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      A new species of the genus Leptobrachella Smith, 1925 (Anura, Megophryidae) from Guizhou, China

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          Abstract

          Asian leaf-litter toads of the genus Leptobrachella represent charismatic anuran diversification with 80 species, of which 25 are from China. Recent new discoveries suggest that the diversity of this genus is underestimated. Here, we describe a new species of Leptobrachella , Leptobrachella bashaensis sp. nov. from the Basha Nature Reserve, Congjiang County, Guizhou Province, China. The new species is distinguished from its congeners by the following suite of morphological traits: small body size (SVL 22.9–25.6 mm in six adult males and 27.1 mm in one adult female); head longer than wide; dorsal skin slightly shagreened with small tubercles; creamy-white chest and belly with irregular black spots; distinct ventrolateral glands forming a white line; finger webbing and fringes absent; toe webbing rudimentary and lateral fringes narrow; iris bicolored with bright orange in upper half and silver in lower half; dorsal surface of tadpole head dark brown with small, brown, irregular spot, air sac-shaped bulges on both sides of body. The new species differs from all known congeners by an uncorrected p-distance of >5.3% of the 16S rRNA gene fragment examined, and the phylogenetic analysis clusters the new species with L. maoershanensis and L. laui . At present, the new species is only known from a small range of montane evergreen secondary forests in Basha Nature Reserve approximately 900 m elevation. Its natural history and conservation status are discussed.

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          MUSCLE: multiple sequence alignment with high accuracy and high throughput.

          We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.
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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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              jModelTest 2: more models, new heuristics and parallel computing.

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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
                31 December 2020
                : 1008
                : 139-157
                Affiliations
                [1 ] Guizhou Institute of Biology, Guizhou Academy of Sciences, Guiyang, 550002, China Guizhou Institute of Biology, Guizhou Academy of Sciences Guiyang China
                [2 ] Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming 650224, Yunnan, China Southwest Forestry University Kunming China
                [3 ] Forestry Bureau of Congjiang County, Congjiang, 557400, Guizhou, China Forestry Bureau of Congjiang County Guizhou China
                [4 ] Mt. Foding National Nature Reserve Bureau, shiqian, 555100, Guizhou, China Mt. Foding National Nature Reserve Bureau Shiqian China
                [5 ] Biodiversity Conservation Key Laboratory, Guiyang College, Guiyang, 550002, China Guiyang College Guiyang China
                Author notes

                Academic editor: Anthony Herrel

                Author information
                https://orcid.org/0000-0001-5991-3021
                Article
                56412
                10.3897/zookeys.1008.56412
                7790805
                33505191
                c733b166-b009-409c-ae81-85d49c3d9c6e
                Jing-Cai Lyu, Liang-Liang Dai, Ping-Fan Wei, Yan-Hong He, Zhi-Yong Yuan, Wen-Li Shi, Sheng-lun Zhou, Si-yu Ran, Zhong-Fan Kuang, Xuan Guo, Gang Wei, Guo Yuan

                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
                : 15 July 2020
                : 05 December 2020
                Categories
                Research Article
                Amphibia
                Anura
                Biodiversity & Conservation
                Cenozoic
                Asia

                Animal science & Zoology
                integrated taxonomy,morphology,tadpole,vocalization
                Animal science & Zoology
                integrated taxonomy, morphology, tadpole, vocalization

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