Abstract
A molecular phylogenetic analysis of the genus Scomber was conducted based on mitochondrial (COI, Cyt b and control region) and nuclear (5S rDNA) DNA sequence data in multigene perspective. A variety of phylogenetic analytic methods were used to clarify the current taxonomic Classification and to assess phylogenetic relationships and the evolutionary history of this genus. The present study produced a well-resolved phylogeny that strongly supported the monophyly of Scomber. We confirmed that S. japonicus and S. colias were genetically distinct. Although morphologically and ecologically similar to S. colias, the molecular data showed that S. japonicus has a greater molecular affinity with S. australasicus, which conflicts with the traditional taxonomy. This phylogenetic pattern was corroborated by the mtDNA data, but incompletely by the nuclear DNA data. Phylogenetic concordance between the mitochondrial and nuclear DNA regions for the basal nodes Supports an Atlantic origin for Scomber. The present-day geographic ranges of the species were compared with the resultant molecular phylogeny derived from partition Bayesian analyses of the combined data sets to evaluate possible dispersal routes of the genus. The present-day geographic distribution of Scomber species might be best ascribed to multiple dispersal events. In addition, our results suggest that phylogenies derived from multiple genes and long sequences exhibited improved phylogenetic resolution, from which we conclude that the phylogenetic reconstruction is a reliable representation of the evolutionary history of Scomber.
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Akaike H. 1973. Information theory and an extension of the maximum likelihood principle. In: Petrov B N, Csaki F ed. International Symposium of Information Theory, 2nd. Akademiai Kiado, Budapest, p. 267–281.
Anderson F E. 2000. Phylogeny and historical biogeography of the loliginid squids (Mollusca: Cephalopoda) based on mitochondrial DNA sequence data. Mol. Phylogenet. Evol., 2: 191–214.
Benton M J, Ayala F J. 2003. Dating the tree of life. Science, 300: 1 698–1 700.
Berggren W A. 1978. Recent advances in Cenozoic planktonic foraminiferal biostratigraphy, biochronology, and biogeography: Atlantic Ocean. Micropaleontology, 24: 337–370.
Bermingham E S, McCaVerty A, Martin P. 1997. Fish biogeography and molecular clocks: perspectives from the Panamanian Isthmus. In: Kocher T, Stepien C ed. Molecular Systematics of Fishes. Academic Press, New York. p. 113–126.
Bowen B W, Bass A L, Rocha L A, Grant W S, Robertson D R. 2001. Phylogeography of the trumpetfishes (Aulostomus): ring species complex on a global scale. Evolution, 55: 1 029–1 039.
Brandley M C, Schmitz A, Reeder T W. 2005. Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards. Syst. Biol., 54: 373–390.
Briggs J C. 1984. Centres of origin in biogeography. Biogeographical Monographs No. 1. Biogeography Study Group, University of Leeds, Leeds. 106p.
Campo D, Machado-Schiaffmo G, Perez J, Garcia-Vazquez E. 2007. Phylogeny of the genus Merluccius based on mitochondrial and nuclear genes. Gene, 406: 171–179.
Cantatore P, Roberti M, Pesole G, Ludovico A, Milella F, Gadaleta M N, Saccore G 1994. Evolutionary analysis of cytochrome b sequence in some Perciformes: evidence for a slower rate of evolution than in mammals. J. Mol. Evol., 39: 589–597.
Catanese G, Manchado M, Fernández-Trujillo A, Infante C. 2010b. A multiplex-PCR assay for the authentication of mackereis of the genus Scomber in processed fish products. Food Chem., 122: 319–326.
Catanese G, Manchado M, Infante C. 2010a. Evolutionary relatedness of mackereis 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, 452: 35–43.
Collette B B. 1999. Mackereis, molecules, and morphology. In: Séret B, Sire J Y ed. Proceedings of the 5th Indo-Pacific Fish Conference, Nouméa 1997. Société Française d’Ichtyologie, Paris, p. 149–164.
Collette B B. 2003. Family Scombridae Rafinisque 1815-mackerels, tunas, and bonitos. In: California Academy Sciences ed. Annotated Checklist of Fishes No. 19. San Francisco, California. 28p.
Collette B B, Chao L N. 1975. Systematic and morphology of the bonitos (Sarda) and their relatives (Scombridae, Sardini). Fish. Bull., 73: 516–625.
