Phylogenetic relationships and divergence times of the genusTokudaiawithin Murinae (Muridae; Rodentia) inferred from the nucleotide sequences encoding the Cytbgene, RAG 1, and IRBP

Abstract

The phylogenetic relationships of six genera of Murinae (Apodemus, Diplothrix, Micromys, Mus, Rattus, and Tokudaia) were examined using the nucleotide sequences for the mitochondrial cytochrome b (Cytb), as well as the nuclear recombination activating gene 1 (RAG1) and interphotoreceptor retinoid-binding protein (IRBP), with special emphasis on the position of the genus Tokudaia, which is endemic to the Ryukyu Islands. Compared with Cytb at all codon positions, the first and second codon positions of Cytb, RAG1 (1002 base pairs (bp)), and IRBP (1586 bp) sequences were less prone to saturation. Close affinity between the genera Tokudaia and Apodemus was observed in the analyses using the IRBP (1586 bp) and combined nuclear (2588 bp; RAG1 + IRBP) sequences. The divergence time for the Tokudaia–Apodemus clade was estimated at approximately 6.5–8.0 Ma, which is more recent than previously reported, thereby indicating the recent colonization of the Ryukyu Islands by the genus Tokudaia. The other relationships among the main genera were highly ambiguous, owing either to saturation or insufficient phylogenetic information. The radiation of the main genera within a relatively short period of evolutionary time may explain the unresolved topologies, although molecular sources that are less subject to saturation are required to resolve the outstanding issues.