A barcode of life database for the Cephalopoda? Considerations and concerns

Reviews in Fish Biology and Fisheries

Volumn 17, Issue 2-3, 2007, Pages 337-344

  Strugnell, Jan M ^a,b   Lindgren, Annie R ^c  

^a QUEEN'S UNIVERSITY BELFAST   (United Kingdom)

^b BRITISH ANTARCTIC SURVEY   (United Kingdom)

^c OHIO STATE UNIVERSITY   (United States)

Author keywords

Barcode of life database (BoLD); Cephalopoda; Cytochrome c oxidase subunit I (COI); Mitochondrial DNA

Indexed keywords

CEPHALOPOD; CONFERENCE PROCEEDING; DATABASE; MITOCHONDRIAL DNA;

AUSTRALASIA; AUSTRALIA; HOBART; TASMANIA;

CEPHALOPODA; MOLLUSCA;

EID: 34249869528     PISSN: 09603166     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11160-007-9043-0     Document Type: Conference Paper

References (50)

1. Anderson FE (2000a) Phylogenetic relationships among loliginid squids (Cephalopoda: Myopsida) based on analyses of multiple datasets. Zool J Linnean Soc 130:603-633
2. Anderson FE (2000b) Phylogeny and historical biogeography of the loliginid squids (Mollusca: Cephalopoda) based on mitochondrial DNA sequence data. Mol Phylogenet Evol 15(2):191-214
3. Ballard JW, Kreitman M (1995) Is mitochondrial DNA a strictly neutral marker? Trends Ecol Evol 10(12): 485-488
4. Benesh DP, Hasu T, Suomalainen LR, Valtonen ET, Tiirola M (2005) Reliability of mitochondrial DNA in an acanthocephalan: The problem of pseudogenes. Int J Parasitol 36(2):247-254
5. Bensasson D, Zhang D-X, Hewit GM (2000) Frequent assimilation of mitochondrial DNA by grasshopper nuclear genomes. Mol Biol Evol 17:406-415
6. Bonnaud L, Boucher-Rodoni R, Monnerot M (1997) Phylogeny of cephalopods inferred from mitochondrial DNA sequences. Mol Phylogenet Evol 7(1):44-54
7. Boore JL (1994) Complete DNA sequence of the mitochondrial genome of the black chiton, Katharina tunicata. Genetics 138:423-443
8. Boore JL (1999) Animal mitochondrial genomes. Nucleic Acids Res 27:1767-1780
9. Boore JL, Brown WM (1994) Mitochondrial genomes and the phylogeny of mollusks. Nautilus Suppl 2:61-78
10. Boore JL, Brown WM (1995) Complete sequence of the mitochondrial DNA of the annelid worm Lumbricus terretris. Genetics 141:305-319
11. Brown WM, George Jr M, Wilson AC (1979) Rapid evolution of animal mitochondrial DNA. Proc Natl Acad Sci USA 76:1967-1971
12. Brown WM, Prager EM, Wang A, Wilson AC (1982) Mitochondrial DNA sequences of primates: Tempo and mode of evolution. J Mol Evol 18:225-239
13. Brower AVZ (1994) Rapid morphological radiation and convergence among races of the butterfly Heliconius erato inferred from patterns of mitochondrial DNA evolution. Proc Natl Acad Sci USA. 91:6491-6495
14. Carlini DB, Graves JE (1999) Phylogenetic analysis of cytochrome c oxidase I sequences to determine higher-level relationships within the coleoid cephalopods. Bull Mar Sci 64(1):57-76
15. Carlini DB, Young RE, Vecchione M (2001) A molecular phylogeny of the Octopoda (Mollusca: Cephalopoda) evaluated in light of morphological evidence. Mol Phyl Evol 21(3):388-397
16. Carlini DB, Kunkle LK, Vecchione M (2006) A molecular systematic evaluation of the squid genus Illex (Cephalopoda: Ommastrephidae) in the North Atlantic Ocean and Mediterranean Sea. Mol Phylogenet Evol 41(2):496-502
17. Dasmahapatra KK, Mallet J (2006) DNA barcodes: Recent successes and future prospects. Heredity, June: 1-2
18. DeSalle R, Egan MG, Siddall M (2005) The unholy trinity: Taxonomy, species delimitation and DNA barcoding. Phil Trans R Soc B 360:1905-1916
19. Erpenbeck D, Hooper JNA, Worheide G (2006) COI phylogenies in diploblasts and the 'Barcoding of Life - are we sequencing a suboptimal partition? Mol Ecol Notes 6:550-553
20. Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek RC (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol 3: 294-299
21. Funk DJ, Omland KE (2003) Species level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Ann Rev Ecol Syst 34:397-423
22. Hanner R (2005) Proposed Standards for BARCODE Records in INSDC (BRIs). Available online at the Consortium for the Barcode of Life:
23. Hebert PD, Ratnasingham S, deWaard JR (2003) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc R Soc Lond B 270:S96-S99
24. Hebert PD, Penton EH, Burns JM, Janzen, DH, Hallwachs W (2004) Proc Natl Acad Sci USA 101:14812-14817
25. Hoeh WR, Steward DT, Sutherland BW, Zouros E (1996) Cytochrome c oxidase sequence comparisons suggest and unusually high rate of mitochondrial DNA evolution in Mytilus (Mollusca: Bivalvia). Mol Biol Evol 13(2):418-421
