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
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The hijacking of a receptor kinase-driven pathway by a wheat fungal pathogen leads to disease
Gongjun Shi,Zengcui Zhang,Timothy L. Friesen,Timothy L. Friesen,Dina Raats,Tzion Fahima,Robert Brueggeman,Shunwen Lu,Harold N. Trick,Zhaohui Liu,Wun Chao,Zeev Frenkel,Steven S. Xu,Jack B. Rasmussen,Justin D. Faris +14 more
TL;DR: This work reports the positional cloning of Snn1, a member of the wall-associated kinase class of receptors, which is known to drive pathways for biotrophic pathogen resistance, and demonstrates that necrotrophic pathogens such as P. nodorum hijack host molecular pathways that are typically involved in resistance toBiotrophic pathogens.
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DNA metabarcoding of insects and allies: an evaluation of primers and pipelines
Guo-Jie Brandon-Mong,Han Ming Gan,Kong-Wah Sing,Ping-Shin Lee,Phaik-Eem Lim,John-James Wilson +5 more
TL;DR: It is suggested that metabarcode is slowly becoming as cheap, fast and easy as conventional DNA barcoding, and that Malaise trap metabarcoding may soon fulfill its potential, providing a thermometer for biodiversity.
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Genomic-assisted haplotype analysis and the development of high-throughput SNP markers for salinity tolerance in soybean
Gunvant Patil,Tuyen D. Do,Tri D. Vuong,Babu Valliyodan,Jeong-Dong Lee,Juhi Chaudhary,J. Grover Shannon,Henry T. Nguyen +7 more
TL;DR: High quality whole-genome resequencing was utilized on 106 diverse soybean lines and three major structural variants and allelic variation in the promoter and genic regions of the GmCHX1 gene were identified, identifying salt-tolerant/sensitive genotypes and different structural-variants.
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Two linked pairs of Arabidopsis TNL resistance genes independently confer recognition of bacterial effector AvrRps4
Simon B. Saucet,Yan Ma,Panagiotis F. Sarris,Oliver J. Furzer,Kee Hoon Sohn,Jonathan D. G. Jones +5 more
TL;DR: An R gene pair is revealed that resembles and is linked to RRS1/RPS4, designated as R RS1B/R PS4B, which confers recognition of AvrRps4 but not PopP2, which provides novel insights into paired R gene function and evolution.
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The divorce of Sporothrix and Ophiostoma: solution to a problematic relationship.
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References
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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.
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