Complete mitochondrial genome of the Leishan moustache toad,  Vibrissaphora leishanensis  (Anura: Megophryidae)

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Abstract

The complete mitogenome of Leishan moustache toad, Vibrissaphora leishanensis, is determined. The mitogenome size is 17,485 bp, containing 13 protein-coding genes, 2 rRNA genes, 23 tRNA genes and a control region (D-loop). The base composition of the whole genome is 28.1% A, 32.6% T, 24.4% C and 14.8% G. As observed in this genus before, this mitogenome also appears a tandem duplication of tRNA ^Met gene. This study will provide fundamental data for further research to resolve population genetics of this species and systematic problems of the genus Vibrissaphora.

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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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New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

Stéphane Guindon, Jean-François Dufayard, Vincent Lefort … (2010)

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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Colored atlas of Chinese amphibians and their distributions

L. Fei, C. Y. Ye, J. JIANG … (2012)

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Journal

Journal ID (nlm-ta): Mitochondrial DNA B Resour

Journal ID (iso-abbrev): Mitochondrial DNA B Resour

Title: Mitochondrial DNA. Part B, Resources

Publisher: Taylor & Francis

ISSN (Electronic): 2380-2359

Publication date (Electronic, pub): 29 March 2016

Publication date (Electronic, collection): 2016

Volume: 1

Issue: 1

Pages: 275-276

Affiliations

[a ]Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu, China;

[b ]University of Chinese Academy of Sciences , Beijing, China

Author notes

CONTACT Feng Xie xiefeng@ 123456cib.ac.cn Chengdu Institute of Biology, Chinese Academy of Sciences, PO Box 416, Chengdu 610041 , China

Article

Publisher ID: 1159937

DOI: 10.1080/23802359.2016.1159937

PMC ID: 7871820

SO-VID: 19f0e08a-d6f3-42b6-8c94-987274deed03

License:

This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/Licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Complete mitochondrial genome of the Leishan moustache toad, Vibrissaphora leishanensis (Anura: Megophryidae)

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Most cited references 5

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

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

Colored atlas of Chinese amphibians and their distributions

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