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      Genetic evidence illuminates the origin and global spread of the slug Deroceras invadens

      1 , 1 , 1 , 1 , 2
      Journal of Molluscan Studies
      Oxford University Press (OUP)

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          ABSTRACT

          The terrestrial slug Deroceras invadens has spread across much of the world over the last century. What is there to learn about its origin, colonizations and diversity by comparing barcoding sequences of the mitochondrial gene COI (cytochrome c oxidase subunit I)? Samples from 317 localities covering most of the species’ range yielded 87 haplotypes. Higher diversity, the predominance of private haplotypes and geographic structuring all indicate a native range centred on southern Italy, including eastern Sicily. In contrast, central Italy is dominated by one haplotype, although accompanied by both close and more distant relatives; the lack of geographic structuring suggests recent expansion from a restricted distribution within that region. Beyond the Alps, two haplotypes predominate, accompanied by very similar variants; such star-shaped genealogies characterize recent population growth. Also, some rarer haplotypes have been independently introduced. Generally, haplotypes are well mixed here, often co-occurring at a locality. In North America and Australasia, some frequent haplotypes were likely directly introduced from Italy, because they were not found elsewhere in Europe. The rarity or absence in these continents of one or other of the two dominant European haplotypes suggests that import inspections have restricted repeated introductions. A skyline plot detects the recent demographic expansion but also indicates an earlier population decline in the native area. This may explain why the one-dimensional summary statistics FS and R2 did not signal population growth. A review of 41 other studies that used DNA to analyse invasions of terrestrial molluscs documents considerable diversity in methodology. Studies using genetic data to date recent invasions probably should adjust standard substitution rates upwards.

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          MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types-e.g. morphological, nucleotide, and protein-and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters.
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            DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets.

            We present version 6 of the DNA Sequence Polymorphism (DnaSP) software, a new version of the popular tool for performing exhaustive population genetic analyses on multiple sequence alignments. This major upgrade incorporates novel functionalities to analyze large data sets, such as those generated by high-throughput sequencing technologies. Among other features, DnaSP 6 implements: 1) modules for reading and analyzing data from genomic partitioning methods, such as RADseq or hybrid enrichment approaches, 2) faster methods scalable for high-throughput sequencing data, and 3) summary statistics for the analysis of multi-locus population genetics data. Furthermore, DnaSP 6 includes novel modules to perform single- and multi-locus coalescent simulations under a wide range of demographic scenarios. The DnaSP 6 program, with extensive documentation, is freely available at http://www.ub.edu/dnasp.
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              Is Open Access

              BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

              We present a new open source, extensible and flexible software platform for Bayesian evolutionary analysis called BEAST 2. This software platform is a re-design of the popular BEAST 1 platform to correct structural deficiencies that became evident as the BEAST 1 software evolved. Key among those deficiencies was the lack of post-deployment extensibility. BEAST 2 now has a fully developed package management system that allows third party developers to write additional functionality that can be directly installed to the BEAST 2 analysis platform via a package manager without requiring a new software release of the platform. This package architecture is showcased with a number of recently published new models encompassing birth-death-sampling tree priors, phylodynamics and model averaging for substitution models and site partitioning. A second major improvement is the ability to read/write the entire state of the MCMC chain to/from disk allowing it to be easily shared between multiple instances of the BEAST software. This facilitates checkpointing and better support for multi-processor and high-end computing extensions. Finally, the functionality in new packages can be easily added to the user interface (BEAUti 2) by a simple XML template-based mechanism because BEAST 2 has been re-designed to provide greater integration between the analysis engine and the user interface so that, for example BEAST and BEAUti use exactly the same XML file format.
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                Author and article information

                Journal
                Journal of Molluscan Studies
                Oxford University Press (OUP)
                0260-1230
                1464-3766
                November 2020
                October 29 2020
                September 02 2020
                November 2020
                October 29 2020
                September 02 2020
                : 86
                : 4
                : 306-322
                Affiliations
                [1 ]Senckenberg Museum of Natural History Görlitz, Am Museum 1, 02826 Görlitz, Germany
                [2 ]Landcare Research, PO Box 69040, Lincoln 7640, New Zealand
                Article
                10.1093/mollus/eyaa016
                fcee21f3-05af-4470-be83-ab01b993e82d
                © 2020

                https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model

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