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      Phylogeography using mitogenomes: A rare Dipodidae, Sicista betulina, in North‐western Europe

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          Abstract

          Repeated climatic and vegetation changes during the Pleistocene have shaped biodiversity in Northern Europe including Denmark. The Northern Birch Mouse ( Sicista betulina) was one of the first small rodent species to colonize Denmark after the Late Glacial Maximum. This study analyses complete mitochondrial genomes and two nuclear genes of the Northern Birch Mouse to investigate the phylogeographical pattern in North‐western Europe and test whether the species colonized Denmark through several colonization events. The latter was prompt by (i) the present‐day distinct northern and southern Danish distribution and (ii) the subfossil record of Northern Birch Mouse, supporting early Weichselian colonization. Samples from Denmark, Norway, Sweden, Russia, Latvia, Estonia, and Slovakia were included. Mitogenomes were obtained from 54 individuals, all representing unique mitogenomes supporting high genetic variation. Bayesian phylogenetic analysis identified two distinct evolutionary linages in Northern Europe diverging within the Elster glaciation period. The results of the two nuclear genomes showed lower genetic differentiation but supported the same evolutionary history. This suggests an allopatric origin of the clades followed by secondary contact. Individuals from southern Denmark were only found in one clade, while individuals from other areas, including northern Denmark, were represented in both clades. Nevertheless, we found no evidence for repeated colonization's explaining the observed fragmented distribution of the species today. The results indicated that the mitogenome pattern of the Northern Birch Mouse population in southern Denmark was either (i) due to the population being founded from northern Denmark, (ii) a result of climatic and anthropogenic effects reducing population size increasing genetic drift or (iii) caused by sampling bias.

          Abstract

          The phylogeographical pattern of the Northern Birch Mouse ( Sicista betulina) in Northwestern Europe was investigated using complete mitochondrial genomes and two nuclear genes. Samples representing Denmark, Norway, Sweden, Russia, Latvia, Estonia and Slovakia were analysed. Mitogenomes were obtained from 54 individuals, all unique, supporting high genetic variation. Two distinct evolutionary linages diverging within the Elster glaciation period was found suggesting an allopatric origin and vicariance followed by secondary contact throughout the northern range. The results indicated that the mitogenome pattern of the Northern Birch Mouse population in southern Denmark was either (i) due to the population being founded from northern Denmark, (ii) a result of climatic and anthropogenic effects reducing population size increasing genetic drift or (iii) caused by sampling bias.

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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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            MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.

            We announce the release of an advanced version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables the inference of timetrees, as it implements the RelTime method for estimating divergence times for all branching points in a phylogeny. A new Timetree Wizard in MEGA6 facilitates this timetree inference by providing a graphical user interface (GUI) to specify the phylogeny and calibration constraints step-by-step. This version also contains enhanced algorithms to search for the optimal trees under evolutionary criteria and implements a more advanced memory management that can double the size of sequence data sets to which MEGA can be applied. Both GUI and command-line versions of MEGA6 can be downloaded from www.megasoftware.net free of charge.
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              Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows.

              We present here a new version of the Arlequin program available under three different forms: a Windows graphical version (Winarl35), a console version of Arlequin (arlecore), and a specific console version to compute summary statistics (arlsumstat). The command-line versions run under both Linux and Windows. The main innovations of the new version include enhanced outputs in XML format, the possibility to embed graphics displaying computation results directly into output files, and the implementation of a new method to detect loci under selection from genome scans. Command-line versions are designed to handle large series of files, and arlsumstat can be used to generate summary statistics from simulated data sets within an Approximate Bayesian Computation framework. © 2010 Blackwell Publishing Ltd.
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                Author and article information

                Contributors
                lwa@bios.au.dk
                Journal
                Ecol Evol
                Ecol Evol
                10.1002/(ISSN)2045-7758
                ECE3
                Ecology and Evolution
                John Wiley and Sons Inc. (Hoboken )
                2045-7758
                21 April 2022
                April 2022
                : 12
                : 4 ( doiID: 10.1002/ece3.v12.4 )
                : e8865
                Affiliations
                [ 1 ] Department of Ecoscience Aarhus University Aarhus C Denmark
                [ 2 ] Section for Marine Living Resources National Institute of Aquatic Resources Technical University of Denmark Silkeborg Denmark
                [ 3 ] Højbjerg Denmark
                [ 4 ] Møller Consultansy Frøstrup Denmark
                [ 5 ] Natural History Museum, Aarhus Aarhus Denmark
                Author notes
                [*] [* ] Correspondence

                Liselotte Wesley Andersen, Department of Ecoscience, Aarhus University, CF Møllers Allé 4‐8, build. 1110, 8000 Aarhus C, Denmark.

                Email: lwa@ 123456bios.au.dk

                Author information
                https://orcid.org/0000-0003-3225-9917
                Article
                ECE38865
                10.1002/ece3.8865
                9022092
                35475180
                efe03bdd-3402-41df-8a75-f02e5f6d0ccd
                © 2022 The Authors. Ecology and Evolution 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
                : 07 April 2022
                : 01 November 2021
                : 08 April 2022
                Page count
                Figures: 5, Tables: 4, Pages: 16, Words: 12483
                Funding
                Funded by: Danish Ministry of Cultural Affairs
                Award ID: 2011‐7.40.01/75104‐0001
                Categories
                Phylogenetics
                Research Article
                Research Articles
                Custom metadata
                2.0
                April 2022
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.1.4 mode:remove_FC converted:21.04.2022

                Evolutionary Biology
                divergence time,genetic diversity,mitogenomes,phylogeography,population structure,sicista betulina

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