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Phylogenetic relationships and divergence times of the genus Tokudaia within Murinae (Muridae; Rodentia) inferred from the nucleotide sequences encoding the Cytb gene, RAG 1, and IRBP

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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 TokudaiaApodemus 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.

L'étude des séquences de nucléotides codant pour le cytochrome b (Cytb) mitochondrial, ainsi que les séquences nucléaires du gène 1 de l'activation de la recombinaison (RAG1) et de la protéine liant le rétinol entre les photorécepteurs (IRBP), nous a permis d'examiner les relations phylogénétiques de six genres de Murinae (Apodemus, Diplothrix, Micromys, Mus, Rattus et Tokudaia) avec une attention particulière pour Tokudaia qui est endémique aux îles Ryukyu. Par comparaison avec Cytb à toutes les positions du codon, les premières et secondes positions du codon des séquences Cytb, RAG1 (1002 paires de bases (pb)) et IRBP (1586 pb) sont moins sujettes à la saturation. Les analyses basées sur les séquences IRBP (1586 pb) et les séquences nucléaires combinées (2588 pb; RAG1 + IRBP) font ressortir la forte affinité entre les genres Tokudaia et Apodemus. Le moment de la divergence du clade TokudaiaApodemus est estimé à environ 6,5–8,0 Ma, donc plus tardivement que ce qui a été signalé antérieurement, ce qui indique que la colonisation des îles Ryukyu par le genre Tokudaia est récente. Les autres relations entre les genres principaux sont très ambiguës, soit à cause de la saturation, soit par manque d'information phylogénétique. La radiation des genres principaux sur une période relativement courte de temps évolutif peut vraisemblablement expliquer les topologies encore irrésolues; il faudra des sources moléculaires moins sujettes à la saturation pour résoudre les questions encore en suspends.[Traduit par la Rédaction]

Document Type: Research Article

Publication date: August 1, 2004

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