Evolutionary relatedness of mackerels of the genus Scomber based on complete mitochondrial genomes: Strong support to the recognition of Atlantic Scomber colias and Pacific Scomber japonicus as distinct species

Gene

Volumn 452, Issue 1, 2010, Pages 35-43

  Catanese, Gaetano ^a   Manchado, Manuel ^a   Infante, Carlos ^a  

^a IFAPA CENTRO EL TORUÑO   (Spain)

Author keywords

Mitochondrial genome; Phylogeny; Scomber; Scomber colias; Scomber japonicus

Indexed keywords

ARTICLE; DNA SEQUENCE; FISH; FISH GENETICS; GENETIC ANALYSIS; GENETIC CONSERVATION; MITOCHONDRIAL GENOME; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; SCOMBER COLIAS; SCOMBER JAPONICUS; SPECIES DIFFERENCE;

ANIMALS; ATLANTIC OCEAN; BASE COMPOSITION; BASE SEQUENCE; DNA, INTERGENIC; EVOLUTION, MOLECULAR; GENES, RRNA; GENETIC SPECIATION; GENOME, MITOCHONDRIAL; MOLECULAR SEQUENCE DATA; MUTATION; OPEN READING FRAMES; PACIFIC OCEAN; PERCIFORMES; PHYLOGENY; RNA, TRANSFER; SPECIES SPECIFICITY;

SCOMBER; SCOMBER AUSTRALASICUS; SCOMBER COLIAS; SCOMBER JAPONICUS; SCOMBER SCOMBRUS; SCOMBRIDAE; VERTEBRATA;

EID: 74549177042     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2009.12.004     Document Type: Article

References (65)

