The complete mitochondrial genome of the relict frog Leiopelma archeyi: Insights into the root of the frog Tree of Life

References

• Abascal F, Zardoya R, Posada D. 2005. ProtTest: Selection of best-fit models of protein evolution. Bioinformatics. 21:2104–2105.
   PubMed Web of Science ®Google Scholar
• Adachi J, Hasegawa H. 1996. Model of amino acid substitution in proteins encoded by mitochondrial DNA. J Mol Evol. 42:459–468.
   PubMed Web of Science ®Google Scholar
• Akaike H. 1973. Information theory as an extension of the maximum likelihood principle. In: Petrov BN, Csaki F. editors. Second international symposium of information theory. Budapest: Akademiai Kiado.
   Google Scholar
• Altig RI, Johnston GF. 1989. Guilds of anuran larvae: Relationships among developmental modes, morphologies, and habitats. Herpetol Monogr. 3:81–109.
   Google Scholar
• Archey G. 1922. The habitat and life history of Leiopelma hochtetteri. Rec Canterbury Mus. 2:59–71.
   Google Scholar
• Báez AM, Basso NG. 1996. The earliest known frogs of the Jurassic of South America: Review and cladistic appraisal of their relationships. Münchener Geowiss Abh (A). 30:131–158.
   Google Scholar
• Bell BD, Wassersug RJ. 2003. Anatomical features of Leiopelma embryos and larvae: Implications for anuran evolution. J Morphol. 256:160–170.
   PubMed Web of Science ®Google Scholar
• Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. 2007. GenBank. Nucleic Acids Res. 35:D21–D25.
   Web of Science ®Google Scholar
• Bidnenko V, Ehrlich SD, Michel B. 2002. Replication fork collapse at replication terminator sequences. EMBO J. 21:3898–3907.
   Google Scholar
• Biju SD, Bossuyt F. 2003. New frog family from India reveals an ancient biogeographical link with the Seychelles. Nature. 425:711–714.
   PubMed Web of Science ®Google Scholar
• Boore JL. 1999. Animal mitochondrial genomes. Nucleic Acids Res. 27:1767–1780.
   PubMed Web of Science ®Google Scholar
• Boore JL. 2000. The duplication/random loss model for gene rearrangement exemplified by mitochondrial genomes of deuterostome animals. In: Sankoff D, Nadeau JH. editors. Comparative genomics. Boston, MA: Kluwer Academic Publisher133–147.
   Google Scholar
• Bossuyt F, Roelants K. 2009. Frogs and toads. In: Hedges SB, Kumar S. editors. The Timetree of Life. New York: Oxford University Press357–364.
   Google Scholar
• Bowmaker M, Yang MY, Yasukawa T, Reyes A, Jacobs HT, Huberman JA, Holt IJ. 2003. Mammalian mitochondrial DNA replicates bidirectionally from an initiation zone. J Biol Chem. 278:50961–50969.
   PubMed Web of Science ®Google Scholar
• Carroll RL. 2007. The Palaeozoic ancestry of salamanders, frogs and caecilians. Zool J Linn Soc. 150:1–140.
   Web of Science ®Google Scholar
• Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 17:540–552.
   PubMed Web of Science ®Google Scholar
• Clayton DA. 1982. Replication of animal mitochondrial DNA. Cell. 28:693–705.
   PubMed Web of Science ®Google Scholar
• Curole JP, Kocher TD. 1999. Mitogenomics: Digging deeper with complete mitochondrial genomes. Trends Ecol Evol. 14:394–398.
   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 USA. 78:6116–6120.
   PubMed Web of Science ®Google Scholar
• Dowton M, Austin AD. 1999. Evolutionary dynamics of a mitochondrial rearrangement “hot spot” in the Hymenoptera. Mol Biol Evol. 16:298–309.
   PubMed Web of Science ®Google Scholar
• Duellman WE. 1975. On the classification of frogs. Occas Pap Mus Nat His Univ Kansas. 42:1–14.
   Google Scholar
• Duellman WE, Trueb L. 1986. Biology of amphibians. New York: MacGraw-Hill.
   Google Scholar
• Estes R, Reig OA. 1973. The early fossil record of frogs: A review of the evidence. In: Vial JL. editors. Evolutionary biology of the anurans: Contemporary research on major problems. Columbia, MO: University of Missouri Press11–63.
