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      Evolutionary relationships, biogeography and morphological characters of Glinus (Molluginaceae), with special emphasis on the genus composition in Sub-Saharan Africa

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          Glinus is a small genus of Molluginaceae with 8–10 species mostly distributed in the tropics of the World. Its composition and evolutionary relationships were poorly studied. A new molecular phylogeny constructed here using nuclear (ITS) and chloroplast ( rbcL, trnK-matK) markers confirmed the monophyly of the genus. Based on ITS analysis, the following well-supported lineages are present within Glinus : the G. bainesii lineage is recovered as sister to the remainder of the genus followed by G. oppositifolius. Three other clades are: G. hirtus with G. orygioides ; G. radiatus and G. lotoides ; the latter is represented by a sample from North America, and G. zambesiacus as sister to G. setiflorus + G. lotoides + G. dictamnoides . On the plastid gene tree, G. bainesii + G. oppositifolius form a sister clade to all other Glinus species. The next clade is formed by G. hirtus and G. orygioides followed by G. radiatus plus an American sample of G. lotoides . The next branch comprises G. setiflorus as sister to G. zambesiacus + G. lotoides + G. dictamnoides . Glinus seems to have originated from Africa around the Late Eocene or Early Miocene, with further radiations to Australia and the Americas during the Late Miocene or Late Pliocene. Compared with the previous limited character set used for the diagnostics, we have found ten new morphological and carpological traits distinguishing Glinus members. In both trees based on nuclear and plastid datasets, the major phylogenetic clades cannot be characterized by the peculiar morphological characters. Many shared character states leading to their contrasting pattern in the multivariate analysis model are interpreted as a high homoplasy in the phylogenetically distant species. We paid special attention to the composition of the genus in Sub-Saharan Africa, a region with the greatest species diversity. Our results provide new insight into the taxonomy of Glinus in this region. Glinus lotoides var. virens accepted in many previous works is a synonym of G. dictamnoides that is closely related to G. lotoides based on molecular analysis and morphological characters. The status of the American populations of G. lotoides needs further investigation due to different characters of the specimens from the Old and the New World. Many specimens previously identified as G. lotoides var. virens and as the intermediates G. lotoides × G. oppositifolius belong to G. zambesiacus sp. nov. and G. hirtus comb. nov. (≡ Mollugo hirta ); the latter species is resurrected from synonymy after 200 years of unacceptance. In some African treatments, G. hirtus was known under the invalidly published name G. dahomensis . Glinus zambesiacus is distributed in the southern and eastern parts of tropical Africa, and G. hirtus previously assumed to be endemic to West Africa is indeed a species with a wide distribution across the tropical part of the continent. Glinus microphyllus previously accepted as endemic to West Tropical Africa together with other new synonyms ( G. oppositifolius var. lanatus , G. herniarioides , Wycliffea rotundifolia ) is considered here as G. oppositifolius var. keenanii comb. nov. (≡ Mollugo hirta var. keenanii ), a variety found across the entire distribution of G. oppositifolius (Australia, Asia, and Africa). The presence of the American G. radiatus in Africa is not confirmed, and all records of this species belong to G. hirtus . The lectotypes of some names ( G. dictamnoides , G. herniarioides , Mollugo hirta , M. setiflora , Pharnaceum pentagynum , Wycliffea ) as well as a neotype of G. trianthemoides are designated. A new key to the identification of all Glinus species in Sub-Saharan Africa is provided. A checklist is given of all accepted species in this region ( G. bainesii , G. hirtus , G. lotoides , G. oppositifolius s.l., G. setiflorus , and G. zambesiacus ) with their nomenclature, morphological description and geographical distribution.

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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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            MUSCLE: multiple sequence alignment with high accuracy and high throughput.

             Robert Edgar (2004)
            We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.
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              jModelTest 2: more models, new heuristics and parallel computing.


                Author and article information

                Pensoft Publishers
                22 February 2021
                : 173
                : 1-92
                [1 ] Department of Higher Plants, Biological Faculty, Lomonosov Moscow State University, 119234, Moscow, Russia
                [2 ] Laboratory Herbarium (TK), Tomsk State University, Lenin Ave. 36, 634050, Tomsk, Russia
                [3 ] Botanical Museum, Finnish Museum of Natural History, P.O. Box 7, 00014 University of Helsinki, Finland
                [4 ] Herbarium, Komarov Botanical Institute of Russian Academy of Sciences, Prof. Popov St. 2, 197376 St. Petersburg, Russia
                [5 ] Institut für Molekulare Physiologie, Johannes Gutenberg–Universität Mainz, Germany
                [6 ] Department of Plant Physiology, Biological Faculty, Lomonosov Moscow State University, 119234, Moscow, Russia
                [7 ] University of Botswana, Plot 4775, Notwane Road, Gaborone, Botswana
                [8 ] Royal Botanic Gardens, Kew, Richmond, TW9 3AE, United Kingdom
                [9 ] Department of Hydrobiology, Biological Faculty, Lomonosov Moscow State University, 119234, Moscow, Russia
                Author notes
                Corresponding author: Alexander P. Sukhorukov ( suchor@ 123456mail.ru )

                Academic editor: G.P.G. del Galdo

                Alexander P. Sukhorukov, Alexander Sennikov, Marie Claire Veranso-Libalah, Maria Kushunina, Maya V. Nilova, Roger Heath, Alison Heath, Yuri Mazei, Maxim A. Zaika

                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.

                Tomsk State University competitiveness improvement programme
                Biodiversity & Conservation
                Evolutionary biology
                Floristics & Distribution
                Identification key
                Molecular systematics


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