What can the mitochondrial genome reveal about higher-level phylogeny of the molluscan class Cephalopoda?

Zoological Journal of the Linnean Society

Volumn 161, Issue 3, 2011, Pages 573-586

  Allcock, A Louise ^a   Cooke, Ira R ^b,c   Strugnell, Jan M ^b,d  

^a NATIONAL UNIVERSITY OF IRELAND   (Ireland)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c Physical Sciences 3   (United Kingdom)

^d LA TROBE UNIVERSITY   (Australia)

Author keywords

Cuttlefish; Molecular systematics; Octopus; Squid

Indexed keywords

CEPHALOPODA; COLEOIDEA; DECAPODIFORMES; NEOCOLEOIDEA; OCTOPODIFORMES; OCTOPUS; OEGOPSIDA; SEPIIDAE; SPIRULIDA;

EID: 79951922231     PISSN: 00244082     EISSN: 10963642     Source Type: Journal    
DOI: 10.1111/j.1096-3642.2010.00656.x     Document Type: Article

References (75)

1. Abascal F, Posada D, Zardoya R. 2007. MtArt: a new model of amino acid replacement for Arthropoda. Molecular Biology and Evolution 24: 1-5.
2. Abascal F, Zardoya R, Posada D. 2005. ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21: 2104-2105.
3. Akasaki T, Nikaido M, Tsuchiya K, Segawa S, Hasegawa M, Okada N. 2006. Extensive mitochondrial gene arrangments in coleoid Cephalopoda and their phylogenetic implications. Molecular Phylogenetics and Evolution 38: 648-658.
4. Bader DA, Moret BME, Yan M. 2001. A linear-time algorithm for computing inversion distances between signed permutations with an experimental study. Journal of Computational Biology 8: 483-491.
5. Berry SS. 1911. Note on a New Abraliopsis from Japan. Nautilus 25 (8): 93-94.
6. Berry SS. 1913. Some New Hawaiian Cephalopods. Proceedings of the United States National Museum 45 (1996): 563-566.
7. Blanchette M, Bourque G, Sankoff D. 1997. Breakpoint phylogenies. In: Miyano S, Takagi T, eds. Genome informatics. Tokyo: University Academy Press, 25-34.
8. Boletzky SV. 1978/79. Nos connaissances actuelles sur le développement des Octopodes. Vie Et Milieu 28-29: 85-120.
9. Boletzky SV. 2006. From head to foot - and back again: brachial crown development in the Coleoidea (Mollusca, Cephalopoda). Acta Universitatis Carolinae - Geologica 49: 33-42.
10. Bonnaud L, Boucher-Rodoni R, Monnerot M. 1997. Phylogeny of cephalopods inferred from mitochondrial DNA sequences. Molecular Phylogenetics and Evolution 7: 44-54.
11. Boore JL. 2006. The use of genome-level characters for phylogenetic reconstruction. Trends in Ecology and Evolution 21: 439-446.
12. Boore JL, Brown WM. 2000. Mitochondrial genomes of Galathealinum, Helobdella, and Platynereis: sequence and gene arrangement comparisons indicate that Pogonophora is not a phylum and Annelida and Arthropoda are not sister taxa. Molecular Biology and Evolution 17: 87-106.
13. Boore JL, Collins TM, Stanton D, Daehler LL, Brown WM. 1995. Deducing arthropod phylogeny from mitochondrial DNA rearrangements. Nature 376: 163-165.
14. Boore JL, Lavrov DV, Brown WM. 1998. Gene translocation links insects and crustaceans. Nature 392: 667-668.
15. Boore JL, Staton JL. 2002. The mitochondrial genome of the sipunculid Phascolopsis gouldii supports its association with Annelida rather than Mollusca. Molecular Biology and Evolution 19: 127-137.
16. Carlini DB, Graves JE. 1999. Phylogenetic analysis of cytochrome c oxidase I sequences to determine higher-level relationships within the coleoid cephalopods. Bulletin of Marine Science 64: 57-76.
