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Evolutionary relationships and divergence times among the native rats of Australia

Judith H Robins1*, Patricia A McLenachan2, Matthew J Phillips3, Bennet J McComish4, Elizabeth Matisoo-Smith5 and Howard A Ross6

Author Affiliations

1 Department of Anthropology and School of Biological Sciences, The University of Auckland, Auckland, New Zealand

2 Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand

3 Research School of Biology, Australian National University, Canberra, Australia

4 Allan Wilson Centre for Molecular Ecology and Evolution and Institute of Molecular Biosciences Massey University, Palmerston North, New Zealand

5 Allan Wilson Centre for Molecular Ecology and Evolution and Department of Anatomy and Structural Biology, Otago School of Medical Sciences, Dunedin, New Zealand

6 Allan Wilson Centre for Molecular Ecology and Evolution, Bioinformatics Institute and School of Biological Sciences, The University of Auckland, Auckland, New Zealand

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BMC Evolutionary Biology 2010, 10:375  doi:10.1186/1471-2148-10-375

Published: 2 December 2010



The genus Rattus is highly speciose and has a complex taxonomy that is not fully resolved. As shown previously there are two major groups within the genus, an Asian and an Australo-Papuan group. This study focuses on the Australo-Papuan group and particularly on the Australian rats. There are uncertainties regarding the number of species within the group and the relationships among them. We analysed 16 mitochondrial genomes, including seven novel genomes from six species, to help elucidate the evolutionary history of the Australian rats. We also demonstrate, from a larger dataset, the usefulness of short regions of the mitochondrial genome in identifying these rats at the species level.


Analyses of 16 mitochondrial genomes representing species sampled from Australo-Papuan and Asian clades of Rattus indicate divergence of these two groups ~2.7 million years ago (Mya). Subsequent diversification of at least 4 lineages within the Australo-Papuan clade was rapid and occurred over the period from ~ 0.9-1.7 Mya, a finding that explains the difficulty in resolving some relationships within this clade. Phylogenetic analyses of our 126 taxon, but shorter sequence (1952 nucleotides long), Rattus database generally give well supported species clades.


Our whole mitochondrial genome analyses are concordant with a taxonomic division that places the native Australian rats into the Rattus fuscipes species group. We suggest the following order of divergence of the Australian species. R. fuscipes is the oldest lineage among the Australian rats and is not part of a New Guinean radiation. R. lutreolus is also within this Australian clade and shallower than R. tunneyi while the R. sordidus group is the shallowest lineage in the clade. The divergences within the R. sordidus and R. leucopus lineages occurring about half a million years ago support the hypotheses of more recent interchanges of rats between Australia and New Guinea. While problematic for inference of deeper divergences, we report that the analysis of shorter mitochondrial sequences is very useful for species identification in rats.