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      Description of a new Megophrys Kuhl & Van Hasselt, 1822 (Anura, Megophryidae) from Guizhou Province, China

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          Abstract

          A new species of the genus Megophrys is described from Guizhou Province, China. Molecular phylogenetic analyses based on mitochondrial DNA indicated the new species as a clade clustered into the Megophrys clade. The new species can be distinguished from its congeners by a combination of the following characters: body size moderate (SVL 40.0–45.5 mm in males and 48.9–51.2 mm in females); vomerine teeth absent; tongue not notched behind; tympanum distinctly visible, oval; a small horn-like tubercle at the edge of each upper eyelid; two metacarpal tubercles in hand; toes with rudimentary webbing; heels overlapping when thighs are positioned at right angles to the body; tibiotarsal articulation reaching the level of mid-eye when leg stretched forward; in breeding males, an internal single subgular vocal sac present and brownish nuptial pads, made up of black nuptial spines, present on the dorsal base of the first two fingers.

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          Most cited references 86

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          MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.

          We announce the release of an advanced version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables the inference of timetrees, as it implements the RelTime method for estimating divergence times for all branching points in a phylogeny. A new Timetree Wizard in MEGA6 facilitates this timetree inference by providing a graphical user interface (GUI) to specify the phylogeny and calibration constraints step-by-step. This version also contains enhanced algorithms to search for the optimal trees under evolutionary criteria and implements a more advanced memory management that can double the size of sequence data sets to which MEGA can be applied. Both GUI and command-line versions of MEGA6 can be downloaded from www.megasoftware.net free of charge.
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            New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

            PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.
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              MrBayes 3: Bayesian phylogenetic inference under mixed models.

              MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types-e.g. morphological, nucleotide, and protein-and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters.
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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
                05 November 2020
                : 986
                : 101-126
                Affiliations
                [1 ] Department of Food Science and Engineering, Moutai Institute, Renhuai 564500, China Chengdu Institute of Biology, Chinese Academy of Sciences Chengdu China
                [2 ] CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China Moutai Institute Renhuai China
                Author notes
                Corresponding author: Bin Wang ( wangbin@ 123456cib.ac.cn )

                Academic editor: A. Ohler

                Article
                57119
                10.3897/zookeys.986.57119
                7661479
                Shi-Ze Li, Ning-Ning Lu, Jing Liu, Bin Wang

                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
                Amphibia
                Animalia
                Anura
                Megophryidae
                Vertebrata
                Systematics
                Taxonomy
                Cenozoic
                Neogene
                Asia
                China Seas
                Far East

                Animal science & Zoology

                taxonomy, new species, morphology, molecular phylogenetic analysis

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