Basal Vertebrate Divergences from a Molecular Perspective
Abstract: Fishes (Superclass Pisces) constitute the most numerous and morphologically diverse vertebrate group, yet only a small fraction of all molecular evolutionary studies concern piscine evolution. This thesis aims to investigate the vertebrate tree, through the analysis of mitochondrial (mt) DNA sequences. To this end the coding regions of the mt genome of a jawless fish, the hagfish (Myxine glutinosa), were sequenced, along with the complete mt genomes of two elasmobranch (cartilaginous) fishes, the spiny dogfish (Squalus acanthias) and the starry skate (Raja radiata). Phylogenetic analyses were carried out on both on amino acid and nucleotide sequences and using both the jawless fishes (the hagfish, Myxine glutinosa, and the sea lamprey, Petromyzon marinus). The ?Cyclostomata hypothesis?-which states that hagfishes and lampreys constitute a monophyletic group-was tested against the ?Vertebrate hypothesis?, but neither hypothesis could be statistically rejected. The third possible hypothesis-that hagfishes are the sister group of the jawed vertebrates-was however rejected in all analyses. Phylogenetic analyses showed that the branching order and the evolutionary direction of the fishes was inverted compared to the traditional view on vertebrate evolution. In addition, all of the jawed fishes fell into one group while the amniotes formed a second, distinct group, as opposed to all of the taxa forming one large group as in the traditional tree. This finding suggests that the origin of extant aminotes predated the diversification of extant gnathostomous (jawed) fishes and therefore, if this topology is indeed the correct one, the ancestor of extant amniotes was not more closely related to the lungfish or the coelacanth lineages than to any other extant fishes. In addition to the jawless fishes a number of invertebrates (lancelet and echinoderms) were used to root the vertebrate tree. Irrespective of which invertebrate outgroups were used, the same tree polarity and the same phylogenetic relationship among piscine and amniote taxa were reconstructed. These findings could not be related to violations of the assumptions used in the phylogenetic reconstruction nor could they be ascribed to any random error (due to limited sample size) in the data set. The sequences of two elasmobranchs were used to investigate the relationship between cartilaginous and bony fishes. In contrast with all previous mtDNA studies the cartilaginous fishes were not found to be basal among jawed vertebrates, but instead fell in a crown position among the fishes, constituting the sister group to the teleosts. This terminal position of the elasmobranchs was well-supported in all of the analyses. Rooting the tree with the cartilaginous fishes resulted in the traditional vertebrate tree. This is however an operation inconsistent with the principle of unquestionable outgroup rooting, since cartilaginous fishes have not clearly been shown to be the most basal gnathostomous group. The reconstructed crown position of the elasmobranchs together with their questionable use as an outgroup confirms that rooting, using cartilaginous fishes, is probably the cause for the incongruent topologies reconstructed. This thesis deals with these new, molecular findings, their implications for vertebrate phylogeny and evolution and the validity of the traditional views.
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