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Published April 17, 2016 | Version v1
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Mitogenomics of electric rays: evolutionary considerations within Torpediniformes (Batoidea; Chondrichthyes)

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Gaitan-Espitia, Juan Diego, Solano-Iguaran, Jaiber J., Tejada-Martinez, Daniela, Quintero-Galvis, Julian F. (2016): Mitogenomics of electric rays: evolutionary considerations within Torpediniformes (Batoidea; Chondrichthyes). Zoological Journal of the Linnean Society 178 (2): 257-266, DOI: 10.1111/zoj.12417, URL: http://dx.doi.org/10.1111/zoj.12417

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urn:lsid:plazi.org:pub:7632F11A181FFFC7AE1D934EFFC0C17B

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Publication: 10.2305/IUCN.UK.2007.RLTS.T63142A12622582.en (DOI)
Publication: 10.2305/IUCN.UK.2007.RLTS.T63157A12602819.en (DOI)
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Figure: 10.5281/zenodo.5368134 (DOI)
Figure: 10.5281/zenodo.5368136 (DOI)
Figure: 10.5281/zenodo.5368138 (DOI)

References

  • Abascal F, Zardoya R, Telford M. 2010. TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations. Nucleic Acids Research 38: W7-W13.
  • Alam MT, Petit RA, Read TD, Dove ADM. 2014. The complete mitochondrial genome sequence of the world's largest fish, the whale shark (Rhincodon typus), and its comparison with those of related shark species. Gene 539: 44-49.
  • Aschliman NC, Nishida M, Miya M, Inoue JG, Rosana KM, Naylor GJP. 2012a. Body plan convergence in the evolution of skates and rays (Chondrichthyes: Batoidea). Molecular Phylogenetics and Evolution 63: 28-42.
  • Aschliman NC, Claeson KM, McEachran JD. 2012b. Phylogeny of Batoidea. In: Carrier J, Musick J, Heithaus M, eds. Biology of sharks and their relatives. Boca Raton, FL: CRC Press, 57-94.
  • Austin CM, Tan MH, Lee Y, Croft LJ, Meekan MG, Gan HM. 2014. The complete mitogenome of the cow tail ray Pastinachus atrus (Macleay, 1883) (Elasmobranchii; Myliobatiformes; Dasyatidae). Mitochondrial DNA 1736: 1-2.
  • Bernt M, Bleidorn C, Braband A, Dambach J, Donath A, Fritzsch G, Golombek A, Hadrys H, J uhling € F, Meusemann K, Middendorf M. 2013a. A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny. Molecular Phylogenetics and Evolution 69: 352-364.
  • Bernt M, Braband A, Schierwater B, Stadler PF. 2013b. Genetic aspects of mitochondrial genome evolution. Molecular Phylogenetics and Evolution 69: 328-338.
  • Blier PU, Dufresne F, Burton RS. 2001. Natural selection and the evolution of mtDNA-encoded peptides: evidence for intergenomic co-adaptation. Trends in Genetics 17: 400- 406.
  • Blier PU, Breton S, Desrosiers V, Lemieux H. 2006. Functional conservatism in mitochondrial evolution: insight from hybridization of arctic and brook charrs. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 306: 425-432.
  • Boore JL, Brown WM. 1998. Big trees from little genomes: mitochondrial phylogenetic tool gene order as a phylogenetic tool. Current Opinion in Genetics & Development 8: 668-674.
  • Botero-Castro F, Tilak MKA, Justy F, Catzeflis F, Delsuc F, Douzery EJP. 2013. Next-generation sequencing and phylogenetic signal of complete mitochondrial genomes for resolving the evolutionary history of leaf-nosed bats (Phyllostomidae). Molecular phylogenetics and evolution 69: 728-739.
  • de Carvalho MR, Seret B, Compagno LJV. 2002. A new species of electric ray of the genus Narcine Henle, 1834 from the South-Western Indian Ocean (Chondrichthyes: Torpediniformes: Narcinidae). South African Journal of Marine Science 24: 135-149.
  • de Carvalho MR, McCord ME, Myers RA. 2007. Narcine bancroftii. The IUCN Red List of Threatened Species 2007, e.T63142A12622582. Available at: http://dx.doi.org/10.2305/ IUCN.UK.2007.RLTS.T63142A12622582.en. Accessed on 21 March 2016.
  • Castillo-Paez A, del Rio-Portilla MA, Rocha-Olivares A. 2014. The complete mitochondrial genome of the giant electric ray, Narcine entemedor (Elasmobranchii: Torpediniformes). Mitochondrial DNA 1736: 1-3.
