Molecular characteristics and evolution of the mitochondrial control region in three genera (Hipposideridae: HipposiderosAselliscus and Coelops) of leaf-nosed bats

References

• Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, Schreier PH, Smith AJ, Staden R, Young IG. 1981. Sequence and organization of the human mitochondrial genome. Nature. 290 5806: 457–465.
   PubMed Web of Science ®Google Scholar
• Bogdanowicz W, Owen R. 1998. In the Minotaur's labyrinth: Phylogeny of the bat family Hipposideridae. In: Kunz TH, Racey PA. editors. Bat biology and conservation. Washington, DC: Smithsonian Institution Press27–42.
   Google Scholar
• Chen SF, Rossiter SJ, Faulkes CG, Jones G. 2006. Population genetic structure and demographic history of the endemic Formosan lesser horseshoe bat (Rhinolophus monoceros). Mol Ecol. 15 6: 1643–1656.
   PubMed Web of Science ®Google Scholar
• 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 U S A. 78 10: 6116–6120.
   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 11: 1154–1166.
   PubMed Web of Science ®Google Scholar
• Felsenstein J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution. 39:783–791.
   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
• Gascuel O. 1997. BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol. 14 7: 685–695.
   PubMed Web of Science ®Google Scholar
• Gemmell NJ, Western PS, Watson JM, Graves JA. 1996. Evolution of the mammalian mitochondrial control region—Comparisons of control region sequences between monotreme and therian mammals. Mol Biol Evol. 13 6: 798–808.
   PubMed Web of Science ®Google Scholar
• Guillen A, Francis C. 2006. A new species of bat of the Hipposideros bicolor group (Chiroptera: Hipposideridae) from Central Laos, with evidence of convergent evolution with Sundaic taxa. Acta Chiropterol. 8:39–61.
   Web of Science ®Google Scholar
• Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52 5: 696–704.
   PubMed Web of Science ®Google Scholar
• Hand S, Kirsch J. 1998. A southern origin for the Hipposideridae (Microchiroptera)? Evidence from the Australian fossil record. In: Kunz TH, Racey PA. editors. Bat biology and conservation. Washington, DC: Smithsonian Institution Press72–90.
   Google Scholar
• Hasegawa M, Kishino H, Yano T. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol. 22 2: 160–174.
   PubMed Web of Science ®Google Scholar
• Hill J. 1963. A revision of the genus Hipposideros. Bull Br Mus. 11:1–129.
   Google Scholar
• Huelsenbeck J, Bollback J. 2001. Empirical and hierarchical Bayesian estimation of ancestral states. Syst Biol. 50 3: 351–366.
   PubMed Web of Science ®Google Scholar
• Iyengar A, Diniz FM, Gilbert T, Woodfine T, Knowles J, Maclean N. 2006. Structure and evolution of the mitochondrial control region in oryx. Mol Phylogenet Evol. 40 1: 305–314.
   PubMed Web of Science ®Google Scholar
• Jackson JD, Miller W, Hardison RC. 1996. Sequences within and flanking hypersensitive sites 3 and 2 of the beta-globin locus control region required for synergistic versus additive interaction with the epsilon-globin gene promoter. Nucleic Acids Res. 24 21: 4327–4335.
   PubMed Web of Science ®Google Scholar
• Jones K, Purvis A, MacLarnon A, Binnda-Emonds O, Simmons N. 2002. A phylogenetic supertree of the bats (Mammalia: Chiroptera). Biol Rev. 77 2: 223–259.
   PubMed Web of Science ®Google Scholar
• Kanagaraj C, Mrimuthu G, Rajan K. 2010. Genetic analysis on three South Indian sympatric hipposiderid bats (Chiroptera, Hipposideridae). Anim Biodivers Conserv. 33:187–194.
   Web of Science ®Google Scholar
• Ketmaier V, Bernardini C. 2005. Structure of the mitochondrial control region of the Eurasian otter (Lutra lutra; Carnivora, Mustelidae): Patterns of genetic heterogeneity and implications for conservation of the species in Italy. J Hered. 96 4: 318–328.
