The mitochondrial control region of Cervidae: evolutionary patterns and phylogenetic content

The mitochondrial control region (CR) sequence, also known as the D- loop,has been determined for six Cervidae (Artiodactyla, Ruminantia): the redand fallow deers (subfamily Cervinae), the brocket deer and two roe deers(subfamily Odocoileinae), and the Chinese water deer (Hydropotinae). Thesenew sequences have been aligned with available cervid and bovidorthologues. Comparative analyses indicate that the 5'- peripheral domainexhibits a 75-bp length polymorphism near sequences associated with thetermination of the H-strand replication. The New World Odocoileinae possessthe longest cervid CR due to the presence of an additional 47-bp tandemrepeat, located in the 3'-peripheral domain, downstream of the initiationsite for H-strand replication (OH) and the first conserved sequence block(CSB-1). This insertion represents a duplication spanning the OH to CSB-1region and constitutes an exclusive synapomorphy for New WorldOdocoileinae. Phylogenetic analyses of the complete CR support theparaphyly of antlered deers due to the nesting of the antlerless Hydropoteswithin Odocoileinae. Capreolus is the closest relative of Hydropotes, andthe divergence of this Old World Odocoileinae clade may have occurredbetween 8.7 and 10.4 MYA. The conserved central domain of CR can be alignedacross ungulates and indicates the Pecora monophyly, their closeassociation with cetaceans, and the earlier emergence of suiformes.