DEMOGRAPHY AND PHYLOGENETIC UTILITY OF NUMT PSEUDOGENES IN THE SOUTHERN RED-BACKED VOLE(MYODES GAPPERI)

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Abstract

Nuclear copies of mitochondrial DNA fragments (numts) have been reported in a number of mammalian taxa. The inclusion of these numt pseudogenes within mitochondrial data sets can unknowingly compromise the integrity of phylogenetic, systematic, and biogeographic studies. Here, we evaluate 6 unique cytochrome-b numt sequences isolated in the southern red-backed vole (Myodes [formerly Clethrionomys] gapperi). Each sequence contains features characteristic of numt pseudogenes including premature stop codons, insertionsdeletions (indels), frame-shift substitutions, and transposable element insertions. Mitochondrial and nuclear sequences are evolving at different rates. Molecular dating indicates that this group of mitochondrial transfers originated ∽4.6 million years ago, which predates the presumptive origin of the genus. Phylogenetic analyses of mitochondrial and nuclear sequences suggest that the numts are the result of at least 1 nuclear insertion followed by subsequent duplication events, but pairwise sequence comparisons do not support this assertion. This conflict is likely the result of incomplete numt sampling from the Myodes nuclear genome. Genome sequencing efforts will ultimately provide the data needed to fully characterize numt demography in different lineages, and we predict that numts will have phylogenetic utility as informative synapomorphies in closely related species.

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