The mitogenomic phylogeny of the Elasmobranchii (Chondrichthyes)

References

• Allis EP. 1923. The cranial anatomy of Chlamydoselachus anguineus. Acta Zool. 4:123–221.
   Google Scholar
• Arnason U, Gullberg A, Janke A. 2001. Molecular phylogenetics of gnathostomous (jawed) fishes: old bones, new cartilage. Zool Scripta. 30:249–255.
   Web of Science ®Google Scholar
• Aschliman NC, Nishida M, Miya M, Inoue JG, Rosana KM, Naylor GJP. 2012. Body plan convergence in the evolution of skates and rays (Chondrichthyes: Batoidea). Mol Phylogenet Evol. 63:28–42.
   PubMed Web of Science ®Google Scholar
• Carvalho MR. 1996. Higher-level elasmobranch phylogeny, basal squaleans, and paraphyly. In: Stiassny MJ, Parenti LR, Johnson GD, editors. Interrelationships of fishes. London (UK): Academic Press; p. 35–62.
   Google Scholar
• Carvalho MR, Maisey JG. 1996. Phylogenetic relationships of the Late Jurassic shark Protospinax Woodward 1919 (Chondrichthyes: Elasmobranchii). In: Mesozoic fishes: systematics and paleoecology. Munich: Verlag Dr Friedrich Pfeil; p. 9–46.
   Google Scholar
• Compagno LJV. 1973. Interrelationships of living elasmobranchs. Zool J Linn Soc. 53:15–61.
   Google Scholar
• Compagno LJV. 1977. Phyletic relationships of living sharks and rays. Am Zool. 17:303.
   Google Scholar
• Compagno LJV. 1988. Sharks of the order Carcharhiniformes. Princeton (NJ): Princeton University Press.
   Google Scholar
• Compagno LJV. 1990. Relationships of the megamouth shark, Megachasma pelagios (Lamniformes, Megachasmidae), with comments on its feeding habits. NOAA Technical Report NMFS 90, p. 357–379.
   Google Scholar
• Compagno LJV. 1999. Systematics and body form. In: Hamlett WC, editor. Sharks, skates, and rays: the biology of elasmobranch fishes. Baltimore (MD): Johns Hopkins University Press; p. 1–42.
   Google Scholar
• Compagno LJV. 2005. Checklist of living chondrichthyan fishes. In: Fowler SL, Cavanagh RD, Camhi M, Burgess GH, Caillet GM, Fordham SV, Simpfendorfer CA, Musick JA, editors. Sharks, rays, and chimaeras: the status of the chondrichthyan fishes: status survey. Gland (Switzerland); Cambridge (UK): IUCN; p. 401–423.
   Google Scholar
• Corrigan S, Beheregaray LB. 2009. A recent shark radiation: molecular phylogeny, biogeography and speciation of wobbegong sharks (family: Orectolobidae). Mol Phylogenet Evol. 52:205–216.
   PubMed Web of Science ®Google Scholar
• Douady CJ, Dosay M, Shivji MS, Stanhope MJ. 2003. Molecular phylogenetic evidence refuting the hypothesis of Batoidea (rays and skates) as derived sharks. Mol Phylogenet Evol. 26:215–221.
   PubMed Web of Science ®Google Scholar
• Dulvy NK, Baum JK, Clarke S, Compagno LJV, Cortés E, Domingo A, Fordham S, Fowler S, Francis MP, Gibson C. 2008. You can swim but you can’t hide: the global status and conservation of oceanic pelagic sharks and rays. Aquat Conserv Mar Freshwat Ecosys. 18:459–482.
   Web of Science ®Google Scholar
• Dunn KA, Morrissey JF. 1995. Molecular phylogeny of elasmobranchs. Copeia. 3:526–531.
   Google Scholar
• Dunn KA, McEachran JD, Honeycutt RL. 2003. Molecular phylogenetics of myliobatiform fishes (Chondrichthyes: Myliobatiformes), with comments on the effects of missing data on parsimony and likelihood. Mol Phylogenet Evol. 27:259–270.
