Molecular phylogeny and species identification of sardines

Journal of Agricultural and Food Chemistry

Volumn 51, Issue 1, 2003, Pages 43-50

  Jérôme, Marc ^a   Lemaire, Christophe ^a   Bautista, José M ^b   Fleurence, Joël ^a   Etienne, Monique ^a  

^a IFREMER   (France)

^b UNIVERSIDAD COMPLUTENSE DE MADRID   (Spain)

Author keywords

Clupeidae; Cytochrome b gene; Genetic divergence; PCR RFLP; Sardine; Species identification

Indexed keywords

CYTOCHROME B; DEOXYRIBONUCLEASES, TYPE II SITE SPECIFIC; DNA; ENDODEOXYRIBONUCLEASE HINFI; ENDODEOXYRIBONUCLEASE MNLI; MITOCHONDRIAL DNA; RESTRICTION ENDONUCLEASE; TYPE II SITE SPECIFIC DEOXYRIBONUCLEASE;

ANIMAL; ARTICLE; CANNED FOOD; CLASSIFICATION; COMPARATIVE STUDY; CONTROLLED STUDY; DNA SEQUENCE; FISH; FOOD ANALYSIS; GENETIC CODE; GENETIC PARAMETERS; GENETICS; ISOLATION PROCEDURE; METABOLISM; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SARDINA PILCHARDUS; SPECIES IDENTIFICATION;

ANIMALS; CYTOCHROME B GROUP; DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; DNA, MITOCHONDRIAL; FISHES; PHYLOGENY; POLYMERASE CHAIN REACTION; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH;

ANIMALIA; CLUPEIDAE; CLUPEOMORPHA; SARDINA PILCHARDUS;

EID: 0037223855     PISSN: 00218561     EISSN: None     Source Type: Journal    
DOI: 10.1021/jf020713w     Document Type: Article

References (56)

