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      Potamophylax coronavirus sp. n. (Trichoptera: Limnephilidae), a new species from Bjeshkët e Nemuna National Park in the Republic of Kosovo, with molecular and ecological notes

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          Abstract

          Background

          The Western Balkans are an important hotspot of caddisfly diversity in Europe, with several microscale endemics, many of which were discovered during the recent years. The genus Potamophylax Wallengren, 1891 likely originated and diversified in Europe, with the Balkan Peninsula being one of the most important diversity hotspots.

          New information

          In this paper, we describe the new species Potamophylax coronavirus sp. n. from Bjeshkët e Nemuna National Park in the Republic of Kosovo. The new species belongs to the Potamophylax winneguthi species group and is morphologically most similar to Potamophylax juliani Kumanski, 1999, currently known only from Bulgaria and Potamophylax winneguthi Klapalek, 1902, known from Bosnia and Herzegovina and Serbia. The male of the new species differs from its most similar congeners mainly in exhibiting: (1) elongated subrectangular superior appendages in lateral view; (2) hardly acuminate, almost rounded apex of intermediate appendages; (3) differently shaped, irregular and higher inferior appendages; (4) narrow spinate area, roughly rectangular in dorsal view, slightly wider at the base and (5) different paramere shape and/or spine pattern. The new species also differs by its considerably smaller size and association with open, high altitude eucrenal zones.

          The uncorrected interspecific pairwise distance between P. coronavirus and other species of the P. winneguthi species group is on par with those amongst other recognised species in the group, as well as with the yet ambiguously identified taxa from the Sharr, Rila and Bajgorë Mountains.

          The new species is most probably a microendemic of Bjeshkët e Nemuna, thus highlighting further this area as an important hotspot of caddisfly biodiversity in Europe.

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          Most cited references 47

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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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            MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

            Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d N /d S rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
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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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                Author and article information

                Contributors
                Journal
                Biodivers Data J
                Biodivers Data J
                1
                urn:lsid:arphahub.com:pub:F9B2E808-C883-5F47-B276-6D62129E4FF4
                urn:lsid:zoobank.org:pub:245B00E9-BFE5-4B4F-B76E-15C30BA74C02
                Biodiversity Data Journal
                Pensoft Publishers
                1314-2836
                1314-2828
                2021
                07 April 2021
                : 9
                Affiliations
                [1 ] University of Prishtina "Hasan Prishtina", Faculty of Mathematics and Natural Sciences, Department of Biology, Eqrem Çabej nn., Prishtina, Kosovo University of Prishtina "Hasan Prishtina", Faculty of Mathematics and Natural Sciences, Department of Biology, Eqrem Çabej nn. Prishtina Kosovo
                [2 ] University of Peja "Haxhi Zeka", Faculty of Agribusiness, UÇK str. nn., Peja, Kosovo University of Peja "Haxhi Zeka", Faculty of Agribusiness, UÇK str. nn. Peja Kosovo
                [3 ] University of Natural Resources and Life Sciences, Vienna Institute of Hydrobiology and Aquatic Ecosystem Management (IHG) Gregor-Mendel-Straße 33, 1180, Vienna, Austria University of Natural Resources and Life Sciences, Vienna Institute of Hydrobiology and Aquatic Ecosystem Management (IHG) Gregor-Mendel-Straße 33 1180, Vienna Austria
                [4 ] WasserCluster Lunz – Biologische Station, Dr. Carl Kupelwieserpromenade 5, 3293, Lunz am See, Austria WasserCluster Lunz – Biologische Station, Dr. Carl Kupelwieserpromenade 5 3293, Lunz am See Austria
                [5 ] University of Vienna, Department of Functional and Evolutionary Ecology, Althanstraße 14, 1090, Vienna, Austria University of Vienna, Department of Functional and Evolutionary Ecology, Althanstraße 14 1090, Vienna Austria
                [6 ] Institute of Insect Biotechnology, Justus-Liebig-University Gießen, Heinrich-Buff-Ring 26, 35392, Gießen, Germany Institute of Insect Biotechnology, Justus-Liebig-University Gießen, Heinrich-Buff-Ring 26, 35392 Gießen Germany
                [7 ] Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, 60388, Frankfurt a. M., Germany Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, 60388 Frankfurt a. M. Germany
                [8 ] Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60388, Frankfurt a. M., Germany Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60388 Frankfurt a. M. Germany
                Author notes
                Corresponding author: Astrit Bilalli ( astritbilalli@ 123456yahoo.com ).

                Academic editor: Henrique Paprocki

                Article
                64486 16219
                10.3897/BDJ.9.e64486
                8046748
                Halil Ibrahimi, Astrit Bilalli, Simon Vitecek, Steffen U. Pauls, Felicitas Erzinger, Agim Gashi, Linda Grapci Kotori, Donard Geci, Milaim Musliu, Edison Kasumaj

                This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                Page count
                Figures: 7, Tables: 1, References: 40
                Categories
                Taxonomic Paper
                Insecta
                Limnephiloidea
                Limnephilidae
                Trichoptera
                Hexapoda
                Arthropoda
                Invertebrata
                Animalia
                Biodiversity & Conservation
                Southern Europe and Mediterranean
                Balkans
                Kosovo
                Europe

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