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      A new species of Nanorana Günther, 1896 (Anura, Dicroglossidae) from Yunnan, China

      research-article
      1 , , 2 , 3 ,
      ZooKeys
      Pensoft Publishers
      12S, 16S, morphology, phylogeny, spiny frog, systematic, taxonomy

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          Abstract

          A new species of Nanorana Günther, 1896 is described from Yunnan Province, China, based on morphological and molecular evidence. Morphologically, Nanorana xuelinensis sp. nov. is distinguished from its congeners by a combination of the following diagnostic characters: body size large; adult males with keratinized spines on chest, belly, lateral body, posterior dorsum, buttocks, outer side of the fore limbs, the inner metacarpal tubercle, fingers I and II, and upper eyelids; no spines on the inner side of the lower and upper arm; forelimbs strongly hypertrophied in adult males; anterior dorsum skin smooth; dorsolateral folds absent; finger I longer than finger II; webbing deeply incurved between tips of toes; present outer metacarpal tubercle and absent outer metatarsal tubercle. The new species is separated from all other congeners by uncorrected genetic distances ranging from 5.2% to 7.3% based on mitochondrial 16S rRNA gene and ranging from 3.9% to 7.6% based on mitochondrial 12S rRNA gene.

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          MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

          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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            IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

            Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%.
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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
                2021
                07 July 2021
                : 1048
                : 49-67
                Affiliations
                [1 ] Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, the Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, Yunnan 650223, China Kunming Natural History Museum of Zoology Kunming China
                [2 ] Research Institute of Xishuangbanna National Nature Reserve, No. 6 North Galan Road, Jinghong, Yunnan 666100, China Research Institute of Xishuangbanna National Nature Reserve Jinghong China
                [3 ] Kunming Institute of Zoology, the Chinese Academy of Sciences, No. 17 Longxin Road, Kunming, Yunnan 650201, China Kunming Institute of Zoology Kunming China
                Author notes
                Corresponding authors: Dingqi Rao ( raodq@ 123456mail.kiz.ac.cn ); Shuo Liu ( liushuo@ 123456mail.kiz.ac.cn )

                Academic editor: A. Ohler

                Article
                65620
                10.3897/zookeys.1048.65620
                8280097
                c7d9bcca-1b38-46b7-9a28-e2355271d168
                Shuo Liu, Peisong Zhang, Dingqi Rao

                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
                : 07 March 2021
                : 14 June 2021
                Categories
                Research Article
                Amphibia
                Animalia
                Anura
                Chordata
                Dicroglossidae
                Vertebrata
                Molecular Systematics
                Phylogeny
                Systematics
                Taxonomy
                Asia
                Central Asia
                China

                Animal science & Zoology
                12s,16s,morphology,phylogeny,spiny frog,systematic,taxonomy
                Animal science & Zoology
                12s, 16s, morphology, phylogeny, spiny frog, systematic, taxonomy

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