  • Cea G, Gaitan-Espitia JD, Cardenas L. 2015. Complete mitogenome of the edible sea urchin Loxechinus albus: genetic structure and comparative genomics within Echinozoa. Molecular Biology Reports 42: 1081-1089.
  • Chen X, Ai W, Xiang D, Pan L, Shi X. 2014. Complete mitogenome of the brown guitarfish Rhinobatos schlegelii (Rajiformes, Rhinobatidae). Mitochondrial DNA 1736: 1-2.
  • Claeson KM. 2014. The impacts of comparative anatomy of electric rays (Batoidea: Torpediniformes) on their systematic hypotheses. Journal of Morphology 275: 597-612.
  • Compagno LJV. 1999. Checklist of living elasmobranchs. In: Hamlett WC, ed. Sharks, Skates, and Rays: The Biology of Elasmobranch Fishes. Baltimore: The John Hopkins University Press, 471-498.
  • Dilly GF, Gaitan-Espitia JD, Hofmann GE. 2015. Characterization of the Antarctic sea urchin (Sterechinus neumayer i) transcriptome and mitogenome: a molecular resource for phylogenetics, ecophysiology and global change biology. Molecular Ecology Resources 15: 425-436.
  • Douady CJ, Dosay M, Shivji MS, Stanhope MJ. 2003. Molecular phylogenetic evidence refuting the hypothesis of Batoidea (rays and skates) as derived sharks. Molecular Phylogenetics and Evolution 26: 215-221.
  • Drummond A, Ashton B, Buxton S, Cheung M, Cooper A, Duran C, Field M, Heled J, Kearse M, Markowitz S, Moir R, Stones-Havas S, Sturrock S, Thierer T, Wilson A. 2010. GENEIOUS Version 8.1. Available at: http:// www.geneious.com.
  • Fowler SL. 2005. Sharks, Rays and Chimaeras: The Status of the Chondrichthyan Fishes: Status Survey. IUCN/SSC Shark Specialist Group. IUCN: Gland, Switzerland x + 461 pp.
  • Franklin O, Palmer C, Dyke G. 2014. Pectoral fin morphology of batoid fishes (Chondrichthyes: Batoidea): Explaining phylogenetic variation with geometric morphometrics. Journal of Morphology 275: 1173-1186.
  • Gaitan-Espitia JD, Hofmann GE. 2016. Mitochondrial genome architecture of the giant red sea urchin Mesocentrotus franciscanus (Strongylocentrotidae, Echinoida). Mitochondrial DNA 27: 591-592.
  • Gaitan-Espitia JD, Lopez A. 2008. Presencia de juveniles de tiburon aletinegro Carcharhinus limbatus (Carcharhiniformes: Carcharhinidae) en la zona norte de la ecoregion Tayrona, Caribe colombiano. Latin American Journal of Aquatic Research 36: 115-119.
  • Gaitan-Espitia JD, Nespolo RF, Opazo JC. 2013. The complete mitochondrial genome of the land snail Cornu aspersum (Helicidae: Mollusca): intra-specific divergence of protein-coding genes and phylogenetic considerations within Euthyneura. PLoS ONE 8: e67299.
  • Galtier N, Nabholz B, Glemin S, Hurst GDD. 2009. Mitochondrial DNA as a marker of molecular diversity: a reappraisal. Molecular Ecology 18: 4541-4550.
  • Gillett CPDT, Crampton-Platt A, Timmermans MJTN, Jordal BH, Emerson BC, Vogler AP. 2014. Bulk de novo mitogenome assembly from pooled total DNA elucidates the phylogeny of weevils (Coleoptera: Curculionoidea). Molecular Biology and Evolution 31: 2223-2237.
  • Inoue JG, Miya M, Lam K, Tay BH, Danks J a., Bell J, Walker TI, Venkatesh B. 2010. Evolutionary origin and phylogeny of the modern holocephalans (Chondrichthyes: Chimaeriformes): a mitogenomic perspective. Molecular Biology and Evolution 27:2576-2586.
  • Iwasaki W, Fukunaga T, Isagozawa R, Yamada K, Maeda Y, Satoh T, Sado T, Mabuchi K, Takeshima H, Miya Nishida M. 2013. MitoFish and MitoAnnotator: a mitochondrial genome database of fish with an accurate and automatic annotation pipeline. Molecular Biology and Evolution 30: 2531-2540.
  • Lanfear R, Calcott B, Ho SYW, Guindon S. 2012. PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Molecular Biology and Evolution 29: 1695-1701.
  • Laslett D, Canb ack € B. 2008. ARWEN, a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics 24: 172-175.
  • Leavitt JR, Hiatt KD, Whiting MF, Song H. 2013. Searching for the optimal data partitioning strategy in mitochondrial phylogenomics: a phylogeny of Acridoidea (Insecta: Orthoptera: Caelifera) as a case study. Molecular Phylogenetics and Evolution 67: 494-508.
  • Luo C, Tsementzi D, Kyrpides N, Read T, Konstantinidis KT. 2012. Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PLoS ONE 7: e30087.
