J OURNAL OF FISH ERIES OF CHINA. ,, M EGA version ,, 16 S rrna. [ ] mtdna 16 S rrna [ 20 ]

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1 J OURNAL OF FISH ERIES OF CHINA Vol. 32, No. 6 Nov., 2008 : (2008) S r RNA 12 1,2, 1,2, 3, 1,2, 1 (1., ; 2., ; 3., ) : PCR (Carangidae) S rrna 598 bp, GenBank 3,,, M EGA version 31 0 /, : (1) 16S rrna, 146 bp, / 21 17,,81 22 % ; (2) (,,, ) ; (3) ; (4),16S rrna %, : ;DNA ;16S rrna ; : S 917 : A ( Carangidae) ( Perciformes),, ( ),, ( ), [ 1-2 ], [ 3 ],74 [ 4 ] [ 5-10 ],, : [ 2,5,11 ],, [ 10,12-14 ],,, DNA ( mitochondrial DNA, mtdna) [ ] mtdna 16 S rrna,,, mtdna DNA,rRNA [ 20 ],,16 S rrna [ ] 9 16 S rrna, GenBank 3 : : ( ) ; ( K06141) : ( ),,,,,E2mail : com :,E2mail : edu. cn

2 ( Pom adasys m aculates) 16 S rrna, ( MP) ( NJ ), GenBank 3 16S rrna, 10 12, ( 1) 1. 2 DNA PCR DNA 95 %, / [ 18 ] PCR 16SAR (5 - GCC T GT T TA TCA AAA ACA T - 3 ) 16SBR ( 5 - CCG GTC T GA ACT CA G A TC ACG T - 3 ) [ 23 ] PCR DNA 100 ng, 50 L, 10 Ex T aq Buffer 5 L, dn TPs 2 L ( 21 5 mmol L - 1 ),1 L (20 mol L - 1 ), Ex T aq 01 3 L (2 U) PCR :94 4 min ;94 45 s,52 45 s,72 1 min,34, min DNA, 1 % 1 Tab. 1 The origins of tissue samples of Carangidae f ishes and DNA data subfamilies genera species GenBank Accession Caranginae A lectis A. indica, R ppell EF A lepes A. djedaba, Forssk l EF A. kleinii, Bloch EF Caranx C. melam py gus, Cuvier AP Carangoi des C. armatus, R ppell AP C. chrysophrys, Cuvier EF Decapterus D. maruadsi, Temminck and Schlegel EF Selaroi des S. leptolepis, Cuvier EF T rachurus T. j aponicus, Temminck and Schlegel AP Seriolinae Zonichthys Z. ni grof asciata, R ppell EF Trachinotinae Chorineminae Pomadasyidae T rachinotus Scomberoi des Pomadasys T. blochii, Lacep de S. commersonianus Lacep deef P. maculates, Bloch EF AF : 3 Notes : 3 The sequences were sequenced in this study

3 6, : 16S rrna PCR, ( ), p UCm2T ( ),D H 5,,, M13 (Applied Biosystems 3730, ),,, GenBank Clustal W, M EGA version 31 0 / (MP) (NJ ) PAU P Version 41 0 b10 [ 24 ] ( MP) (heuristic search), :1 000 random stepwise addition sequence replicates, tree bisection reconnection ( TBR), Kimura 22 parameter (Boot strap analysis), [ 25 ] S r RNA 16S rrna PCR, bp, GenBank 3 16S rrna Clustal W, 608 bp,, bp bp, 146 bp, 78 bp 16S rrna T C A G % % % %, A + T ( %) G + C (481 0 %),, [ 23,26 ], % %, %, %, S rrna ( ) / ( ) Tab. 2 Percentage divergence( below diagonal) and number of transitions / transversions ( above diagonal) for partial 16S rrna sequences in Carangidae and the outgroup / 8 19/ 8 23/ 8 17/ 4 19/ 1 16/ 6 26/ 11 14/ 10 29/ 22 26/ 19 36/ 29 42/ / 0 18/ 4 27/ 12 27/ 9 21/ 10 22/ 5 20/ 10 29/ 22 32/ 19 42/ 27 40/ / 4 26/ 12 27/ 9 23/ 10 23/ 5 20/ 10 30/ 22 27/ 19 39/ 27 41/ / 10 19/ 9 19/ 12 21/ 5 20/ 12 36/ 22 28/ 19 38/ 27 40/ / 5 20/ 8 27/ 13 20/ 12 27/ 22 27/ 17 36/ 25 48/ / 7 22/ 10 24/ 9 23/ 23 29/ 20 34/ 28 43/ / 13 8/ 6 32/ 20 30/ 19 41/ 29 41/ / 11 28/ 23 28/ 18 41/ 26 39/ / 18 33/ 17 41/ 25 44/ / 17 43/ 29 46/ / 22 48/ / Codes 1-13 : A. indica, A. d jedaba, A. kleinii, C. melam p y gus, C. armatus, C. chrysophrys, D. maruadsi, S. leptolepis, T. j aponicus, Z. ni grof asciata, T. blochii, S. commersonianus, P. maculates, / ( Ts/ Tv ) ( Kimura 22 parameter), Ts/ Tv 21 0, [ 27 ]

