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SUDHIR KUMAR Professor Ph.D., 1996, Pennsylvania State University Send e-mail to s.kumar@asu.edu

Molecular Evolution of genes, genomes, and developmental complexity

The scope of molecular evolutionary biology has expanded greatly with advances in laboratory techniques and development of statistical methods for analyzing molecular data. Molecular evolutionary analyses have provided valuable insight into the short- term and long-term evolutionary histories of organisms, relative rates of gene and genome evolution, adaptive evolution at molecular level, and the striking conservation of developmental genes in diverse animals. The rapid increase in the amount of DNA sequences and other molecular data is allowing us to study these problems using larger datasets. To facilitate molecular evolutionary analyses using large data sets, we are developing new computational and statistical methods and easy-to-use computer softwares. Interdisciplinary research projects in my laboratory include: (1) Revision and expansion of Molecular Evolutionay Genetics Analysis [MEGA] Software for Windows 95 and NT, (2) Multigene analysis for studying dynamics of gene and genome evolution and for establishing a molecular timescale of animal evolution, (3) Comparative sequence analysis to study the molecular basis of functional diversification of genes leading to developmental complexity in diverse organisms, and (4) Development of new phylogenetic inference methods and examination of their utility in recovering correct phylogenies by means of computer simulation.

Selected Publications

Tamura K, Subramanian S & Kumar S (2004) Temporal patterns of fruit fly evolution revealed by mutation clocks. Molecular Biology and Evolution 21:36-44.

Miller MP, Parker JD, Rissing SW, & Kumar S (2003) Quantifying the intragenic distribution of disease mutations. Annals of Human Genetics 67:567-579.

Hedges SB & Kumar S (2003) Genomic clocks and evolutionary timescales. Trends in Genetics 19:200-206.

Rosenberg MS & Kumar S (2003) Heterogeneity of nucleotide frequencies among evolutionary lineages and phylogenetic inference. Molecular Biology & Evolution 20:610-621.

Rosenberg MS & Kumar S (2003) Patterns of transitional mutation biases within and among mammalian genomes. Molecular Biology & Evolution 20:988-993.

Subramanian S & Kumar S (2003) Neutral substitutions occur as a faster rate in exons than in noncoding DNA in primate genomes. Genome Research 13:838-844.

Kumar S, Jayaraman K, Panchanathan S, Gurunathan R, Marti-Subirana A & Newfeld SJ (2002) BEST: A novel computational approach for comparing gene expression patterns from early stages of Drosophila melanogaster development. Genetics 162: 2037-2047.

Hedges SB & Kumar S (2002) Vertebrate genomes compared. Science 297: 1283-1285.

Tamura K & Kumar S (2002) Evolutionary distance estimation under heterogeneous substitution pattern among lineages. Molecular Biology & Evolution 19:1727-1736.

Kumar S & Subramanian S (2002) Mutation rates in mammalian genomes. Proceedings of the National Academy of Sciences (USA) 99:803-808.

Miller MP & Kumar S (2001) Understanding human disease mutations through the use of interspecific genetic variation. Human Molecular Genetics 10: 2319-2328.

Kumar S, Tamura K, Jakobsen IB, & Nei M (2001) MEGA2: Molecular Evolutionary Genetics Analysis software. Bioinformatics 17:1244-1245.

Rosenberg MS & Kumar S (2001) Incomplete taxon sampling is not a problem for phylogenetic inference. Proceedings of the National Academy of Sciences (USA) 98:10751-10756.

Kumar S and Gadagkar SR (2001) Disparity Index: A simple statistic to measure and test the homogeneity of substitution pattern between molecular sequences. Genetics 158:1321-1327.

Kumar S, Gadagkar SR, Filipski A & Gu X (2001) Determination of the number of conserved chromosomal segments between species. Genetics 157:1387-1395.

Hedrick P & Kumar S (2001) Mutations and linkage disequilibrium in Human mtDNA. European Journal of Human Genetics 9:969-972.

Nei M & Kumar S (2000) Molecular Evolution and Phylogenetics. Oxford University Press, New York. (333 pp).

Kumar S & Gadagkar SR (2000) Efficiency of the Neighbor-Joining method in reconstructing deep and shallow evolutionary relationships in large phylogenies. Journal of Molecular Evolution 51:544-553.

Kumar S, Hedrick P, Dowling T, & Stoneking M (2000) Questioning evidence for recombination in human mitochondrial DNA. Science 288:1931a.

Kumar S, Mitnik C, Valente G & Floyd-Smith G (2000) Expansion and molecular evolution of the interferon-induced 2'-5' oligoadenylate synthetase gene family. Molecular Biology & Evolution 17:738-750.

Newfeld SJ, Wisotzkey RG & Kumar S (1999) Molecular evolution of a development pathway: Phylogenetic analyses of transforming growth factor- family ligands, receptors, and Smad signal transducers. Genetics 152:783-795.

Nei M, Kumar S & Takahashi K (1998) The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small. Proceedings of the National Academy of Sciences (USA) 95:12390-12397.

Kumar S & Hedges SB (1998) A molecular timescale for vertebrate evolution.Nature 392:917-920.

Balczarek KA, Lai Z-C & Kumar S (1997) Evolution and functional diversification of the Paired-box (Pax) DNA-binding domains. Molecular Biology & Evolution 14: 829-842.

Kumar S & Rzhetsky A (1996) Evolutionary relationships of eukaryotic kingdoms. Journal of Molecular Evolution 42:183-193.

Kumar S, Balczarek KA & Lai Z-C (1996) Evolution of the hedgehog gene family. Genetics 142:965-972.

Kumar S (1996) Patterns of nucleotide substitution in mitochondrial protein coding genes of vertebrates. Genetics 143:537-548.

Kumar S (1996) A stepwise algorithm for finding minimum evolution trees. Molecular Biology & Evolution 13:584-593.

Hedges SB, Parker PH, Sibley CG & Kumar S (1996) Continental breakup and the ordinal diversification of birds and mammals. Nature 381:226-229.

Yang Z, Kumar S & Nei M (1995) A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141:1641-1650.

Kumar S, Tamura K & Nei M (1994) MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers. Computer Applications in Biosciences 10:189-191.

Hedges SB, Kumar S, Tamura K & Stoneking M (1992) Human origins and analysis of mitochondrial DNA sequences. Science 255:737-739.