   PubMed Web of Science ®Google Scholar
• Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792–1797.
   PubMed Web of Science ®Google Scholar
• Ferretti F, Myers RA, Serena F, Lotze HK. 2008. Loss of large predatory sharks from the Mediterranean Sea. Conserv Biol. 22:952–964.
   PubMed Web of Science ®Google Scholar
• Gaitán-Espitia JD, Solano-Iguaran JJ, Tejada-Martinez D, Quintero-Galvis JF. 2016. Mitogenomics of electric rays: evolutionary considerations within Torpediniformes (Batoidea; Chondrichthyes). Zoolog J Linnean Soc. 178:257–266.
   Web of Science ®Google Scholar
• Goodrich ES. 1909. Vertebrata craniata. First fascicle: cyclostomes and fishes. In: Lankester R, editor. A treatise on zoology. Vol. 9. London (UK): A&C Black; p. 1–518.
   Google Scholar
• Gudger EW, Smith BG. 1933. The natural history of the frilled shark Chlamydoselachus anguineus. In: Gudger EW, editor. Bashford Dean memorial volume: Archaic fishes, article 5. New York: American Museum of Natural History; p. 245–319.
   Google Scholar
• Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52:696–704.
   PubMed Web of Science ®Google Scholar
• Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 59:307–321.
   PubMed Web of Science ®Google Scholar
• Heinicke MP, Naylor GJP, Hedges SB. 2009. Cartilaginous fishes (Chondrichthyes). In: Hedges SB, Kumar S, editors. The timetree of life. New York: Oxford University Press; p. 320.
   Google Scholar
• Holmgren N. 1940. Studies on the head in fishes. Part I: development of the skull in sharks and rays. Acta Zool Stockh. 21:51–257.
   Google Scholar
• Holmgren N. 1941. Studies on the head in fishes. Embryological, morphological, and phylogenetical researches. Part II: comparative anatomy of the adult selachian skull, with remarks on the dorsal fins in sharks. Acta Zool Stockh. 22:1–100.
   Google Scholar
• Human BA, Owen EP, Compagno LJV, Harley EH. 2006. Testing morphologically based phylogenetic theories within the cartilaginous fishes with molecular data, with special reference to the catshark family (Chondrichthyes; Scyliorhinidae) and the interrelationships within them. Mol Phylogenet Evol. 39:384–391.
   PubMed Web of Science ®Google Scholar
• Kitamura T, Takemura A, Watabe S, Taniuchi T, Shimizu M. 1996. Molecular phylogeny of the sharks and rays of the superorder Squalea based on mitochondrial cytochrome b gene. Fish Sci. 62:340–343.
   Web of Science ®Google Scholar
• Kriwet J, Benton MJ. 2004. Neoselachian (Chondrichthyes, Elasmobranchii) diversity across the Cretaceous-Tertiary boundary. Palaeogeogr Palaeocl. 214:181–194.
   Web of Science ®Google Scholar
• Lassmann T, Sonnhammer ELL. 2005. Kalign: an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics. 6:298.
   PubMed Web of Science ®Google Scholar
• Libralato S, Christensen V, Pauly D. 2005. A method for identifying keystone species in food web models. Ecol Model. 195:153–171.
   Web of Science ®Google Scholar
• Lim KC, Lim P-E, Chong VC, Loh K-H. 2015. Molecular and morphological analyses reveal phylogenetic relationships of stingrays focusing on the family Dasyatidae (Myliobatiformes). PLoS One. 10:e0120518
   PubMed Web of Science ®Google Scholar
• Lopez JA, Ryburn JA, Fedrigo O, Naylor GJ. 2006. Phylogeny of sharks of the family Triakidae (Carcharhiniformes) and its implications for the evolution of carcharhiniform placental viviparity. Mol Phylogenet Evol. 40:50–60.
   PubMed Web of Science ®Google Scholar
• Lovejoy NR, Bermingham E, Martin AP. 1998. Marine incursion into South America. Nature. 296:421–422.
