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      Integrative taxonomy tests possible hybridisation between Central Asian cerambycids (Coleoptera)

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          Abstract

          Hybridisation can lead to the formation of new evolutionary lineages and some described insect species may in fact be first‐generation hybrids of their parental species. Anoplistes forticornis and Agalusoi are two closely related cerambycid taxa endemic to Central Asia that exhibit a peculiar geographical distribution. Although the common diagnostic elytral pattern makes these beetles superficially easily distinguishable, there are marked resemblances in their morphology. By applying an integrative taxonomy approach, we verify the taxonomic status of Aforticornis and Agalusoi and test the possibility of hybridisation. The results of our comprehensive morphological examination and molecular analyses targeting mitochondrial (COI, 16S rRNA) and nuclear (arginine kinase, CAD, 28S rRNA) genes support the specific status of these taxa. In mtDNA, the putative hybrid specimen is more closely related to Aforticornis, which indicates that a female of this species bred with a male of Agalusoi. The supposed ecotypic variability (manifested in elytral pattern) is apparently not related to the topography or spatial structure of habitat. The phylogenetic hypothesis supports a peripatric scenario in which populations of the common ancestor had been separated for a significant period of time, first by the mountain ranges of Dzungarian Alatau (~11–10 Ma) and ultimately by the Ili River. The diverged taxa came into recent secondary contact following these isolation events. The methodology presented herein can be widely applied to identify first‐generation hybridisation in Coleoptera.

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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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            MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

            We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge.
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              MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

              Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d N /d S rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
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                Author and article information

                Contributors
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                Journal
                Zoologica Scripta
                Zoologica Scripta
                0300-3256
                1463-6409
                January 2023
                October 02 2022
                January 2023
                : 52
                : 1
                : 70-85
                Affiliations
                [1 ] Museum and Institute of Zoology Polish Academy of Sciences Warsaw Poland
                [2 ] Department of Entomology Michigan State University East Lansing USA
                [3 ] Department of Organismic and Evolutionary Biology Harvard University Cambridge USA
                [4 ] Department of Forest Protection Forest Research Institute Sękocin Stary Poland
                [5 ] Department of Natural History Upper Silesian Museum in Bytom Bytom Poland
                Article
                10.1111/zsc.12570
                d78c4fea-2c3d-44a9-9c97-a4b7c4d2c6ed
                © 2023

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