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      Reinstatement of Eschatoporiini Blaisdell, 1906, a unique tribe of blind cavernicolous Tenebrionidae from California, with a new species from Napa County (Coleoptera, Tenebrionidae, Lagriinae)

      1 , 2 , 2

      ZooKeys

      Pensoft Publishers

      Eschatoporis, Blind, Subterranean, Cave, endemicity

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          Abstract

          Abstract

          The tribe Eschatoporini Blaisdell, 1906 is reinstated, based on molecular and morphological data, and the spelling corrected as Eschatoporiini . The tribe currently includes only the cave-dwelling genus Eschatoporis Blaisdell, 1906 from California, which is associated with underground aquifers. A second species of Eschatoporis is described from a cave in Napa County, California. The phylogenetic placement of Eschatoporiini within the Lagriinae is examined, and notes on the biology of Eschatoporis are provided.

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          Most cited references 21

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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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            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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              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

                Journal
                Zookeys
                Zookeys
                ZooKeys
                ZooKeys
                Pensoft Publishers
                1313-2989
                1313-2970
                2017
                10 August 2017
                : 688
                : 135-149
                Affiliations
                [1 ] Department of Entomology, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA
                [2 ] Northern Arizona University Department of Biological Sciences 617 S. Beaver St., Flagstaff, AZ 86011-5640, USA
                Author notes
                Corresponding author: Aaron D. Smith ( pimeliinae@ 123456gmail.com )

                Academic editor: P. Bouchard

                Article
                10.3897/zookeys.688.13575
                5672585
                29118594
                Rolf L. Aalbu, Kojun Kanda, Aaron D. Smith

                This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                Categories
                Research Article

                Animal science & Zoology

                endemicity, eschatoporis, blind, subterranean, cave

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