With the aim of understanding the evolutionary history of genes and organisms and the mechanisms of evolution, two mutually related research projects are proposed. (l) Statistical methods for phylogenetic inference. Phylogenetic analysis of DNA sequences has become an important tool for studying population genetics and evolution. In this analysis the neighbor- joining, maximum parsimony (MP), and maximum likelihood (ML) methods are commonly used. However, the MP and ML methods are very time-consuming when the number of sequences used is large. In the proposed research, we plan to explore fast MP and ML algorithms that give a reliable bootstrap consensus tree (close to the true tree-rather than to the optimal tree) by using computer simulation. Efficient algorithms for constructing linearized trees with a reliable timescale will also be developed. In addition, a computer program package for studying molecular evolution will be developed. (2) Statistical analysis of genome diversity. Using abundant DNA sequence data recently generated by the genome projects, we plan to study the evolution and maintenance of genome diversity in different groups of organisms. We are particularly interested in understanding the evolution and maintenance of genetic variability of the major histocompatibility complex molecules, immunoglobulins, and T-cell receptors, all of which are concerned with generation of antibody diversity. We plan to conduct phylogenetic analyses of these multigene families using sequence data from diverse groups of vertebrate species. Special attention will be given to the coevolution of the variable region genes of immunoglobulins and T-cell receptors. We are also interested in extending our phylogenetic analysis to several multigene families that produce highly conserved proteins (e.g., ubiquitin, histone, and globins) to understand whether the highly conserved proteins are due to concerted evolution or to purifying selection or combinations of several factors.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
2R01GM020293-29
Application #
6046040
Study Section
Genetics Study Section (GEN)
Program Officer
Eckstrand, Irene A
Project Start
1990-08-01
Project End
2004-01-31
Budget Start
2000-02-01
Budget End
2001-01-31
Support Year
29
Fiscal Year
2000
Total Cost
$188,757
Indirect Cost
Name
Pennsylvania State University
Department
Biology
Type
Schools of Arts and Sciences
DUNS #
City
University Park
State
PA
Country
United States
Zip Code
16802
Nozawa, Masafumi; Miura, Sayaka; Nei, Masatoshi (2012) Origins and evolution of microRNA genes in plant species. Genome Biol Evol 4:230-9
Nei, Masatoshi; Nozawa, Masafumi (2011) Roles of mutation and selection in speciation: from Hugo de Vries to the modern genomic era. Genome Biol Evol 3:812-29
Miura, Sayaka; Nozawa, Masafumi; Nei, Masatoshi (2011) Evolutionary changes of the target sites of two microRNAs encoded in the Hox gene cluster of Drosophila and other insect species. Genome Biol Evol 3:129-39
Nei, Masatoshi; Suzuki, Yoshiyuki; Nozawa, Masafumi (2010) The neutral theory of molecular evolution in the genomic era. Annu Rev Genomics Hum Genet 11:265-89
Das, Sabyasachi; Mohamedy, Uzra; Hirano, Masayuki et al. (2010) Analysis of the immunoglobulin light chain genes in zebra finch: evolutionary implications. Mol Biol Evol 27:113-20
Takezaki, Naoko; Nei, Masatoshi; Tamura, Koichiro (2010) POPTREE2: Software for constructing population trees from allele frequency data and computing other population statistics with Windows interface. Mol Biol Evol 27:747-52
Nozawa, Masafumi; Miura, Sayaka; Nei, Masatoshi (2010) Origins and evolution of microRNA genes in Drosophila species. Genome Biol Evol 2:180-9
Nozawa, Masafumi; Suzuki, Yoshiyuki; Nei, Masatoshi (2009) Reliabilities of identifying positive selection by the branch-site and the site-prediction methods. Proc Natl Acad Sci U S A 106:6700-5
Das, Sabyasachi; Nikolaidis, Nikolas; Nei, Masatoshi (2009) Genomic organization and evolution of immunoglobulin kappa gene enhancers and kappa deleting element in mammals. Mol Immunol 46:3171-7
Xu, Guixia; Ma, Hong; Nei, Masatoshi et al. (2009) Evolution of F-box genes in plants: different modes of sequence divergence and their relationships with functional diversification. Proc Natl Acad Sci U S A 106:835-40

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