   Google Scholar
• Evans SE, Borsuk-Bialynicka M. 1998. A stem-group frog from the early Triassic of Poland. Acta Palaeontol Pol. 43:573–580.
   Web of Science ®Google Scholar
• Feller AE, Hedges SB. 1998. Molecular evidence for the early history of living amphibians. Mol Phylogenet Evol. 9:509–516.
   PubMed Web of Science ®Google Scholar
• Felsenstein J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool. 27:401–410.
   Google Scholar
• Felsenstein J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol. 17:368–376.
   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
• Fernández-Silva P, Enriquez JA, Montoya J. 2003. Replication and transcription of mammalian mitochondrial DNA. Exp Physiol. 88:41–56.
   PubMed Web of Science ®Google Scholar
• Ford L, Cannatella DC. 1993. The major clades of frogs. Herpetol Monogr. 7:93–117.
   Google Scholar
• Frost DR, Grant T, Faivovich J, Bain RH, Haas A, Haddad CFB, de Sá RO, Channing A, Wilkinson M, Donnellan SC, Raxworthy CJ, Campbell JA, Blotto BL, Moler P, Drewes RC, Nussbaum R, Lynch JD, Green DM, Wheeler WC. 2006. The amphibian Tree of Life. Bull Am Mus Nat Hist. 297:1–370.
   Web of Science ®Google Scholar
• García-París M, Buchholz DR, Parra-Olea G. 2003. Phylogenetic relationships of Pelobatoidea re-examined using mtDNA. Mol Phylogenet Evol. 28:12–23.
   PubMed Web of Science ®Google Scholar
• Gissi C, San Mauro D, Pesole G, Zardoya R. 2006. Mitochondrial phylogeny of Anura (Amphibia): A case study of congruent phylogenetic reconstruction using amino acid and nucleotide characters. Gene. 366:228–237.
   Google Scholar
• Green DM, Cannatella DC. 1993. Phylogenetic significance of the amphicoelous frogs. Ascaphidae and Leiopelmatidae. Ecol Ethol Evol. 5:233–245.
   Web of Science ®Google Scholar
• Green DM, Sharbel TF, Hitchmough RA, Daugherty CH. 1989. Genetic variation in the genus Leiopelma and relationships to other primitive frogs. J Zoolog Syst Evol Res. 27:65–79.
   Google Scholar
• Haas A. 2003. Phylogeny of frogs as inferred from primarily larval characters (Amphibia: Anura). Cladistics. 19:23–89.
   PubMed Web of Science ®Google Scholar
• Hay JM, Ruvinsky I, Hedges SB, Maxson LR. 1995. Phylogenetic relationships of amphibian families inferred from DNA sequences of mitochondrial 12S and 16S ribosomal RNA genes. Mol Biol Evol. 12:928–937.
   PubMed Web of Science ®Google Scholar
• Hedges SB, Maxson LR. 1993. A molecular perspective on lissamphibian phylogeny. Herpetol Monogr. 7:27–42.
   Google Scholar
• Hillis DM, Ammerman LK, Dixon MT, de Sá RO. 1993. Ribosomal DNA and the phylogeny of frogs. Herpetol Monogr. 7:1118–1200.
   Google Scholar
• Hixson JE, Wong TW, Clayton DA. 1986. Both the conserved stem-loop and divergent 5′-flanking sequences are required for initiation at the human mitochondrial origin of light-strand DNA replication. J Biol Chem. 261:2384–2390.
   PubMed Web of Science ®Google Scholar
• Hoegg S, Vences M, Brinkmann H, Meyer A. 2004. Phylogeny and comparative substitution rates of frogs inferred from sequences of three nuclear genes. Mol Biol Evol. 21:1188–1200.
   PubMed Web of Science ®Google Scholar
• Huelsenbeck JP, Ronquist F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics. 17:754–755.
   PubMed Web of Science ®Google Scholar
• Hugall AF, Foster R, Lee MSY. 2007. Calibration choice, rate smoothing, and the pattern of tetrapod diversification according to the long nuclear gene RAG-1. Syst Biol. 56:543–563.
   PubMed Web of Science ®Google Scholar
• Hyrien O. 2000. Mechanisms and consequences of replication fork arrest. Biochimie. 82:5–17.
   PubMed Web of Science ®Google Scholar
• Igawa T, Kurabayashi A, Usuki C, Fujii T, Sumida M. 2008. Complete mitochondrial genomes of three neobatrachian anurans: A case study of divergence time estimation using different data and calibration settings. Gene. 407:116–129.
