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      Lichens and associated fungi from Glacier Bay National Park, Alaska

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          Abstract

          Lichens are widely acknowledged to be a key component of high latitude ecosystems. However, the time investment needed for full inventories and the lack of taxonomic identification resources for crustose lichen and lichenicolous fungal diversity have hampered efforts to fully gauge the depth of species richness in these ecosystems. Using a combination of classical field inventory and extensive deployment of chemical and molecular analysis, we assessed the diversity of lichens and associated fungi in Glacier Bay National Park, Alaska (USA), a mixed landscape of coastal boreal rainforest and early successional low elevation habitats deglaciated after the Little Ice Age. We collected nearly 5000 specimens and found a total of 947 taxa, including 831 taxa of lichen-forming and 96 taxa of lichenicolous fungi together with 20 taxa of saprotrophic fungi typically included in lichen studies. A total of 98 species (10.3% of those detected) could not be assigned to known species and of those, two genera and 27 species are described here as new to science: Atrophysma cyanomelanos gen. et sp. nov., Bacidina circumpulla, Biatora marmorea, Carneothele sphagnicola gen. et sp. nov., Cirrenalia lichenicola, Corticifraga nephromatis, Fuscidea muskeg, Fuscopannaria dillmaniae, Halecania athallina, Hydropunctaria alaskana, Lambiella aliphatica, Lecania hydrophobica, Lecanora viridipruinosa, Lecidea griseomarginata, L. streveleri, Miriquidica gyrizans, Niesslia peltigerae, Ochrolechia cooperi, Placynthium glaciale, Porpidia seakensis, Rhizocarpon haidense, Sagiolechia phaeospora, Sclerococcum fissurinae, Spilonema maritimum, Thelocarpon immersum, Toensbergia blastidiata and Xenonectriella nephromatis. An additional 71 ‘known unknown’ species are cursorily described. Four new combinations are made: Lepra subvelata (G. K. Merr.) T. Sprib., Ochrolechia minuta (Degel.) T. Sprib., Steineropsis laceratula (Hue) T. Sprib. & Ekman and Toensbergia geminipara (Th. Fr.) T. Sprib. & Resl. Thirty-eight taxa are new to North America and 93 additional taxa new to Alaska. We use four to eight DNA loci to validate the placement of ten of the new species in the orders Baeomycetales, Ostropales, Lecanorales, Peltigerales, Pertusariales and the broader class Lecanoromycetes with maximum likelihood analyses. We present a total of 280 new fungal DNA sequences. The lichen inventory from Glacier Bay National Park represents the second largest number of lichens and associated fungi documented from an area of comparable size and the largest to date in North America. Coming from almost 60°N, these results again underline the potential for high lichen diversity in high latitude ecosystems.

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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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            RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

            Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
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              Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses.

              In phylogenetic analyses of molecular sequence data, partitioning involves estimating independent models of molecular evolution for different sets of sites in a sequence alignment. Choosing an appropriate partitioning scheme is an important step in most analyses because it can affect the accuracy of phylogenetic reconstruction. Despite this, partitioning schemes are often chosen without explicit statistical justification. Here, we describe two new objective methods for the combined selection of best-fit partitioning schemes and nucleotide substitution models. These methods allow millions of partitioning schemes to be compared in realistic time frames and so permit the objective selection of partitioning schemes even for large multilocus DNA data sets. We demonstrate that these methods significantly outperform previous approaches, including both the ad hoc selection of partitioning schemes (e.g., partitioning by gene or codon position) and a recently proposed hierarchical clustering method. We have implemented these methods in an open-source program, PartitionFinder. This program allows users to select partitioning schemes and substitution models using a range of information-theoretic metrics (e.g., the Bayesian information criterion, akaike information criterion [AIC], and corrected AIC). We hope that PartitionFinder will encourage the objective selection of partitioning schemes and thus lead to improvements in phylogenetic analyses. PartitionFinder is written in Python and runs under Mac OSX 10.4 and above. The program, source code, and a detailed manual are freely available from www.robertlanfear.com/partitionfinder.
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                Author and article information

                Journal
                Lichenologist
                Lichenologist (Lond.)
                LIC
                Lichenologist (London, England)
                Cambridge University Press (Cambridge, UK )
                0024-2829
                1096-1135
                March 2020
                11 May 2020
                : 52
                : 2
                : 61-181
                Affiliations
                [1 ]Department of Biological Sciences, CW405, University of Alberta , Edmonton, Alberta T6G 2R3, Canada
                [2 ]Department of Plant Sciences, Institute of Biology, University of Graz , NAWI Graz, Holteigasse 6, 8010 Graz, Austria
                [3 ]Division of Biological Sciences, University of Montana , 32 Campus Drive, Missoula, Montana 59812, USA
                [4 ]Herbarium, Department of Plant Biology, Michigan State University , East Lansing, Michigan 48824, USA
                [5 ]Real Jardín Botánico (CSIC) , Departamento de Micología, Calle Claudio Moyano 1, E-28014 Madrid, Spain
                [6 ]Museum of Evolution, Uppsala University , Norbyvägen 16, SE-75236 Uppsala, Sweden
                [7 ]Department of Natural History, University Museum of Bergen Allégt. 41 , P.O. Box 7800, N-5020 Bergen, Norway
                [8 ]Faculty of Bioscience and Aquaculture, Nord University , Box 2501, NO-7729 Steinkjer, Norway
                [9 ]NTNU University Museum, Norwegian University of Science and Technology , NO-7491 Trondheim, Norway
                [10 ]Faculty of Biology, Department I, Systematic Botany and Mycology, University of Munich (LMU) , Menzinger Straße 67, 80638 München, Germany
                [11 ]Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow , Glasgow G12 8QQ, UK
                [12 ]Botany Department, State Museum of Natural History Stuttgart , Rosenstein 1, 70191 Stuttgart, Germany
                [13 ]Natural History Museum , Cromwell Road, London SW7 5BD, UK
                [14 ]Institute of Botany of the Czech Academy of Sciences , Zámek 1, 252 43 Průhonice, Czech Republic
                [15 ]Department of Botany, Faculty of Science, University of South Bohemia , Branišovská 1760, CZ-370 05 České Budějovice, Czech Republic
                [16 ]Glacier Bay National Park & Preserve , P.O. Box 140, Gustavus, Alaska 99826, USA
                Author notes
                Author for correspondence: Toby Spribille. E-mail: toby.spribille@ 123456ualberta.ca
                Author information
                https://orcid.org/0000-0002-9855-4591
                https://orcid.org/0000-0002-5310-9232
                https://orcid.org/0000-0002-5411-3698
                https://orcid.org/0000-0003-3021-1821
                https://orcid.org/0000-0002-7841-6060
                https://orcid.org/0000-0001-7381-2139
                Article
                S0024282920000079
                10.1017/S0024282920000079
                7398404
                32788812
                fa377bc3-071e-4d1a-a92f-6900469f5598
                © British Lichen Society 2020

                This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 08 October 2019
                Page count
                Figures: 44, Tables: 1, References: 330, Pages: 121
                Categories
                Standard Paper

                biodiversity,evolution,floristics,key,latitudinal diversity gradient,molecular,new species,phylogenetics,symbiosis,taxonomy,temperate rainforest

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