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      Narrow-clawed crayfish in Finland: Aphanomyces astaci resistance and genetic relationship to other selected European and Asian populations

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          Abstract

          The narrow-clawed crayfish ( Pontastacus leptodactylus) is an alien species in Finland with only a few populations reported from the southeastern region during the last century. We discovered a productive population in the lake Jängynjärvi, which is upstream from the previously reported wild narrow-clawed crayfish population in that region. Preliminary studies indicated that this population is not infected with Aphanomyces astaci. We collected narrow-clawed crayfish samples from the lake Jängynjärvi population for both infection challenge and genetic studies, in order to investigate possible A. astaci resistance among this Finnish population and to evaluate their phylogenetic position that would enable us to speculate different scenarios of distribution pathways or origin of the population. The infection studies indicated that the narrow-clawed crayfish in this population were more resistant against A. astaci infection (B haplogroup A. astaci) compared to the noble crayfish ( Astacus astacus) from the lake Rytky in North Savo, while all crayfish of both species in the B haplogroup A. astaci challenged groups died within 58 days post-infection. Results of the phylogenetic reconstruction indicate that the lake Jängynjärvi narrow-clawed crayfish are closely related to narrow-clawed crayfish from the lake Bolshoye near Krasnoye, located on the White Sea island of Solovestky and also populations from Tyumen region, both in Russia. This could confirm previous speculations about introduction of the narrow-clawed crayfish from Russia into Finland or could indicate previous hydrological connection.

          Abstract

          L'écrevisse à pattes grêles ( Pontastacus leptodactylus) est une espèce exotique en Finlande, avec seulement quelques populations signalées dans la région sud-est au cours du siècle dernier. Nous avons découvert une population productive dans le lac Jängynjärvi, qui se trouve en amont de la population sauvage d'écrevisses à pinces étroites signalée précédemment dans cette région. Des études préliminaires ont indiqué que cette population n'est pas infectée par Aphanomyces astaci. Nous avons prélevé des échantillons d'écrevisses à pinces étroites dans la population du lac Jängynjärvi, à la fois pour des études sur le test de l'infection et des études génétiques, afin d'étudier la résistance possible à A. astaci dans cette population finlandaise et d'évaluer leur position phylogénétique, ce qui nous permettrait de spéculer sur différents scénarios de voies de diffusion ou d'origine de la population. Les études d'infection ont montré que les écrevisses à pinces étroites de cette population étaient plus résistantes à l'infection par A. astaci (haplogroupe B A. astaci) que les écrevisses nobles ( Astacus astacus) du lac Rytky dans le nord du Savo, tandis que toutes les écrevisses des deux espèces de l'haplogroupe B A. astaci ayant été infectées sont mortes dans les 58 jours suivant l'infection. Les résultats de la reconstitution phylogénétique indiquent que les écrevisses à pinces étroites du lac Jängynjärvi sont étroitement apparentées aux écrevisses à pinces étroites du lac Bolshoye près de Krasnoïe, situé sur l'île de Solovestky dans la mer Blanche, ainsi qu'aux populations de la région de Tioumen, toutes deux en Russie. Cela pourrait confirmer les hypothèses antérieures sur l'introduction en Finlande d'écrevisses à pinces étroites en provenance de Russie ou pourrait indiquer un lien hydrologique antérieur.

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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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            New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

            PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.
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              Geographical patterns in range extension of Ponto-Caspian macroinvertebrate species in Europe

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                Author and article information

                Journal
                Knowledge & Management of Aquatic Ecosystems
                Knowl. Manag. Aquat. Ecosyst.
                EDP Sciences
                1961-9502
                2020
                July 09 2020
                2020
                : 421
                : 30
                Article
                10.1051/kmae/2020022
                87d03eed-7fc1-4055-8ff7-710a80e1027d
                © 2020

                https://creativecommons.org/licenses/by-nd/4.0/

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