17. Carlini DB, Reece KS, Graves JE. 2000. Actin gene family evolution and the phylogeny of coleoid cephalopods (Mollusca: Cephalopoda). Molecular Biology and Evolution 17: 1353-1370.
18. Chun C. 1903. Aus den Tiefen des Weltmeeres. Gustav Fischer, 2nd edition, Jena, 592 pages.
19. Clarke MR. 1988. Evolution of recent cephalopods - a brief review. In: Clarke MR, Trueman ER, eds. The Mollusca, vol. 12. Paleontology and neontology of cephalopods.San Diego: Academic Press, 331-341.
20. Clarke MR, Maddock L. 1988. Statoliths from living species of cephalopods and evolution. In: Clarke MR, Trueman ER, eds. The Mollusca, vol. 12. Paleontology and neontology of cephalopods. San Diego: Academic Press, 169-184.
21. Cowles MK, Carlin BP. 1996. Markov Chain Monte Carlo convergence diagnostics: a comparative review. Journal of the American Statistical Association 91: 883-904.
22. Cuvier G. 1797. Tableau elementaire de l'histoire naturelle des animaux. 710 pages, 14 plates. Paris.
23. Fioroni VP. 1981. The exceptional position of sepiolids, a comparison of the orders of recent cephalopods. Zoologische Jahrbucher 108: 178-228.
24. Geweke J. 1992. Evaluating the accuracy of sampling-based approaches to the calculation of posterior moments. In: Bernardo JM, Berger J, David AP, Smith AFM, eds. Bayesian statistics 4. Oxford: Oxford University Press, 169-193.
25. Gray JE. 1849. Catalogue of the Mollusca in the Collection of the British Museum. Part I. Cephalopoda Antepedia. London, 614 pages.
26. Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology 52: 696-704.
27. Guindon S, Lethiec F, Duroux P, Gascuel O. 2005. PHYML Online - a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Research 33: W557-W559.
28. Hoyle WE. 1885. Diagnoses of New Species of Cephalopoda Collected During the Cruise of H.M.S. Challenger. - II. The Decapoda. Annals and Magazine of Natural History, (series 5) 16: 181-203.
29. Hylleberg J, Nateewathana A. 1991a. Morphology, internal anatomy, and biometrics of the cephalopod Idiosepius pygmaeus Voss, 1962. A new record for the Andaman Sea. Phuket Marine Biological Center Research Bulletin 56: 1-9.
30. Hylleberg J, Nateewathana A. 1991b. Redescription of Idiosepius pygmaeus Steenstrup, 1881 (Cephalopoda:Idiosepiidae), with mention of additional morphological characters. Phuket Marine Biological Center Research Bulletin 55: 33-42.
31. Keferstein W. 1866. Malacozoa, pages 523-1500. In: Bronn HG. Die Klassen und Ordnungen des Thier-reichs. Leipzig und Heidelberg, 1862-1866.
32. Larget B, Kadane JB, Simon DL. 2005. A Bayesian approach to the estimation of ancestral genome arrangements. Molecular Phylogenetics and Evolution 36: 214-223.
33. Lavrov DV, Brown WM, Boore JL. 2004. Phylogenetic position of the Pentastomida and (pan)crustacean relationships. Proceedings of the Royal Society Series B 271: 537-544.
34. Lavrov DV, Wang XJ, Kelly M. 2008. Reconstructing ordinal relationships in the Demospongiae using mitochondrial genomic data. Molecular Phylogenetics and Evolution 49: 111-124.
35. Lesson RP. 1830. Mollusques, Annelides et Vers. Voyage Autour du Monde, sur la Corvette de la Majeste, La Coquille, pendant les annees 1822, 1823, 1824 et 1825 2 (1): 239-471.
36. Lindgren AR, Daly M. 2007. The impact of length-variable data and alignment criterion on the phylogeny of Decapodiformes (Mollusca Cephalopoda). Cladistics 23: 464-476.
37. Lindgren AR, Giribet G, Nishiguchi MK. 2004. A combined approach to the phylogeny of Cephalopoda (Mollusca). Cladistics 20: 454-486.