1. Alvarado Bremer J.R., Naseri I., Ely B. Orthodox and unorthodox phylogenetic relationships among tunas revealed by the nucleotide sequence analysis of the mitochondrial DNA control region. J. Fish Biol. 1997, 50:540-554.
2. Alvarado Bremer J.R., Viñas J., Mejuto J., Ely B., Pla C. Comparative phylogeography of Atlantic bluefin tuna and swordfish: the combined effects of vicariance, secondary contact, introgression, and population expansion on the regional phylogenies of two highly migratory pelagic fishes. Mol. Phylogenet. Evol. 2005, 36:169-187.
3. Avise J.C. Molecular population structure and the biogeographis history of a regional fauna: a case history with lessons for conservation biology. Oikos 1992, 62:62-76.
4. Boore J.L. Animal mitochondrial genomes. Nucleic Acids Res. 1999, 27:1767-1780.
5. Broughton R.E., Reneau P.C. Spatial covariation of mutation and nonsynonymous substitution rates in vertebrate mitochondrial genomes. Mol. Biol. Evol. 2006, 23:1516-1524.
6. Broughton R.E., Milam J.E., Roe B.A. The complete sequence of the zebrafish (Danio rerio) mitochondrial genome and evolutionary patterns in vertebrate mitochondrial DNA. Genome Res. 2001, 11:1958-1967.
7. Brown W.M., George M., Wilson A.C. Rapid evolution of animal mitochondrial DNA. Proc. Natl. Acad. Sci. U. S. A. 1979, 76:1967-1971.
8. Catanese G., Infante C., Manchado M. Complete mitochondrial DNA sequences of the frigate tunas Auxis thazard and the bullet tuna Auxis rochei. DNA Seq. 2008, 19:159-166.
9. Chow S., Kishino H. Phylogenetic relationships between tuna species of the genus Thunnus (Scombridae: Teleostei): inconsistent implications from morphology, nuclear and mitochondrial genomes. J. Mol. Evol. 1995, 41:741-748.
10. Clayton D.A. Nuclear gadgets in mitochondrial DNA replication and transcription. Trends Biochem. Sci. 1991, 16:107-111.
11. Clayton D.A. Transcription and replication of animal mitochondrial DNAs. Int. Rev. Cytol. 1992, 141:217-232.
12. Collette B.B. Family Scombridae Rafinisque 1815-Mackerels, Tunas, and Bonitos, Annotated Checklist of Fishes California Academy Sciences 2003, 28 pp.
13. Collette B.B., Nauen C.E. Scombrids of the world. An annotated and illustrated catalogue of tunas, mackerels, bonitos, and related species known to date. FAO 1983, FAO, Rome. F.A.O. Species Catalogue (Ed.).
14. Collette B.B., Reeb C., Block B.A. Systematics of the tunas and mackerels (Scombridae). Fish Physiol. 2001, 19:1-33.
15. Curole J.P., Kocher T.D. Mitogenomics: digging deeper with complete mitochondrial genomes. Trends Ecol. Evol. 1999, 14:394-398.
16. Espiñeira M., González-Lavín N., Vieites J.M., Santaclara F.J. Development of a method for the identification of scombroid and common substitute species in seafood products by FINS. Food Chem. 2009, 117:698-704.
17. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985, 39:783-791.
18. Food and Agriculture Organization (FAO), 2007. Fishery statistical collection. Global capture production. Available from. http://www.fao.org/fishery/statistics/global-capture-production/.
19. Galtier N., Lobry J.R. Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes. J. Mol. Evol. 1997, 44:632-636.
20. Hixson J.E., Wong T.W., Clayton D.A. Both the conserved stem-loop and divergent 5'-flanking sequences are required for initiation at the human mitochondrial origin of light-strand DNA replication. J. Biol. Chem. 1986, 261:2384-2390.
21. Hurst C.D., Bartlett S.E., Davidson W.S., Bruce I.J. The complete mitochondrial DNA sequence of the Atlantic salmon, Salmo salar. Gene 1999, 239:237-242.
22. Infante C., Blanco E., Zuasti E., Crespo A., Manchado M. Phylogenetic differentiation between Atlantic Scomber colias and Pacific Scomber japonicus based on nuclear DNA sequences. Genetica 2007, 130:1-8.
23. Inoue J.G., Miya M., Tsukamoto K., Nishida M. A mitogenomic perspective on the basal teleostean phylogeny: resolving higher-level relationships with longer DNA sequences. Mol. Phylogenet. Evol. 2001, 20:275-285.
24. Inoue J.G., Miya M., Tsukamoto K., Nishida M. Complete mitochondrial DNA sequence of the Japanese anchovy Engraulis japonicus. Fish Sci. 2001, 67:828-835.
25. Kartavtsev Y.P., Lee J.S. Analysis of nucleotide diversity at the cytochrome b and cytochrome oxidase 1 genes at the population, species, and genus levels. Genetika 2006, 42:437-461.
26. Kartavtsev Y.P., Jung S.O., Lee Y.M., Byeon H.K., Lee J.S. Complete mitochondrial genome of the bullhead torrent catfish, Liobagrus obesus (Siluriformes, Amblycipididae): genome description and phylogenetic considerations inferred from the Cyt b and 16S rRNA genes. Gene 2007, 396:13-27.
27. Kawahara R., et al. Interrelationships of the 11 gasterosteiform families (sticklebacks, pipefishes, and their relatives): a new perspective based on whole mitogenome sequences from 75 higher teleosts. Mol. Phylogenet. Evol. 2008, 46:224-236.
28. Keigwin L.D. Pliocene closing of the isthmus of Panamá, based on biostratigraphic evidence from nearby Pacific Ocean and Caribbean Sea cores. Geology 1978, 6:630-634.
29. Keigwin L. Isotopic paleoceanography of the Caribbean and East Pacific: role of Panama uplift in Late Neogene time. Science 1982, 217:350-353.
30. Kijima A., Taniguchi N., Ochiai A. Genetic divergence and morphological difference between the spotted and common mackerel. Japan J. Ichthyol. 1986, 33:152-161.
31. Lavoué S., Miya M., Saitoh K., Ishiguro N.B., Nishida M. Phylogenetic relationships among anchovies, sardines, herrings and their relatives (Clupeiformes), inferred from whole mitogenome sequences. Mol. Phylogenet. Evol. 2007, 43:1096-1105.
32. Lavoué S., Miya M., Poulsen J.Y., Moller P.R., Nishida M. Monophyly, phylogenetic position and inter-familial relationships of the Alepocephaliformes (Teleostei) based on whole mitogenome sequences. Mol. Phylogenet. Evol. 2008, 47:1111-1121.
33. Librado P., Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 2009, 25:1451-1452.