   PubMed Web of Science ®Google Scholar
• Johnson GD, Patterson C. 1993. Percomorph phylogeny: A survey of acanthomorphs and a new proposal. Bull Mar Sci. 52:554–626.
   Web of Science ®Google Scholar
• Kurabayashi A, Sumida M, Yonekawa H, Glaw F, Vences M, Hasegawa M. 2008. Phylogeny, recombination, and mechanisms of stepwise mitochondrial genome reorganization in mantellid frogs from Madagascar. Mol Biol Evol. 25:874–891.
   PubMed Web of Science ®Google Scholar
• Laurent RF. 1979. Esquisse d'une phylogenèse des anoures. Bull Soc Zool France. 104:397–422.
   Google Scholar
• Laurent RF. 1986. Sous classe des lissamphibiens (Lissamphibia). In: Grassé P, Delsol M. editors. Traité de zoologie: Anatomie, systematique, biologie. Paris: Masson594–797.
   Google Scholar
• Lupi R, de Meo PDO, Picardi E, D'Antonio M, Paoletti D, Castrignanò T, Pesole G, Gissi C. 2010. MitoZoa: A curated mitochondrial genome database of metazoans for comparative genomics studies. Mitochondrion. 10:192–199.
   PubMed Web of Science ®Google Scholar
• Lynch JD. 1973. The transition from archaic to advanced frogs. In: Vial JL. editors. Evolutionary biology of the anurans: Contemporary research on major problems. Columbia, MO: University of Missouri Press133–182.
   Google Scholar
• Macey JR, Papenfuss TJ, Kuehl JV, Fourcade HM, Boore JL. 2004. Phylogenetic relationships among amphisbaenian reptiles based on complete mitochondrial genomic sequences. Mol Phylogenet Evol. 33:22–31.
   PubMed Web of Science ®Google Scholar
• MacKay SLD, Olivo PD, Laipis PJ, Hauswirth WW. 1986. Template-directed arrest of mammalian mitochondrial DNA synthesis. Mol Cell Biol. 6:1261–1267.
   PubMedGoogle Scholar
• Milner AR. 1988. The relationships and origin of living amphibians. In: Benton MJ. editors. The phylogeny and classification of the tetrapods. Oxford: Clarendon Press59–102.
   Google Scholar
• Mindell DP, Sorenson MD, Dimcheff DE. 1998. Multiple independent origins of mitochondrial gene order in birds. Proc Natl Acad Sci USA. 95:10693–10697.
   PubMed Web of Science ®Google Scholar
• Miya M, Takeshima H, Endo H, Ishiguro NB, Inoue JG, Mukai T, Satoh TP, Yamaguchi M, Akira K. 2003. Major patterns of higher teleostean phylogenies: A new perspective based on 100 complete mitochondrial DNA sequences. Mol Phylogenet Evol. 26:121–138.
   PubMed Web of Science ®Google Scholar
• Moritz C, Brown WM. 1986. Tandem duplications of D-loop and ribosomal RNA sequences in lizard mitochondrial DNA. Science. 233:1425–1427.
   PubMed Web of Science ®Google Scholar
• Moritz C, Brown WM. 1987. Tandem duplications in animal mitochondrial DNAs: Variation in incidence and gene content among lizards. Proc Natl Acad Sci USA. 84:7183–7187.
   PubMed Web of Science ®Google Scholar
• Moritz C, Dowling TE, Brown WM. 1987. Evolution of animal mitochondrial DNA: Relevance for population biology and systematics. Annu Rev Ecol Syst. 18:269–292.
   Google Scholar
• Mueller RL, Macey JR, Jaekel M, Wake DB, Boore JL. 2004. Morphological homoplasy, life history evolution, and historical biogeography of plethodontid salamanders inferred from complete mitochondrial genomes. Proc Natl Acad Sci USA. 101:13820–13825.
   PubMed Web of Science ®Google Scholar
• Nelson JS. 2006. Fishes of the world. Hoboken, NJ: John Wiley & Sons, Inc.
   Google Scholar
• Noble GK. 1924. A new spadefoot toad from the Oligocene of Mongolia with a summary of the evolution of the Pelobatidae. Am Mus Novit. 132:1–15.
