Journal ArticleDOI
MEGA2 : Molecular evolutionary genetics analysis software
TLDR
MEGA2 vastly extends the capabilities of MEGA version 1 by facilitating analyses of large datasets, enabling creation and analyses of groups of sequences, and expanding the repertoire of statistical methods for molecular evolutionary studies.Abstract:
Summary: We have developed a new software package, Molecular Evolutionary Genetics Analysis version 2 (MEGA2), for exploring and analyzing aligned DNA or protein sequences from an evolutionary perspective. MEGA2 vastly extends the capabilities of MEGA version 1 by: (1) facilitating analyses of large datasets; (2) enabling creation and analyses of groups of sequences; (3) enabling specification of domains and genes; (4) expanding the repertoire of statistical methods for molecular evolutionary studies; and (5) adding new modules for visual representation of input data and output results on the Microsoft Windows platform. Availability: http://www.megasoftware.net.read more
Citations
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Transgenic modification of gai or rgl1 causes dwarfing and alters gibberellins, root growth, and metabolite profiles in Populus
Victor Busov,Richard Meilan,David W. Pearce,Stewart B. Rood,Caiping Ma,Timothy J. Tschaplinski,Steven H. Strauss +6 more
TL;DR: Through transgenic modification, it is found that DELLA-less versions of GAI and RGL1 (rgl1) in a Populus tree have profound, dominant effects on phenotype, producing pleiotropic changes in morphology and metabolic profiles.
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Changes in Nitrogen-Fixing and Ammonia-Oxidizing Bacterial Communities in Soil of a Mixed Conifer Forest after Wildfire
TL;DR: The decreased microbial biomass and shift in nitrogen-fixing and ammonia-oxidizing communities were still evident in fire-impacted soils collected 14 months after the fire, and sequence types was positively correlated with soil pH and NH3-N levels, both of which were higher in burned soils.
Journal ArticleDOI
Nitrogen‐fixing chemo‐organotrophic bacteria isolated from cyanobacteria‐deprived lichens and their ability to solubilize phosphate and to release amino acids and phytohormones
C. M. Liba,F.I.S. Ferrara,Gilson P. Manfio,Fabiana Fantinatti-Garboggini,R.C. Albuquerque,C. Pavan,Patrícia Locosque Ramos,Carlos Alberto Moreira-Filho,Heloiza Ramos Barbosa +8 more
TL;DR: Cyanobacteria‐deprived lichens of the species Canoparmelia caroliniana, canoparm Amelia crozalsiana, CanopArmelia texana, Parmotrema sancti‐angeli and Parmot rema tinctorum were screened for the presence of chemo‐organotrophic nitrogen‐fixing bacteria.
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A genetic regulatory network for Xenopus mesendoderm formation.
Matthew Loose,Roger Patient +1 more
TL;DR: A genetic regulatory network summarising the functional relationships between the transcription factors (TFs) and embryonic signals involved in Xenopus mesendoderm formation is constructed and identifies conserved features of the deuterostome ancestral pathway.
Journal ArticleDOI
Burkholderia silvatlantica sp. nov., a diazotrophic bacterium associated with sugar cane and maize
Liamara Perin,Liamara Perin,Lourdes Martínez-Aguilar,Guadalupe Paredes-Valdez,José Ivo Baldani,P. Estrada-de los Santos,Veronica Massena Reis,Jesús Caballero-Mellado +7 more
TL;DR: Novel isolates were recovered from the roots of different sugar-cane varieties cultivated in diverse geographical regions of Brazil and confirmed that these isolates belong to a novel species within the genus Burkholderia, for which the name Burk holderia silvatlantica sp.
References
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Book
Molecular Evolution and Phylogenetics
Masatoshi Nei,Sudhir Kumar +1 more
TL;DR: This chapter discusses the molecular basis of evolution, the evolution of organisms based on the fossil record, and the implications of these events for phylogenetic inference.
Journal ArticleDOI
MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers
TL;DR: In this program, various methods for estimating evolutionary distances from nucleotide and amino acid sequence data, three different methods of phylogenetic inference (UPGMA, neighbor-joining and maximum parsimony) and two statistical tests of topological differences are included.
Book
Molecular Evolution: A Phylogenetic Approach
TL;DR: The Archaeology of the Genome Trees Genes: Organization, Function and Evolution Genes in Populations Measuring Genetic Change Inferring Molecular Phylogeny Models of Molecular Evolution Applications of molecular phylogenetics as mentioned in this paper.
Journal ArticleDOI
Phylogenetic test of the molecular clock and linearized trees.
TL;DR: To estimate approximate divergence times of species or species groups with molecular data, a method of constructing a linearized tree under the assumption of a molecular clock is developed and used to analyze hominoid mitochondrial DNA and drosophilid Adh gene sequences.
Journal ArticleDOI
Molecular Evolution — A Phylogenetic Approach.
TL;DR: The authors set themselves the tasks of showing how evolutionary information is written into gene sequences and describing the methods by which such information can be recovered and succeed, providing a wealth of examples and setting many of them in a historical perspective.
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The neighbor-joining method: a new method for reconstructing phylogenetic trees.
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