Assessing divergence time of Spirulida and Sepiida (Cephalopoda) based on hemocyanin sequences

Molecular Phylogenetics and Evolution

Volumn 58, Issue 2, 2011, Pages 390-394

  Warnke, Kerstin Martina ^a   Meyer, Achim ^b   Ebner, Bettina ^b   Lieb, Bernhard ^b  

^a FREIE UNIVERSITÄT BERLIN   (Germany)

^b JOHANNES GUTENBERG UNIVERSITY   (Germany)

Author keywords

Cephalopoda; Hemocyanin; Molecular clock; Sepia; Spirula

Indexed keywords

HEMOCYANIN;

ANIMAL; ARTICLE; CEPHALOPOD; CLASSIFICATION; DNA SEQUENCE; GENETICS; MOLECULAR EVOLUTION; PHYLOGENY; SEQUENCE ALIGNMENT;

ANIMALS; CEPHALOPODA; EVOLUTION, MOLECULAR; HEMOCYANIN; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

CEPHALOPODA; DECAPODIFORMES; GASTROPODA; HETEROBRANCHIA; MYA; SEPIA; SEPIA OFFICINALIS; SEPIIDA; SEPIIDAE; SPIRULA; SPIRULIDA; VETIGASTROPODA;

EID: 79951579818     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2010.11.024     Document Type: Article

References (42)

