Review of the Merodon natans group with description of a new species, a key to the adults of known species of the natans lineage and first descriptions of some preimaginal stages

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Abstract

Abstract Merodon natans group (Diptera, Syrphidae) taxa are reviewed using an integrative taxonomic approach combining morphological, morphometric and molecular techniques. The approach substantiates recognition of the three species: M. calcaratus (Fabricius, 1794), M. natans (Fabricius, 1794) and M. pulveris Vujić & Radenković in Radenković et al. 2011, and reveals the existence of a new species, M. makrisi Vujić, Radenković & Tot sp. nov., which is described. It also highlights the existence of a series of natans group populations, especially on some of the Mediterranean islands, in the Levant and in the Afrotropical Region, for which more comprehensive data are required to clarify their status. A key is provided to the natans lineage species currently recognised, and preimaginal stages of some natans-group species are described for the first time. Redescriptions for M. calcaratus and M. natans are provided. A neotype is selected for M. natans. Lectotypes are designated for M. annulatus (Fabricius, 1794) and M. melancholicus (Fabricius, 1794). Merodon annulatus is recognised as a synonym of M. natans.

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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Kazutaka Katoh, Daron Standley (2013)

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.

Sudhir Kumar, Glen Stecher, Koichiro Tamura (2016)

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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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

Alexandros Stamatakis (2014)

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.