Base compositions of the (A) 18S and (B) 28S rRNA genes, averaged over all 88 mite strains used in this study.

<p>Error bars depict range. Results of the homogeneity test are given for each gene.</p

Bayesian phylogenetic tree of the sub-family Tetranychinae based on the 18S and 28S rRNA genes using the GTR Gamma model.

<p>Bayesian posterior probabilities (>0.50) are indicated at nodes. Each operational taxonomic unit is indicated by the voucher specimen no. and scientific name. Black circles with numbers indicate the clade no. which corresponds with the article. The tree is divided into three sections: (A) The entire tree, (B) Tetranychini-1, (C) Tetranychini-1, Eurytetranychini and Tetranychini-2 and (D) Tetranychini-3.</p

Maximum likelihood (ML) phylogenetic tree of the sub-family Tetranychinae based on the 18S and 28S rRNA genes using the GTR Gamma model.

<p>Bootstrap values (>50%) based on 1,000 replications are indicated at nodes. Each operational taxonomic unit is indicated by the voucher specimen no. and scientific name. Black circles with numbers indicate the clade no. which corresponds with the article. The tree is divided into three sections: (A) The entire tree, (B) Tetranychini-1, (C) Tetranychini-1, Eurytetranychini and Tetranychini-2 and (D) Tetranychini-3.</p

Maximum likelihood (ML) phylogenetic tree of the sub-family Tetranychinae based on the mitochondrial COI gene using the GTR Gamma model.

<p>Bootstrap values (>50%) based on 1,000 replications are indicated at nodes. Each operational taxonomic unit is indicated by the voucher specimen no. and scientific name. Black circles with numbers indicate the clade no. which corresponds with the article.</p

Base compositions of the codons of the mitochondrial COI gene.

<p>(A) All codon positions, (B) 1st codon position, (C) 2nd codon position, (D) 3rd codon position, averaged over all 68 mite strains used in this study. Error bars depict range. Results of the homogeneity test are given for each codon position.</p

Phylogenetic Analysis of the Spider Mite Sub-Family Tetranychinae (Acari: Tetranychidae) Based on the Mitochondrial COI Gene and the 18S and the 5′ End of the 28S rRNA Genes Indicates That Several Genera Are Polyphyletic

<div><p>The spider mite sub-family Tetranychinae includes many agricultural pests. The internal transcribed spacer (ITS) region of nuclear ribosomal RNA genes and the cytochrome <i>c</i> oxidase subunit I (COI) gene of mitochondrial DNA have been used for species identification and phylogenetic reconstruction within the sub-family Tetranychinae, although they have not always been successful. The 18S and 28S rRNA genes should be more suitable for resolving higher levels of phylogeny, such as tribes or genera of Tetranychinae because these genes evolve more slowly and are made up of conserved regions and divergent domains. Therefore, we used both the 18S (1,825–1,901 bp) and 28S (the 5′ end of 646–743 bp) rRNA genes to infer phylogenetic relationships within the sub-family Tetranychinae with a focus on the tribe Tetranychini. Then, we compared the phylogenetic tree of the 18S and 28S genes with that of the mitochondrial COI gene (618 bp). As observed in previous studies, our phylogeny based on the COI gene was not resolved because of the low bootstrap values for most nodes of the tree. On the other hand, our phylogenetic tree of the 18S and 28S genes revealed several well-supported clades within the sub-family Tetranychinae. The 18S and 28S phylogenetic trees suggest that the tribes Bryobiini, Petrobiini and Eurytetranychini are monophyletic and that the tribe Tetranychini is polyphyletic. At the genus level, six genera for which more than two species were sampled appear to be monophyletic, while four genera (<i>Oligonychus</i>, <i>Tetranychus</i>, <i>Schizotetranychus</i> and <i>Eotetranychus</i>) appear to be polyphyletic. The topology presented here does not fully agree with the current morphology-based taxonomy, so that the diagnostic morphological characters of Tetranychinae need to be reconsidered.</p></div

Classification and sources of Tetranychid mites used in this study.

<p><i>^a</i>Voucher specimens are preserved at the Laboratory of Applied Entomology and Zoology, Faculty of Agriculture, Ibaraki University under the serial voucher specimen number.</p><p>Classification and sources of Tetranychid mites used in this study.</p

Primers used in polymerase chain reaction amplification and sequencing of the mitochondrial COI gene and the 18S and 28S rRNA genes.

<p>Primers used in polymerase chain reaction amplification and sequencing of the mitochondrial COI gene and the 18S and 28S rRNA genes.</p