data are made freely available to support further scientific developments and conservation action.
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            AdapterRemoval: easy cleaning of next-generation sequencing reads

            Background With the advent of next-generation sequencing there is an increased demand for tools to pre-process and handle the vast amounts of data generated. One recurring problem is adapter contamination in the reads, i.e. the partial or complete sequencing of adapter sequences. These adapter sequences have to be removed as they can hinder correct mapping of the reads and influence SNP calling and other downstream analyses. Findings We present a tool called AdapterRemoval which is able to pre-process both single and paired-end data. The program locates and removes adapter residues from the reads, it is able to combine paired reads if they overlap, and it can optionally trim low-quality nucleotides. Furthermore, it can look for adapter sequence in both the 5’ and 3’ ends of the reads. This is a flexible tool that can be tuned to accommodate different experimental settings and sequencing platforms producing FASTQ files. AdapterRemoval is shown to be good at trimming adapters from both single-end and paired-end data. Conclusions AdapterRemoval is a comprehensive tool for analyzing next-generation sequencing data. It exhibits good performance both in terms of sensitivity and specificity. AdapterRemoval has already been used in various large projects and it is possible to extend it further to accommodate application-specific biases in the data.
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              The state and conservation of Southeast Asian biodiversity

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                Author and article information

                Journal
                R Soc Open Sci
                R Soc Open Sci
                RSOS
                royopensci
                Royal Society Open Science
                The Royal Society Publishing
                2054-5703
                October 2017
                25 October 2017
                25 October 2017
                : 4
                : 10
                : 171096
                Affiliations
                [1 ]Institute of Zoology, Zoological Society of London , Regent's Park, London NW1 4RY, UK
                [2 ]Earth Sciences Department, Natural History Museum , Cromwell Road, London SW7 5BD, UK
                [3 ]School of Geography, Royal Holloway University of London , Egham TW20 0EX, UK
                Author notes
                Author for correspondence: Samuel T. Turvey e-mail: samuel.turvey@ 123456ioz.ac.uk

                Electronic supplementary material is available online at https://doi.org/10.6084/m9.figshare.c.3900508.

                Author information
                http://orcid.org/0000-0002-3717-4800
                Article
                rsos171096
                10.1098/rsos.171096
                5666285
                1eb49032-0571-4ef3-b577-9b4caf5341ba
                © 2017 The Authors.

                Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.

                History
                : 15 August 2017
                : 25 September 2017
                Funding
                Funded by: Royal Society, http://dx.doi.org/10.13039/501100000288;
                Award ID: UF130573
                Categories
                1001
                60
                70
                Genetics
                Research Article
                Custom metadata
                October, 2017

                ancient dna,conservation biology,elaphurus davidianus,extinction dynamics,mammal extinction,range collapse

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