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      The minnow Phoxinus lumaireul (Leuciscidae) shifts the Adriatic–Black Sea basin divide in the north‐western Dinaric Karst region

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          Abstract

          Karst landscapes are characterized by intermittent and sinking streams. The most common method used to study underground hydrological connections in karst is tracing tests. However, a more biologically oriented approach has been suggested: analysis of the genetic structure of aquatic organisms. Biological tracers can be sought among trogloxenes, that is, surface species that occasionally enter caves and groundwater. One such example is the fish genus Phoxinus, which exhibits high genetic diversity and complex phylogeography in the Balkan Peninsula. In the north‐western Dinaric Karst, the complex hydrological network was digitalized in 2020. Contemporaneously, Phoxinus lumaireul populations in the Slovenian Dinaric Karst were intensively sampled and analysed for fragments of two mitochondrial genes and one nuclear gene. The derived phylogeographic structure and data on hydrological connections were compared to evaluate support for three alternative scenarios: The genetic structure (1) is a consequence of the ongoing geneflow through underground connections, (2) reflects a previous hydrological network or (3) is an outcome of anthropogenic translocations. The results suggest that the first two scenarios seem to have played a major role, while the third has not had profound effects on the genetic composition. Comparison between the genetic structure of Slovenian Dinaric Karst sampling sites and that of hydrologically isolated reference sampling sites indicated a greater genetic connectivity in the former. Moreover, the range of Adriatic (1a) and Black Sea (1c) haplotypes does not correspond to the Adriatic–Black Sea basin divide but is shifted northwards.

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          MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

          We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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            MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

            The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
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              RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

              Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
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                Author and article information

                Contributors
                susanne.reier@nhm-wien.ac.at
                Journal
                Ecohydrology
                Ecohydrology
                10.1002/(ISSN)1936-0592
                ECO
                Ecohydrology
                John Wiley and Sons Inc. (Hoboken )
                1936-0584
                1936-0592
                13 July 2022
                September 2022
                : 15
                : 6 ( doiID: 10.1002/eco.v15.6 )
                : e2449
                Affiliations
                [ 1 ] First Zoological Department Natural History Museum Vienna Vienna Austria
                [ 2 ] Department of Evolutionary Biology University of Vienna Vienna Austria
                [ 3 ] Central Research Laboratories Natural History Museum Vienna Vienna Austria
                [ 4 ] Department of Animal Science, Biotechnical Faculty University of Ljubljana Domžale Slovenia
                [ 5 ] Department of Biology, Biotechnical Faculty University of Ljubljana Ljubljana Slovenia
                Author notes
                [*] [* ] Correspondence

                Susanne Reier, First Zoological Department, Natural History Museum Vienna, Burgring 7, Vienna 1010, Austria.

                Email: susanne.reier@ 123456nhm-wien.ac.at

                Author information
                https://orcid.org/0000-0001-6839-7137
                https://orcid.org/0000-0001-8708-4347
                https://orcid.org/0000-0003-4708-0370
                https://orcid.org/0000-0003-4057-6912
                https://orcid.org/0000-0002-4555-5240
                Article
                ECO2449
                10.1002/eco.2449
                9539529
                36245897
                d23f2b12-a700-45be-955f-08b2725f571e
                © 2022 The Authors. Ecohydrology published by John Wiley & Sons Ltd.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 25 May 2022
                : 04 January 2022
                : 26 June 2022
                Page count
                Figures: 7, Tables: 4, Pages: 22, Words: 14805
                Funding
                Funded by: Austrian Science Fund , doi 10.13039/501100002428;
                Award ID: I4131‐B25
                Funded by: Slovenian Research Agency , doi 10.13039/501100004329;
                Award ID: N1‐0096
                Categories
                Research Article
                Research Articles
                Custom metadata
                2.0
                September 2022
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.2.0 mode:remove_FC converted:07.10.2022

                dinaric karst,paleohydrology,phoxinus,underground connections,underground migration

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