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.

Dental Shape Variation and Phylogenetic Signal in the Rattini Tribe Species of Mainland Southeast Asia

“…To avoid these problems, we focused on comparative specimens that were consistently identified by a single research group (Ceropath project, http://www.ceropath.org/). Although extremely important to future understanding of the diversification of the genus Rattus, the taxonomic status and systematics of Sahulian Rattus from New Guinea and Australia remain little known, despite recent biomolecular investigation (Rowe et al 2008(Rowe et al , 2011Robins et al 2014). As such, it has been excluded from our analyses.…”

Emergence of Neural Angiostrongyliasis in Eastern Australia

“…The presence of only a single native Angiostrongylus is intriguing because there is a diverse range of native Rattus species in Australia and an even more diverse range of species in New Guinea and South East Asia countries (Robins et al 2014). Several other native rodent species occur in this country that frequently eat molluscs or other invertebrate prey (e.g., Hydromys chrysogaster and Uromys caudimaculatus).…”

Commensal Rats and Humans: Integrating Rodent Phylogeography and Zooarchaeology to Highlight Connections between Human Societies

“…[ 4 ] To date, mitochondrial phylogenies have included 26 or fewer species, [ 5 ] and comparisons between phylogenies with and without nuclear data identify mito‐nuclear discordance for some species. [ 4,6,7 ]…”

“…[ 10 ] for R. rattus complex (RrC), Robins et al. [ 6 ] for R. exulans , and Puckett et al. [ 81 ] for R. norvegicus .…”