4 S rrna,, (BP = MP ( 1), 334, C I = , R I = Boot strap (BP), :, : (BP = 41), (BP = 50), 65) : (A),; (B), ; ( C),, NJ MP, MP ( 2) 1 16S rrna ( MP ) Fig. 1 Molecular phylogenetic tree on the partial 16S rrna sequences of Carangidae fishes constructed by MP method of PAU P Version 410 b 10 with Bootstrap Test (1 000 replications). The values of boot strap confidence level (BCL) of nodes are indicated above the branch 2 16S rrna ( NJ ) Fig. 2 Molecular phylogenetic tree on partial 16S rrna sequences of Carangidae fishes constructed by Neighbor2Joining method of PAU P Version 410 b 10 with Boot strap Test (1 000 replications). The values of boot strap confidence level (BCL) of nodes are indicated above the branch

5 6, : 16S rrna MP NJ : :, :,,, Cyt b [ 14 ], (MP) (ML) Bayesian Cyt b [ 10 ],,,, [ 5-6 ] : A le pes 1839, [ 7 ] ; Gushiken [ 9 ],,,,, [ 4 ] [ 28 ] : MP NJ, [ 10 ],, [ 1-3 ] 3. 2,,,,,, [ 5-6 ] ( Cit ul a) (U ras pis ) ( Carangoi des) ( Caranx ) ( A t ule) (L ongi rost rum) : ( A lectis) A, ( S el aroi des) C, [ 5 ] [ 4 ], [ 2-3,28-29 ],,, A B C, 16S rrna 3. 3 Swaison, A t ule 1922 Jordan, [ 2,5,29-30 ] [ 5-6 ], A t ule d j ed d aba, A t ule kall a ( A t ule) [ 2 ] [ 5 ], A t ule kall a, A lepes d j edaba A lepes, ( Shrimp scad) [ 3 ] Lin and Shao [ 11 ] [ 30 ] Smit h2vaniz (2000) [ 11,30-31 ] A lepes, : A lepes klei nii, http :/ / www. itis. gov/ servlet/ SingleRp t/ SingleRp t? search _ topic = TSN &sear ch _ value = A lepes klei nii ( A lepes d j edaba ) : A lepes d j ed daba A t ule d j ed daba Caranx ( A t ule ) d j ed daba, ( : ht tp :/ / fishdb. sinica. edu. t w/ 2001new/ fishpic. asp? gen = Alepes &spe = djedaba),, :,, 1,,;

6 852 32,1 2,,1 3, [ 3 ] [ 5,29 ],, [ 5,29 ], [ 6 ] [ 6 ] 1,1-2, 3,,, : ;,;, ;, ;,,, [ 6 ],,,,MP NJ, [ 5,29 ] (MP - BP = 92, NJ - BP = 100 ), %, (81 22 %), cyt b %, ( %), cyt b % [ 14 ] :,,,, ( A lepes klei nii) [ 1 ] Nelson J S. Fishes of the World. Third edition [ M ]. New York : John Wiley & Sons, Inc., 1994 :600. [ 2 ],,. [ M ]. :,1999 :26,944,1015. [3 ],,. [ M ]. :,1995, [ 4 ]. [ M ]. :,1994, [ 5 ],. [ M ]. :,1987, [ 6 ],,. [ M ]. :,1962, [ 7 ] Smith2Vaniz W F. Carangidae : relationship s[ M ] Moser H G,Richards W J,Cohen D M,Fahay M P, Kendall A W, Richardson S L. ( Eds. ), Ontogeny and Systematics of Fishes. Am Soc Ichthyol Herpetol Spec Publ, 1984,1 : [ 8 ] Kijima A, Taniguchi N, Ochiai A. Genetic relationships in the family Carangidae [ C ] Uyeno T,Arai R, Taniuchi T,Matsuura K. ( Eds. ), Indo2 Pacific Fish Biology : Proceedings of the Second International Conference on Indo2Pacific Fishes. Tokyo : Ichthyological Society of Japan, 1986, [ 9 ] Gushiken S. Phylogenetic relationship s of the Perciformes genera of the family Carangidae [ J ]. J ap J Ichthyol,1988,34 : [10 ] Reed D L,Carpenter K E,de Gravelle M J. Molecular systematics of the Jacks ( Perciformes : Carangidae) based on mitochondrial cytochrome b sequences using parsimony, likelihood, and Bayesian approaches [ J ]. Mol Phylogenetics, 2002,23 : [11 ] Lin P L,Shao K T. A review of the carangid fishes (family Carangidae) f rom Taiwan with description of four new records [J ]. Zoological Studies, 1999, 38 (1) : [ 12 ] Reed D L, de Gravelle M J, Carpenter K E. Molecular systematics of Selene ( Perciformes : Carangidae) based on cytochrome b sequences [J ]. Mol Phylogenetics Evol,2001,21 : [13 ] Cardenas L, Hernandez C E,Poulin E,et al. Origin, diversification, and historical biogeography of the genus T rachurus ( Perciformes : Carangidae) [J ]. Mol Phylogenetics Evol,2005,35 : [14 ],,,. b [J ].,2007,53 (4) : [ 15 ] Miya M, Nishida M. Use of mitogenome information in teleostean molecular p hylogenetics : A tree2based exploration under the maximum2 parsimony optimality criterion [J ]. Mol Phylogent

