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      The Lichen Genus Sticta in South Korea

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          Abstract

          Sticta (Schreber.) Ach. is one of the common lichen genera in tropical and subtropical regions, but not in the Korean Peninsula. For almost two decades, no detailed taxonomic or revisionary study has been done on this genus. This study was based on the specimens deposited in the lichen herbarium at the Korean Lichen Research Institute, and the samples were identified on the basis of recent literature. In this revisionary study, a total of eight species of Sticta, including a newly recorded one are documented. These species include Sticta fuliginosa (Dicks.) Ach., Sticta gracilis (Müll. Arg.) Zahlbr., Sticta limbata (Sm.) Ach., Sticta nylanderiana Zahlbr., Sticta sublimbata (J. Steiner) Swinscow & Krog, Sticta weigelii (Ach.) Vain., Sticta wrightii Tuck., and Sticta yatabeana Müll. Arg. Detailed descriptions of S. nylanderiana, S. sublimbata, S. weigelii, and S. yatabeana with their morphological, anatomical, and chemical characteristics are provided. A key description of all known Sticta species of the Korean Peninsula is also presented.

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          Positional effect of single bulge nucleotide on PNA(peptide nucleic acid)/DNA hybrid stability

          We report positional effect of bulge nucleotide on PNA/DNA hybrid stability. CD spectra showed that PNA/DNA hybrids required at least seven base pairings at a stem region to form a bulged structure. On the other hand, DNA/DNA could form bulged structure when there are only four base pairings adjacent to the bulge nucleotide. We discuss why PNA requests such a many base pairings to form bulged structure from a nearest neighbor standpoint.
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            Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology.

            Phylogenetic analyses of non-protein-coding nucleotide sequences such as ribosomal RNA genes, internal transcribed spacers, and introns are often impeded by regions of the alignments that are ambiguously aligned. These regions are characterized by the presence of gaps and their uncertain positions, no matter which optimization criteria are used. This problem is particularly acute in large-scale phylogenetic studies and when aligning highly diverged sequences. Accommodating these regions, where positional homology is likely to be violated, in phylogenetic analyses has been dealt with very differently by molecular systematists and evolutionists, ranging from the total exclusion of these regions to the inclusion of every position regardless of ambiguity in the alignment. We present a new method that allows the inclusion of ambiguously aligned regions without violating homology. In this three-step procedure, first homologous regions of the alignment containing ambiguously aligned sequences are delimited. Second, each ambiguously aligned region is unequivocally coded as a new character, replacing its respective ambiguous region. Third, each of the coded characters is subjected to a specific step matrix to account for the differential number of changes (summing substitutions and indels) needed to transform one sequence to another. The optimal number of steps included in the step matrix is the one derived from the pairwise alignment with the greatest similarity and the least number of steps. In addition to potentially enhancing phylogenetic resolution and support, by integrating previously nonaccessible characters without violating positional homology, this new approach can improve branch length estimations when using parsimony.
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              Molecular phylogeny of the genus Sticta (lichenized Ascomycota: Lobariaceae) in Colombia

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                Author and article information

                Journal
                Mycobiology
                Mycobiology
                MB
                Mycobiology
                The Korean Society of Mycology
                1229-8093
                2092-9323
                March 2014
                31 March 2014
                : 42
                : 1
                : 6-11
                Affiliations
                [1 ]Korean Lichen Research Institute, Sunchon National University, Suncheon 540-742, Korea.
                [2 ]Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca 400015, Romania.
                Author notes
                Corresponding author: jshur1@ 123456sunchon.ac.kr
                Article
                10.5941/MYCO.2014.42.1.6
                4004950
                24808727
                fef13fb8-959f-42ee-aa79-6bf263b289b9
                © The Korean Society of Mycology

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/3.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 15 October 2013
                : 05 November 2013
                : 09 December 2013
                Funding
                Funded by: Korean Forest Service Program through the Korea National Arboretum
                Award ID: KNA 2013
                Funded by: Korean National Research Resource Center Program
                Award ID: NRF: 2012M3A9B8021726
                Categories
                Research Article

                Plant science & Botany
                foliose,lobariaceae,nostoc,south korea,sticta
                Plant science & Botany
                foliose, lobariaceae, nostoc, south korea, sticta

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