38. Linnaeus C. 1758. Systema naturae per regna tria naturae, secundum classes, ordines, genera, species cum characteribus, diferentiis, synonymis, locis. Holmiae, 1758, Leipzig 1894, (Ed. 10), 824 pages.
39. Moret BME, Wang L-S, Warnow T, Wyman SK. 2001b. New approaches for reconstructing phylogenies from gene order data. Bioinformatics 17: S165-S173.
40. Moret BM, Wyman S, Bader D, Warnow T, Yan M. 2001a. A new implementation and detailed study of breakpoint analysis. Proceedings of the 6th Pacific symposium on biocomputing, Hawaii. World Scientific Publications, 583-594.
41. Moretti S, Armougom F, Wallace IM, Higgins DG, Jongeneel CV, Notredame C. 2007. The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Nucleic Acids Research 35: W645-W648.
42. Naef A. 1916. Systematische übersicht der mediterranen Cephalopoden. Pubblicazione Della Stazione Zoologica Di Napoli 1: 11-19.
43. Naef A. 19211923. Fauna und Flora des Golfes von Neapel und der angrenzenden Meeres-Abschnitte [Fauna and flora of the Bay of Naples], English translation by Israeli Program for Scientific Translations. Jerusalem: Keter Press.
44. Nateewathana A. 1997. The Sepiolidae (Cephalopoda) of the Andaman Sea, Thailand, with description of Euprymna hyllebergi sp. nov. Phuket Marine Biological Center Special Publication 17 (2): 465-481, 7 figures.
45. Orbigny Ad'. 1834183518431847. Mollusques. Voyage dans l'Amerique Méridionale 5 (3): 1-758. Atlas of 85 plates.
46. Ortmann A. 1888. Japanische Cephalopoden. Zoologische Jahrbücher 3: 639-670.
47. Pickford GE. 1936. A new order of dibranchiate cephalopods. The Anatomical Record 67: 77-78. [Abstract].
48. Pickford GE. 1938. The Vampyromorpha - a new order of dibranchiate cephalopods. British Association for the Advancement of Science, Report of the 108th Annual Meeting. pp. 427-428. [Abstract].
49. Pickford GE. 1940. The Vampyropmorpha, living fossil Cephalopoda. Transactions of the New York Academy of Sciences II 2: 169-181.
50. Plummer M, Best N, Cowles K, Vines K. 2009. Coda: output analysis and diagnostics for MCMC. R package version 0.13-4.
51. Robson GC. 1929. On the rare abyssal octopod Melanoteuthis beebei (sp. n.): a contribution to the phylogeny of the Octopoda. Proceedings of the Royal Society of London 3: 469-486.
52. Roper CFE. 1969. Systematics and zoogeography of the worldwide bathypelagic squid Bathyteuthis (Cephalopoda: Oegopsida). Bulletin of the United States National Museum 291: 1-210.
53. Simison WB, Boore JL. 2008. Molluscan evolutionary genomics. In: Ponder WF, Lindberg DR, eds. Phylogeny and evolution of the Mollusca. Berkeley: University of California Press, 447-461.
54. Sowerby GB. 1849. Monograph of the Genus Nautilus. Thesaurus Concyliorum 2: 463-465.
55. Steenstrup J. 1857. Oplysninger om Atlanterhavets Colossale Blaekprutter. Forhandlinger ved de Skandinaviske Naturforskeres 7: 182-185.
56. Steenstrup J. 1880. De Ommatostrephagtige Blaeksprutter indbyrdes Forhold, en Oreintering. Oversigt over det Kongelige Danske Videnskabernes Selskabs Forhandlinger 1880: 73-110.
57. Steenstrup J. 1881. Sepiadarium og Idiosepius to nye Slaegter af Sepiernes Familie. Med Bemaerknin ger om de to beslaegted e former Sepioloide a D'Orb. og Spirula Lmk. Det Kongelige dansk Videnskabernes Selskabs Skrif ter, (series 6) 1: 213-242.
58. Strugnell J, Nishiguchi MK. 2007. Molecular phylogeny of coleoid cephalopods (Mollusca Cephalopoda) inferred from three mitochondrial and six nuclear loci: a comparison of alignment, implied alignment and analysis methods. Journal of Molluscan Studies 73: 399-410.
