Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolutionReport as inadecuate




Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution - Download this document for free, or read online. Document in PDF available to download.

BMC Evolutionary Biology

, 9:95

First Online: 11 May 2009Received: 03 October 2008Accepted: 11 May 2009

Abstract

BackgroundThe 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.

ResultsIn 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.

ConclusionSatisfactory 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

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2148-9-95 contains supplementary material, which is available to authorized users.

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Author: Eske Willerslev - M Thomas P Gilbert - Jonas Binladen - Simon YW Ho - Paula F Campos - Aakrosh Ratan - Lynn P Tomsho -

Source: https://link.springer.com/article/10.1186/1471-2148-9-95



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