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My Memory of Walter Fitch (1929–2011) and Starting Molecular Biology and Evolution

Masatoshi Nei 0 0 Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University - More than 3 years have passed after Walter Fitch died on March 10, 2011 ... came up with the proposal of President Walter Fitch, President-elect Masatoshi Nei, Secretary and Treasurer Linda Maxson, New Editor Barry Hall, and Interim Councilor Caro-Beth Stewart. This slate was

Origins and Evolution of MicroRNA Genes in Plant Species

MicroRNAs (miRNAs) are among the most important regulatory elements of gene expression in animals and plants. However, their origin and evolutionary dynamics have not been studied systematically. In this paper, we identified putative miRNA genes in 11 plant species using the bioinformatic technique and examined their evolutionary changes. Our homology search indicated that no...

Roles of Mutation and Selection in Speciation: From Hugo de Vries to the Modern Genomic Era

Masatoshi Nei 0 Masafumi Nozawa 0 0 Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University One of the most important problems in evolutionary biology

Evolutionary Changes of the Target Sites of Two MicroRNAs Encoded in the Hox Gene Cluster of Drosophila and Other Insect Species

Sayaka Miura 0 Masafumi Nozawa 0 Masatoshi Nei 0 0 Institute of Molecular Evolutionary Genetics, Department of Biology, Pennsylvania State University MicroRNAs (miRs) are noncoding RNAs that

Genomic Drift and Evolution of Microsatellite DNAs in Human Populations

Naoko Takezaki 0 Masatoshi Nei 0 Life Science Research Center, Kagawa University , Japan ; and Department of Biology, Institute of Molecular Evolutionary Genetics, Pennsylvania State University In

POPTREE2: Software for Constructing Population Trees from Allele Frequency Data and Computing Other Population Statistics with Windows Interface

Currently, there is a demand for software to analyze polymorphism data such as microsatellite DNA and single nucleotide polymorphism with easily accessible interface in many fields of research. In this article, we would like to make an announcement of POPTREE2, a computer program package, that can perform evolutionary analyses of allele frequency data. The original version...

Origins and Evolution of MicroRNA Genes in Drosophila Species

Masafumi Nozawa 0 Sayaka Miura 0 Masatoshi Nei 0 0 Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, University Park MicroRNAs (miRs) regulate

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building...

Extensive Gains and Losses of Olfactory Receptor Genes in Mammalian Evolution

Odor perception in mammals is mediated by a large multigene family of olfactory receptor (OR) genes. The number of OR genes varies extensively among different species of mammals, and most species have a substantial number of pseudogenes. To gain some insight into the evolutionary dynamics of mammalian OR genes, we identified the entire set of OR genes in platypuses, opossums...

Ultraconserved coding regions outside the homeobox of mammalian Hox genes

Background All bilaterian animals share a general genetic framework that controls the formation of their body structures, although their forms are highly diversified. The Hox genes that encode transcription factors play a central role in this framework. All Hox proteins contain a highly conserved homeodomain encoded by the homeobox motif, but the other regions are generally...

Analysis of the Immunoglobulin Light Chain Genes in Zebra Finch: Evolutionary Implications

All jawed vertebrates produce immunoglobulins (IGs) as a defense mechanism against pathogens. Typically, IGs are composed of two identical heavy chains (IGH) and two identical light chains (IGL). Most tetrapod species encode more than one isotype of light chains. Chicken is the only representative of birds for which genomic information is currently available and is an exception...

The origins and early evolution of DNA mismatch repair genes—multiple horizontal gene transfers and co-evolution

To understand the evolutionary process of the DNA mismatch repair system, we conducted systematic phylogenetic analysis of its key components, the bacterial MutS and MutL genes and their eukaryotic homologs. Based on genome-wide homolog searches, we identified three new MutS subfamilies (MutS3-5) in addition to the previously studied MutS1 and MutS2 subfamilies. Detailed...

Evolutionary dynamics of olfactory and other chemosensory receptor genes in vertebrates

The numbers of functional olfactory receptor (OR) genes in humans and mice are about 400 and 1,000 respectively. In both humans and mice, these genes exist as genomic clusters and are scattered over almost all chromosomes. The difference in the number of genes between the two species is apparently caused by massive inactivation of OR genes in the human lineage and a substantial...

MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences

Sudhir Kumar Masatoshi Nei Joel Dudley Koichiro Tamura The Molecular Evolutionary Genetics Analysis (MEGA) software is a desktop application designed for comparative analysis of homologous gene ... of the Center for Evolutionary Functional Genomics at Arizona State University, AZ, USA. Masatoshi Nei is one of the founders of molecular evolutionary genetics and pursues statistical analysis of

Evolutionary Change of the Numbers of Homeobox Genes in Bilateral Animals

Jongmin Nam 0 Masatoshi Nei 0 0 Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University It has been known that the conservation or diversity of homeobox

Origins and Evolution of the Formin Multigene Family That Is Involved in the Formation of Actin Filaments

In eukaryotes, the assembly and elongation of unbranched actin filaments is controlled by formins, which are long, multidomain proteins. These proteins are important for dynamic cellular processes such as determination of cell shape, cell division, and cellular interaction. Yet, no comprehensive study has been done about the origins and evolution of this gene family. We therefore...

MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0

Koichiro Tamura Joel Dudley Masatoshi Nei Sudhir Kumar We announce the release of the fourth version of MEGA software, which expands on the existing facilities for editing DNA sequence data from

False-Positive Selection Identified by ML-Based Methods: Examples from the Sig1 Gene of the Diatom Thalassiosira weissflogii and the tax Gene of a Human T-cell Lymphotropic Virus

Yoshiyuki Suzuki 0 Masatoshi Nei 0 Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Japan; and Institute of Molecular Evolutionary Genetics and Department of

Concerted and Nonconcerted Evolution of the Hsp70 Gene Superfamily in Two Sibling Species of Nematodes

Nikolas Nikolaidis 0 Masatoshi Nei 0 0 Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University We have identified the Hsp70 gene superfamily of the

Birth-and-Death Evolution in Primate MHC Class I Genes: Divergence Time Estimates

Helen Piontkivska 0 Masatoshi Nei 0 0 Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University The major histocompatibility complex (MHC) is a multigene