1. Abascal F., Zardoya R., Telford M.J. TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations. Nucl. Acids Res. 2010, gkq291.
2. Altenhein B., Markl J., Lieb B. Gene structure and hemocyanin isoform HtH2 from the mollusc Haliotis tuberculata indicate early and late intron hot spots. Gene 2002, 301:53-60.
3. Benton M.J. The Fossil Record 2 1993, Chapman and Hall, London.
4. Bergmann S., Markl J., Lieb B. The first complete cDNA sequence of the hemocyanin from a bivalve, the protobranch Nucula nucleus. J. Mol. Evol. 2007, 64:500-510.
5. Bergmann S., Lieb B., Ruth P., Markl J. The hemocyanin from a living fossil, the cephalopod Nautilus pompilius: protein structure, gene organization, and evolution. J. Mol. Evol. 2006, 62:362-374.
6. Boletzky S.v. Brève mise au point sur la classification des céphalopodes actuels. Bull. Soc. Zool. France 1999, 124:271-278.
7. Bonnaud L., Boucher-Rodoni R., Monnerot M. Phylogeny of decapod cephalopods based on partial 16S rDNA nucleotide sequences. C.R. Acad. Sci. 1994, 317:581-588.
8. Bruun A.F. The biology of Spirula spirula (L.). DanaRep 1943, 24:1-49.
9. Carlini D.B., Reece K.S., Graves J.E. Actin gene family evolution and the phylogeny of coleoid cephalopods (Mollusca: Cephalopoda). Mol. Biol. Evol. 2000, 17:1353-1370.
10. Dinapoli A., Klussmann-Kolb A. The long way to diversity-Phylogeny and evolution of the Heterobranchia (Mollusca: Gastropoda). Mol. Phyl. Evol. 2010, 55:60-76.
11. Doguzhaeva L.A., Mapes R., Mutvei H. A late Carboniferous spirulid coleoid from the southern midcontinent (USA): shell wall ultrastructure and evolutionary implications. Advancing Research on Living and Fossil Cephalopods 1999, 47-58. Kluwer Academic/Plenum Publishers, New York. F. Oloriz, F.J. Rodriguez-Tovar (Eds.).
12. Donovan D.T. Evolution of dibranchiate Cephalopoda. Symp. Zool. Soc. Lond. 1977, 38:15-48.
13. Drummond A., Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 2007, 7:214.
14. Engeser T. Phylogeny of the fossil coleoid Cephalopoda (Mollusca). Berliner Geowiss. Abh. 1990, 124:123-191.
15. Erben H.K. Über den Ursprung der Ammonoidea. Biol. Rev. 1966, 41:641-658.
16. Frýda J., Blodgett R.B. The oldest known heterobranch gastropod, Kuskokwimia gen. nov., from the Early Devonian of west-central Alaska, with notes on the early phylogeny of higher gastropods. Vestnik Ceského Geol. Ú stavu (Bull. Geol. Soc., Prague) 2001, 76:39-53.
17. Fuchs D. Fossil erhaltungsfähige Merkmalskomplexe der Coleoidea (Cephalopoda) und ihre phylogenetische Bedeutung. Berliner Paläobiol. Abh. 2006, 8:1-122. (doctoral thesis, Freie Universität Berlin).
18. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids Symp. Ser. 1999, 41:95-98.
19. Hewitt R.A., Jagt J.W.M. Maastrichtian Ceratisepia and Mesozoic cuttlebone homeomorphs. Acta Palaeontol. Pol. 1999, 44:305-326.
20. House M.R. Major features of cephalopod evolution. Cephalopods, Present and Past 1988, 1-16. Schweizerbart, Stuttgart. J. Wiedmann, J. Kullmann (Eds.).
21. Katoh K., Misawa K., Kuma K.-I., Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucl. Acids Res. 2002, 30:3059-3066.
22. Keller H., Lieb B., Altenhein B., Gebauer D., Richter S., Stricker S., Markl J. Abalone (Haliotis tuberculata) hemocyanin type 1 (HtH1). Organization of the approximately 400kDa subunit, and amino acid sequence of its functional units f, g and h. Eur. J. Biochem. 1999, 264:27-38.
23. Lamy J., You V., Taveau J.C., Boisset N., Lamy J.N. Intramolecular localization of the functional units of Sepia officinalis hemocyanin by immunoelectron microscopy. J. Mol. Biol. 1998, 284:1051-1074.
24. Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H., Valentin F., Wallace I.M., Wilm A., Lopez R., Thompson J.D., Gibson T.J., Higgins D.G. Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23:2947-2948.
25. Lieb B., Altenhein B., Markl J. The sequence of a gastropod hemocyanin (HtH1 from Haliotis tuberculata). J. Biol. Chem. 2000, 275:5675-5681.
26. Lieb B., Markl J. Evolution of molluscan hemocyanins as deduced from DNA sequencing. Micron 2004, 35:117-119.
27. Lieb B., Boisguérin V., Gebauer W., Markl J. CDNA sequence, protein structure, and evolution of the single hemocyanin from Aplysia californica, an opisthobranch gastropod. J. Mol. Evol. 2004, 59:536-545.
28. Lieb B., Todt C. Hemocyanin in mollusks - a molecular survey and new data on hemocyanin genes in Solenogastres and Caudofoveata. Mol. Phyl. Evol. 2008, 49:382-385.
29. Lieb B., Altenhein B., Markl J., Vincent A., van Olden E., van Holde K.E., Miller K.I. Structures of two molluscan hemocyanin genes: significance for gene evolution. Proc. Natl. Acad. Sci. USA 2001, 98:4546-4551.
30. Mouche F., Boisset N., Lamy J., Zal F., Lamy J.N. Structural comparison of cephalopod hemocyanins: phylogenetic significance. J. Struct. Biol. 1999, 127:199-212.
31. Naef A. Die fossilen Tintenfische 1922, Fischer, Jena, (English Translation: Berliner Paläobiol Abh 5).
32. Nesis K.N. Cephalopods of the World. Squids, Cuttlefishes, Octopuses and Allies 1987, TFH Publication, Neptune City, New Jersey.
33. Norman M. Cephalopods, a World Guide 2000, ConchBooks, Hackenheim.
34. Posada D. JModelTest: Phylogenetic Model Averaging. Mol. Biol. Evol. 2008, 25:1253-1256.
35. Schindewolf O.H. Vergleichende Morphologie und Phylogenie der Anfangskammern tetrabranchiater Cephalopoden. Abh. Preuss. Geol. Landesanst. N.F. 1933, 148:1-115.
36. Rambaut, A., Drummond, A., 2007. Tracer v1.4, http://beast.bio.ed.ac.uk/Tracer.
37. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
38. Strugnell J., Jackson J., Drummond A.J., Cooper A. Divergence time estimates for major cephalopod groups: evidence from multiple genes. Cladistics 2006, 22:89-96.
39. Talavera G., Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 2007, 56:564-577.
40. Tamura K., Dudley J., Nei M., Kumar S. Mega4: Molecular evolutionary. Genetics Analysis (Mega) software version 4.0. Mol. Biol. Evol. 2007, 24:1596-1599.
41. Warnke K., Plötner J., Santana J.I., Rueda M.J., Llinas O. Reflections on the phylogenetic position of Spirula (Cephalopoda): preliminary evidence from the 18S ribosomal RNA gene. Berliner Paläobiol. Abh. 2003, 3:253-260.
42. Warnke K., Keupp H. Spirula - a recent model for ammonoids? Molecular indication for a palaeontological hypothesis. Facies 2005, 51:60-65.