An examination of the origin and evolution of additional tandem repeats in the mitochondrial DNA control region of Japanese sika deer (Cervus Nippon)

References

• Arnason E, Rand DM. (1992). Heteroplasmy of short tandem repeats in mitochondrial DNA of Atlantic cod, Gadus morhua. Genetics 132:211–20
   PubMed Web of Science ®Google Scholar
• Ba H, Yang F, Xing X, Li C. (2013). Classification and phylogeny of sika deer (Cervus nippon) subspecies based on the mitochondrial control region DNA sequence using an extended sample set. Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736.2013.836509
   Google Scholar
• Bandelt HJ, Forster P, Rohl A. (1999). Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37–48
   PubMed Web of Science ®Google Scholar
• Broughton RE, Dowling TE. (1994). Length variation in mitochondrial DNA of the minnow Cyprinella spiloptera. Genetics 138:179–90
   PubMed Web of Science ®Google Scholar
• Broughton RE, Dowling TE. (1997). Evolutionary dynamics of tandem repeats in the mitochondrial DNA control region of the minnow Cyprinella spiloptera. Mol Biol Evol 14:1187–96
   PubMed Web of Science ®Google Scholar
• Brown JR, Beckenbach AT, Smith MJ. (1992). Mitochondrial DNA length variation and heteroplasmy in populations of white sturgeon (Acipenser transmontanus). Genetics 132:221–8
   PubMed Web of Science ®Google Scholar
• Buroker NE, Brown JR, Gilbert TA, O'hara PJ, Beckenbach AT, Thomas WK, Smith MJ. (1990). Length heteroplasmy of sturgeon mitochondrial DNA: An illegitimate elongation model. Genetics 124:157–63
   PubMed Web of Science ®Google Scholar
• Clayton DA. (1992). Transcription and replication of animal mitochondrial DNAs. Int Rev Cytol 141:217–32
   PubMedGoogle Scholar
• Cook CE, Wang Y, Sensabaugh G. (1999). A mitochondrial control region and cytochrome b phylogeny of sika deer (Cervus nippon) and report of tandem repeats in the control region. Mol Phylogenet Evol 12:47–56
   PubMed Web of Science ®Google Scholar
• Douzery E, Randi E. (1997). The mitochondrial control region of Cervidae: Evolutionary patterns and phylogenetic content. Mol Biol Evol 14:1154–66
   PubMed Web of Science ®Google Scholar
• Fumagalli L, Taberlet P, Favre L, Hausser J. (1996). Origin and evolution of homologous repeated sequences in the mitochondrial DNA control region of shrews. Mol Biol Evol 13:31–46
   PubMed Web of Science ®Google Scholar
• Hoelzel AR. (1993). Evolution by DNA turnover in the control region of vertebrate mitochondrial DNA. Curr Opin Genet Dev 3:891–5
   PubMedGoogle Scholar
• Hoelzel AR, Lopez JV, Dover GA, O'brien SJ. (1994). Rapid evolution of a heteroplasmic repetitive sequence in the mitochondrial DNA control region of carnivores. J Mol Evol 39:191–9
   PubMed Web of Science ®Google Scholar
• Kawamura Y. (1991). Quaternary mammalian faunas in the Japanese islands. Quaternary Res 28:213–20
   Google Scholar
• Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, et al. (2007). Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–8
   PubMed Web of Science ®Google Scholar
• Librado P, Rozas J. (2009). DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–2
   PubMed Web of Science ®Google Scholar
• Lopez JV, Cevario S, O'brien SJ. (1996). Complete nucleotide sequences of the domestic cat (Felis catus) mitochondrial genome and a transposed mtDNA tandem repeat (Numt) in the nuclear genome. Genomics 33:229–46
   PubMed Web of Science ®Google Scholar
• Lunt DH, Hyman BC. (1997). Animal mitochondrial DNA recombination. Nature 387:247
   PubMed Web of Science ®Google Scholar
• Mathews DH, Burkard ME, Freier SM, Wyatt JR, Turner DH. (1999). Predicting oligonucleotide affinity to nucleic acid targets. RNA 5:1458–69
   PubMed Web of Science ®Google Scholar
• Mundy NI, Helbig AJ. (2004). Origin and evolution of tandem repeats in the mitochondrial DNA control region of shrikes (Lanius spp.). J Mol Evol 59:250–7
   PubMed Web of Science ®Google Scholar
• Nagata J, Masuda R, Tamate HB, Hamasaki S, Ochiai K, Asada M, Tatsuzawa S, et al. (1999). Two genetically distinct lineages of the sika deer, Cervus nippon, in Japanese islands: Comparison of mitochondrial D-loop region sequences. Mol Phylogenet Evol 13:511–19
   PubMed Web of Science ®Google Scholar
• Purdue JR, Oleksyk TK, Smith MH. (2006). Independent occurrences of multiple repeats in the control region of mitochondrial DNA of white-tailed deer. J Hered 97:235–43
   PubMed Web of Science ®Google Scholar
• Rand DM. (1993). Endotherms, ectotherms, and mitochondrial genome-size variation. J Mol Evol 37:281–95
   PubMed Web of Science ®Google Scholar
• Randi E, Mucci N, Claro-Hergueta F, Bonnet A, Douzery EJ. (2001). A mitochondrial DNA control region phylogeny of the Cervinae: Speciation in Cervus and implications for conservation. Anim Conserv 4:1–11
   Web of Science ®Google Scholar
• Stewart DT, Baker AJ. (1994). Patterns of sequence variation in the mitochondrial D-loop region of shrews. Mol Biol Evol 11:9–21
   PubMed Web of Science ®Google Scholar
• Tamura K, Nei M. (1993). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512–26
   PubMed Web of Science ®Google Scholar
• Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. (2011). MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–9
   PubMed Web of Science ®Google Scholar
• Tatarenkov A, Avise JC. (2007). Rapid concerted evolution in animal mitochondrial DNA. Proc Biol Sci 274:1795–8
   PubMed Web of Science ®Google Scholar
• Wilkinson GS, Chapman AM. (1991). Length and sequence variation in evening bat D-loop mtDNA. Genetics 128:607–17
   PubMed Web of Science ®Google Scholar
• Wilkinson GS, Mayer F, Kerth G, Petri B. (1997). Evolution of repeated sequence arrays in the D-loop region of bat mitochondrial DNA. Genetics 146:1035–48
   PubMed Web of Science ®Google Scholar