7 6, : 16S rrna Evol, 2000, 17 : [ 16 ] Miya M, Kawaguchi A, Nishida M. Mitogenomic exploration of higher teleostean phylogenies : a case study formoderate2scale evolutionary genomics with 38 newly determined complete mitochondrial DNA sequences [J ]. Mol Biol Evol,2001,18 : [ 17 ] Miya M, Takeshima H, Endo H, et al. Major patterns of higher teleostean phylogenies : a new perspective based on 100 complete mitochondrial DNA sequences [ J ]. Mol Phylogenet Evol, 2003, 26 : [ 18 ],,,. b [J ].,2004,39 (5) : [19 ],,,. b [J ].,2006,30 (4) : [ 20 ],,,. 16S rrna [J ].,2005,15 (1) : [ 21 ],,,. 16S rrna [J ].,2004, 49 (14) : [ 22 ] Near T J, Pesavento J J,Cheng C H C. Phylogenetic investigations of Antarctic notothenioid fishes ( Perciformes : Notothenioidei ) using complete gene sequences of the mitochondrial encoded 16S rrna [J ]. Mol Biol Evol,2004,32 : [ 23 ],,,. 8 16S rrna [J ].,2004,14 (5) : [ 24 ] Swofford D L. PAU P 3 : Phylogenetic analysis using parsimony ( 3 and Other Methods), Version 410 b 10 [ M ]. Sinauer Associates, Inc., Sunderland,MA,US [25 ] Kumar S, Tamura K, Nei M. M EGA3 : Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment [ J ]. Briefings in Bioinformatics,2004,5 : [26 ],,,. 16S rdna 30 [J ].,2006,52 (3) : [27 ],,,. 6 16S rrna [J ].,2004,11 (2) : [28 ] Masuda H,Amaoka K,Araga C, et al. The Fishes of the J apanese Archipelago [ M ]. J apan : Tokai University Press,1984 :137. [29 ] Van der Elst R. A guide to the common sea fishes of Southern Africa[ M ]. Struick, Cape Town,1981 : [30 ], %,,. [ M ]. :,1993 : [31 ] Randall J E, Lim K K P. A checklist of the fishes of the South China Sea[J ]. Raffles Bull Zool,2000, (8) :

8 Molecular phylogenetic relationship of Carangidae based on partial sequence of mitochondrial 16S ribosomal RNA gene Z H EN G We n2jua n 1,2, Z HU Shi2hua 1,2, ZO U J i2xi ng 3, YA N G Yi ng2chun 1,2, S H EN Xi2qua n 1 (1. Key L aboratory of A p plied M arine B iotechnolog y Certi f icated by Minist ry of Education, N ingbo Universit y, N ingbo , China; 2. Department of B iology, Facult y of L i f e S cience and B iotechnolog y, N ingbo Universit y, N ingbo , China; 3. College of A nimal S cience, S outh China A g ricultural Universit y, Guangz hou , China) Abstract : The classificatio n and evolutio nary relatio nship of Carangidae have remained much co nt roversy bet ween co nventio nal morp hological st udies and molecular p hylogenetic st udies. In t his st udy, t he 16S ribosomal RNA partial sequences of 9 species of 8 genera from Carangidae in China sea were amplified using PCR technique. App ro ximately, 598 bp gene f ragment s were o btained. The resulting data were co mbined wit h Pom a d as ys m acul ates designed o ut gro up and additio nal homologous sequences of 3 species f rom Carangidae downloaded from GenBank to form t he analysis mat rix. N ucleotide co mpo sitio n f requencies, Kimura22 parameter genetic distance and t ransitio n/ transversion ratios were analyzed wit h t he M EGA 31 0 software. Molecular p hylogenetic trees were constructed by maximum parsimony (MP) and neighbor2joining (NJ ) methods. The result s were as follow s : (1) There were insertio ns and deletio ns of base pair s in t he aligned base pair s. 146 bp variable sites were fo und in t he t he analysis mat rix. The average t s/ t v ratio amo ng all pairwise co mpariso ns was 21 17, suggesting t hat t he sequences had not reached sat uratio n. The average percentage divergence was % ; ( 2 ) Fish classificatio n system of Carangidae classified fo ur subfamilies as Caranginae, Seriolinae, Trachinotinae, Chorineminae was acceptable, according to t he partial sequence of mitocho ndrial 16 S ribo so mal RNA gene ; ( 3) Itπs imp roper to define subgenus in Caranx of Caranginae ; (4) A le pes d j ed daba and A le pes klei nii had a close relationship, and should belong to t he same Alepes genus, as t he difference of partial 16S ribosomal RNA gene between t hem was only %. Key words : Carangidae ; mitochondrial DNA ( mtdna ) ; 16S ribosomal RNA ( 16S rrna ) ; molecular p hylogeny