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      Evolutionary Dynamics of Host Organs for Microbial Symbiosis in Tortoise Leaf Beetles (Coleoptera: Chrysomelidae: Cassidinae)

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          ABSTRACT

          Diverse insects host specific microbial symbionts that play important roles for their growth, survival, and reproduction. They often develop specialized symbiotic organs for harboring the microbial partners. While such intimate associations tend to be stably maintained over evolutionary time, the microbial symbionts may have been lost or replaced occasionally. How symbiont acquisitions, replacements, and losses are linked to the development of the host’s symbiotic organs is an important but poorly understood aspect of microbial symbioses. Cassidine leaf beetles are associated with a specific gammaproteobacterial lineage, Stammera, whose reduced genome is streamlined for producing pectin-degrading enzymes to assist the host’s digestion of food plants. We investigated the symbiotic system of 24 Japanese cassidine species and found that (i) most species harbored Stammera within paired symbiotic organs located at the foregut-midgut junction, (ii) the host phylogeny was largely congruent with the symbiont phylogeny, indicating stable host-symbiont association over evolutionary time, (iii) meanwhile, the symbiont was not detected in three distinct host lineages, uncovering recurrent losses of the ancient microbial mutualist, (iv) the symbiotic organs were vestigial but present in the symbiont-free lineages, indicating evolutionary persistence of the symbiotic organs even in the absence of the symbiont, and (v) the number of the symbiotic organs was polymorphic among the cassidine species, either two or four, unveiling a dynamic evolution of the host organs for symbiosis. These findings are discussed as to what molecular mechanisms and evolutionary trajectories underpin the recurrent symbiont losses and the morphogenesis of the symbiotic organs in the herbivorous insect group.

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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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            Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

            Abstract Bayesian inference of phylogeny using Markov chain Monte Carlo (MCMC) plays a central role in understanding evolutionary history from molecular sequence data. Visualizing and analyzing the MCMC-generated samples from the posterior distribution is a key step in any non-trivial Bayesian inference. We present the software package Tracer (version 1.7) for visualizing and analyzing the MCMC trace files generated through Bayesian phylogenetic inference. Tracer provides kernel density estimation, multivariate visualization, demographic trajectory reconstruction, conditional posterior distribution summary, and more. Tracer is open-source and available at http://beast.community/tracer.
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              RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

              Abstract Motivation Phylogenies are important for fundamental biological research, but also have numerous applications in biotechnology, agriculture and medicine. Finding the optimal tree under the popular maximum likelihood (ML) criterion is known to be NP-hard. Thus, highly optimized and scalable codes are needed to analyze constantly growing empirical datasets. Results We present RAxML-NG, a from-scratch re-implementation of the established greedy tree search algorithm of RAxML/ExaML. RAxML-NG offers improved accuracy, flexibility, speed, scalability, and usability compared with RAxML/ExaML. On taxon-rich datasets, RAxML-NG typically finds higher-scoring trees than IQTree, an increasingly popular recent tool for ML-based phylogenetic inference (although IQ-Tree shows better stability). Finally, RAxML-NG introduces several new features, such as the detection of terraces in tree space and the recently introduced transfer bootstrap support metric. Availability and implementation The code is available under GNU GPL at https://github.com/amkozlov/raxml-ng . RAxML-NG web service (maintained by Vital-IT) is available at https://raxml-ng.vital-it.ch/ . Supplementary information Supplementary data are available at Bioinformatics online.

                Author and article information

                Contributors
                Role: Editor
                Journal
                mBio
                mBio
                mbio
                mBio
                American Society for Microbiology (1752 N St., N.W., Washington, DC )
                2150-7511
                25 January 2022
                Jan-Feb 2022
                25 January 2022
                : 13
                : 1
                : e03691-21
                Affiliations
                [a ] National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
                [b ] Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Japan
                [c ] Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan
                [d ] Graduate School of Human Development and Environment, Kobe University, Kobe, Japan
                [e ] Department of Applied Chemistry, National Chiao Tung University, Hsinchu, Taiwan
                [f ] Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
                [g ] Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
                University of Hawaii at Manoa
                Author notes

                Kayoko Fukumori and Kohei Oguchi contributed equally to this work. Author order was determined both alphabetically and in order of increasing seniority.

                The authors declare no conflict of interest.

                Author information
                https://orcid.org/0000-0001-5987-2602
                Article
                03691-21 mbio.03691-21
                10.1128/mbio.03691-21
                8787481
                35073753
                e83152db-b6d3-4cb0-98fd-b40ed9d66377
                Copyright © 2022 Fukumori et al.

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                : 10 December 2021
                : 21 December 2021
                Page count
                supplementary-material: 8, Figures: 8, Tables: 0, Equations: 0, References: 94, Pages: 17, Words: 10778
                Funding
                Funded by: MEXT | Japan Science and Technology Agency (JST), FundRef https://doi.org/10.13039/501100002241;
                Award ID: JPMJER1803
                Award Recipient :
                Funded by: MEXT | Japan Science and Technology Agency (JST), FundRef https://doi.org/10.13039/501100002241;
                Award ID: JPMJER1902
                Award Recipient :
                Funded by: MEXT | Japan Society for the Promotion of Science (JSPS), FundRef https://doi.org/10.13039/501100001691;
                Award ID: JP17H06388
                Award Recipient :
                Funded by: MEXT | Japan Society for the Promotion of Science (JSPS), FundRef https://doi.org/10.13039/501100001691;
                Award ID: JP16J40021
                Award Recipient :
                Categories
                Research Article
                host-microbial-interactions, Host-Microbial Interactions
                Custom metadata
                January/February 2022

                Life sciences
                tortoise leaf beetle,cassidinae,symbiotic bacteria,stammera capleta,symbiotic organ,symbiont loss

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