Two new cryptic species of <i>Microhyla</i> Tschudi, 1838 (Amphibia, Anura, Microhylidae) related to the <i>M. heymonsi </i> group from central Vietnam

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Abstract

The Microhyla heymonsi species complex from central Vietnam was examined, and based upon morphological and molecular evidence, two new species are described. The discovery of Microhyla daklakensis sp. nov. and Microhyla ninhthuanensis sp. nov. brings the total number of known species in the genus to 46 and the species number of Microhyla in Vietnam to 13. The Truong Son Range harbors the highest diversity of the genus Microhyla with 11 recorded species so far. However, this apparent micro-endemic diversity is at risk because of habitat loss by deforestation, which highlights the necessity of further research leading to improved conservation measures.

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MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

Sudhir Kumar, Glen Stecher, Koichiro Tamura (2016)

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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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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The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.

J. Thompson (1997)

CLUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W. The new system is easy to use, providing an integrated system for performing multiple sequence and profile alignments and analysing the results. CLUSTAL X displays the sequence alignment in a window on the screen. A versatile sequence colouring scheme allows the user to highlight conserved features in the alignment. Pull-down menus provide all the options required for traditional multiple sequence and profile alignment. New features include: the ability to cut-and-paste sequences to change the order of the alignment, selection of a subset of the sequences to be realigned, and selection of a sub-range of the alignment to be realigned and inserted back into the original alignment. Alignment quality analysis can be performed and low-scoring segments or exceptional residues can be highlighted. Quality analysis and realignment of selected residue ranges provide the user with a powerful tool to improve and refine difficult alignments and to trap errors in input sequences. CLUSTAL X has been compiled on SUN Solaris, IRIX5.3 on Silicon Graphics, Digital UNIX on DECstations, Microsoft Windows (32 bit) for PCs, Linux ELF for x86 PCs, and Macintosh PowerMac.

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Author and article information

Contributors

Tao Thien Nguyen:

ORCID: https://orcid.org/0000-0002-5640-4536

Jianping Jiang

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: 2021

Publication date (Electronic): 05 May 2021

Volume: 1036

Pages: 47-74

Affiliations

[1 ] CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China Chengdu Institute of Biology, Chinese Academy of Sciences Chengdu China

[2 ] University of Chinese Academy of Sciences, Beijing 810000, China University of Chinese Academy of Sciences Beijing China

[3 ] Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Hanoi, Vietnam Forest Resources and Environment Center Hanoi Vietnam

[4 ] Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Hanoi, Vietnam Vietnam National Museum of Nature, Vietnam Academy of Science and Technology Hanoi Vietnam

[5 ] Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Cau Giay, Hanoi, Vietnam Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology Hanoi Vietnam

[6 ] Zoological Institute, Russian Academy of Sciences, Universitetskaya nab 1, St. Petersburg 199034, Russia Graduate University of Science and Technology Hanoi Vietnam

[7 ] AG Zoologischer Garten Köln, Riehler Strasse 173, D-50735 Cologne, Germany Zoological Institute, Russian Academy of Sciences St. Petersburg Russia

[8 ] Institute of Zoology, University of Cologne, Zülpicher Strasse 47b, D-50674 Cologne, Germany AG Zoologischer Garten Köln Cologne Germany

[9 ] Forest Resources and Environment Center, 300 Ngoc Hoi Road, Thanh Tri, Hanoi, Vietnam University of Cologne Cologne Germany

Author notes

Corresponding authors: Jianping Jiang ( jiangjp@ 123456cib.ac.cn ); Tao Thien Nguyen ( nguyenthientao@ 123456gmail.com )

Academic editor: J. Penner

Author information

Chung Van Hoang https://orcid.org/0000-0002-0709-974X

Tao Thien Nguyen https://orcid.org/0000-0002-5640-4536

Truong Quang Nguyen https://orcid.org/0000-0002-6601-0880

Bin Wang https://orcid.org/0000-0001-6036-5579

Article

Publisher ID: 56919

DOI: 10.3897/zookeys.1036.56919

PMC ID: 8116321

SO-VID: 79fd9711-e508-4431-822f-9cd3c14d7a6f

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.

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Two new cryptic species of Microhyla Tschudi, 1838 (Amphibia, Anura, Microhylidae) related to the M. heymonsi group from central Vietnam

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Most cited references 57

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.

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