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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Analysis of microbial communities developed on the fouling layers of a membrane-coupled anaerobic bioreactor applied to wastewater treatment
TL;DR: Significant differences in structure of the Bacteria communities were observed amongst the different fouling layers analyzed in the UASB membranes, particularly following a chemical cleaning step (NaClO), while the Archaea communities retained more similarity in all samples.
Journal ArticleDOI
A global study of forensically significant calliphorids: implications for identification.
TL;DR: This study used phylogenetic analysis to assess the species status of 27 forensically important calliphorid species based on 1167 base pairs of the COI gene of 119 specimens from 22 countries, and confirmed the utility of theCOI gene in identifying most species.
Journal ArticleDOI
Genetic diversity of hydrogen-producing bacteria in an acidophilic ethanol-H2-coproducing system, analyzed using the [Fe]-hydrogenase gene.
TL;DR: The ability to produce H2 gas during anaerobic fermentation was previously thought to be restricted to a few species within the genera Clostridium and Enterobacter.
Journal ArticleDOI
Mitochondrial Sequence Reveals High Levels of Gene Flow Between Breeds of Domestic Sheep from Asia and Europe
J. R. S. Meadows,Kui Li,Juha Kantanen,Miika Tapio,W. Sipos,V. C. Pardeshi,Vidya S. Gupta,Jorge H. Calvo,V. Whan,B. Norris,James W. Kijas +10 more
TL;DR: The distribution of haplotypes indicates sheep appear to have the weakest population structure and the highest rate of intercontinental dispersal of any domestic animal reported to date.
Journal ArticleDOI
Dating Dispersal and Radiation in the Gymnosperm Gnetum (Gnetales)--clock Calibration When Outgroup Relationships Are Uncertain
Hyosig Won,Susanne S. Renner +1 more
TL;DR: In this article, the effects of resolved and polytomous input topologies in a rate-heterogeneous sequence data set for Gnetum, a member of the seed plant lineage Gnetales, were explored.
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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