Abstract
BackgroundThe 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.ResultsAnalyses 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.ConclusionsOur 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.
Highlights
The genus Rattus is highly speciose and has a complex taxonomy that is not fully resolved
Differences in the relationships among Australian species were inferred when New Guinean sequences were included in the analysis of Australian species
The greatest uncertainty in relationships among the Australian species was due to different root placements being optimal for the Australo-Papuan clade in some analyses of the different datasets
Summary
The genus Rattus is highly speciose and has a complex taxonomy that is not fully resolved. Over the last five million years (My) a combination of tectonic and climatic change meant that this geographic region experienced major fluctuations in sea level and in the extent of Previous studies [4,5] based on mitochondrial DNA (mtDNA) identified two major groups within Rattus. These are the Asian group, comprising rats from Southeast Asia and Island Southeast Asia, and the AustraloPapuan group comprising rats from Australia and New Guinea. The focus of this investigation is to use mtDNA, including whole mitochondrial genomes, to help evaluate these evolutionary relationships and to date the divergences among the Rattus species of Australia
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