本試驗目的解讀臺灣梅花鹿（Cervus nippon taiounanus , Formosan Sika deer）、臺灣水鹿(Rusa unicolor swinhoei , Formosan sambar) 、蘭嶼豬 （Sus scrofa vittatus, Lanyu pig）與桃園豬（Sus scrofa vittatus, Taoyuan pig）粒線體全長序列，並以核苷酸變異探討鹿科與豬種動物之間親緣關係。本試驗分別設計27對、28對、34對與33對引子成功定序臺灣梅花鹿、臺灣水鹿、蘭嶼豬與桃園豬粒線體全長序列，上述鹿種與豬種是國家級保種動物，四條序列成功定序並公開發表至美國生物資訊資料庫NCBI GenBank網站，其粒線體完整序列長度與序列編號為臺灣梅花鹿16,436 bp (DQ985076)、臺灣水鹿16,505 bp (DQ989636)、蘭嶼豬16,747 bp (DQ518915)與桃園豬16,728 bp (DQ534707) 。粒線體全長序列共包括1個D-loop控制區、2個rRNA (12S與16S)、22個tRNA及 13 個mRNA基因 (NADH1；NADH2； NADH3； NADH4； NADH4L； NADH5； NADH6； ATP6； ATP8； Cytb； CO1; CO2；CO3)。
利用鄰接法(neighbor-joining methods)統計模式將臺灣水鹿以D-loop與13種鹿科動物比較，鹿科動物可區分成歐洲型與亞洲型，臺灣水鹿與中國水鹿(Rusa unicolor hainana, GQ304777)屬於同一分支，兩者皆屬於亞洲型。試驗又收集臺灣水鹿保種場與商用水鹿繁殖場共24隻血液樣品，分析粒線體D-loop區域，親緣關係顯示，以Rusa unicolor hainana作為外群 (out-group)，商用水鹿與保種場之臺灣水鹿可區分成2個分群（clade），此結果代表商用水鹿場與保種場水鹿種原基因交流頻繁。
The purpose of this study is to investigate the complete nucleotide sequence of the mitochondrial genome of the Formosan Sika deer (Cervus nippon taiounanus), Formosan sambar (Rusa unicolor swinhoei),Taiwan Lanyu pig (Sus scrofa vittatus) and Taoyuan pig (Sus scrofa vittatus) and its phylogenetic relationships with other species within family Cervidae and pig breeds. This study used Twenty-seven, Twenty-eight, Thirty-four and Thirty-three forward and reverse primers were designed. Sequencing was performed in both directions. Formosan Sika deer, Formosan sambar, Taiwan Lanyu pig and Taiwan Taoyuan pig there all Nation Germplasm Conservation animal in Taiwan. That the complete sequence of the mitochondrial genome of the Formosan Sika deer is 16,436 bp (DQ985076) , Formosan sambar deer is 16,505 bp (DQ989636), Lanyu pig is 16,747 bp (DQ518915) and Taoyuan pig is 16,728 bp (DQ534707), which was submitting in NCBI GenBank. The complete sequence includes one D-loop, two rRNA (12S and 16S), 22 tRNA and 13 mRNA genes.
The mitochondrial D-loop region was also analyzed for comparative purposes among the Formosan Sambar and 13 other species within family Cervidae using neighbor-joining methods. The phylogenetic tree demonstrated that there are two separate groups, European type and Asian type, Formosan sambar (Rusa unicolor swinhoei) and China sambar belong to the same clades , both genus Rusa. When the mtDNA D-loop sequences of Twenty-four Formosan Sambar DNA were compared, Rusa unicolor hainana was used as out-group. According to this result, we can divide Formosan sambar into two clades, therefore that LRI sambar exchanges with the commercial farms sambar gene flow frequently.
The phylogenetic relationships of the Lanyu by comparing the sequence of the mitochondrial genome and the D-loop region of Asian and European pig breeds were investigated. It revealed that, the genetic distance of the Lanyu is high when compared with both the European and Asian pig breeds; the genetic exchange between the Lanyu and other breeds is not frequent. There is also no evidence of genetic exchange or introgression caused by population migration. Therefore, we conclude that the Lanyu is an independent branch among the breeds.