Gene Rearrangement and Molecular Evolution in Animal Mitochondrial Genomes

Abstract

<p> Phylogenetic analysis of gene order data is a developing area, and many questions on gene orders are still unresolved. In this project, we started from the OGRe database, where we obtained the mitochondrial genome information (after some corrections), designed a logarithm correction for breakpoint distance, applied distance matrix methods to both breakpoint distance and the logarithm of breakpoint distance for gene orders, and then focused on Arthropoda phylogeny We tried many phylogenetic methods to infer Arthropod phylogeny; however, no method yielded a satisfying result. We constructed an Arthropod phylogenetic tree based on both molecular and morphological evidences. After we estimated the phylogenetic tree, we used maximum likelihood methods to estimate branch lengths for tRNAs and proteins, calculated the breakpoint numbers and inversion numbers for gene orders, and calculated the correlations among these four measures. We found that: when gene order rearrangements and mutations on sequences are small, the changes are independent, and, when the rearrangements and mutations are large, the changes seem to be correlated. The branch lengths in the tRNA and protein trees are highly correlated in low mutation situations and less correlated when mutation rates are larger. </p>