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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Journal ArticleDOI
Duplication of growth hormone receptor (GHR) in fish genome: gene organization and transcriptional regulation of GHR type I and II in gilthead sea bream (Sparus aurata).
TL;DR: Searching by RT-PCR for GHR type II in trout, gilthead sea bream, European sea bass, and turbot provides suitable evidence for tissue-specific regulation of fish GHRs, but further research is needed to determine whether these duplicated genes are evolved in a new or redundant fashion.
Journal ArticleDOI
Molecular diversity of nitrite reductase genes (nirK) in nitrifying bacteria.
Jason L. Cantera,Lisa Y. Stein +1 more
TL;DR: Insight is provided to the use of nirK genes for molecular diversity studies, a framework to resolve the origins and diversification of nitrite reduction among the nitrifiers is established, and the database of nIRK orthologues is expanded.
Characterization of a novel P[24], G11 human group A rotavirus
Mustafizur Rahman,Tasnim Azim,Jelle Matthijnssens,G Poddar,Sofie De Vos,David A. Sack,Marc Van Ranst +6 more
Journal ArticleDOI
Multilocus Sequence Typing for Differentiation of Strains of Candida tropicalis
Arianna Tavanti,Amanda Denise Davidson,Elizabeth M. Johnson,Martin C. J. Maiden,Duncan James Shaw,Neil A. R. Gow,Frank C. Odds +6 more
TL;DR: Five of six isolates in one cluster that may acquire clade status were resistant to flucytosine, and this study adds C. tropicalis to Candida albicans and Candida glabrata as Candida species for which a multilocus sequence typing (MLST) system has been set up.
Journal ArticleDOI
Effects of historical climate change, habitat connectivity, and vicariance on genetic structure and diversity across the range of the red tree vole ( Phenacomys longicaudus ) in the Pacific Northwestern United States.
TL;DR: Examination of phylogeographical patterns of red tree voles in western Oregon demonstrated distinct North/South genetic discontinuities that have been attributed to Pleistocene glaciation, and suggested the presence of two haplotype groups corresponding to northern and southern regions of P. longicaudus.
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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