Phylogenetic Studies of Complete Mitochondrial DNA Molecules Place Cartilaginous Fishes Within the Tree of Bony Fishes

Abstract

It is commonly acknowledged that cartilaginous fishes, Chondrichthyes, have a basal position among the Gnathostomata (jawed vertebrates). In order to explore this relationship we have sequenced the complete mitochondrial genome of the spiny dogfish, Squalus acanthias, and included it in a phylogenetic analysis together with a number of bony fishes and amniotes. The phylogenetic reconstructions placed the dogfish among the bony fishes. Thus, and contrary to the common view, the analyses have shown that the position of the sharks is not basal among the gnathostomes. The presently recognized phylogenetic position of the dogfish was identified irrespective of the outgroup used, echinoderms or agnathan fishes. The lungfish was the most basal gnathostome fish, while the teleosteans had an apical position in the piscine tree. A basal position of the dogfish among the gnathostomes was statistically rejected, but the phylogenetic relationship among the coelacanth, spiny dogfish, and teleosts was not conclusively resolved. The findings challenge the current theory that sharks and other chondrichthyans, if monophyletic, are the sister group to all other extant gnathostomes. The results open to question the status of several morphological characters commonly used in piscine phylogenetic reconstruction, most notably the presence versus absence of endochondral bone in the endoskeleton, the macromeric versus micromeric structure of the exoskeleton, and the presence/absence of swimbladder and/or lung. The study also confirmed recent findings demonstrating that the origin of the amniotes is deeper than the diversification of extant bony fishes.

Molecular studies suggest that cartilaginous fishes have a terminal position in the piscine tree

“…Compared with the previous study (9), the present analysis improved the resolution of the relationship between the coelacanth, the chondrichthyans, and the teleosts. In other respects, the phylogenetic findings of this study were consistent with recent findings applying unambiguous rooting of the gnathostome tree (8,9), showing, inter alia, that the divergence between amniotes and extant gnathostomous fishes took place before the diversification of extant gnathostome fishes.…”

“…The conclusions based on the teleostean and chondrichthyan rooting have been challenged in two recent molecular studies (8,9) in which the gnathostome tree was rooted by using non-gnathostome taxa. The first study indicated that the lungfishes have a basal position in the piscine tree and that the separation between extant bony fishes and amniotes preceded the divergence of the extant bony fishes.…”

Going nuclear: gene family evolution and vertebrate phylogeny reconciled

“…Outgroups for each gene family were found using sequence similarity searches against a number of sequence databases to identify related genes: either invertebrate orthologues or vertebrate paralogues. Due to the size of the dataset, amino acid sequences were aligned in ClustalW (Thompson et The maximumlikelihood tree from Rasmussen & Arnason (1999). Figures on branches are neighbour-joining (top) and maximum-parsimony (middle) bootstrap values based on 100 replicates, and maximum-likelihood (bottom) support values from 1000 puzzle replicates.…”

Extracting Species Trees From Complex Gene Trees: Reconciled Trees And Vertebrate Phylogeny

“…None of the genes (lactate dehydrogenase, rhodopsin, trypsinogen, Wnt-7) that have both chondrichthyian and teleost sequences support this conventional relationship. Interestingly, trees inferred from complete mitochondrial genomes place chondrichthyians within the teleosts (Rasmussen and Arnason, 1999).…”