1. Durand, P.; Landrein, A.; Quéro, J. C. Catalogue Électrophorétique Des Poissons Commerciaux; IFREMER: Nantes, France, 1985.
2. Lundstrom, R. Fish species identification by thin-layer polyacrylamide gel isoelectric focusing: Collaborative study. J. Assoc. Off. Anal. Chem. 1980, 63, 69-73.
3. Rehbein, H.; Mackie, I. M.; Gonzales-Sotelo, C.; Perez-Martin, R.; Quinteiro, J.; Rey-Mendez, M. Fish species identification in canned tuna by DNA analysis (PCR-SSCP). Inf. Fischwirtsch. 1995, 42, 209-212.
4. Piñeiro, C.; Sotelo, C. G.; Medina, I.; Gallardo, J. M.; Pérez-Martín, R. Reverse-phase HPLC as a method for the identification of gadoid fish species. Z. Lebensm.-Unters.-Forsch., A 1997, 204, 411-416.
5. Osman, M. A.; Ashoor, S. H.; Marsh, P. C. Liquid chromatographic identification of common fish species. J. Assoc. Off. Anal. Chem. 1987, 70, 618-625.
6. Etienne. M.; Jérôme. M.; Fleurence, J.; Rehbein, H.; Kundiger, R.; Yman, I.; Ferm, M.; Craig, A.; Mackie, I.; Jessen, F.; Smelt, A.; Luten, J. A standardized method of identification of raw and heat-processed fish by urea isoelectric focusing: A collaborative study. Electrophoresis 1999, 20, 1923-1933.
7. Etienne, M.; Jérôme. M.; Fleurence, J.; Rehbein, H.; Kündiger, R.; Mendes, R.; Costa, H.; Perez-Martin, R.; Pineiro-Gonzalez, C.; Craig-A.; Mackie, I.; Yman, I. M.; Ferm, M.; Martinez, I.; Jessen, F.; Smelt, A.; Luten, J. Identification of fish species after cooking by SDS-PAGE and urea IEF: A collaborative study. J. Agric. Food Chem. 2000, 48, 2653-2658.
8. Etienne, M.; Jérôme, M.; Fleurence, J.; Rehbein, H.; Kündiger, R.; Mendes, R.; Costa, H.; Martinez, I. Species identification of formed fishery products and high pressure-treated fish by electrophoresis: A collaborative study. Food Chem. 2001, 72, 105-112.
9. Mackie, I.; Craig, A.; Etienne, M.; Jérôme, M.; Fleurence, J.; Jessen, F.; Smelt, A.; Kruijt, A.; Yman, I. M.; Ferm, M.; Martinez, I.; Perez-Martin, R.; Pineiro, C.; Rehbein, H.; Kundiger, R. Species identification of smoked and gravad fish products by sodium dodecylsulphate polyacrylamide gel electrophoresis, urea isoelectric focusing and native isoelectric focusing: A collaborative study. Food Chem. 2000, 71, 1-7.
10. Piñeiro, C.; Barros-Velazquez, J.; Perez-Martin, R. I.; Martinez, I.; Jacobsen, T.; Rehbein, H.; Kundiger, R.; Mendes, R.; Etienne, M.; Jérôme, M.; Craig, A.; Mackie, I. M.; Jessen, F. Development of a sodium dodecyl sulfate-polyacrylamide gel electrophoresis reference method for the analysis and identification of fish species in raw and heat-processed samples: A collaborative study. Electrophoresis 1999, 20, 1425-1432.
11. Rehbein, H.; Kundiger, R.; Yman, I. M.; Ferm, M.; Etienne, M.; Jérôme, M.; Craig, A.; Mackie, I.; Jessen, F.; Martinez, I.; Mendes, R.; Smelt, A.; Luten, J.; Pineiro, C.; Perez-Martin, R. Species identification of cooked fish by urea isoelectric focusing and sodium dodecyl sulfate polyacrylamide gel electrophoresis: A collaborative study. Food Chem. 1999, 67, 333-339.
12. Bossier, P. Authentication of seafood products by DNA patterns. J. Food Sci. 1999, 64, 189-193.
13. Lockley, A. K.; Bardsley, R. G. DNA-based methods for food authentication. Trends Food Sci. Technol. 2000, 11, 67-77.
14. Kocher, T. D.; Thomas, W. K.; Meyer, A.; Edwards, S. V.; Paabo, S.; Villablanca, F. X.; Wilson, A. C. Dynamics of mitochondrial DNA evolution in animals: Amplification and sequencing with conserved primers. Proc. Natl. Acad. Sci. U.S.A. 1989, 86, 6196-6200.
15. Bartlett, S. E.; Davidson, W. S. Identification of Thunnus tuna species by the polymerase chain reaction and direct sequence analysis of their mitochondrial cytochrome b genes. Can. J. Fish. Aquat. Sci 1991, 48, 309-317.
16. Bartlett, S. E.; Davidson, W. S. FINS (Forensically Informative Nucleotide Sequencing): A procedure for identifying the animal origin of biological specimens. Biotechnology 1991, 12, 408-411.
17. Albert, B.; Lewis, D.; Raff, J.; Roberts, K.; Watson, J. D. In Molecular Biology of the Cell; Garland Publishing: New York, 1994; p 94.
18. Carvalho, G. R.; Hauser, L. Advances in the molecular analysis of fish population structure. It. J. Zool. 1998, 65, 21-33.
19. Sezaki, K.; Kuboshima, Y.; Mitani, I.; Fukui, A.; Watabe, S. Identification of chub and spotted mackerels with mitochondrial cytochrome b genes and its application to respective pelagic eggs fixed with formalin. Nippon Suisan Gakkaishi 2001, 67, 17-22.
20. Bembo, D. G.; Carvalho, G. R.; Snow, M.; Cingolani, N.; Pitcher, T. J. Stock discrimination among European anchovies, Engraulis encrasicolus, by means of PCR-amplified mitochondrial DNA analysis. Fish. Bull. 1995, 94, 31-40.
21. Grant, W. S.; Clark, A. M.; Bowen, B. W. Why restriction fragment length polymorphism analysis of mitochondrial DNA failed to resolve sardine (Sardinops) biogeography: Insights from mitochondrial DNA cytochrome b sequences. Can. J. Fish. Aquat. Sci. 1998, 55, 2539-2547.
22. Hauser, L.; Ward, R. D. Population identification in pelagic fish: The limits of molecular markers. Adv. Mol. Ecol. 1998, 191-224.
23. Meyer, A. DNA technology and phylogeny of fish. In Genetics and Evolution of Aquatic Organisms; Chapman and Hall: Beaumont, AR, 1994.
24. Grant, W. S.; Bowen, B. W. Shallow population histories in deep evolutionary lineages of marine fishes: Insights from sardines and anchovies and lessons for conservation. J. Hered. 1998, 89, 415-426.