34. Lowe T.M., Eddy S.R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997, 25:955-964.
35. Manchado M., Catanese G., Infante C. Complete mitochondrial DNA sequence of the Atlantic bluefin tuna Thunnus thynnus. Fish Sci. 2004, 70:68-73.
36. Manchado M., Catanese G., Infante C. Estudio comparativo del ADN mitocondrial en miembros de la familia Scombridae. Libro de Actas IX Congreso Nacional de Acuicultura Cádiz 2003 2005, 149-153. Consejería de Agricultura y Pesca. Junta de Andalucía, Sevilla. C. Andalucía (Ed.).
37. Manchado M., Catanese G., Ponce M., Funes V., Infante C. The complete mitochondrial genome of the Senegal sole, Solea senegalensis Kaup. Comparative analysis of tandem repeats in the control region among soles. DNA Seq. 2007, 18:169-175.
38. Martin A.P., Kessing B.D., Palumbi S.R. Accuracy of estimating genetic distance between species from short sequences of mitochondrial DNA. Mol. Biol. Evol. 1990, 7:485-488.
39. Matsui T. Review of the mackerel genera Scomber and Rastrelliger with description of a new species of Rastrelliger. Copeia 1967, 1967:71-83.
40. Miya M., Kawaguchi A., Nishida M. Mitogenomic exploration of higher teleostean phylogenies: a case study for moderate-scale evolutionary genomics with 38 newly determined complete mitochondrial DNA sequences. Mol. Biol. Evol. 2001, 18:1993-2009.
41. Miya M., et al. Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Mol. Phylogenet. Evol. 2003, 26:121-138.
42. Nakashima H., Fukuchi S., Nishikawa K. Compositional changes in RNA, DNA and proteins for bacterial adaptation to higher and lower temperatures. J. Biochem. 2003, 133:507-513.
43. Naylor G.J., Collins T.M., Brown W.M. Hydrophobicity and phylogeny. Nature 1995, 373:565-566.
44. Oh D.J., Kim J.Y., Lee J.A., Yoon W.J., Park S.Y., Jung Y.H. Complete mitochondrial genome of the rock bream Oplegnathus fasciatus (Perciformes, Oplegnathidae) with phylogenetic considerations. Gene 2007, 392:174-180.
45. Ojala D., Montoya J., Attardi G. tRNA punctuation model of RNA processing in human mitochondria. Nature 1981, 290:470-474.
46. Oliva M.E., et al. What can metazoan parasites reveal about the taxonomy of Scomber japonicus Houttuyn in the coast of South America and Madeira Islands?. J. Fish Biol. 2008, 72:545-554.
47. Peng Z., Wang J., He S. The complete mitochondrial genome of the helmet catfish Cranoglanis bouderius (Siluriformes: Cranoglanididae) and the phylogeny of otophysan fishes. Gene 2006, 376:290-297.
48. Ponce M., Infante C., Jiménez-Cantizano R.M., Pérez L., Manchado M. Complete mitochondrial genome of the blackspot seabream, Pagellus bogaraveo (Perciformes: Sparidae), with high levels of length heteroplasmy in the WANCY region. Gene 2008, 409:44-52.
49. Posada D., Crandall K.A. Modeltest: testing the model of DNA substituion. Bioinformatics 1998, 14:817-818.
50. Rasmussen R.S., Morrissey M.T. DNA-based methods for the identification of commercial fish and seafood species. Compr. Rev. Food Sci. F. 2008, 7:280-295.
51. Saitoh K., et al. Mitogenomic evolution and interrelationships of the Cypriniformes (Actinopterygii: Ostariophysi): the first evidence toward resolution of higher-level relationships of the world's largest freshwater fish clade based on 59 whole mitogenome sequences. J. Mol. Evol. 2006, 63:826-841.
52. Sbisa E., Tanzariello F., Reyes A., Pesole G., Saccone C. Mammalian mitochondrial D-loop region structural analysis: identification of new conserved sequences and their functional and evolutionary implications. Gene 1997, 205:125-140.
53. Scoles D.L., Collette B.B., Graves J.E. Global phylogeografy of mackerels of the genus Scomber. Fish Bull. 1998, 96:823-842.
54. Setiamarga D.H., et al. Interrelationships of Atherinomorpha (medakas, flyingfishes, killifishes, silversides, and their relatives): The first evidence based on whole mitogenome sequences. Mol. Phylogenet. Evol. 2008, 49:598-605.
55. Shadel G.S., Clayton D.A. Mitochondrial DNA maintenance in vertebrates. Annu. Rev. Biochem. 1997, 66:409-435.
56. Swofford D.L. PAUP* Phylogenetic Analysis Using Parsimony (*and Other Methods) Version 4.0b2 2000, Sinauer, Sunderland, MA.
57. Takashima Y., Morita T., Yamashita M. Complete mitochondrial DNA sequence of the Atlantic horse mackerel Trachurus trachurus and molecular identification of two commercially important species T. trachurus and T. japonicus using PCR-RFLP. Fish Sci. 2006, 72:1054-1065.
58. Tamura K., Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 1993, 10:512-526.
59. Tzeng C.H., Chen C.S., Tang P.C., Chiu T.S. Microsatellite and mitochondrial haplotype differentiation in blue mackerel (Scomber australasicus) from the western North Pacific. ICES J. Mar. Sci. 2009, 66:816-825.
60. Wang H.C., Hickey D.A. Evidence for strong selective constraint acting on the nucleotide composition of 16S ribosomal RNA genes. Nucleic Acids Res. 2002, 30:2501-2507.
61. Wang C., Chen Q., Lu G., Xu J., Yang Q., Li S. Complete mitochondrial genome of the grass carp (Ctenopharyngodon idella, Teleostei): insight into its phylogenic position within Cyprinidae. Gene 2008, 424:96-101.
62. Wang X., Wang J., He S., Mayden R.L. The complete mitochondrial genome of the Chinese hook snout carp Opsariichthys bidens (Actinopterygii: Cypriniformes) and an alternative pattern of mitogenomic evolution in vertebrate. Gene 2007, 399:11-19.
63. Yamanoue Y., Miya M., Matsuura K., Katoh M., Sakai H., Nishida M. A new perspective on phylogeny and evolution of tetraodontiform fishes (Pisces: Acanthopterygii) based on whole mitochondrial genome sequences: basal ecological diversification?. BMC Evol. Biol. 2008, 8:212.
64. Zardoya R., Garrido-Pertierra A., Bautista J.M. The complete nucleotide sequence of the mitochondrial DNA genome of the rainbow trout, Oncorhynchus mykiss. J. Mol. Evol. 1995, 41:942-951.
65. Zhu Z.Y., Yue G.H. The complete mitochondrial genome of red grouper Plectropomus leopardus and its applications in identification of grouper species. Aquaculture 2008, 276:44-49.