Two genetically distinct lineages of the sika deer, Cervus nippon, in Japanese islands: Comparison of mitochondrial D-loop region sequences

To investigate genetic diversity among populations of the sika deer, Cervus nippon, nucleotide sequences (705-824 bases) of the mitochondrial D-loop r egions were determined in animals from 13 localities in the Japanese island s. Phylogenetic trees constructed by the sequences indicated that the Japan ese sika deer is separated into two distinct lineages: the northern Japan g roup (the Hokkaido island and most of the Honshu mainland) and the southern Japan group (a part of the southern Honshu mainland, the Kyushu island, an d small islands around the Kyushu island). All sika deer examined in this s tudy shared four to seven units of repetitive sequences (37 to 40 bases eac h) within the D-loop sequences. The number of tandem repeats was different among the populations, and it was specific to each population. Six or seven repeats occurred in populations of the northern Japan group, while four or five repeats occurred in populations of the southern Japan group. Each rep eat unit included several nucleotide substitutions, compared with others, a nd 26 types were identified from 31 animals. Sequences of the first, second , and third units in arrays were clearly different between the northern and the southern groups. Based on these D-loop data, colonization and separati on of the sika deer populations in the Japanese islands were estimated to h ave occurred less than 0.5 million years before present. Our results provid e an invaluable insight into better understanding the evolutionary history, phylogeny, taxonomy, and population genetics of the sika deer. (C) 1999 Ac ademic Press.