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
Marked host specificity and lack of phylogeographic population structure of Campylobacter jejuni in wild birds
Petra Griekspoor,Frances M. Colles,Noel D. McCarthy,Philip M. Hansbro,Chris Ashhurst‐Smith,Bjorn R. Olsen,Dennis Hasselquist,Martin C. J. Maiden,Jonas Waldenström +8 more
TL;DR: To assess C. jejuni population structure more broadly and investigate host adaptation, wild bird isolates from Europe and Australia were genotyped by multilocus sequencing and compared to the genotypes recovered from domestic animal and human isolates, indicating that domesticated animals may represent a novel niche for C.Jejuni and driving the evolution of those bacteria as they exploit this niche.
Journal ArticleDOI
Explorative Multivariate Analyses of 16S rRNA Gene Data from Microbial Communities in Modified-Atmosphere-Packed Salmon and Coalfish
TL;DR: The explorative multivariate approach gave a picture of the total microbial biodiversity in MAP fish that was more comprehensive than the picture that could be obtained previously and crucial in controlled food production when, for example, the hazard analysis of critical control points principle is used.
Journal ArticleDOI
Psychromonas ingrahamii sp. nov., a novel gas vacuolate, psychrophilic bacterium isolated from Arctic polar sea ice
TL;DR: DNA-DNA hybridization experiments revealed a level of relatedness of 37 % between strain 37T and P. antarctica, providing further support that it represents a distinct species.
Journal ArticleDOI
Historical Biogeography of the New-World Pupfish Genus Cyprinodon (Teleostei: Cyprinodontidae)
Anthony A. Echelle,Evan W. Carson,Alice F. Echelle,R. A. Van Den Bussche,Thomas E. Dowling,Axel Meyer +5 more
TL;DR: Analysis of mtDNA sequence variation indicates that the genus Cyprinodon began diverging in the Late Miocene from a common ancestor with Megupsilon, a monotypic genus on the Mesa del Norte of Mexico.
Journal ArticleDOI
Molecular phylogeography and evolutionary history of the estuarine copepod, Acartia tonsa, on the Northwest Atlantic coast
TL;DR: It is hypothesized that the observed patterns of molecular genetic diversity and structure of A. tonsa resulted from responses to historical climatic variation, including episodic range compression and displacement, and alteration of NW Atlantic coastal and estuarine environments.
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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