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      Lamproderma vietnamense: a new species of myxomycetes with reticulate spores from Phia Oắc - Phia Đén National Park (northern Vietnam) supported by molecular phylogeny and morphological analysis

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          Abstract

          A new species of Lamproderma ( Myxomycetes), described herein as L. vietnamense, was recovered in the field on ground litter from mountain subtropical forests (Phia Oắc - Phia Đén National Park) of northern Vietnam. Morphological details were examined by light and scanning electron microscopy. The species is characterized by a distinct and unique combination of morphological features, including a bright blue, shiny and very thin membranous peridium, a small dome-shaped columella, rigid, straight, branched, brown capillitial threads which gradually become pale at the periphery and finally colorless at the tips and small-meshed, banded-reticulate spores with 9-12 meshes across the spore diameter and solid walls without perforations 0.3-0.5 µm high. The stability of the taxonomic characters of L. vietnamense is supported by two well-developed collections found in 2018 and 2019. Partial sequences of three molecular markers (SSU, EF1α, COI) for both collections are identical. A two-gene phylogeny of the first two markers displays the two known accessions as a well-separated entity and indicates affinity of the new species with L. columbinum (the type taxon of the genus), L. violaceum, and several nivicolous Lamproderma species.

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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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            IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

            Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%.
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              ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates

              Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates. The improvement is achieved by incorporating a model of rate-heterogeneity across sites not previously considered in this context, and by allowing concurrent searches of model-space and tree-space.
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                Author and article information

                Contributors
                yurinovozhilov@gmail.com
                Journal
                Mycoscience
                Mycoscience
                mycosci
                Mycoscience
                The Mycological Society of Japan (Tokyo, JAPAN )
                1340-3540
                1618-2545
                31 July 2022
                2022
                : 63
                : 4
                : 149-155
                Affiliations
                [a] a V.L. Komarov Botanical Institute of the Russian Academy of Sciences
                [b] b Saint Petersburg State University
                [c] c Lomonosov Moscow State University
                [d] d Polistovsky National Nature Reserve
                [e] e Institute of Botany and Landscape Ecology, Ernst-Moritz-Arndt University Greifswald
                Author notes
                * Corresponding author. V.L. Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Prof. Popov St. 2, Russia E-mail address: yurinovozhilov@ 123456gmail.com (Yu. K. Novozhilov)
                Article
                mycosci.2022.05.003
                10.47371/mycosci.2022.05.003
                10043568
                5c0494c7-bd8e-43bf-b6cc-3c662812f92c
                2022, by The Mycological Society of Japan

                This is an open-access paper distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivative 4.0 international license (CC BY-NC-ND 4.0: https://creativecommons.org/licenses/by-nc-nd/4.0/).

                History
                : 1 November 2021
                : 29 April 2022
                : 10 May 2022
                Funding
                Funded by: the state task “Biodiversity, ecology, structural and functional features of fungi and fungus-like protists” (BIN RAS, 122011900033-4) and the project “Taxonomic and ecological diversity of mycobiota of tropical forests in Vietnam, Ecolan E-1.5” of the state task “Tropical Ecology” of the Joint Russian-Vietnamese Tropical Research and Technological Centre. The molecular work for YKN, ISP, and ONS were supported by the Ministry of Science and Higher Education of the Russian Federation (agreement No. 075-15-2021-1056) and for MS by the German Research Foundation (DFG, grants RTG 2010, SCHN 1080/2-1).
                Categories
                Full Paper

                dna barcodes,fungus-like protists,new taxon,slime molds,subtropics

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