Collette B B, Nauen C E. 1983. Scombrids of the world: An annotated and illustrated catalogue of tunas, mackereis, bonitos and related species known to date. FAO species catalogue, vol. 2. FAO Fish Synop, 125: 1–137.
Collette B B, Reeb C, Block B A. 2001. Systematics of the tunas and mackereis (Scombridae). In: Block B A, Stevens E D ed. Tuna: Physiology, Ecology, and Evolution. Academic Press, San Diego, California. p.1–33.
Collette B B, Russo J L. 1979. An introduction to the Spanish mackereis, genus Scomberomorus. In: Nakamura E L, Bullis H R J ed. Proceedings of Colloquium on the Spanish and King Mackerei Resources of the Gulf of Mexico. Marine Fish Community, Gulf States, p.3–16.
Espineira M, González-Lavín N, Vieites J M, Santaclara F J. 2009. Development of a method for the identification of scombroid and common Substitute species in seafood products by FINS. Food Chem., 117: 698–704.
Felsenstein J. 1985. Confidence limits on a phylogenies: an approach using the bootstrap. Evolution, 39: 783–791.
Fessler J L, Westneat M W. 2007. Molecular phylogenetics of the butterflyfishes (Chaetodontidae): Taxonomy and biogeography of a global coral reef fish family. Mol. Phylogenet. Evol., 45: 50–68.
Gojobori T. 1983. Codon Substitution in evolution and the “Saturation” of synonymous changes. Genetics, 105: 1011–1027.
Heads M. 2005. Towards a panbiogeography of the seas. Biol. J. Linn. Soc., 84: 675–723.
Hewitt G 2000. The genetic legacy of the Quaternary ice ages. Nature, 405: 907–913.
Holder M, Lewis P O. 2003. Phylogeny estimation: traditional and Bayesian approaches. Genetics, 4: 275–284.
Hrbek T, Meyer A. 2003. Closing of the Tethys Sea and the phylogeny of Eurasian killifishes (Cyprinodontiformes: Cyprinodontidae). J. Evolution. Biol., 16: 17–36.
Infante C, Blanco E, Zuasti E, Crespo A, Manchado M. 2007. Phylogenetic differentiation between Atlantic Scomber colias and Pacific Scomber japonicus based on nuclear DNA sequences. Genetica, 130: 1–8.
Johns G C, Avise J C 1998. A comparative summary of genetic distances in the vertebrates from the mitochondrial cytochrome b gene. Mol. Biol. Evol., 15: 1 481–1 490.
Kimura M. 1980. A simple method for estimating evolutionary rate of base Substitution through comparative studies of nucleotide sequences. J. Mol. Evol., 16: 111–120.
Kishino H, Thorne J L, Bruno W J. 2001. Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol. Biol. Evol., 18: 352–361.
Kocher T D, Thomas W K, Meyer A, Edwards S V. 1989. Dynamic of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. P. Natl. Acad. Sci. USA, 86: 6196–6 200.
Kumar S, Tamura K, Nei M. 2004. MEGA3: Integrated Software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform., 5: 150–163.
Matsui T. 1967. Review of the mackerei genera Scomber and Rastrelliger with description of a new species of Rastrelliger. Copeia, 1967: 71–83.
Meyer A. 1993. Phylogenetic relationship and evolutionary processes in east African cichlid fishes. Trends Ecol. Evol., 8: 279–284.
Minegishi Y, Aoyama J, Inoue J G, Miya M, Nishida M, Tsukamoto K. 2005. Molecular phylogeny and evolution of the freshwater eels genus Anguilla based on the whole mitochondrial genome sequences. Mol. Phylogenet. Evol., 34: 134–146.
Miya M, Takeshima H, Endo H, Ishiguro N B, Inoue J G, Mukai T, Satoh T P, Yamaguchi M, Kawaguchi A, Mabuchi K. 2003. Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Mol. Phylogenet. Evol., 26: 121–138.
Nylander J A A. 2004. MrModeltest v2. Program distributed by the author. Evolutionary Biology Centre, Uppsala University, Uppsala.
Nylander J A A, Ronquist F, Huelsenbeck J P, Nieves-Aldrey J L. 2004. Bayesian phylogenetic analysis of combined data. Syst. Biol., 53: 47–67.
Ohdachi S, Masuda R, Abe H, Adachi J, Dokuchaev N E, Haukisalmi V, Yoshida M C. 1997. Phylogeny of Eurasian soricine shrews (Insectivora, Mammalia) inferred from the mitochondrial cytochrome b gene sequences. Zool. Sci., 14: 527–532.
