90 



Fishery Bulletin 93(1). 1995 





NHj 



COOH 



Figure 6 



Variability in amino acid sequence superimposed over a structural model for cyto- 

 chrome b (Howell, 1989). Hypervariable residues, present in three or more amino 

 acid states, are indicated by solid circles. Variable residues, present in two states, 

 are indicated by open circles. The amino acids present at invariant residues are 

 specified on the diagram. Residue 1 of this fragment is equivalent to the forty-sixth 

 residue from the amino terminal of the protein in humans. 



The strength of the evidence that billfishes are not 

 scombroids can be emphasized by directly examining 

 the amino acid characters that are informative about 

 this issue. Of the 38 informative amino acid sites, no 

 sites unite billfishes and other scombroids to the ex- 

 clusion of other perciforms, whereas eight sites unam- 

 biguously separate billfishes from all other scombroids, 

 i.e. sites where all billfishes possess one character state 

 and all other scombroids possess some other character 

 state (characters 12, 14, 15, 16, 113, 117, 140, and 169; 

 Fig. 5). At all of these sites, billfishes share the same 

 character state as one or more of the percoid fishes. 

 Furthermore, at three of these eight sites (15, 16, and 

 169), Gempylidae, Scombridae, and Trichiuridae share 

 a common state with Sphyraena to the exclusion of all 

 other species in the study As this character analysis 

 emphasizes, the amino acids are consistent with the 

 hypothesis that billfishes are not scombroids and that 

 Sphyraena is the sister group of a clade consisting of 

 Gempylidae, Scombridae, and Trichiuridae. 



Intrafamilial relationships 



Within the family Istiophoridae (Istiophorus, Makaira, 

 and Tetrapturus), cytochrome b nucleotide sequence 

 provides a particularly well resolved and strongly sup- 

 ported phylogenetic signal. This is probably due to the 

 recency of the istiophorid radiation. The maximum se- 

 quence divergence between any two species within this 

 clade is less than five percent. We have performed a 

 more in depth analysis of the interrelationships of 

 istiophorids using the exhaustive search option of PAUP 

 3.1 (Swofford, 1991). Use of the exhaustive search op- 

 tion guarantees identification of the most parsimoni- 

 ous tree. The topology of this tree is identical to the 

 topology of the istiophorid clade within the more inclu- 

 sive scombroid phylogeny (Fig. 8, cf. Fig. 2). Neighbor- 

 joining and UPGMA analyses produce an identical to- 

 pology. Computer simulations suggest that agreement 

 between these three methods should increase our con- 

 fidence in a phylogenetic hypothesis (Kim, 1993). 