  • Martin AP. 1995. Mitochondrial DNA sequence evolution in sharks: rates, patterns, and phylogenetic inferences. Molecular Biology and Evolution 12: 1114-1123.
  • Martin AP, Naylor GJ, Palumbi SR. 1992. Rates of mitochondrial DNA evolution in sharks are slow compared with mammals. Nature 357: 153-155.
  • McEachran JD, Aschliman N. 2004. Phylogeny of Batoidea. In: Carrier J, Musick J, Heithaus M, eds. Biology of sharks and their relatives. Boca Raton, Florida: CRC Press, 115-135.
  • McEachran JD, Carvalho MD. 2002. Batoid fishes. The living marine resources of the Western Central Atlantic FAO Species Identification. Guide for Fishery Purposes and American Society of Ichthyologists and Herpetologists. Rome: FAO. 507-589.
  • Naylor GJ, Caira JN, Jensen K, Rosana KA, Straube N, Lakner C. 2012. Elasmobranch Phylogeny: A Mitochondrial Estimate Based on 595 Species. In: Carrier JC, Musick JA, Heithaus MR eds. The biology of sharks and their relatives, 2nd edn. Boca Raton, FL: CRC Press. 31-56.
  • Nelson J. 2006. Fishes of the world. New York, USA: John Wiley & Sons.
  • Pavan-Kumar A, Gireesh-Babu P, Babu P, Jaiswar A, Krishna V, Prasasd K, Chaudhari A, Raje S, Chakraborty S, Krishna G, Lakra W. 2014. Molecular phylogeny of elasmobranchs inferred from mitochondrial and nuclear markers. Molecular Biology Reports 41: 447-457.
  • Perseke M, Golombek A, Schlegel M, Struck TH. 2013. The impact of mitochondrial genome analyses on the understanding of deuterostome phylogeny. Molecular Phylogenetics and Evolution 66: 898-905.
  • Poortvliet M, Hoarau G. 2013. The complete mitochondrial genome of the Spinetail Devilray, Mobula japanica. Mitochondrial DNA 24: 28-30.
  • Poortvliet M, Olsen J, Croll DA, Bernardi G, Newton K, Kollias S, O'Sullivan J, Fernando D, Stevens G, Maga na ~ F, Seret B. 2015. A dated molecular phylogeny of manta and devil rays (Mobulidae) based on mitogenome and nuclear sequences. Molecular Phylogenetics and Evolution 83: 72-85.
  • Rambaut A, Drummond A. 2009. Tracer: MCMC trace analysis tool v1.5.0. Available at: http://beast. bio. ed. ac. uk.
  • Ramirez-Hernandez A, Palacios-Barreto P, Gaitan- Espitia JD, Reyes F, Ramirez J. 2011. Morphological abnormality in the longnose stingray Dasyatis guttata (Myliobatiformes: Dasyatidae) in the Colombian Caribbean. Cybium 35: 79-80.
  • Ray D, Densmore L. 2002. The crocodilian mitochondrial control region: general structure, conserved sequences, and evolutionary implications. Journal of Experimental Zoology 294: 334-345.
  • Rocco L. 2013. Molecular and Chromosomal Markers for Evolutionary Considerations in Torpediniformes (Chondrichthyes, Batoidea). ISRN Genetics 2013: 1-10.
  • Rocco L, Liguori I, Costagliola D, Morescalchi MA, Tinti F, Stingo V. 2007. Molecular and karyological aspects of Batoidea (Chondrichthyes, Elasmobranchi) phylogeny. Gene 389: 80-86.
  • Ronquist F, Huelsenbeck J. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
  • Rosa RS, Furtado M. 2007. Narcine brasiliensis. The IUCN Red List of Threatened Species 2007, e.T63157A12602819. Available at: http://dx.doi.org/10.2305/IUCN.UK.2007.RLTS. T63157A12602819.en. Accessed on 21 March 2016.
  • Schaefer JT, Summers AP. 2005. Batoid wing skeletal structure: Novel morphologies, mechanical implications, and phylogenetic patterns. Journal of Morphology 264: 298-313.
  • Schattner P, Brooks AN, Lowe TM. 2005. The tRNAscan- SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Research 33: W686- W689.
  • Silvestro D, Michalak I. 2011. RaxmlGUI: a graphical front-end for RAxML. Organisms Diversity & Evolution 12: 335-337.
  • Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihoodbased phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics (Oxford, England) 22:2688- 2690.
  • Yang B, Zhang J, Yamaguchi A, Zhang B. 2013. Mitochondrial genome of Dasyatis bennettii (Chondrichthyes: Dasyatidae). Mitochondrial DNA 24: 344-346.
  • Zhang J, Yang B, Yamaguchi A, Furumitsu K, Zhang B. 2015. Mitochondrial genome of longheaded eagle ray Aetobatus flagellum (Chondrichthyes: Myliobatidae). Mitochondrial DNA 26: 763-764.