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      Successful post-glacial colonization of Europe by single lineage of freshwater amphipod from its Pannonian Plio-Pleistocene diversification hotspot

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          Abstract

          Gammarus roeselii Gervais, 1835 is a morphospecies with a wide distribution range in Europe. The Balkan Peninsula is known as an area of pre-Pleistocene cryptic diversification within this taxon, resulting in at least 13 Molecular Operational Taxonomic Units (MOTUs). The morphospecies diversified there during Neogene and has probably invaded other parts of the continent very recently, in postglacial or even historical times. Thus, the detailed goals of our study were to (1) identify which lineage(s) colonized Central-Western Europe (CWE), (2) determine their possible geographical origin, (3) verify, whether the colonisation was associated with demographic changes. In total, 663 individuals were sequenced for the cytochrome oxidase I (COI) barcoding fragment and 137 individuals for the internal transcribed spacer II (ITS2). We identified two MOTUs in the study area with contrasting Barcode Index Number and haplotype diversities. The Pannonian Basin (PB) appeared to be a potential ice age refugium for the species, while CWE was colonised by a single lineage (also present in PB), displaying low genetic diversity. Our results suggest that G. roeselii is a relatively recent coloniser in CWE, starting demographic expansion around 10 kya.

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          Basic local alignment search tool.

          A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
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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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              Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

              Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl. Contact: peter@biomatters.com
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                Author and article information

                Contributors
                tomasz.rewicz@biol.uni.lodz.pl
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                29 October 2020
                29 October 2020
                2020
                : 10
                : 18695
                Affiliations
                [1 ]GRID grid.425054.2, Institute of Oceanology Polish Academy of Sciences, ; 81-712 Sopot, Poland
                [2 ]GRID grid.10789.37, ISNI 0000 0000 9730 2769, Faculty of Biology and Environmental Protection, Department of Invertebrate Zoology and Hydrobiology, , University of Lodz, ; 90-237 Lodz, Poland
                [3 ]GRID grid.9679.1, ISNI 0000 0001 0663 9479, Faculty of Sciences, Department of Hydrobiology, , University of Pecs, ; Pecs, 7634 Hungary
                [4 ]GRID grid.5613.1, ISNI 0000 0001 2298 9313, UMR CNRS 6282 Biogéosciences, , Université Bourgogne Franche Comté, ; 21000 Dijon, France
                [5 ]GRID grid.6612.3, ISNI 0000 0004 1937 0642, Zoological Institute, , University of Basel, ; 4051 Basel, Switzerland
                [6 ]Department of Natural Sciences, Varaždin City Museum, 42000 Varaždin, Croatia
                [7 ]GRID grid.34429.38, ISNI 0000 0004 1936 8198, Centre for Biodiversity Genomics, , University of Guelph, ; Guelph, ON N1G 2W1 Canada
                Author information
                http://orcid.org/0000-0002-3659-685X
                http://orcid.org/0000-0002-4551-3454
                http://orcid.org/0000-0001-5772-4681
                http://orcid.org/0000-0003-4498-5107
                http://orcid.org/0000-0002-0524-3015
                http://orcid.org/0000-0003-4119-3948
                http://orcid.org/0000-0002-2085-4973
                Article
                75568
                10.1038/s41598-020-75568-7
                7596225
                33122728
                bd7fb0b3-fafb-49f0-8538-4b38304171b4
                © The Author(s) 2020

                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
                : 4 June 2020
                : 14 October 2020
                Funding
                Funded by: internal funds of the University of Lodz
                Funded by: ERASMUS Mobility Grant
                Award ID: 17/1/KA103/035116/SMP-063
                Award Recipient :
                Funded by: New National Excellence Program of the Hungarian Ministry of Human Capacities
                Award ID: ÚNKP-18-2-I-PTE-146
                Award Recipient :
                Funded by: Polish Ministry of Science and Education
                Award ID: N N303 579439
                Award ID: N N303 579439
                Award Recipient :
                Funded by: National Science Centre, Poland
                Award ID: 2014/15/B/NZ8/00266
                Award ID: 2014/15/B/NZ8/00266
                Award Recipient :
                Funded by: Polish National Agency for Academic Exchange (NAWA) within Polonium Programme
                Award ID: PPN/BIL/2018/1/00138
                Award ID: PPN/BIL/2018/1/00138
                Award ID: PPN/BIL/2018/1/00138
                Award ID: PPN/BIL/2018/1/00138
                Award ID: PPN/BIL/2018/1/00138
                Award Recipient :
                Funded by: internal funds of the UMR-CNRS-Ub-6282 Biogéosciences and the Burgundy Region
                Funded by: Scholarship of the Polish National Agency for Academic Exchange (NAWA) at Bekker Programme
                Award ID: PPN/BEK/2018/1/00225
                Award ID: PPN/BEK/2018/1/00162
                Award Recipient :
                Categories
                Article
                Custom metadata
                © The Author(s) 2020

                Uncategorized
                ecology,evolution,zoology
                Uncategorized
                ecology, evolution, zoology

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