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
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Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers
Martin Sikora,Andaine Seguin-Orlando,Vitor C. Sousa,Vitor C. Sousa,Vitor C. Sousa,Anders Albrechtsen,Thorfinn Sand Korneliussen,Amy Ko,Simon Rasmussen,Isabelle Dupanloup,Isabelle Dupanloup,Philip R. Nigst,Marjolein Bosch,Marjolein Bosch,Gabriel Renaud,Morten E. Allentoft,Ashot Margaryan,Ashot Margaryan,Sergey Vasilyev,Elizaveta Veselovskaya,Svetlana B. Borutskaya,Thibaut Devièse,Dan Comeskey,Thomas Higham,Andrea Manica,Robert Foley,Robert Foley,David J. Meltzer,David J. Meltzer,Rasmus Nielsen,Laurent Excoffier,Laurent Excoffier,Marta Mirazón Lahr,Marta Mirazón Lahr,Ludovic Orlando,Ludovic Orlando,Eske Willerslev,Eske Willerslev,Eske Willerslev +38 more
TL;DR: It is shown that individuals at Sunghir derive from a population of small effective size, with limited kinship and levels of inbreeding similar to HG populations, suggesting that Upper Paleolithic social organization was similar to that of living HGs, withlimited relatedness within residential groups embedded in a larger mating network.
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Chimpanzee genomic diversity reveals ancient admixture with bonobos
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TL;DR: It is found that chimpanzee population substructure makes genetic information a good predictor of geographic origin at country and regional scales and also provides population-specific genetic markers that may be valuable for conservation efforts.
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Mitochondrial phylogenomics of Hemiptera reveals adaptive innovations driving the diversification of true bugs.
Hu Li,John Moeller Leavengood Jr.,Eric G. Chapman,Daniel Burkhardt,Fan Song,Pei Jiang,Jinpeng Liu,Xuguo Zhou,Wanzhi Cai +8 more
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Genome-wide Association Mapping Identifies a New Arsenate Reductase Enzyme Critical for Limiting Arsenic Accumulation in Plants
Dai-Yin Chao,Yi Chen,Jiugeng Chen,Shulin Shi,Zi-Ru Chen,Chengcheng Wang,John Danku,Fang-Jie Zhao,David E. Salt +8 more
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References
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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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