25. Froese, R.; Pauly, D. World Wide Web electronic publication, FishBase: www.fishbase.org, 2002.
26. Parrish, R. H.; Serra, R.; Grant, W. S. The monotypic sardines Sardina and Sardinpos: Their taxonomy, distribution, stock structure, and zoogeography. Can. J. Fish. Aquat. Sci. 1989, 46, 2019-2036.
27. Chickhi, L.; Agnèse, J.-F.; Bonhomme, F. Fortes différences des ADN mitochondriaux de populations de Sardinella aurita de la mer Méditerranée et de l'Atlantique Est. C. R. Acad. Sci., Ser. 3 1997, 289-297.
28. Chickhi, L.; Bonhomme, F.; Agnèse, J.-F. Low genetic variability in a widely distributed and abundant clupeid species, Sardinella aurita. New empirical results and interpretations. J. Fish Biol. 1998, 52, 861-878.
29. Magoulas, A.; Tsimenides, N.; Zouros, E. Mitochondrial DNA phylogeny and the reconstruction of population history of a species: The case of the European anchovy (Engraulis encrasicolus). Mol. Biol. Evol. 1996, 13, 178-190.
30. Tringali, M. D.; Wilson, R. R. Differences in haplotype frequencies of mtDNA of the Spanish sardine Sardinella aurita between specimens from the eastern Gulf of Mexico and southern Brazil. Fish. Bull. U.S. 1993, 91, 362-370.
31. Kimura, M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 1980, 16, 111-120.
32. Grant, W. S.; Leslie, R. W. Late Pleitocene dispersal of Indian-Pacific sardine populations in an ancient lineage of the genus Sardinops. Mar. Biol. 1996, 126, 133-142.
33. Quinteiro, J.; Sotelo, C. G.; Rehbein, H.; Pryde, S. E.; Medina, I.; Perez-Martin, R. I.; Rey-Mendez, M.; Mackie, I. M. Use of mtDNA direct polymerase chain reaction (PCR) sequencing and PCR-restriction fragment length polymorphism methodologies in species identification of canned tuna. J. Agric. Food Chem. 1998, 46, 1662-1669.
34. Hall, T. A. BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 1999, 41, 95-98.
35. Kumar, S.; Tamura, K.; Jakobsen, I.; Nei, M. MEGA2: Molecular Evolutionary Genetics Analysis Software. Bioinformatics 2001, 17, 1244-1245.
36. Brown, W. M.; Prager, E. M.; Wang, A.; Wilson, A. C. Mitochondrial DNA sequence of primates: Tempo and mode evolution. J. Mol. Evol. 1982, 18, 239-255.
37. Holmquist, R. Transitions and transversions in evolutionary descent: An approach to understanding. J. Mol. Evol. 1983, 19, 134-144.
38. Tamura, K.; Nei, M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in human and chimpanzees. Mol. Biol. Evol. 1993, 10, 512-526.
39. Saitou, N.; Nei, M. The Neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1987, 4, 406-425.
40. Fitch, W. M. Toward defining the course of evolution: Minimum change for a specific tree topology. Syst. Zool. 1971, 20, 406-416.
41. Felsenstein, J. Phylip 3.5 (Phylogeny Inference Package); University of Washington: Seattle, WA, 1993.
42. Inoue, J. G.; Miya, M.; Tsukamoto, K.; Nishida, M. Complete mitochondrial DNA sequence of the Japanese sardine Sardinops melanosticus. Fish. Sci. 2000, 66, 924-932.
43. Miya, M.; Nishida, M. Organization of the mitochondrial genome of a deep-sea fish, Gonostoma gracile (Teleostei: Stomiiformes): First example of transfer RNA gene rearrangements in bony fishes. Mar. Biotechnol. 1999, 1, 416-426.
44. Quinteiro, J.; Vidal, R.; Rey-Mendez, M. Phylogeny and biogeographic history of hake (genus Merluccius), inferred from mitochondrial DNA control-region sequences. Mar. Biol. 2000, 136, 163-174.
45. Tinti, F.; Piccinetti, C.; Tommasini, S.; Vallisneri, M. Mitochondrial DNA variation, phylogenetic relationships, and evolution of four Mediterranean genera of soles (Soleidae, Pleuronectiformes). Mar. Biotechnol. 2000, 2, 274-284.
46. Graur, D.; Li, W.-H. Fundamentals of Molecular Evolution, 2nd Ed.; Sinauer Associates: Sunderland, MA, 1999.
47. Johns, G. C.; Avise, J. C. A comparative summary of genetic distances in the vertebrates from the mitochondrial cytochrome b gene, Mol. Biol. Evol. 1998, 15, 1481-1490.
48. Okazaki, T.; Kobayashi, T.; Uozomi, Y. Genetic relationships of pilchards (genus Sardinops) with anti-tropical distributions. Mar. Biol. 1996, 126, 585-590.
49. Bowen, B. W.; Grant, W. S. Phylogeography of the sardines (Sardinops spp): Assessing biogeographic models and population histories in temperate upwelling zones. Evolution 1997, 51, 1601-1610.
50. Svetovidov, A. N. Fishes: Clupeidae. Fauna U.S.S.R. (New Ser.) 1952, 2, 1.
51. Pamilo, P.; Nei, M. Relationship between gene trees and species trees. Mol. Biol. Evol. 1988, 5, 568-583.
52. Avise, J. C. Molecular Markers, Natural History and Evolution; Chapman and Hall: London, 1994.
53. Lydeard, C.; Roe, K. J. The Phylogenetic Utility of the Mitochondrial Cytochrome b Gene for Inferring Relationships Among Actinopterygian Fishes; Kocher, T. D., Stepien, C. A., Eds.; Academic Press: San Diego, CA; pp 285-303.
54. Rehbein, H.; Kress, G.; Schmidt, T. Application of PCR-SSCP to species identification of fishery products. J. Sci. Food Agric. 1997, 74, 35-41.
55. Ram, J. L.; Ram, M. L.; Baidoun, F. F. Authentication of canned tuna and bonito by sequence and restriction site analysis of polymerase chain reaction products of mitochondrial DNA. J. Agric. Food Chem. 1996, 44, 2460-2467.
56. Wolf, C.; Burgener, M.; Hubner, P.; Luthy, J. PCR-RFLP analysis of mitochondrial DNA: Differentiation of fish species, Lebensm.-Wiss. Technol. 2000, 144-150.