Analysis of full‐length mitochondrial DNA D‐loop sequences from Macaca fascicularis of different geographical origin reveals novel haplotypes

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. CONCLUSION 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.