Posada D, Buckley T R. 2004. Model selection and model averaging in phylogenetics: advantages of Akaike Information criterion and Bayesian approaches over likelihood ratio tests. Syst. Biol., 53: 793–808.
Posada D, Crandall K. 1998. Modeltest: testing the model of DNA Substitution. Bioinformatics, 14: 817–818.
Rodriguez-Trelles F, Tarrio R, Ayala F J. 2002. A methodological bias toward overestimation of molecular evolutionary time scales. P. Natl. Acad. Sci. USA, 99: 8112–8115.
Rögl F. 1999. Mediterranean and paratethys. Facts and hypothesis of an Oligocene to Miocene paleogeography (short overview). Geol. Carpath., 50: 339–349.
Rohde K, Hayward C J. 2000. Oceanic barriers as indicated by scombrid fishes and their parasites. Int. I. Parasitol., 30: 579–583.
Ronquist F, Huelsenbeck J P. 2003. Mrbayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19: 1 572–1 574.
Rozas J, Sánchez-DelBarrio J C, Messeguer X, Rozas R. 2003. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19: 2496–2497.
Sambrook J, Russell D W. 2001. Molecular Cloning: a Laboratory Manual. 3rd edn. Cold Spring Harbor Laboratory Press, New York. 2 344p.
Schneider S, Roessli D, Excoffier L. 2000. Arlequin Version 2.0: A Software for population genetic data analysis. Genetics and Biometry Laboratory, University of Geneva.
Scoles D R, Collette B B, Graves J E. 1998. Global phylogeography of mackereis of the genus Scomber. Fish. Bull, 96: 823–842.
Smith A B, Peterson K J. 2002. Dating the time of origin of major clades: molecular clocks and the fossil record. Annu. Rev. Earth. PL Sc, 30: 65–88.
Strugnell J, Norman M, Jackson J, Drummond A J, 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: 426–441.
Swofford D L. 2002. PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.
Thorne J L, Kishino H. 2002. Divergence time and evolutionary rate estimation with multilocus data. Syst. Biol., 51: 689–702.
Tzeng C H, Chen C S, Tang P C, Chiu T S. 2009. Microsatellite and mitochondrial haplotype differentiation in blue mackerei (Scomber australasicus) from the western North Pacific. ICES J. Mar. Sci., 66: 816–825.
Vrielynck B, Odin G S, Dercourt J. 1997. Miocene palaeogeography of the Tethys Ocean; potential global correlations in the Mediterranean. In: Montanari A, Odin G, Coccioni R ed. Miocene Stratigraphy: An Integrated Approach. Elsevier Science, Amsterdam, p. 157–165.
Ward R D, Zemlak T S, Innes B H, Last P R, Hebert P D N. 2005. DNA barcoding Australia’s fish species. Philos. T. Roy. Soc. B., 360: 1 847–1 857.
Wood A R, Apte S, MacAvoy E S, Gardner J P A. 2007. A molecular phylogeny of the marine mussei genus Perna (Bivalvia: Mytilidae) based on nuclear (ITS1&2) and mitochondrial (COI) DNA sequences. Mol. Phylogenet. Evol., 44: 685–698.
Xiao W H, Zhang Y P, Liu H Z. 2001. Molecular systematics of Xenocyprinae (Teleostei: Cyprinidae): taxonomy, biogeography, and coevolution of a special group restricted in East Asia. Mol. Phylogenet. Evol., 18: 163–173.
Yang Z, Yoder A D. 2003. Comparison of likelihood and Bayesian methods for estimating divergence times using multiple gene loci and calibration points, with application to a radiation of cute-looking mouse lemur species. Syst. Biol., 52: 705–716.
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Supported by the International Cooperation and Exchange of the National Natural Science Foundation of China (No. 31061160187), and Special Fund for Agro-scientific Research in the Public Interest (No. 200903005)
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Cheng, J., Gao, T., Miao, Z. et al. Molecular phylogeny and evolution of Scomber (Teleostei: Scombridae) based on mitochondrial and nuclear DNA sequences. Chin. J. Ocean. Limnol. 29, 297–310 (2011). https://doi.org/10.1007/s00343-011-0033-7
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DOI: https://doi.org/10.1007/s00343-011-0033-7