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      Two new species of Neofoleyellides (Nematoda: Onchocercidae) parasitising anuran amphibians in South Africa

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          Abstract

          The genus Neofoleyellides was recently erected for a single species, Neofoleyellides boerewors from bufonid hosts in South Africa. In present study, we discovered two undescribed species of Neofoleyellides, namely N. steyni n. sp. and N. martini n. sp. parasitising frogs Amietia delalandii and Leptopelis natalensis, respectively. Both species differ from N. boerewors and between each other in shape and relative length of oesophagus, size of spicules, arrangement of genital papillae and morphology of caudal alae in males. Phylogenetic analysis based on concatenated fragments of the 18S ribosomal ribonucleic acid (18S rRNA) and the Cytochrome oxidase c subunit I (COI) genes confirmed both species as Neofoleyellides sister to Icosiellinae and Oswaldofilariinae.

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          Highlights

          • Two new species of Neofoleyellides described from frogs Amietia delalandii and Leptopelis natalensis.

          • Morphological characters of N. boerewors, N. steyni n. sp. and N. martini n. sp. compared.

          • Phylogenetic tree based on 18S rDNA and COI mtDNA sequences generated.

          • Morphological and phylogenetic characteristics of three Neofoleyellides spp. discussed.

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          Most cited references14

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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.

            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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              Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.

              The use of some multiple-sequence alignments in phylogenetic analysis, particularly those that are not very well conserved, requires the elimination of poorly aligned positions and divergent regions, since they may not be homologous or may have been saturated by multiple substitutions. A computerized method that eliminates such positions and at the same time tries to minimize the loss of informative sites is presented here. The method is based on the selection of blocks of positions that fulfill a simple set of requirements with respect to the number of contiguous conserved positions, lack of gaps, and high conservation of flanking positions, making the final alignment more suitable for phylogenetic analysis. To illustrate the efficiency of this method, alignments of 10 mitochondrial proteins from several completely sequenced mitochondrial genomes belonging to diverse eukaryotes were used as examples. The percentages of removed positions were higher in the most divergent alignments. After removing divergent segments, the amino acid composition of the different sequences was more uniform, and pairwise distances became much smaller. Phylogenetic trees show that topologies can be different after removing conserved blocks, particularly when there are several poorly resolved nodes. Strong support was found for the grouping of animals and fungi but not for the position of more basal eukaryotes. The use of a computerized method such as the one presented here reduces to a certain extent the necessity of manually editing multiple alignments, makes the automation of phylogenetic analysis of large data sets feasible, and facilitates the reproduction of the final alignment by other researchers.
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                Author and article information

                Contributors
                Journal
                Int J Parasitol Parasites Wildl
                Int J Parasitol Parasites Wildl
                International Journal for Parasitology: Parasites and Wildlife
                Elsevier
                2213-2244
                18 March 2021
                April 2021
                18 March 2021
                : 14
                : 298-307
                Affiliations
                [a ]I.I. Schmalhausen Institute of Zoology NAS of Ukraine, 15 B. Khmelnytskogo str., 01030, Kyiv, Ukraine
                [b ]African Amphibian Conservation Research Group, Unit for Environmental Sciences and Management, North-West University, Private Bag X6001, Potchefstroom, 2520, South Africa
                [c ]South African Institute for Aquatic Biodiversity, Somerset Street, Machanda, 6140, South Africa
                Author notes
                []Corresponding author. Department of Invertebrate Fauna and Systematics, I.I. Schmalhausen Institute of Zoology NAS of Ukraine, 15 B. Khmelnytskogo str., 01030, Kyiv, Ukraine. romasvit@ 123456izan.kiev.ua
                Article
                S2213-2244(21)00032-8
                10.1016/j.ijppaw.2021.02.018
                8056133
                33898231
                26475676-da5b-4129-9ca1-e62106eda1b0
                © 2021 The Authors

                This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

                History
                : 24 December 2020
                : 14 February 2021
                : 27 February 2021
                Categories
                Articles from the Special Issue 'Africa-Parasites of Wildlife'

                nematode,neofoleyellides,amphibia,anura,amietia,leptopelis,limpopo,kwazulu-natal,south africa

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