title: Analysis of full-length mitochondrial DNA D-loop sequences from Macaca fascicularis of different geographical origin reveals novel haplotypes.
abstract: BACKGROUND
  Cynomolgus macaques are indigenous to Asia occupying a range of geographical areas. A non-indigenous population established on Mauritius approximately 500 years ago. Mauritian cynomolgus macaques are recognised as having low genetic diversity compared to Indonesian macaques, from which they originated. As cynomolgus macaques are widely used as a biomedical model, there have been many studies of their genetic relationships. However, population diversity and relationships have only been assessed through analysis of either the hypervariable region I or II separately within the D-loop region of the mitochondrial genome in these macaques.
  
  
  METHODS
  Using sequencing, we defined haplotypes encompassing the full D-loop sequence for Mauritian and Indonesian cynomolgus macaques.
  
  
  RESULTS
  We evaluated the haplotype relationships by constructing a median-joining network based on full-length D-loop sequences, which has not been reported previously.
  
  
  CONCLUSIONS
  Our data allow a complete D-loop haplotype, including a hereto unreported polymorphic region, to be defined to aid the resolution of populations of cynomolgus macaques and which highlights the value in analysing both D-loop hypervariable regions in concert.
authors.affiliation: Division of Virology, National Institute for Biological Standards and Control, Medicines and Healthcare Products Regulatory Authority, South Mimms, Hertfordshire, UK.
authors.forename: Anjna
authors.initials: A
authors.lastname: Badhan
authors.affiliation: Division of Biological Anthropology, Department of Archaeology and Anthropology, University of Cambridge, Cambridge, UK.
authors.forename: Christina A
authors.initials: CA
authors.lastname: Eichstaedt
authors.affiliation: Division of Virology, National Institute for Biological Standards and Control, Medicines and Healthcare Products Regulatory Authority, South Mimms, Hertfordshire, UK.
authors.forename: Neil M
authors.initials: NM
authors.lastname: Almond
authors.affiliation: Division of Biological Anthropology, Department of Archaeology and Anthropology, University of Cambridge, Cambridge, UK.
authors.forename: Leslie A
authors.initials: LA
authors.lastname: Knapp
authors.affiliation: Division of Virology, National Institute for Biological Standards and Control, Medicines and Healthcare Products Regulatory Authority, South Mimms, Hertfordshire, UK.
authors.forename: Nicola J
authors.initials: NJ
authors.lastname: Rose
mesh_terms: D000818:Animals; D001483:Base Sequence; D004272:DNA, Mitochondrial / Q000737:chemistry* / Q000235:genetics*; D014644:Genetic Variation; D006239:Haplotypes / Q000235:genetics*; D007214:Indonesia; D008252:Macaca fascicularis / Q000235:genetics*; D008436:Mauritius; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000662:veterinary; D011110:Polymorphism, Genetic / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D004272:DNA, Mitochondrial
keywords: Indonesia; Mauritius; control region; cynomolgus macaque; diversity; mtDNA