59. Strugnell J, Norman M, Jackson J, Drummond AJ, Cooper A. 2005. Molecular phylogeny of coleoid cephalopods (Mollusca: Cephalopoda) using a multigene approach; the effect of data partitioning on resolving phylogenies in a Bayesian framework. Molecular Phylogenetics and Evolution 37: 426-441.
60. Swofford DL. 1998. PAUP*4.0: phylogenetic analysis using parsimony (* and other methods). Sunderland, MA: Sinauer.
61. Takumiya M, Kobayashi M, Tsuneki K, Furuya H. 2005. Phylogenetic relationships among major species of Japanese coleoid cephalopods (Mollusca: Cephalopoda) using three mitochondrial DNA sequences. Zoological Science 22: 147-155.
62. Teichert C. 1988. Main features of cephalopod evolution. In: Clarke MR, Trueman ER, eds. The Mollusca, vol. 12. Paleontology and neontology of cephalopods. San Diego: Academic Press, 11-79.
63. Tomita K, Yokobori S, Oshima T, Ueda T, Watanabe K. 2002. The cephalopod Loligo bleekeri mitochondrial genome: multiplied noncoding regions and transposition of tRNA genes. Journal of Molecular Evolution 54: 486-500.
64. Vecchione M, Young RE. 2008. Sepioidea Naef, 1916. Version 21 April 2008 (under construction). Available at: in The Tree of Life Web Project.
65. Vecchione M, Young RE, Carlini DB. 2000. Reconstruction of ancestral character states in neocoleoid cephalopods based on parsimony. American Malacological Bulletin 15: 179-193.
66. Verany JB. 1851. Céphalopodes de la Méditerranée. Mollusques Médit erané ens obser vés, décri ts figurés et chromolithographiés d'apr? s le vivant ouvrage dedie a SM le Roi Charles Albert 1: 1-137.
67. Wang LS, Jansen R, Moret B, Raubeson L, Warnow T. 2002. Fast phylogenetic methods for the analysis of genome rearrangement data: an empirical study. Proceedings of the Fifth Pacific Symposium of Biocomputing (PSB 02), pp 524-535.
68. Wang X, Lavrov DV. 2008. Seventeen new complete mtDNA sequences reveal extensive mitochondrial genome evolution within the Demospongiae. Plos ONE 3: e2723.
69. Wiens JJ. 1998. Does adding characters with missing data increase or decrease phylogenetic accuracy? Systematic Biology 47: 625-640.
70. Yokobori SI, Fukuda N, Nakamura M, Aoyama T, Oshima T. 2004. Long-term conservation of six duplicated structural genes in cephalopod mitochondrial genomes. Molecular Biology and Evolution 21: 2034-2046.
71. Yokobori S, Lindsay DJ, Yoshida M, Tsuchiya K, Yamagishi A, Maruyama T, Oshima T. 2007. Mitochondrial genome structure and evolution in the living fossil vampire squid, Vampyroteuthis infernalis, and extant cephalopods. Molecular Phylogenetics and Evolution 44: 898-910.
72. Young RE, Vecchione M. 1996. Analysis of morphology to determine primary sister taxon relationships within coleoid cephalopods. American Malacological Bulletin 12: 91-112.
73. Young RE, Vecchione M. 1999. Morphological observations on a hatchling and a paralarva of the vampire squid, Vampyroteuthis infernalis Chun (Mollusca, Cephalopoda). Proceedings of the Biological Society of Washington 112: 661-666.
74. Young RE, Vecchione M, Donovan DT. 1998. The evolution of coleoid cephalopods and their present biodiversity and ecology. South African Journal of Marine Science 20: 393-420.
75. Young RE, Vecchione M, Mangold KM. 2008. Decapodiformes Leach, 1817. Squids, cuttlefishes and their relatives. Version 21 April 2008. Available at: in The Tree of Life Web Project.