   Google Scholar
• Maisey JG. 1983. Cranial anatomy of Hybodus basanus Egerton from the Lower Cretaceous of England. Am Mus Novit. 2758:1–64.
   Google Scholar
• Maisey JG, Naylor GJP, Ward DJ. 2004. Mesozoic elasmobranchs, neoselachian phylogeny and the rise of modern elasmobranch diversity. In: Arratia G, Tintori A, editors. Mesozoic fishes 3. München: Verlag Dr Friedrich Pfeil; p. 17–56.
   Google Scholar
• Mallatt J, Winchell CJ. 2007. Ribosomal RNA genes and deuterostome phylogeny revisited: more cyclostomes, elasmobranchs, reptiles, and a brittle star. Mol Phylogenet Evol. 43:1005–1022.
   PubMed Web of Science ®Google Scholar
• Martin AP. 1999. Substitution rates of organelle and nuclear genes in sharks: implicating metabolic rate (again). Mol Biol Evol. 16:996–1002.
   PubMed Web of Science ®Google Scholar
• Martin AP, Burg TM. 2002. Perils of paralogy: using HSP70 genes for inferring organismal phylogenies. Syst Biol. 51:570–587.
   PubMed Web of Science ®Google Scholar
• Martin AP, Pardini AT, Noble LR, Jones CS. 2002. Conservation of a dinucleotide simple sequence repeat locus in sharks. Mol Phylogenet Evol. 23:205–213.
   PubMed Web of Science ®Google Scholar
• McEachran JD, Aschliman N. 2004. Phylogeny of Batoidea. In: Carrier JC, Musick JA, Heithaus MR, editors. Biology of sharks and their relatives. Boca Raton (FL): CRC Press; p. 79–113.
   Google Scholar
• McEachran JD, Dunn KA, Miyake T. 1996. Interrelationships of the batoid fishes (Chondrichthyes: Batoidea). In: Stiassny MJ, Parenti LR, Johnson GD, editors. Interrelationships of fishes. London (UK): Academic Press; p. 63–82.
   Google Scholar
• Myers RA, Worm B. 2003. Rapid worldwide depletion of predatory fish communities. Nature. 423:280–283.
   PubMed Web of Science ®Google Scholar
• Myers RA, Baum JK, Shepherd TD, Powers SP, Peterson CH. 2007. Cascading effects of the loss of apex predatory sharks from a coastal ocean. Science. 315:1846–1850.
   PubMed Web of Science ®Google Scholar
• Naylor GJP, Martin AP, Mattison E, Brown WM. 1997. The inter-relationships of lamniform sharks: testing phylogenetic hypotheses with sequence data. In: Kocher TD, Stepien C, editors. Molecular systematics of fishes. New York: Academic Press; p. 199–218.
   Google Scholar
• Naylor GJP, Ryburn JA, Fedrigo O, López JA. 2005. Phylogenetic relationships among the major lineages of modern elasmobranchs. In: Hamlett WC, Jamieson BGM, editors. Reproductive biology and phylogeny. Vol. 3. Enfield (NH): Science Publishers, Inc.; p. 1–25.
   Google Scholar
• Naylor GJP, Caira JN, Jensen K, Rosana KAM, Straube N, Lakne C. 2012. Elasmobranch phylogeny: a mitochondrial estimate based on 595 species. In: Carrier JC, Musick JA, Heithaus MR, editors. The biology of sharks and their relatives. Boca Raton (FL): CRC Press, Taylor & Francis Group; p. 31–56.
   Google Scholar
• Nishida K. 1990. Phylogeny of the suborder Myliobatoidei. Mem Facul Fish Hokkaido Univ. 37:1–108.
   Google Scholar
• Nye TMW, Liò P, Gilks WR. 2005. A novel algorithm and web-based tool for comparing two alternative phylogenetic trees. Bioinformatics. 22:117–119.
   PubMed Web of Science ®Google Scholar
• Posada D. 2008. jModelTest: phylogenetic model averaging. Mol Biol Evol. 25:1253–1256.
   PubMed Web of Science ®Google Scholar
• Regan CT. 1906. A classification of the selachian fishes. Proc Zool Soc London. 1906:722–758.
