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

Eske Willerslev1*, M Thomas P Gilbert1, Jonas Binladen1, Simon YW Ho2, Paula F Campos1, Aakrosh Ratan3, Lynn P Tomsho3, Rute R da Fonseca4, Andrei Sher5, Tatanya V Kuznetsova6, Malgosia Nowak-Kemp7, Terri L Roth8, Webb Miller3 and Stephan C Schuster3*

Author Affiliations

1 Centre for Ancient Genetics, University of Copenhagen, Universitetsparken 15, DK-2100, Denmark

2 Centre for Macroevolution and Macroecology, School of Biology, Australian National University, Canberra, ACT 0200, Australia

3 Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, 310 Wartik Building, University Park, PA 16802, USA

4 Department of Integrative Biology, University of California, Berkeley, CA 9472-3140, USA

5 Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 33 Leninsky Prospect, 119071 Moscow, Russia

6 Department of Paleontology, Faculty of Geology, Lomonosov Moscow State University, Leninskiye Gory, 119992 Moscow, Russia

7 Oxford University Museum of Natural History, Parks Road, Oxford, OX1 3PW, UK

8 Center for Conservation and Research of Endangered Wildlife (CREW), Cincinnati Zoo & Botanical Garden, 3400 Vine St, Cincinnati, OH 45220, USA

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BMC Evolutionary Biology 2009, 9:95  doi:10.1186/1471-2148-9-95

Published: 11 May 2009



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.


In this study we report the first complete mitochondrial genome sequences of the extinct ice-age woolly rhinoceros (Coelodonta antiquitatis), and the threatened Javan (Rhinoceros sondaicus), Sumatran (Dicerorhinus sumatrensis), and black (Diceros bicornis) rhinoceroses. In combination with the previously published mitochondrial genomes of the white (Ceratotherium simum) and Indian (Rhinoceros unicornis) 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 vs 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.


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.

"The human factor in classification is nowhere more evident than in dealing with this superfamily (Rhinocerotoidea)." G. G. Simpson (1945)