Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution

<p>Abstract</p> <p>Background</p> <p>The scientific literature contains many examples where DNA sequence analyses have been used to provide definitive answers to phylogenetic problems that traditional (non-DNA based) approaches alone have failed to resolve. One notable example concerns the rhinoceroses, a group for which several contradictory phylogenies were proposed on the basis of morphology, then apparently resolved using mitochondrial DNA fragments.</p> <p>Results</p> <p>In this study we report the first complete mitochondrial genome sequences of the extinct ice-age woolly rhinoceros (<it>Coelodonta antiquitatis</it>), and the threatened Javan (<it>Rhinoceros sondaicus</it>), Sumatran (<it>Dicerorhinus sumatrensis</it>), and black (<it>Diceros bicornis</it>) rhinoceroses. In combination with the previously published mitochondrial genomes of the white (<it>Ceratotherium simum</it>) and Indian (<it>Rhinoceros unicornis</it>) rhinoceroses, this data set putatively enables reconstruction of the rhinoceros phylogeny. While the six species cluster into three strongly supported sister-pairings: (i) The black/white, (ii) the woolly/Sumatran, and (iii) the Javan/Indian, resolution of the higher-level relationships has no statistical support. The phylogenetic signal from individual genes is highly diffuse, with mixed topological support from different genes. Furthermore, the choice of outgroup (horse <it>vs </it>tapir) has considerable effect on reconstruction of the phylogeny. The lack of resolution is suggestive of a hard polytomy at the base of crown-group Rhinocerotidae, and this is supported by an investigation of the relative branch lengths.</p> <p>Conclusion</p> <p>Satisfactory resolution of the rhinoceros phylogeny may not be achievable without additional analyses of substantial amounts of nuclear DNA. This study provides a compelling demonstration that, in spite of substantial sequence length, there are significant limitations with single-locus phylogenetics. We expect further examples of this to appear as next-generation, large-scale sequencing of complete mitochondrial genomes becomes commonplace in evolutionary studies.</p> <p><it>"The human factor in classification is nowhere more evident than in dealing with this superfamily (Rhinocerotoidea)." G. G. Simpson (1945)</it></p