   PubMed Web of Science ®Google Scholar
• Kimura M. 1981. Estimation of evolutionary distances between homologous nucleotide sequences. Proc Natl Acad Sci USA. 78 1: 454–458.
   PubMed Web of Science ®Google Scholar
• Koopman K. 1994. Chiroptera: Systematics. In: Niethammer J, Schliemann H, Starck D. editors. Mammalia part 60 of handbook of zoology: A natural history of the phyla of the animal kingdom. Vol VIII. Berlin/New York: Walter de Gruyter. 1–217.
   Google Scholar
• Larizza A, Pesole G, Reyes A, Sbisà E, Saccone C. 2002. Lineage specificity of the evolutionary dynamics of the mtDNA D-loop region in rodents. J Mol Evol. 54 2: 145–155.
   PubMed Web of Science ®Google Scholar
• Levinson G, Gutman GA. 1987. Slipped-strand mispairing: A major mechanism for DNA sequence evolution. Mol Biol Evol. 4 3: 203–221.
   PubMed Web of Science ®Google Scholar
• Li G, Liang B, Wang Y, Zhao HH, Helgen K, Lin L, Jones G, Zhang SY. 2007. Echolocation calls, diet, and phylogenetic relationships of Stoliczka's trident bat, Aselliscus stoliczkanus (Hipposideridae). J Mammal. 88:736–744.
   Web of Science ®Google Scholar
• Liu F, Song Y, Yan S, Luo J, Jiang F. 2009. Structure and sequence variation of the mitochondrial DNA control region in Myotis macrodactylus. Chin J Zool. 44 4: 19–27.
   Google Scholar
• Madsen CS, Ghivizzani SC, Hauswirth WW. 1993. In vivo and in vitro evidence for slipped mispairing in mammalian mitochondria. Proc Natl Acad Sci U S A. 90 16: 7671–7675.
   PubMed Web of Science ®Google Scholar
• Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH. 2004. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci USA. 101 19: 7287–7292.
   PubMed Web of Science ®Google Scholar
• Matson CW, Baker RJ. 2001. DNA sequence variation in the mitochondrial control region of red-backed voles (Clethrionomys). Mol Biol Evol. 18 8: 1494–1501.
   PubMed Web of Science ®Google Scholar
• Murray SW, Campbell P, Kingston T, Zubaid A, Francis CM, Kunz TH. 2012. Molecular phylogeny of hipposiderid bats from Southeast Asia and evidence of cryptic diversity. Mol Phylogenet Evol. 62 2: 597–611.
   PubMed Web of Science ®Google Scholar
• Nilsson MA. 2009. The structure of the Australian and South American marsupial mitochondrial control region. Mitochondrial DNA. 20 5–6: 126–138.
   PubMed Web of Science ®Google Scholar
• Pereira SL, Grau ET, Wajntal A. 2004. Molecular architecture and rates of DNA substitutions of the mitochondrial control region of cracid birds. Genome. 47 3: 535–545.
   PubMed Web of Science ®Google Scholar
• Pesole G, Gissi C, De Chirico A, Saccone C. 1999. Nucleotide substitution rate of mammalian mitochondrial genomes. J Mol Evol. 48 4: 427–434.
   PubMed Web of Science ®Google Scholar
• Petri B, von Haeseler A, Pääbo S. 1996. Extreme sequence heteroplasmy in bat mitochondrial DNA. Biol Chem. 377 10: 661–668.
   PubMed Web of Science ®Google Scholar
• Posada D. 2008. jModelTest: Phylogenetic model averaging. Mol Biol Evol. 25 7: 1253–1256.
   PubMed Web of Science ®Google Scholar
• Reyes A, Nevo E, Saccone C. 2003. DNA sequence variation in the mitochondrial control region of subterranean mole rats, Spalax ehrenbergi superspecies. Mol Biol Evol. 20 4: 622–632.
