References
- Avise JC. (1994). Molecular markers, natural history and evolution. New York: Chapman & Hall
- Bandelt HJ, Forster P, Rhl A. (1999). Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37–48
- Barker FK, Benesh MK, Vandergon AJ, Lanyon SM. (2012). Contrasting evolutionary dynamics and information content of the avian mitochondrial control region and ND2 gene. PLoS One 7:1–12
- Bernatchez L, Danzmann RG. (1993). Congruence in control-region sequence and restriction-site variation in mitochondrial DNA of brook charr (Salvelinus fontinalis Mitchill). Mol Biol E 10:1002
- Bradman H, Grewe P, Appleton B. (2011). Direct comparison of mitochondrial markers for the analysis of swordfish population structure. Fish Res 109:95–9
- Brown GG, Gadaleta G, Pepe G, Saccone C, Sbisà E. (1986). Structural conservation and variation in the D-loop-containing region of vertebrate mitochondrial DNA. J Mol Biol 192:503–11
- Brown WM. (1985). The mitochondrial genome of animals. New York: Plenum Press
- Burland TG. (1999). DNASTAR’s Laser gene sequence analysis software. In: Misener S, Krawetz SA, editors. Bioinformatics methods and protocols. New York: Springer. p. 71–75
- Carmichael LE, Nagy JA, Larter NC, Strobeck C. (2001). Prey specialization may influence patterns of gene flow in wolves of the Canadian Northwest. Mol Ecol 10:2787–98
- Doda JN, Wright CT, Clayton DA. (1981). Elongation of displacement-loop strands in human and mouse mitochondrial DNA is arrested near specific template sequences. Proc Natl Acad Sci USA 78:6116–20
- Drummond AJ, Rambaut A. (2007). BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7:214
- Drummond AJ, Suchard MA, Xie D, Rambaut A. (2012). Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 29:1969–73
- Eriksson J, Hohmann GG, Boesch C, Vigilant L. (2004). Rivers influence the population genetic structure of bonobos (Pan paniscus). Mol Ecol 13:3425–35
- Fei L, Ye CY, Jiang JP. (2010). Colored atlas of Chinese amphibians. Chengdu: Sichuan Publishing House of Science and Technology
- Galtier N, Nabholz B, Glémin S, Hurst GD. (2009). Mitochondrial DNA as a marker of molecular diversity: A reappraisal. Mol Ecol 8:4541–50
- Johnson JR, Thomson RC, Micheletti SJ, Shaffer HB. (2011). The origin of tiger salamander (Ambystoma tigrinum) populations in California, Oregon, and Nevada: Introductions or relicts? Conservat Genet 12:355–70
- Lampert KP, Rand AS, Mueller UG, Ryan MJ. (2003). Fine-scale genetic pattern and evidence for sex-biased dispersal in the túngara frog, Physalaemus pustulosus. Mol Ecol 12:3325–34
- Lee WJ, Conroy J, Howell WH, Kocher TD. (1995). Structure and evolution of teleost mitochondrial control regions. J Mol Evol 41:54–66
- Li R, Chen W, Tu L, Fu J. (2009). Rivers as barriers for high elevation amphibians: A phylogeographic analysis of the alpine stream frog of the Hengduan Mountains. J Zool 277:309–16
- Librado P, Rozas J. (2009). DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–2
- Lind AJ, Spinks PQ, Fellers GM, Shaffer HB. (2011). Range wide phylogeography and landscape genetics of the Western US endemic frog Rana boylii (Ranidae): Implications for the conservation of frogs and rivers. Conserv Genet 12:269–84
- Liu HZ, Chen YY. (2003). Phylogeny of the East Asian cyprinids inferred from sequences of the mitochondrial DNA control region. Can J Zool 81:1938–46
- Meng SQ, Li GF. (2006). Research advances of Ichthyophis bannanicus. Sichuan J Zool China 25:423–5
- Meyer A. (1993). Evolution of mitochondrial DNA in fishes. Biochem Mol Biol Fish 2:1–38
- Moum T, Arnason E. (2001). Genetic diversity and population history of two related seabird species based on mitochondrial DNA control region sequences. Mol Ecol 10:2463–78
- Pan T, Wang H, Hu CC, Shi WB, Zhao K, Huang X, Zhang BW. (2014). Range-wide phylogeography and conservation genetics of a narrowly endemic stream salamander, Pachyhynobius shangchengensis (Caudata, Hynobiidae): Implications for conservation. Genet Mol Res 13:2873–85
- Rambaut A. (2009). FigTreeversion1.3.1.Computer program distributed by the author. Available at: http://tree.bio.ed.ac.uk/software/figtree/ (Accessed 4 January 2011)
- Rambaut A, Drummond A. (2007). Tracer. Version 1.5
- Rambaut A, Drummond A. (2010). Tree Annotator version 1.6.1
- Randi E, Lucchini V. (1998). Organization and evolution of the mitochondrial DNA control region in the avian genus Alectoris. J Mol Evol 47:449–62
- Saccone C, Pesole G, Sbisà E. (1991). The main regulatory region of mammalian mitochondrial DNA: Structure–function model and evolutionary pattern. J Mol Evol 33:83–91
- Sambrook J, Fritsch EF, Maniatis T. (1989). Molecular cloning: A laboratory manual. New York: Cold Spring Harbor Laboratory Press
- Saunders MA, Edwards SV. (2000). Dynamics and phylogenetic implications of mtDNA control region sequences in New World jays (Aves: Corvidae). J Mol Evol 51:97–109
- Sbisà E, Tanzariello F, Reyes A, Pesole G, Saccone C. (1997). Mammalian mitochondrial D-loop region structural analysis: Identification of new conserved sequences and their functional and evolutionary implications. Gene 205:125–40
- Shedlock AM, Parker JD, Crispin DA, Pietsch TW, Burmer GC. (1992). Evolution of the salmonid mitochondrial control region. Mol Phylogenet Evol 1:179–92
- Southern SO, Southern PJ, Dizon AE. (1988). Molecular characterization of a cloned dolphin mitochondrial genome. J Mol Evol 28:32–42
- Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. (2013). MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–9
- Tang QY, Liu HZ, Mayden R, Xiong BX. (2006). Comparison of evolutionary rates in the mitochondrial DNA cytochrome b gene and control region and their implications for phylogeny of the Cobitoidea (Teleostei: Cypriniformes). Mol Phylogenet Evol 39:347–57
- Taylor MF, Mckechnie SW, Pierce N, Kreitman M. (1993). The lepidopteran mitochondrial control region: Structure and evolution. Mol Biol Evol 10:1259–72
- Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. (1997). The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–82
- Wang H, Luo X, Meng S, Bei Y, Song T, Meng T, Li G, Zhang B. (2015). The phylogeography and population demography of the Yunnan Caecilian (Ichthyophis bannanicus): Massive rivers as barriers to gene flow. PLoS One 10:1–18
- Zhao Y, Zhang Y, Li X. (2013). Molecular phylogeography and population genetic structure of an endangered species Pachyhynobius shangchengensis (hynobiid Salamander) in a fragmented habitat of southeastern China. PLoS One 8:1–11
- Zhu DQ, Jamieson BG, Hugall A, Moritz C. (1994). Sequence evolution and phylogenetic signal in control-region and cytochrome b sequences of rainbow fishes (Melanotaeniidae). Mol Biol Evol 11:672–83