   Google Scholar
• Robbins WD, Hisano M, Connolly SR, Choat JH. 2006. Ongoing collapse of coral-reef shark populations. Curr Biol. 16:2314–2319.
   PubMed Web of Science ®Google Scholar
• Schindler DE, Essington TE, Kitchell JF, Boggs C, Hilborn R. 2008. Sharks and tunas: fisheries impacts on predators with contrasting life histories. Ecol Appl. 12:735–748.
   Google Scholar
• Shirai S. 1992a. Phylogenetic relationships of the angel sharks, with comments on elasmobranch phylogeny (Chondrichthyes, Squatinidae). Copeia. 2:505–518.
   Google Scholar
• Shirai S. 1992b. Squalean phylogeny: a new framework of ‘squaloid’ sharks and related taxa. Sapporo: Hokkaido University Press.
   Google Scholar
• Shirai S. 1996. Phylogenetic interrelationships of neoselachians (Chondrichthyes: Euselachii). In: Stassny MLJ, Parenti LR, Johnson GD, editors. Interrelationships of fishes. San Diego: Academic Press; p. 9–34.
   Google Scholar
• Stock DW. 1992. A molecular phylogeny of fishes [dissertation]. Urbana-Champaign: University of Illinois.
   Google Scholar
• Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Mol Biol Evol. 30:2725–2729.
   PubMed Web of Science ®Google Scholar
• Tanaka K, Shiina T, Tomita T, Suzuki S, Hosomichi K, et al. 2013. Evolutionary relations of Hexanchiformes deep-sea sharks elucidated by whole mitochondrial genome sequence. BioMed Res Int. 2013:147064.
   PubMed Web of Science ®Google Scholar
• Toffoli D, Hrbek T, Araújo MLG, Almeida MP, Charvet-Almeida P, Farias IP. 2008. A test of the utility of DNA barcoding in the radiation of the freshwater stingray genus Potamotrygon (Potamotrygonidae, Myliobatiformes). Genet Mol Biol. 31(Suppl. 1), 324–336.
   Web of Science ®Google Scholar
• Vaudo JJ, Heithaus MR. 2009. Spatiotemporal variability in a sandflat elasmobranch fauna in Shark Bay, Australia. Mar Biol. 156:2579–2590.
   Web of Science ®Google Scholar
• Vélez-Zuazo X, Agnarsson I. 2011. Shark tales: a molecular species-level phylogeny of sharks (Selachimorpha, Chondrichthyes). Mol Phylogenet Evol. 58:207–217.
   PubMed Web of Science ®Google Scholar
• Vié J-C, Hilton-Taylor C, Stuart SN. 2008. The 2008 review of the IUCN Red List of threatened species. Gland (Switzerland): IUCN.
   Google Scholar
• White EG. 1936. A classification and phylogeny of the elasmobranch fishes. Am Mus Novit. 837:1–16.
   Google Scholar
• White EG. 1937. Interrelationships of the elasmobranchs with a key to the order Galea. Bull Am Mus Nat Hist. 74:25–138.
   Google Scholar
• Winchell CJ, Martin AP, Mallatt J. 2004. Phylogeny of elasmobranchs based on LSU and SSU ribosomal RNA genes. Mol Phylogenet Evol. 31:214–224.
   PubMed Web of Science ®Google Scholar
• Xia X, Xie Z. 2001. DAMBE: software package for data analysis in molecular biology and evolution. J Hered. 92:371–373.
   PubMed Web of Science ®Google Scholar
• Xia X, Xie Z, Salemi M, Chen L, Wang Y. 2003. An index of substitution saturation and its application. Mol Phylogenet Evol. 26:1–7.
   PubMed Web of Science ®Google Scholar
• Xia X, Lemey P. 2009. Assessing substitution saturation with DAMBE. In: Lemey P, Salemi M, Vandamme A-M, editors. The phylogenetic handbook: a practical approach to DNA and protein phylogeny. 2nd ed. Cambridge: Cambridge University Press; p. 615–630.
   Google Scholar