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

Tomoko Matsuda,Norihide Hinomoto,Maiko Morishita,Tetsuo Gotoh,Dorothee Huchon

doi:10.1371/journal.pone.0108672

Tomoko Matsuda, Norihide Hinomoto + Show 3 more

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https://doi.org/10.1371/journal.pone.0108672

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Abstract

The spider mite sub-family Tetranychinae includes many agricultural pests. The internal transcribed spacer (ITS) region of nuclear ribosomal RNA genes and the cytochrome c 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 (Oligonychus, Tetranychus, Schizotetranychus and Eotetranychus) 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.

Highlights

The spider mite sub-family Tetranychinae includes some pests that cause serious economic losses throughout the world [1], [2], [3]
As observed in previous studies, our tree based on the c oxidase subunit I (COI) gene did not resolve deep-level phylogeny because of the low bootstrap values for deep nodes of tree (Figure 2)
Our phylogenetic trees based on the 18S and 28S ribosomal RNA (rRNA) genes suggest that the tribes Bryobiini and Petrobiini of the sub-family Bryobiinae are both monophyletic, but the tribe Tetranychini is polyphyletic because the monophyletic clade of Eurytetranychini is placed inside Tetranychini (Figures 4A and 5A)

Summary

Introduction

The spider mite sub-family Tetranychinae includes some pests that cause serious economic losses throughout the world [1], [2], [3]. Tetranychus urticae Koch, Panonychus citri (McGregor) and Oligonychus coffeae (Nietner), have an especially strong effect on agricultural and horticultural crops, and they are polyphagous. These genera include mono-, oligophagous species, such as Tetranychus bambusae Wang & Ma, Panonychus bambusicola Ehara & Gotoh, Oligonychus orthius Rimando, Oligonychus modestus (Banks) and Oligonychus rubicundus Ehara which inhabit only gramineous plants. The use of DNA-based methods to identify species has increasingly been used for some genera of the Tetranychinae. Matsuda et al [10], [11] revealed that almost all species of Japanese Oligonychus (17 of 18 species) and all species of Tetranychus (13 species) can be identified by using the cytochrome c oxidase subunit I (COI) gene of mitochondrial DNA

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