   Google Scholar
• Noble GK. 1931. The biology of Amphibia. New York: Dover Publishing.
   Google Scholar
• Ojala D, Montoya J, Attardi G. 1981. tRNA punctuation model of RNA processing in human mitochondria. Nature. 290:470–474.
   PubMed Web of Science ®Google Scholar
• Púgener LA, Maglia AM, Trueb L. 2003. Revisiting the contribution of larval characters to an analysis of phylogenetic relationships of basal anurans. Zool J Linn Soc. 139:129–155.
   Web of Science ®Google Scholar
• Rage J, Roček Z. 1989. Redescription of Triadobatrachus massinoti (Piveteau, 1936) an anuran amphibian from the early Triassic. Palaeontogr Abt A. 206:1–16.
   Google Scholar
• Reeves JH. 1992. Heterogeneity in the substitution process of amino acid sites of proteins coded by mitochondrial DNA. J Mol Evol. 35:17–31.
   PubMed Web of Science ®Google Scholar
• Reig OA. 1958. Proposiciones para una nueva macrosistemática de los anuros (nota preliminar). Physis. 21:109–118.
   Google Scholar
• Reyes A, Gissi C, Pesole G, Saccone C. 1998. Asymmetrical directional mutation pressure in the mitochondrial genome of mammals. Mol Biol Evol. 15:957–966.
   PubMed Web of Science ®Google Scholar
• Ritland RM. 1955. Studies on the post-cranial morphology of Ascaphus truei. J Morphol. 97:215–282.
   Google Scholar
• Roe BA, Ma DP, Wilson RK, Wong JF. 1985. The complete nucleotide sequence of the Xenopus laevis mitochondrial genome. J Biol Chem. 260:9759–9774.
   PubMed Web of Science ®Google Scholar
• Roelants K, Bossuyt F. 2005. Archaeobatrachian paraphyly and Pangaean diversification of crown-group frogs. Syst Biol. 54:111–126.
   PubMed Web of Science ®Google Scholar
• Roelants K, Gower DJ, Wilkinson M, Loader S, Biju SD, Guillaume K, Moriau L, Bossuyt F. 2007. Global patterns of diversification in the history of modern amphibians. Proc Natl Acad Sci USA. 104:887–892.
   PubMed Web of Science ®Google Scholar
• Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 19:1572–1574.
   PubMed Web of Science ®Google Scholar
• Rothstein R, Michel B, Gangloff S. 2000. Replication fork pausing and recombination or “gimme a break”. Genes Dev. 14:1–10.
   PubMed Web of Science ®Google Scholar
• Ruta M, Coates MI. 2007. Dates, nodes and character conflict: Addressing the lissamphibian origin problem. J Syst Palaeontol. 5:69–122.
   Web of Science ®Google Scholar
• Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular cloning: A laboratory manual. New York: Cold Spring Harbor Laboratory Press.
   Google Scholar
• San Mauro D. 2010. A multilocus timescale for the origin of extant amphibians. Mol Phylogenet Evol. 56:554–561.
   PubMed Web of Science ®Google Scholar
• San Mauro D, García-París M, Zardoya R. Phylogenetic relationships of discoglossid frogs (Amphibia: Anura: Discoglossidae) based on complete mitochondrial genomes and nuclear genes. Gene. 2004a; 343:357–366.
   PubMed Web of Science ®Google Scholar
• San Mauro D, Gower DJ, Oommen OV, Wilkinson M, Zardoya R. Phylogeny of caecilian amphibians (Gymnophiona) based on complete mitochondrial genomes and nuclear RAG1. Mol Phylogenet Evol. 2004b; 33:413–427.
   PubMed Web of Science ®Google Scholar
• San Mauro D, Vences M, Alcobendas M, Zardoya R, Meyer A. 2005. Initial diversification of living amphibians predated the breakup of Pangaea. Am Nat. 165:590–599.
   PubMed Web of Science ®Google Scholar
• San Mauro D, Gower DJ, Zardoya R, Wilkinson M. 2006. A hotspot of gene order rearrangement by tandem duplication and random loss in the vertebrate mitochondrial genome. Mol Biol Evol. 23:227–234.
   PubMed Web of Science ®Google Scholar
• San Mauro D, Gower DJ, Massingham T, Wilkinson M, Zardoya R, Cotton JA. 2009. Experimental design in caecilian systematics: Phylogenetic information of mitochondrial genomes and nuclear rag1. Syst Biol. 58:425–438.
