Finnerty and Block: Evolution of cytochrome b in the Scombroidei 



85 



1 Istiophorus platypterus 



2 Makaira nigricans 



3 Makaira indica 



4 Tetrapturus albidus 



5 Tetrapturus audax 



6 Tetrapturus angustirostris 



7 Tetrapturus belane 



8 Tetrapturus pfluegeri 



9 Xiphias gladius 



10 Acanthocybiun solandri 



11 Sccmberamorus cavalla 



12 Sccnteranorus maculata 



13 Gasterochisma melampus 



14 Auxis thazard 



15 Euthynnus affinis 



16 Euthynnus alletteratus 



17 Katswonus pelamis 



18 Thunnus alalunga 



19 Thunnus albacares 



20 Thunnus maccoyii 



21 Thunnus obesus 



22 Thunnus thynnus 



23 Sarda chiliensis 



24 Sarda sarda 



25 Scomber japonicus 



26 Scomber scombrus 



27 Gempylus serpens 



28 Lepidccybium flavobrunneum 



29 Ruvettus pretiosus 



30 Trichiurus lepturus 



31 Sphyraena sphyraena 



32 Coryphaena equiselis 



33 Morane saxatilis 



34 Myctoperca interstitialis 



20 40 60 80 100 120 



TCCTTACACoc rmTLi ' ia xTATGCACTACACCTCAGACATCCc^^ 



A Y T A R 



.A..T. 

 .A..T. 



A. 



.A. .A. 



.T..A 



.T. ..C.T. 



..G. .R. 

 .A.T. .. 



.A.T.G. 



.T 



.TG... 

 ..G.C. 



.C C G. .A. ... 



AT. A T. .A. .A. -T. 



.C... 

 .C.T. 



. .G. ..A.T.G. 

 ..G.. .AGT... 

 .TG. ..A.T... 



.TG.C. 

 . .G.T. 

 . .G.T. 



A. .C. 

 A. . . 

 A. X 



.A. .T. 

 C. 



.T..T. 



..T..A. 

 ,T. . .G. 



.C T. 



.T. .T 



.A 



.A 



.A. .T. 



.C. .C.T. 

 .C..C.T. 



G.RC 



T.X. .A. 



.A. .A. 

 .A. .A. 



.C.C. 

 .C.T. 



TG.. .A.T. 

 TG...A.T. 

 .G.A.A.T. 



.G.C. 

 .G.C. 

 .G.C. 



.C.T. 

 .C.T. 



.A.T. 

 .A.T. 



.TG.C. 

 ..G.C. 



T. 



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.A..C.TT 



.A. .C.T. ..T. 

 A. .C.T. ..A. 



C. 



.T..C. 



CC 



.T..CC 

 CC 



.A..T..A 

 .A T 



C 



C.C. 



.CC. 

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X. .T. 



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C 



C.C. .A. 



.A. .A. 



.A. 



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TG.. .A.T. 

 YG...A.T. 

 A.T. 



.G.C. 

 .G.C. 

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 .C. 



C 



.T. .C 



G..CC 

 G..CC 



C.C. 

 C.C. 



.T..C A.. 



.A. .A. .T..T. 

 .A. .A 



..C.T. 

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.TG...A.T. 

 .TG.T.AGT. . 



A. 



A. .C. 

 C 



.T. 

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CC 



• R..CC 



C.C .A. 

 C.C .A. 



A. .C.T. ..A 

 A. .C.T. . .A 

 A. .C.T. . .A 

 C. .C.T. ..T 



C.T. .TG. . .A.T G.C. .A C.T A. .T. .C .C.T. . .T 



C T. ..T 



C.CT...T. 



A A A .T. .T. . .C.T. .TG. . .A.T G.C. .A. .C C. .T G T T A. .C CCC. .C .A 



T T 



A. .C.T... A 

 A. .C.T. ..A 

 T. .C.T. . .T 

 A. .C.T. . .A 



A. .TG.T. .T C A A. .C.T. . .A T. .C CC 



C.C.T..G 



T..C.T 



A. .C.T. .A 



.C -T. 

 .C. .T. 



.G.C 

 .GAC 

 .GC.C . .G. . .A.T A AC. .A. .C T. .T. 



.A. -C 

 .A. .C 



.CC< 

 .CC( 



.C A. .C... 



.A. .T. .T..A. .A 



.C.C 

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TG.T. A.T. 

 .G.7.A.T. 



.TG.C 

 .TG.C 



.A. .C. 



.A..C. 



.C. 



• A. .C. 

 C. 



.T..CC 

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A. 



G. .C.A. 



.A. X. 

 C. 



T..CCI 

 CC' 



.A T.X... 



-A A.. C.A 



..C.T. 

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 T..T G. 



.A AC. 



.T..TGAC. 

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.T.X. 

 X.A. 



C A A 



T..C..A. .T..T 



.G..A. .T..T. 



.T.G 



.T.A. X. 



X..C 

 CC 



G..C 

 G 



.G..A. 

 -AA.C 



.A. X 



.A. .A. .A. 



.T.X. .. 

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T. .T C. -T A. -T. 



. . .T. .A. X A. .T. .A T C. .CCC X. . . 



AA.T. .T. X. . .AC . .A. .T. .ACA T. X. .T.X T. 



240 260 280 



CCGCCTTajICGaCT3uT3raCICOCCTGAGGACAAAT 



Figure 3 



Alignment of partial cytochrome b sequence (590 base pairs) across 34 species of perciform fishes and two species of Cypriniformes. 

 Nucleotide position 1 is equivalent to position 134 of the human cytochrome b gene. Intraspecific polymorphism is indicated as 

 follows: R=A/G, Y=C/T, M=A/C, S=C/G, K=G/T, W=A/T, H=A/T/C, D=A/G/T. Ambiguities are indicated by '?' 



thirty-six species included in the analysis (Fig. 3). 

 No deletions or insertions were detected. Overall, 293 

 nucleotide positions are variable; 248 were poten- 

 tially phylogenetically informative. As expected for 

 a protein coding sequence, the degree of nucleotide 

 variability differs according to codon position (Table 

 3). The third position is most variable and the sec- 



ond position is least variable. Differences in nucle- 

 otide variability at the three codon positions are due 

 to the fact that many third position substitutions are 

 silent, whereas many second position substitutions 

 result in nonconservative amino acid replacements. 

 The differences in substitution rates between codon 

 positions becomes more apparent when we compare 



