title: Phylogenetic species identification in Rattus highlights rapid radiation and morphological similarity of New Guinean species.
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.
authors.affiliation: School of Biological Sciences and Department of Anthropology, The University of Auckland, Auckland, New Zealand.
authors.forename: Judith H
authors.initials: JH
authors.lastname: Robins
authors.affiliation: Department of Anthropology, The University of Auckland, Auckland, New Zealand.
authors.forename: Vernon
authors.initials: V
authors.lastname: Tintinger
authors.affiliation: Division of Mammals, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of America.
authors.forename: Ken P
authors.initials: KP
authors.lastname: Aplin
authors.affiliation: School of Biological Sciences, The University of Auckland, Auckland, New Zealand.
authors.forename: Melanie
authors.initials: M
authors.lastname: Hingston
authors.affiliation: Department of Anatomy, University of Otago, Dunedin, New Zealand.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Matisoo-Smith
authors.affiliation: Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.
authors.forename: David
authors.initials: D
authors.lastname: Penny
authors.affiliation: School of Biological Sciences and Institute of Marine Science, The University of Auckland, Auckland, New Zealand.
authors.forename: Shane D
authors.initials: SD
authors.lastname: Lavery
mesh_terms: D000818:Animals; D004272:DNA, Mitochondrial / Q000235:genetics*; D019143:Evolution, Molecular; D008928:Mitochondria / Q000235:genetics* / Q000528:radiation effects; D009512:New Guinea; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D011827:Radiation; D051381:Rats / Q000033:anatomy & histology* / Q000145:classification / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D004272:DNA, Mitochondrial