With the aim of understanding the mechanisms of DNA evolution systematic statistical analyses of DNA sequence data will be conducted. Particular attention will be given to the following problems: 1. Evolution of apolipoprotein genes. a. The phylogenetic relationships among apolipoprotein genes will be reconstructed and the evolutionary history of internal repeats in related genes will be inferred. b. Rates of nucleotide substitution in various functional domains will be computed to infer the stringency of structural requirements of various functions such as lipid binding, lipoprotein lipase activation, etc. 2. Evolution of somatostatin genes. a. Did the two duplicate genes in anglerfish and those in catfish arise from a single duplication event? b. What is the divergence time between the 2 genes in bovine? c. How well are the different peptide domains in prosomatostatin, particularly those with unknown function, conserved in evolution? 3. Evolution of cytochrome c genes and pseudogenes. a. What are the phylogenetic relationships among the 7 human, 3 mouse and 3 rat pseudogenes? Were some of them derived from duplication of pseudogenes? Did any of the mouse and rat pseudogenes arise before the mouse-rat split? b. What are the duplication dates for the 2 genes in yeast and the 2 genes in Drosophila? Do these duplicate genes evolve at similar rates? 4. Rates of nucleotide substitution in various regions of nuclear DNA, mitochondrial DNA (mtDNA), and chloroplast DNA (cpDNA). The rates will be compared among different DNA regions in the same type of genomes and among the three types of genomes in the same kind of regions. Causes for differences in substitution rate will be inferred. 5. Patterns of nucleotide substitution in various regions of nuclear DNA, mtDNA and cpDNA. The patterns from the three kinds of genomes will be compared and causes for differences in pattern will be inferred. 6. Molecular clock. a. Is there a generation-time effect on substitution rates? b. Do organisms with similar generation times have similar substitution rates? c. How often does accelerated evolution occur following gene duplication? 7. Deletions and insertions in sequence evolution: their frequency and location of occurrence, the size of gap events and the relative frequencies of spontaneous deletion and insertion.
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