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      Population dynamics and demographic history of Eurasian collared lemmings

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          Abstract

          Background

          Ancient DNA studies suggest that Late Pleistocene climatic changes had a significant effect on population dynamics in Arctic species. The Eurasian collared lemming ( Dicrostonyx torquatus) is a keystone species in the Arctic ecosystem. Earlier studies have indicated that past climatic fluctuations were important drivers of past population dynamics in this species.

          Results

          Here, we analysed 59 ancient and 54 modern mitogenomes from across Eurasia, along with one modern nuclear genome. Our results suggest population growth and genetic diversification during the early Late Pleistocene, implying that collared lemmings may have experienced a genetic bottleneck during the warm Eemian interglacial. Furthermore, we find multiple temporally structured mitogenome clades during the Late Pleistocene, consistent with earlier results suggesting a dynamic late glacial population history. Finally, we identify a population in northeastern Siberia that maintained genetic diversity and a constant population size at the end of the Pleistocene, suggesting suitable conditions for collared lemmings in this region during the increasing temperatures associated with the onset of the Holocene.

          Conclusions

          This study highlights an influence of past warming, in particular the Eemian interglacial, on the evolutionary history of the collared lemming, along with spatiotemporal population structuring throughout the Late Pleistocene.

          Supplementary Information

          The online version contains supplementary material available at 10.1186/s12862-022-02081-y.

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          Most cited references62

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          Trimmomatic: a flexible trimmer for Illumina sequence data

          Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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            The Sequence Alignment/Map format and SAMtools

            Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk
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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
                edana.lord@zoologi.su.se
                love.dalen@zoologi.su.se
                Journal
                BMC Ecol Evol
                BMC Ecol Evol
                BMC Ecology and Evolution
                BioMed Central (London )
                2730-7182
                3 November 2022
                3 November 2022
                2022
                : 22
                : 126
                Affiliations
                [1 ]GRID grid.510921.e, Centre for Palaeogenetics, ; Svante Arrhenius Väg 20C, 10691 Stockholm, Sweden
                [2 ]GRID grid.10548.38, ISNI 0000 0004 1936 9377, Department of Zoology, , Stockholm University, ; 10691 Stockholm, Sweden
                [3 ]GRID grid.425591.e, ISNI 0000 0004 0605 2864, Department of Bioinformatics and Genetics, , Swedish Museum of Natural History, ; Box 50007, 10405 Stockholm, Sweden
                [4 ]GRID grid.12847.38, ISNI 0000 0004 1937 1290, Centre of New Technologies, , University of Warsaw, ; S. Banacha 2C, 02-097 Warsaw, Poland
                [5 ]GRID grid.70738.3b, ISNI 0000 0004 1936 981X, Institute of Arctic Biology, , University of Alaska Fairbanks, ; Fairbanks, AK 99775-7000 USA
                [6 ]GRID grid.17236.31, ISNI 0000 0001 0728 4630, Faculty of Science and Technology, , Bournemouth University, ; Talbot Campus, Fern Barrow, Poole, BH12 5BB Dorset UK
                [7 ]GRID grid.267454.6, ISNI 0000 0000 9422 2878, Department of Archaeology, Anthropology and Geography, , University of Winchester, ; Winchester, SO22 4NR UK
                [8 ]GRID grid.4861.b, ISNI 0000 0001 0805 7253, Service de Préhistoire, , Université de Liège, ; Place du 20 Août 7, 4000 Liège, Belgium
                [9 ]GRID grid.20478.39, ISNI 0000 0001 2171 9581, OD Earth and History of Life, Royal Belgian Institute of Natural Sciences, ; Vautierstraat 29, Brussels, Belgium
                [10 ]GRID grid.7107.1, ISNI 0000 0004 1936 7291, School of Geosciences, , University of Aberdeen, ; Aberdeen, Scotland
                [11 ]GRID grid.439287.3, ISNI 0000 0001 2314 7601, Department of Molecular Systematics, , Zoological Institute RAS, ; St Petersburg, Russia
                [12 ]Far East Branch, N.A. Shilo North-East Interdisciplinary Scientific Research Institute Russian Academy of Sciences (NEISRI FEB RAS), 685000 Magadan, Russia
                [13 ]GRID grid.425585.b, ISNI 0000 0001 2259 6528, Central Research Laboratories, , Natural History Museum Vienna, ; 1010 Vienna, Austria
                [14 ]GRID grid.10420.37, ISNI 0000 0001 2286 1424, Department of Cognitive Biology, , University of Vienna, ; 1090 Vienna, Austria
                [15 ]Konrad Lorenz Institute of Ethology, 1160 Vienna, Austria
                [16 ]GRID grid.452736.1, ISNI 0000 0001 2166 5237, South African National Biodiversity Institute, National Zoological Garden, ; Pretoria, South Africa
                [17 ]GRID grid.426536.0, ISNI 0000 0004 1760 306X, Institute of Plant and Animal Ecology UB RAS, , Russian Academy of Sciences, ; 202 8 Marta Street, 620144 Ekaterinburg, Russia
                [18 ]GRID grid.10548.38, ISNI 0000 0004 1936 9377, Science for Life Laboratory (SciLifeLab), Dept of Biochemistry and Biophysics, , Stockholm University, ; Stockholm, Sweden
                Article
                2081
                10.1186/s12862-022-02081-y
                9632076
                36329382
                cb0a42f9-dbfd-4d08-9f78-e4233246295b
                © The Author(s) 2022

                Open AccessThis 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/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

                History
                : 23 August 2021
                : 19 October 2022
                Funding
                Funded by: Bolin Centre for Climate Research
                Funded by: Polish National Science Centre
                Award ID: 2020/38/E/NZ8/00431
                Award Recipient :
                Funded by: Zoological Institute of Russian Academy of Sciences
                Award ID: 075-15-2021-1069
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000057, National Institute of General Medical Sciences;
                Award ID: P20GM103395
                Award Recipient :
                Funded by: Centre of Biomedical Research Excellence
                Award ID: P20GM130443
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100001862, Svenska Forskningsrådet Formas;
                Award ID: 2018-01640
                Award Recipient :
                Funded by: Stockholm University
                Categories
                Research
                Custom metadata
                © The Author(s) 2022

                collared lemming,palaeogenomics,demographic history,population structure

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