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      Assessing the systematics of Tylodinidae in the Mediterranean Sea and Eastern Atlantic Ocean: resurrecting Tylodina rafinesquii Philippi, 1836 (Heterobranchia: Umbraculida)

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          ABSTRACT

          The systematics of the gastropod clade Umbraculida, particularly the family Tylodinidae, has been a matter of debate. The Tylodinidae of the Mediterranean Sea are a case in point, with no comprehensive molecular assessment of diversity having been carried out to date. Several species and genera have been erected and synonymized in the course of the last two centuries and only a single species from each of the genera Tylodina and Anidolyta are considered to be present in these waters. In order to shed light on the controversial taxonomy of the group, we carried out both morpho-anatomical study and molecular analyses using fragments of two mitochondrial genes, cytochrome c oxidase subunit I and 16S rRNA, and the nuclear gene histone H3. Phylogenetic analyses and species delimitation tests clearly recovered two independent lineages of Tylodina from the Mediterranean and Eastern Atlantic coast, the type species T. perversa and the resurrected T. rafinesquii. We found clear differences in shell and radular morphology between both species, as well as differences in their habitat and food preferences. Interestingly, we found strong evidence that T. rafinesquii is sister to T. fungina from the Eastern Pacific rather than to the sympatric T. perversa. Furthermore, the new morphological data strongly encourage the suppression of the genus Anidolyta, which should be considered a junior synonym of Tylodina.

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          MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

          We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge.
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            MUSCLE: multiple sequence alignment with high accuracy and high throughput.

            We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.
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              MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

              Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d N /d S rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
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                Author and article information

                Journal
                Journal of Molluscan Studies
                Oxford University Press (OUP)
                0260-1230
                1464-3766
                March 2021
                February 13 2021
                March 2021
                February 13 2021
                November 27 2020
                : 87
                : 1
                Affiliations
                [1 ]Catalan Opisthobranch Research Group (GROC), Mas Castellar, 17773 Pontós, Catalonia, Spain
                [2 ]Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
                [3 ]SNSB-Bavarian State Collection of Zoology, Section Mollusca, Münchhausenstrasse 21, D-81247 Munich, Germany
                [4 ]Biozentrum Ludwig Maximilians University and GeoBio-Center LMU Munich, Munich, Germany
                Article
                10.1093/mollus/eyaa031
                d8bc8e8f-6d5e-4090-b1ab-b913f9dc025d
                © 2020

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

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