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      Brahmaculus gen. nov. (Leotiomycetes, Chlorociboriaceae)

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          Abstract

          A second genus in Chlorociboriaceae is described here as Brahmaculus gen. nov. Macroscopically distinctive, all species have bright yellow apothecia with several apothecial cups held on short branches at the tip of a long stipe. The genus is widely distributed across the Southern Hemisphere; the four new species described here include two from Chile ( B. magellanicus sp. nov., B. osornoensis sp. nov.) and one each from New Zealand ( B. moonlighticus sp. nov.) and Australia ( B. packhamiae sp. nov.). They differ from species referred to Chlorociboria , the only other genus in Chlorociboriaceae , in their terrestrial habitat and ascomata that are noticeably more hairy than the known Chlorociboria species, most of which have apothecia with short, macroscopically indistinct hair-like elements. Based on our analyses, Chlorociboria as accepted here is paraphyletic. Additional study is needed to clarify where alternative, monophyletic generic limits should be drawn and how these genera may be recognised morphologically. Also described here are three new Chlorociboria spp. from New Zealand ( C. metrosideri sp. nov., C. solandri sp. nov., C. subtilis sp. nov.), distinctive in developing on dead leaves rather than wood and in two of them not forming the green pigmentation characteristic of most Chlorociboria species. New Zealand specimens previously incorrectly identified as Chlorociboria argentinensis are provided with a new name, C. novae-zelandiae sp. nov.

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          Most cited references 25

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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
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Writing - original draft
                Role: InvestigationRole: Resources
                Role: Data curationRole: ResourcesRole: Writing - review and editing
                Role: InvestigationRole: Resources
                Role: Data curationRole: ResourcesRole: Writing - review and editing
                Journal
                MycoKeys
                MycoKeys
                11
                urn:lsid:arphahub.com:pub:C004A564-9D6A-5F9F-B058-6A3815DFE9C3
                MycoKeys
                Pensoft Publishers
                1314-4057
                1314-4049
                2021
                07 May 2021
                : 80
                : 19-43
                Affiliations
                [1 ] Manaaki Whenua–Landcare Research, Private Bag 92170, Auckland 1142, (Aotearoa) New Zealand Manaaki Whenua–Landcare Research Auckland New Zealand
                [2 ] University of Florida, Department of Plant Pathology, Gainesville FL 32611, USA University of Florida Gainesville United States of America
                [3 ] Royal Botanic Gardens Victoria, Melbourne, Victoria 3004, Australia Royal Botanic Gardens Victoria Melbourne Australia
                Author notes
                Corresponding author: Peter R. Johnston ( johnstonp@ 123456landcareresearch.co.nz )

                Academic editor: Thorsten Lumbsch

                Article
                64435
                10.3897/mycokeys.80.64435
                8121775
                Peter R. Johnston, Duckchul Park, Matthew E. Smith, Alija B. Mujic, Tom W. May

                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.

                Funding
                Funded by: National Science Foundation 100000001 http://doi.org/10.13039/100000001
                Categories
                Research Article
                Ascomycota
                Leotiomycetes
                Taxonomy
                Americas
                Australasia

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