Sequences from complete mitochondrial control regions (mtDNA CR) were used
to infer phylogenetic relationships in 25 Cervinae taxa. Cervus splits into
clades that are partially discordant with current species
delimitations. Nominate Cervus elaphus includes two divergent clades
that must be referred to as species elaphus (European elaphoid deer)
and canadensis (Eurasian and North American wapitoid deer). Cervus
nippon splits into Japanese and continental plus Taiwan sika. Père
David's deer is nested within Cervus, suggesting that Elaphurus should
be merged with Cervus. European and Persian fallow deer are genetically
divergent and distinct species. Sequence length varied due to a CR-I
insertion, tandemly repeated twice in rusa and sambar deer, sika and
wapiti, and repeated up to six times in a clade of Japanese sika. Variable
copy numbers of this repeat are also fixed in different sika subspecies,
and could be used as a diagnostic marker for subspecies. Sequence
variability at the mtDNA CR is informative for defining species and
subspecies boundaries, and for locating the geographical origin of
captive-reared stocks. Natural and farmed populations of some species
have been deeply affected by human management and the conservation of
deer populations would be aided by the appropriate identification of
the different evolutionary and taxonomic units.