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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Mitochondrial genome data support the basal position of Acoelomorpha and the polyphyly of the Platyhelminthes.
Iñaki Ruiz-Trillo,Marta Riutort,H. Matthew Fourcade,Jaume Baguñà,Jeffrey L. Boore,Jeffrey L. Boore +5 more
TL;DR: Phylogenetic analysis of the amino acid sequences inferred from the sequenced genes confirms that the acoelomorph flatworms (acoels+nemertodermatids) do not belong to the Platyhelminthes, but are, instead, the most basal extant bilaterian group.
Journal ArticleDOI
Convergent neofunctionalization by positive Darwinian selection after ancient recurrent duplications of the xanthine dehydrogenase gene
TL;DR: This work shows that Aldehyde oxidase (Ao) evolved independently twice from two different Xdh paralogs, the second time in the chordates, before the diversification of vertebrates, and that the second Ao gene likely endured two periods of redundancy.
Evidence Supporting Zoonotic Transmission of Cryptosporidium spp.
Dawn C. Feltus,Catherine W. Giddings,Brianna L. Schneck,Timothy A. Monson,David M. Warshauer,John McEvoy +5 more
TL;DR: It is found that most sporadic cases of cryptosporidiosis in Wisconsin are caused by zoonotic Cryptosporidium species, indicating thatZoonotic transmission could be more frequently associated with sporadic cases in the United States.
Journal ArticleDOI
Islands within an island: phylogeography and conservation genetics of the endangered Hawaiian tree snail Achatinella mustelina.
TL;DR: Genetic data were used to define evolutionarily significant units for conservation purposes including decisions regarding placement of predator exclusion fences, captive propagation, re‐introduction and translocation in certain areas where forest cover is presently fragmented.
Journal ArticleDOI
Molecular characterization of gilthead sea bream (Sparus aurata) lipoprotein lipase. Transcriptional regulation by season and nutritional condition in skeletal muscle and fat storage tissues
Alfonso Saera-Vila,Josep A. Calduch-Giner,Pedro Gómez-Requeni,Françoise Médale,Sadasivam Kaushik,Jaume Pérez-Sánchez +5 more
TL;DR: This study is the first report in fish of a co-regulated expression of LPL in oxidative and fat storage tissues under different physiological conditions and changes in circulating triglyceride (TG) levels support the key role of L PL in the clearance of TG-rich lipoproteins.
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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