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      Integrative taxonomic revision of the land snail genus Sarika Godwin-Austen, 1907 in Thailand, with descriptions of nine new species (Eupulmonata, Ariophantidae)

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          Abstract

          Members of the land snail genus Sarika Godwin-Austen 1907 are superficially similar and difficult to differentiate by their shell morphology so that their species limits are still unclear. In order to resolve the taxonomy of this group, a phylogenetic reconstruction of Sarika is presented, based on morphological and anatomical characters, as well as on partial sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene. In total, 23 species of Sarika are recognised in Thailand, and nine species are new to science, namely S. caligina Pholyotha & Panha, sp. nov., S. gratesi Pholyotha & Panha, sp. nov., S. inferospira Pholyotha & Panha, sp. nov., S. lactospira Pholyotha & Panha, sp. nov., S. megalogyne Pholyotha & Panha, sp. nov., S. melanospira Pholyotha & Panha, sp. nov., S. pellosa Pholyotha & Panha, sp. nov., S. solemi Pholyotha & Panha, sp. nov., and S. subheptagyra Pholyotha & Panha, sp. nov. Results from genital examination and COI analyses confirm the monophyly of Sarika and its species. The intra- and inter-specific genetic distances of Sarika were 0–3.7% and 4.6–12.0%, respectively. Colour images of the living adults, shell, and genitalia along with SEM images of the spermatophore and radula are given. In addition, an identification key and a geographical distribution map of Sarika species are provided.

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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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            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

                Contributors
                Journal
                Zookeys
                Zookeys
                2
                urn:lsid:arphahub.com:pub:45048D35-BB1D-5CE8-9668-537E44BD4C7E
                urn:lsid:zoobank.org:pub:91BD42D4-90F1-4B45-9350-EEF175B1727A
                ZooKeys
                Pensoft Publishers
                1313-2989
                1313-2970
                2020
                20 October 2020
                : 976
                : 1-100
                Affiliations
                [1 ] Biological Sciences Program, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand Chulalongkorn University Bangkok Thailand
                [2 ] Animal Systematics Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand Chulalongkorn University Bangkok Thailand
                Author notes
                Corresponding author: Chirasak Sutcharit ( jirasak4@ 123456yahoo.com ); Somsak Panha ( somsak.pan@ 123456chula.ac.th )

                Academic editor: E. Gittenberger

                Author information
                https://orcid.org/0000-0001-6677-1164
                Article
                53859
                10.3897/zookeys.976.53859
                7591553
                33173395
                493bed22-eaba-478a-8a81-587ab55f41de
                Arthit Pholyotha, Chirasak Sutcharit, Piyoros Tongkerd, Somsak Panha

                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.

                History
                : 02 May 2020
                : 16 August 2020
                Categories
                Research Article
                Ariophantidae
                Pulmonata
                Systematics
                Cenozoic
                Asia

                Animal science & Zoology
                diversity,dna barcodes,indochina,limestone,systematics
                Animal science & Zoology
                diversity, dna barcodes, indochina, limestone, systematics

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