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      The second known stygomorphic freshwater crab from China, Phasmon typhlops gen. nov. et sp. nov. (Crustacea, Decapoda, Potamidae), diverged at the beginning of the Late Miocene

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      Author(s): 1 , 2 , 4 , 3 ,
      Publication date (Electronic):
      Journal: ZooKeys
      Publisher: Pensoft Publishers
      Keywords: 16S rDNA, blind crab, cave crab, new genus, new species, Guangxi, subterranean

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          Abstract

          A new genus and new species of blind freshwater cave crab are described from Chongzuo City, Guangxi Zhuang Autonomous Region, China based on morphology and mitochondrial 16S rDNA sequences. The new genus, Phasmon gen. nov., is established for P. typhlops sp. nov., which is only the second blind cave crab known from China and East Asia. The combination of a very wide carapace, overall depigmentation, reduced orbits and vestigial unpigmented eyes of Phasmon immediately separates it from all known potamid genera. Molecular divergence estimates based on 16S rDNA suggest that the lineage to which the new genus belongs diverged from other potamids at the beginning of the Late Miocene (10.8 million years ago), much earlier than other Chinese cave crabs.

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          MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

          Sudhir Kumar, Glen Stecher, Michael KaWah Li … (2018)
          The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded 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

            Fredrik Ronquist, Maxim Teslenko, Paul van der Mark … (2012)
            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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              RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.

              Alexandros Stamatakis (2006)
              RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML). Low-level technical optimizations, a modification of the search algorithm, and the use of the GTR+CAT approximation as replacement for GTR+Gamma yield a program that is between 2.7 and 52 times faster than the previous version of RAxML. A large-scale performance comparison with GARLI, PHYML, IQPNNI and MrBayes on real data containing 1000 up to 6722 taxa shows that RAxML requires at least 5.6 times less main memory and yields better trees in similar times than the best competing program (GARLI) on datasets up to 2500 taxa. On datasets > or =4000 taxa it also runs 2-3 times faster than GARLI. RAxML has been parallelized with MPI to conduct parallel multiple bootstraps and inferences on distinct starting trees. The program has been used to compute ML trees on two of the largest alignments to date containing 25,057 (1463 bp) and 2182 (51,089 bp) taxa, respectively. icwww.epfl.ch/~stamatak
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                Author and article information

                Contributors
                Hsi-Te Shih:
                ORCID: https://orcid.org/0000-0003-1317-8783
                Journal
                Journal ID (nlm-ta): Zookeys
                Journal ID (iso-abbrev): Zookeys
                Journal ID (publisher-id): 2
                Journal ID (index): urn:lsid:arphahub.com:pub:45048D35-BB1D-5CE8-9668-537E44BD4C7E
                Journal ID (aggregator): urn:lsid:zoobank.org:pub:91BD42D4-90F1-4B45-9350-EEF175B1727A
                Title: ZooKeys
                Publisher: Pensoft Publishers
                ISSN (Print): 1313-2989
                ISSN (Electronic): 1313-2970
                Publication date Collection: 2020
                Publication date (Electronic): 31 December 2020
                Volume: 1008
                Pages: 1-15
                Affiliations
                [1 ] Unaffiliated, Guangdong, China Unaffiliated Guangdong China
                [2 ] Australian Museum, 1 William St, Sydney NSW 2010, Australia Australian Museum Sydney Australia
                [3 ] Department of Life Science and Research Center for Global Change Biology, National Chung Hsing University, Taichung 402, Taiwan University of New South Wales Kensington Australia
                [4 ] School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, NSW 2052, Australia National Chung Hsing University Taichung Taiwan
                Author notes
                Corresponding author: Hsi-Te Shih ( htshih@ 123456dragon.nchu.edu.tw )

                Academic editor: I.S. Wehrtmann

                Author information
                https://orcid.org/0000-0003-1317-8783
                Article
                Publisher ID: 58854
                DOI: 10.3897/zookeys.1008.58854
                PMC ID: 7790807
                PubMed ID: 33505185
                SO-VID: b4756f09-c221-4682-b1be-28a5f2569857
                Copyright © Chao Huang, Shane T. Ahyong, Hsi-Te Shih
                License:

                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
                Date received : 21 September 2020
                Date accepted : 06 December 2020
                Funding
                Ministry of Science and Technology (MOST), Executive Yuan, Taiwan
                Categories
                Subject: Research Article
                Subject: Potamidae
                Subject: Molecular Systematics
                Subject: Phylogeny
                Subject: Taxonomy
                Subject: China Seas

                ScienceOpen disciplines: Animal science & Zoology
                Keywords: 16s rdna,blind crab,cave crab,new genus,new species,guangxi,subterranean
                Data availability:
                ScienceOpen disciplines: Animal science & Zoology
                Keywords: 16s rdna, blind crab, cave crab, new genus, new species, guangxi, subterranean

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