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      Trypanosoma rangeli Genetic, Mammalian Hosts, and Geographical Diversity from Five Brazilian Biomes

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          Abstract

          Trypanosoma rangeli is a generalist hemoflagellate that infects mammals and is transmitted by triatomines around Latin America. Due to its high genetic diversity, it can be classified into two to five lineages. In Brazil, its distribution outside the Amazon region is virtually unknown, and knowledge on the ecology of its lineages and on host species diversity requires further investigation. Here, we analyzed 57 T. rangeli samples obtained from hemocultures and blood clots of 1392 mammals captured in different Brazilian biomes. The samples were subjected to small subunit (SSU) rDNA amplification and sequencing to confirm T. rangeli infection. Phylogenetic inferences and haplotype networks were reconstructed to classify T. rangeli lineages and to infer the genetic diversity of the samples. The results obtained in our study highlighted both the mammalian host range and distribution of T. rangeli in Brazil: infection was observed in five new species ( Procyon cancrivorous, Priodontes maximum, Alouatta belzebul, Sapajus libidinosus, and Trinomys dimidiatus), and transmission was observed in the Caatinga biome. The coati ( Nasua nasua) and capuchin monkey ( S. libidinosus) are the key hosts of T. rangeli. We identified all four T. rangeli lineages previously reported in Brazil (A, B, D, and E) and possibly two new genotypes.

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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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            MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

            The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
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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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                Author and article information

                Contributors
                Role: Academic Editor
                Journal
                Pathogens
                Pathogens
                pathogens
                Pathogens
                MDPI
                2076-0817
                11 June 2021
                June 2021
                : 10
                : 6
                : 736
                Affiliations
                [1 ]Laboratório de Biologia de Tripanosomatídeos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, Brazil; maria.dario@ 123456ioc.fiocruz.br (M.A.D.); marina.rodrigues@ 123456ioc.fiocruz.br (M.S.R.); crisvarella@ 123456ioc.fiocruz.br (C.V.L.); roque@ 123456ioc.fiocruz.br (A.L.R.R.)
                [2 ]Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-36, Brazil; mgpavan@ 123456ioc.fiocruz.br
                [3 ]Associate Researcher, Naples Zoo at Caribbeans Gardens, Naples, FL 34102, USA; dkluyber@ 123456live.com
                [4 ]Instituto de Conservação de Animais Silvestres (ICAS), Campo Grande 79037-100, Brazil; adesbiez@ 123456hotmail.com
                [5 ]Pós-Graduação em Ciência Ambientais e Sustentabilidade Agropecuária, Universidade Católica Dom Bosco, Campo Grande 79117-900, Brazil; herrera@ 123456ucdb.br
                [6 ]Pós-Graduação em Ecologia e Conservação, Universidade Federal de Mato Grosso do Sul, Campo Grande 79117-900, Brazil
                [7 ]Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo 05508-000, Brazil; lulima@ 123456usp.br (L.L.); mmgteix@ 123456icb.usp.br (M.M.G.T.)
                Author notes
                [* ]Correspondence: jansen@ 123456ioc.fiocruz.br
                Author information
                https://orcid.org/0000-0002-4951-3013
                https://orcid.org/0000-0002-5699-242X
                https://orcid.org/0000-0002-8964-566X
                https://orcid.org/0000-0003-2404-8765
                https://orcid.org/0000-0002-8740-052X
                Article
                pathogens-10-00736
                10.3390/pathogens10060736
                8230690
                64b7116f-8fd4-41d9-bba6-c73b2b986a9a
                © 2021 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( https://creativecommons.org/licenses/by/4.0/).

                History
                : 12 February 2021
                : 30 March 2021
                Categories
                Article

                trypanosoma rangeli,mammals,parasite ecology,lineages,brazilian biomes

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