Abstract
The utility and reliability of mitochondrial DNA sequences in phylogenetic and phylogeographic studies may be compromised by widespread and undetected nuclear mitochondrial copies (numts) as well as heteroplasmy within individuals. Both numts and heteroplasmy are likely to be common across diverse taxa yet few studies have characterised their frequencies and variation at the intra-specific level. Here we report the presence of both numts and heteroplasmy in the mitochondrial control region of the Chinese horseshoe bat Rhinolophus sinicus. In total we generated 123 sequences from 18 bats, which contained two different numt clades (i.e. Numt-1 and Numt-2) and one mtDNA clade. The sequence divergence between Numt-1 and Numt-2 was 16.8% and each numt type was found in all four R. sinicus taxa, suggesting either two ancient translocations of mitochondrial DNA into the nucleus from the same source taxon, or a single translocation from different source taxa that occurred before the split of R. sinicus into different lineages. Within the mtDNA clade, phylogenetic relationships among the four taxa of R. sinicus were similar to those seen in previous results. Based on PCR comparisons, heteroplasmy was inferred between almost all individuals of R. sinicus with respect to sequence variation. Consistent with introgression of mtDNA between Central sinicus and septentrionalis, individuals from these two taxa exhibited similar signatures of repeated sequences in the control region. Our study highlights the importance of testing for the presence of numts and heteroplasmy when applying mtDNA markers to phylogenetic studies.
Highlights
IntroductionMany mitochondrial sequences have been incorporated into the nuclear genome, and the presence of these so-called nuclear mitochondrial copies (numts, [3]) has been recorded in diverse taxa [4,5,6]
Mitochondrial DNA has long been widely used as a source of molecular markers in animal phylogenetic and phylogeographic studies [1,2] due to its high mutation rate and associated intraspecific polymorphism, general assumed lack of recombination [1], and its high copy number within cells.many mitochondrial sequences have been incorporated into the nuclear genome, and the presence of these so-called nuclear mitochondrial copies has been recorded in diverse taxa [4,5,6]
Numts and mitochondrial heteroplasmy have been recorded in multiple species groups [4,6,43], few studies have investigated their patterns at the intra-specific level
Summary
Many mitochondrial sequences have been incorporated into the nuclear genome, and the presence of these so-called nuclear mitochondrial copies (numts, [3]) has been recorded in diverse taxa [4,5,6]. Numts can obscure signals from real mtDNA [4], especially when the translocation of mtDNA to the nucleus has occurred recently. In such cases, insufficient time may have lapsed for mutations to accrue via relaxed selection, leading numts to be amplified by primers designed for their mitochondrial counterparts [7,8]. Potential nuclear copies of mitochondrial coding segments are often inferred from the presence of frameshift mutations and/or stop codons [11], these mutations cannot be used to detect nuclear copies of the mitochondrial control region, in which they can occur naturally
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