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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Gene lineages and eastern North American palaeodrainage basins: phylogeography and speciation in salamanders of the Eurycea bislineata species complex.
TL;DR: The molecular genetic results corroborate geological and faunistic evidence suggesting that palaeodrainage connections altered by glacial advances and headwater erosion occurring between the mid‐Miocene and Pleistocene epochs explain regional patterns of biodiversity in eastern North American streams.
Journal ArticleDOI
Analysis of Primate Genomic Variation Reveals a Repeat-Driven Expansion of the Human Genome
Ge Liu,Nisc Comparative Sequencing Program,Shaying Zhao,Jeffrey A. Bailey,S. Cenk Sahinalp,Can Alkan,Eray Tüzün,Eric D. Green,Evan E. Eichler +8 more
TL;DR: Orthologous comparisons with the chimpanzee suggest that the human genome continues to significantly expand due to shifts in retrotransposition activity, and it is estimated that human euchromatin has expanded 30 Mb and 550 Mb compared to the primate genomes of chimpanzee and lemur, respectively.
Journal ArticleDOI
New Molecular Screening Tools for Analysis of Free-Living Diazotrophs in Soil
TL;DR: A fixed-primer-site approach with six PCR protocols using less degenerate to nondegenerate primer sets that all amplify the same nifH fragment as a previously published PCR protocol for universal amplification, which was better suited to distinguish between diazotroph populations in the different soils.
Journal ArticleDOI
Production and structural characterization of surfactin (C14/Leu7) produced by Bacillus subtilis isolate LSFM-05 grown on raw glycerol from the biodiesel industry
Andreia Fonseca de Faria,Diego Stéfani Teodoro-Martinez,Geraldo Nazareno de Oliveira Barbosa,Boniek G. Vaz,Isis Serrano Silva,Jerusa S. Garcia,Marcos Rogério Tótola,Marcos N. Eberlin,Matthew J. Grossman,Oswaldo Luiz Alves,Lucia Regina Durrant +10 more
TL;DR: In this paper, the synthesis of biosurfactant by Bacillus subtilis LSFM-05 was carried out using raw glycerol, obtained from a vegetable oil biodiesel plant in Brazil, as the sole carbon source.
Journal ArticleDOI
Polymorphisms within the prnD and pltC genes from pyrrolnitrin and pyoluteorin-producing Pseudomonas and Burkholderia spp.
TL;DR: In this article, a 16S rDNA-based phylogenetic analysis of Pseudomonas and Burkholderia species was performed using the restriction fragment length polymorphisms (RFLP) analysis.
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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