26. Juan C, Oromi P, Hewitt GM (1995) Mitochondrial DNA phylogeny and sequential colonization of Canary Islands by darkling beetles of the genus Pimelia (Tenebrionidae). Proc R Soc Lond B 261:173-180
27. Juan C, Oromi P, Hewitt GM (1996) Phylogeny of the genus Hegeter (Tenebrionidae, Coleoptera) and its colonization of the Canary Islands deduced from cytochrome oxidase I mitochondrial DNA sequence. Heredity 76:392-403
28. Kirby RR, Lindley JA (2005) Molecular analysis of Continuous Plankton Recorder samples, an examination of echinoderm larvae in the North Sea. J Mar Biol Ass UK 85:451-459
29. Kocher TD (1991) Sequence evolution of mitochondrial DNA in human and chimpanzees: Control region and protein coding region. In: S. Osawa, T. Honjo (eds) Evolution of life: Fossils, molecules, and culture. Springer, Tokyo, pp 391-413
30. Lindgren AR, Giribet G, Nishiguchi MK (2004) A combined approach to the phylogeny of Cephalopoda (Mollusca). Cladistics 20:454-496
31. Lindgren AR, Katugin ON, Amezquita E, Nishiguchi MK (2005) Evolutionary relationships among squids of the family Gonatidae (Mollusca: Cephalopoda) inferred from three mitochondrial loci. Mol Phyl Evol 36:101-111
32. Meyer CP, Paulay G (2005) DNA barcoding: Error rates based on comprehensive sampling. PLoS Biol 3(12): 0001-0010
33. Moritz C, Dowling TE, Brown WM (1987) Evolution of animal mitochondrial DNA: Relevance for population biology and systematics. Ann Rev Ecol Syst 18:269-292
34. Mundy NI, Pissinatti A, Woodruff DS (2000) Multiple muclear insertions of mitochondrial cytochrome b sequences in callitrichine primates. Mol Biol Evol 17:1075-1080
35. Nishiguchi MK, Lopez JE, Boletzky Sv (2004) Enlightenment of old ideas from new investigations: The evolution of bacteriogenic light organs in squids. Evol Dev 6:41-49
36. Richly E, Leister D (2004) NUMT's in sequenced eukaryotic genomes. Mol Biol Evol 21(6):1081-1084
37. Shearer TL, Van Oppen MJH, Romano SL, Worheide G (2002) Slow mitochondrial DNA sequence evolution in the Anthozoa (Cnidaria). Mol Ecol 11(12):2475-2487
38. Smith MA, Woodley NE, Janzen DH, Hallwachs W, Hebert PD (2006) Proc Natl Acad Sci USA 103:3657-3662
39. Sorenson MD, Fleischer RC (1996) Multiple independent transpositions of mitochondrial DNA control region sequences to the nucleus. Proc Natl Acad Sci USA 93:15239-15243
40. Strugnell J, Norman M, Drummond A, Cooper A (2004) The octopuses that never came back to earth: Neoteny and pelagic octopuses. Curr Biol 14:R300-R301
41. 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. Mol Phylogenet Evol 37(2):426-441
42. Strugnell J, Jackson J, Drummond AJ, Cooper A (2006) Divergence time estimates for major cephalopod groups: Evidence from multiple genes. Cladistics 22:89-96
43. Thalmann O, Serre D, Hofreiter M, Lukas D, Eriksson J, Vigilant L (2005) Nuclear insertions help and hinder inference of the evolutionary history of gorilla mtDNA. Mol Ecol 14:179-188
44. Tomita K, Yokobori S, Oshima T, Ueda T, Watanabe K (2002) Cephalopod Loligo bleekeri mitochondrial genome: Multiplied noncoding regions and transposition of tRNA Genes. J Mol Evol 54:486-500
45. Valverde J, Batuecas B, Moratilla C, Marco R, Garesse R (1994) The complete mitochondrial DNA sequence of the crustacean Artemia franciscana. J Mol Evol 39: 400-408
46. Wakabayashi T, Suzuki N, Sakai M, Ichii T, Chow S (2006) Identification of ommastrephid squid paralarvae collected in northern Hawaiian waters and phylogenetic implications for the family Ommastrephidae using mtDNA analysis. Fish Sci 72(3):494-502
47. Williams ST, Knowlton N (2001) Mitochondrial pseudogenes are pervasive and often insidious in the snapping shrimp genus Alpheus. Mol Biol Evol 18:1484-1493
48. Yamazaki N, Ueshima R, Terrett JA, Yokobori S, Kaifu M, Segawa R, Kobayashi T, Numachi K, Ueda T, Nishikawa K, Watanabe K, Thomas RH (1997) Evolution of pulmonate gastropod mitochondrial genomes: comparisons of gene organizations if Euhadra, Cepaea and Albinaria and implications of unusual tRNA secondary structures. Genetics 145: 749-758
49. Yokobori S, Fukuda N, Nakamura M, Aoyama T, Oshima T (2004) Long-term conservation of six duplicated structural genes in cephalopod mitochondrial genomes. Mol Biol Evol 21(11):2034-2046
50. Zischler H, Geisert H, von Haesler A, Pääbo S (1995) A nuclear 'fossil' of the mitochondrial D-loop and the origin of modern hmans. Nature 387:489-492