Trends in Ecology & Evolution
ReviewMitogenomics: digging deeper with complete mitochondrial genomes
Section snippets
Vertebrate relationships
An accurate phylogeny is the foundation for a complete understanding of vertebrate evolution. Therefore, questions of vertebrate relationships have been a primary focus in the field of molecular systematics. Although fossils provide evidence of morphological change, the genetic changes associated with evolution can only be discerned from comparisons among extant taxa. In Fig. 2, we present the traditional hypothesis of relationships of chordate taxa discussed in this review.
Digging deeper
Although the gene content of animal mtDNA is nearly constant, the relative position of these genes around the molecule varies among major taxonomic groups. The mechanisms responsible for these rearrangements are not well understood, but it is apparent that transfer RNA (tRNA) genes change position more frequently than either rRNAs or protein-coding genes17, 18, 19. It has been suggested that such rearrangements can be used as cladistic characters for studying relationships among higher-level
Conclusions
Mitochondrial sequences have resolved phylogenies deeper than originally expected, but their usefulness as a marker for highly divergent lineages is still controversial. Further studies of nuclear markers are required to confirm these mitochondrial phylogenies. If the hypotheses supported by paleontological data hold up, then slowly evolving nuclear genes will be more useful than complete mtDNA sequences28. If the non-traditional hypothesis is correct, then the utility of this widely used
Acknowledgements
We are grateful to Jessica Bolker, Sarah Cohen, Karen Carleton, Pat Danley, Jeff Markert, Todd Streelman, Ulfur Arnason and an anonymous reviewer for suggestions on the manuscript and to Ying Cao and Ann-Sofie Rasmussen for advance copies of their publications.
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