   PubMed Web of Science ®Google Scholar
• Sano N, Kurabayashi A, Fujii T, Yonekawa H, Sumida M. 2005. Complete nucleotide sequence of the mitochondrial genome of Schlegel's tree frog Rhacophorus schlegelii (family Rhacophoridae): Duplicated control regions and gene rearrangements. Genes Genet Syst. 80:213–224.
   PubMed Web of Science ®Google Scholar
• Satoh TP, Miya M, Endo H, Nishida M. 2006. Round and pointed-head grenadier fishes (Actinopterygii: Gadiformes) represent a single sister group: Evidence from the complete mitochondrial genome sequences. Mol Phylogenet Evol. 40:129–138.
   PubMed Web of Science ®Google Scholar
• Savage JM. 1973. The geographic distribution of frogs: Patterns and predictions. In: Vial JL. editors. Evolutionary biology of the anurans: Contemporary research on major problems. Columbia, MO: Columbia University Press351–445.
   Google Scholar
• Shimodaira H. 2002. An approximately unbiased test of phylogenetic tree selection. Syst Biol. 51:492–508.
   PubMed Web of Science ®Google Scholar
• Shimodaira H, Hasegawa M. 2001. CONSEL: For assessing the confidence of phylogenetic tree selection. Bioinformatics. 17:1246–1247.
   PubMed Web of Science ®Google Scholar
• Shubin NH, Jenkins FA. 1995. An early Jurassic jumping frog. Nature. 377:4952.
   Google Scholar
• Sokol O. 1975. The phylogeny of anuran larvae: A new look. Copeia. 1975:1–23.
   Google Scholar
• Stamatakis A. 2006. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 22:2688–2690.
   PubMed Web of Science ®Google Scholar
• Stamatakis A, Blagojevic F, Nikolopoulos D, Antonopoulos C. 2007. Exploring new search algorithms and hardware for phylogenetics: RAxML meets the IBM Cell. J VLSI Signal Process Syst. 48:271–286.
   Google Scholar
• Stephenson NG. 1951. Observations on the development of the amphicoelous frogs, Leiopelma and Ascaphus. J Linn Soc London. 42:18–28.
   Google Scholar
• Stiassny MLJ. 1986. The limits and relationships of the acanthomorph teleosts. J Zool. 1:411–460.
   Google Scholar
• Swofford DL. 1996. Phylogenetic inference. In: Hillis DM, Moritz C, Mable BK. editors. Molecular systematics. Suderand, MA: Sinauer Associates.
   Google Scholar
• Trueb L, Cloutier R. 1991. Toward an understanding of the amphibians: Two centuries of systematic history. In: Schultze HP, Trueb L. editors. Origins of the major groups of tetrapods: Controversies and consensus. New York: Cornell University Press175–193.
   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. 9:5411–5421.
   PubMed Web of Science ®Google Scholar
• Wiley EO, Johnson GD, Dimmick WW. 2000. The interrelationships of acanthomorph fishes: A total evidence approach using molecular and morphological data. Biochem Syst Ecol. 28:319–350.
   PubMed Web of Science ®Google Scholar
• Yang Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. J Mol Evol. 39:306–314.
   PubMed Web of Science ®Google Scholar
• Yang Z. 1997. PAML: A program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci. 13:555–556.
   PubMedGoogle Scholar
• Zardoya R, Meyer A. 2001. On the origin of and phylogenetic relationships among living amphibians. Proc Natl Acad Sci USA. 98:7380–7383.
   PubMedGoogle Scholar
• Zardoya R, Villalta M, López-Pérez MJ, Garrido-Pertierra A, Montoya J, Bautista JM. 1995. Nucleotide sequence of the sheep mitochondrial DNA D-loop and its flanking tRNA genes. Curr Genet. 28:94–96.
   PubMed Web of Science ®Google Scholar
• Zhang P, Wake DB. 2009. Higher-level salamander relationships and divergence dates inferred from complete mitochondrial genomes. Mol Phylogenet Evol. 53:492–508.
   PubMed Web of Science ®Google Scholar
• Zhang P, Zhou H, Chen Y-Q, Liu Y-F, Qu L-H. 2005. Mitogenomic perspectives on the origin and phylogeny of living amphibians. Syst Biol. 54:391–400.
   PubMed Web of Science ®Google Scholar