   PubMed Web of Science ®Google Scholar
• Saccone C, Attimonelli M, Sbisa E. 1987. Structural elements highly preserved during the evolution of the D-loop-containing region in vertebrate mitochondrial DNA. J Mol Evol. 26 3: 205–211.
   PubMed Web of Science ®Google Scholar
• Saccone C, Pesole G, Sbisá E. 1991. The main regulatory region of mammalian mitochondrial DNA: Structure-function model and evolutionary pattern. J Mol Evol. 33 1: 83–91.
   PubMed Web of Science ®Google Scholar
• Sbisá 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 1–2: 125–140.
   PubMed Web of Science ®Google Scholar
• Simmons N. 2005. Order Chiroptera. In: Wilson DE, Reeder DM. editors. A taxonomic and geographical reference third. Baltimore, MD: The Johns Hopkins University Press312–525.
   Google Scholar
• Stoffberg S, Schoeman MC, Matthee CA. 2012. Correlated genetic and ecological diversification in a widespread southern African horseshoe bat. PloS One. 7 2: e31946.
   Web of Science ®Google Scholar
• Sun K, Feng J, Jin L, Liu Y, Shi L, Jiang T. Structure, DNA sequence variation and phylogenetic implications of the mitochondrial control region in horseshoe bats. Mammal Biol. 2009a; 74 2: 130–144.
   Web of Science ®Google Scholar
• Sun K, Feng J, Zhang Z, Xu L, Liu Y. Cryptic diversity in Chinese rhinolophids and hipposiderids (Chiroptera: Rhinolophidae and Hipposideridae). Mammalia. 2009b; 73:135–141.
   Web of Science ®Google Scholar
• Swofford D. 2002. PAUP^* 4.0. Phylogenetic analysis using parsimony (^* and other methods). Beta version 4.0b4a. Sunderland, MA: Sinauer Associates.
   Google Scholar
• Teeling EC, Springer MS, Madsen O, Bates P, O'Brien SJ, Murphy WJ. 2005. A molecular phylogeny for bats illuminates biogeography and the fossil record. Science. 307 5709: 580–584.
   PubMed Web of Science ®Google Scholar
• 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 24: 4876–4882.
   PubMed Web of Science ®Google Scholar
• Vallo P, Guillen-Servent A, Benda P, Pires D, Koubek P. 2008. Variation in mitochondrial DNA in the Hipposideros caffer complex (Chiroptera: Hipposideridae) and its taxonomic implications. Acta Chiropterol. 10:193–206.
   Web of Science ®Google Scholar
• Walberg MW, Clayton DA. 1981. Sequence and properties of the human KB cell and mouse L cell D-loop regions of mitochondrial DNA. Nucleic Acids Res. 9 20: 5411–5421.
   PubMed Web of Science ®Google Scholar
• Wang H, Liang B, Feng J, Sheng L, Zhang S. 2003. Molecular phylogenetic of hipposiderids (Chiroptera: Hipposideridae) and rhinolophids (Chiroptera: Rhinolophidae) in China based on mitochondrial cytochrome b sequences. Folia Zool. 52:259–268.
   Web of Science ®Google Scholar
• Wang Y. 2003. A complete checklist of mammal species and subspecies in China: A taxonomic and geographic reference. Beijing, China: China Forestry Publishing House.
   Google Scholar
• Wilkinson GS, Chapman AM. 1991. Length and sequence variation in evening bat D-loop mtDNA. Genetics. 128 3: 607–617.
   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 3: 1035–1048.
   PubMed Web of Science ®Google Scholar
• You Y, Sun K, Xu L, Wang L, Feng J, Liu S, Lu G, Berquist S, Feng J. 2010. Pleistocene glacial cycle effects on the phylogeography of the Chinese endemic bat species, Myotis davidii. BMC Evol Biol. 10:208.
   PubMed Web of Science ®Google Scholar