Abstract
The genus Rattus is highly speciose, the taxonomy is complex, and individuals are often difficult to identify to the species level. Previous studies have demonstrated the usefulness of phylogenetic approaches to identification in Rattus but some species, especially among the endemics of the New Guinean region, showed poor resolution. Possible reasons for this are simple misidentification, incomplete gene lineage sorting, hybridization, and phylogenetically distinct lineages that are unrecognised taxonomically. To assess these explanations we analysed 217 samples, representing nominally 25 Rattus species, collected in New Guinea, Asia, Australia and the Pacific. To reduce misidentification problems we sequenced museum specimens from earlier morphological studies and recently collected tissues from samples with associated voucher specimens. We also reassessed vouchers from previously sequenced specimens. We inferred combined and separate phylogenies from two mitochondrial DNA regions comprising 550 base pair D-loop sequences and both long (655 base pair) and short (150 base pair) cytochrome oxidase I sequences. Our phylogenetic species identification for 17 species was consistent with morphological designations and current taxonomy thus reinforcing the usefulness of this approach. We reduced misidentifications and consequently the number of polyphyletic species in our phylogenies but the New Guinean Rattus clades still exhibited considerable complexity. Only three of our eight New Guinean species were monophyletic. We found good evidence for either incomplete mitochondrial lineage sorting or hybridization between species within two pairs, R. leucopus/R. cf. verecundus and R. steini/R. praetor. Additionally, our results showed that R. praetor, R. niobe and R. verecundus each likely encompass more than one species. Our study clearly points to the need for a revised taxonomy of the rats of New Guinea, based on broader sampling and informed by both morphology and phylogenetics. The remaining taxonomic complexity highlights the recent and rapid radiation of Rattus in the Australo-Papuan region.
Highlights
With more than 60 currently recognised species, the genus Rattus features large in the native rodent fauna of mainland Asia, Island South East Asia, Australia and Melanesia [1]
The reassessment of the vouchers held in Sydney at the Australian Museum resulted in ten changes to species identifications of Papua New Guinean rats
These ten corrections were based on morphology, they were subsequently found to be consistent with the DNA results
Summary
With more than 60 currently recognised species, the genus Rattus features large in the native rodent fauna of mainland Asia, Island South East Asia, Australia and Melanesia [1]. Even though species of Rattus are encountered more often than any other group of small mammals in the Asia-Pacific region, they are notoriously difficult to identify in the field, even in reliably distinguishing introduced from native species [6]. This difficulty stems from a combination of intrinsic morphological conservatism, substantial changes in pelage colour and texture through life, and an unusual level of plasticity in both phenotypic and reproductive characters in species that live under multiple bioclimatic regimes [6]
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