title: Detection of mitochondrial insertions in the nucleus (NuMts) of Pleistocene and modern muskoxen.
abstract: BACKGROUND
  Nuclear insertions of mitochondrial sequences (NuMts) have been identified in a wide variety of organisms. Trafficking of genetic material from the mitochondria to the nucleus has occurred frequently during mammalian evolution and can lead to the production of a large pool of sequences with varying degrees of homology to organellar mitochondrial DNA (mtDNA) sequences. This presents both opportunities and challenges for forensics, population genetics, evolutionary genetics, conservation biology and the study of DNA from ancient samples. Here we present a case in which difficulties in ascertaining the organellar mtDNA sequence from modern samples hindered their comparison to ancient DNA sequences.
  
  
  RESULTS
  We obtained mitochondrial hypervariable region (HVR) sequences from six ancient samples of tundra muskox (Ovibos moschatus) that were reproducible but distinct from modern muskox sequences reported previously. Using the same PCR primers applied to the ancient specimens and the primers used to generate the modern muskox DNA sequences in a previous study, we failed to definitively identify the organellar sequence from the two modern muskox samples tested. Instead of anticipated sequence homogeneity, we obtained multiple unique sequences from both hair and blood of one modern specimen. Sequencing individual clones of a >1 kb PCR fragment from modern samples did not alleviate the problem as there was not a consistent match across the entire length of the sequences to Ovibos when compared to sequences in GenBank.
  
  
  CONCLUSIONS
  In specific taxa, due to nuclear insertions some regions of the mitochondrial genome may not be useful for the characterization of modern or ancient DNA.
authors.affiliation: Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA. sk2059@columbia.edu <sk2059@columbia.edu>
authors.forename: Sergios-Orestis
authors.initials: SO
authors.lastname: Kolokotronis
authors.forename: Ross D E
authors.initials: RD
authors.lastname: Macphee
authors.forename: Alex D
authors.initials: AD
authors.lastname: Greenwood
mesh_terms: D000818:Animals; D003001:Cloning, Molecular; D022801:Complementarity Determining Regions / Q000235:genetics*; D004251:DNA Transposable Elements / Q000235:genetics*; D004272:DNA, Mitochondrial / Q000235:genetics*; D019143:Evolution, Molecular; D006239:Haplotypes; D010163:Paleontology; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012418:Ruminants / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D022801:Complementarity Determining Regions; D004251:DNA Transposable Elements; D004272:DNA, Mitochondrial