Assessing the Relative Rate of (Mitochondrial) Genomic Change

Abstract

I report a framework for assessing whether one mitochondrial genome is significantly more rearranged than another. This relative rate of gene rearrangement test (RGR) behaves according to expectation, distinguishing between highly rearranged and mildly rearranged insect mitochondrial genomes. It may be more broadly applied to assess the relative rate of nuclear gene rearrangement. T HE organization of the mitochondrial genome amongMartin and Palumbi 1993; Rand 1994)-have been greatly facilitated by the availability of a test to compare Metazoa is remarkably uniform. Of the Ͼ300 entirely sequenced mitochondrial genomes, the vast majority statistically the relative rate of nucleotide substitution.Here, I present the framework for a relative rate of gene contain the same 37 genes, are circular, and have very little noncoding sequence (Boore 1999). Early comparrearrangement test (RGR). The RGR assesses whether one genome is significantly more rearranged than anisons suggested that the relative positions of genes were similarly highly conserved, at least when comparisons other. Although developed for comparisons of the mitochondrial genome, it may also prove useful for assessing within phyla were made (Moritz et al. 1987). However, more recent studies have exposed many exceptions to the statistical significance of differences in the relative rate of nuclear gene rearrangement (e.g., Coghlan and this prediction ( et al. 1999) genome rearrangement, but in both cases no attempts at nomic lineages [e.g., within the Hymenoptera, Apocrita (Dowton and Austin 1999) and the nonhemipteran assessing the significance of any differences were made. The framework for the RGR follows that developed hemipteroids (Shao et al. 2001b), and the Crustacea, Anomura (Morrison et al. 2002)], leading to speculaby Tajima (1993) to assess the relative rate of nucleotide substitution between two sequences. A comparison of tion that the rate of gene rearrangement is not uniform, but may sporadically increase or decrease during evolutwo sequences can reveal only the absolute number of differences between those two sequences. To determine tion.However, there is currently no means of assessing the whether one sequence is accumulating more substitusignificance of any rearrangement rate increase or detions than another, reference to a third sequence is crease-either lineages have highly rearranged genomes necessary (Figure 1). or they do not. It would be extremely useful to identify m 1 (the number of substitutions between sequence 1 the branches of the metazoan mitochondrial phylogeny and the reference sequence) and m 2 can be measured with significantly increased rates of rearrangement, as directly, and the relative rate of nucleotide divergence this would facilitate investigations of the underlying facis estimated by subtracting these two values. The signifitors associated with such rate changes. Analogously, cance of this value is assessed by performing a chi-square studies identifying factors associated with increased test, with 1 d.f.,...

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