MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0
TLDR
An advanced version of the Molecular Evolutionary Genetics Analysis software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis, is released, which enables the inference of timetrees, as it implements the RelTime method for estimating divergence times for all branching points in a phylogeny.Abstract:
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.read more
Citations
More filters
Journal ArticleDOI
The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication
Weijian Zhuang,Chen Hua,Meng Yang,Jianping Wang,Jianping Wang,Manish K. Pandey,Zhang Chong,Wen Chi Chang,Liangsheng Zhang,Xingtan Zhang,Tang Ronghua,Vanika Garg,Xingjun Wang,Haibao Tang,Chi Nga Chow,Jinpeng Wang,Ye Deng,Depeng Wang,Aamir W. Khan,Aamir W. Khan,Qiang Yang,Tiecheng Cai,Prasad Bajaj,Kangcheng Wu,Baozhu Guo,Baozhu Guo,Xinyou Zhang,Jingjing Li,Fan Liang,Jiang Hu,Boshou Liao,Shengyi Liu,Annapurna Chitikineni,Hansong Yan,Yixiong Zheng,Yixiong Zheng,Shihua Shan,Qinzheng Liu,Dongyang Xie,Zhenyi Wang,Shahid Ali Khan,Niaz Ali,Chuanzhi Zhao,Xinguo Li,Ziliang Luo,Shubiao Zhang,Ruirong Zhuang,Ze Peng,Shuaiyin Wang,Gandeka Mamadou,Yuhui Zhuang,Yuhui Zhuang,Zifan Zhao,Weichang Yu,Faqian Xiong,Weipeng Quan,Mei Yuan,Yu Li,Huasong Zou,Han Xia,Li Zha,Junpeng Fan,Jigao Yu,Wenping Xie,Jiaqing Yuan,Kun Chen,Shanshan Zhao,Wenting Chu,Yuting Chen,Pengchuan Sun,Fanbo Meng,Tao Zhuo,Yuhao Zhao,Chunjuan Li,Guohao He,Yongli Zhao,Congcong Wang,P. B. KaviKishor,Rong Long Pan,Rong Long Pan,Andrew H. Paterson,Andrew H. Paterson,Xiyin Wang,Ray Ming,Ray Ming,Rajeev K. Varshney,Rajeev K. Varshney +86 more
TL;DR: High-quality genome sequence of cultivated peanut provides insights into genome evolution and the genetic mechanisms underlying seed size and leaf resistance in peanut, providing a cornerstone for functional genomics and peanut improvement.
Journal ArticleDOI
Fern genomes elucidate land plant evolution and cyanobacterial symbioses
Fay-Wei Li,Fay-Wei Li,Paul Brouwer,Lorenzo Carretero-Paulet,Shifeng Cheng,Jan de Vries,Pierre-Marc Delaux,Ariana N. Eily,Nils Koppers,Li-Yaung Kuo,Zheng Li,Mathew Simenc,Ian Small,Eric K. Wafula,Stephany Angarita,Michael S. Barker,Andrea Bräutigam,Claude W. dePamphilis,Sven B. Gould,Prashant S. Hosmani,Yao Moan Huang,Bruno Huettel,Yoichiro Kato,Xin Liu,Steven Maere,Rose McDowell,Lukas A. Mueller,Klaas G.J. Nierop,Stefan A. Rensing,Tanner A. Robison,Carl J. Rothfels,Erin M. Sigel,Yue Song,Prakash R. Timilsena,Yves Van de Peer,Yves Van de Peer,Hongli Wang,Per K.I. Wilhelmsson,Paul G. Wolf,Xun Xu,Joshua P. Der,Henriette Schluepmann,Gane Ka-Shu Wong,Kathleen M. Pryer +43 more
TL;DR: The genomes of two fern species, Azolla filiculoides and Salvinia cucullata, are reported and insights into fern-specific whole-genome duplications, f Fern-specific insect-resistant gene evolution and fern–cyanobacterial symbiosis are provided.
Journal ArticleDOI
Beyond Glycolysis: GAPDHs Are Multi-functional Enzymes Involved in Regulation of ROS, Autophagy, and Plant Immune Responses
TL;DR: Results indicate that plant GAPDHs can affect multiple aspects of plant immunity in diverse sub-cellular compartments.
Journal ArticleDOI
Generic concepts in Nectriaceae
TL;DR: A multi-gene phylogenetic analysis using partial sequences for the 28S large subunit (LSU) nrDNA, the internal transcribed spacer region and intervening 5.8S nrRNA gene (ITS) resolved 47 genera in the Nectriaceae, including several genera for which no sequence data was previously available.
Journal ArticleDOI
Variation in the flowering gene SELF PRUNING 5G promotes day-neutrality and early yield in tomato
Sebastian Soyk,Niels A. Müller,Soon Ju Park,Inga Schmalenbach,Ke Jiang,Ryosuke Hayama,Lei Zhang,Joyce Van Eck,José M. Jiménez-Gómez,José M. Jiménez-Gómez,Zachary B. Lippman +10 more
TL;DR: It is shown that loss of day-length-sensitive flowering in tomato was driven by the florigen paralog and flowering repressor SELF-PRUNING 5G (SP5G), and the findings suggest that pre-existing variation in SP5G facilitated the expansion of cultivated tomato beyond its origin near the equator in South America.
References
More filters
Journal ArticleDOI
MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
Koichiro Tamura,Daniel S. Peterson,Nicholas Peterson,Glen Stecher,Masatoshi Nei,Sudhir Kumar +5 more
TL;DR: The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models, inferring ancestral states and sequences, and estimating evolutionary rates site-by-site.
Journal ArticleDOI
MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment
TL;DR: An overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA is provided.
Book
The Neutral Theory of Molecular Evolution
TL;DR: The neutral theory as discussed by the authors states that the great majority of evolutionary changes at the molecular level are caused not by Darwinian selection but by random drift of selectively neutral mutants, which has caused controversy ever since.
Related Papers (5)
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
Naruya Saitou,Masatoshi Nei +1 more