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

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.

Description and phylogenetic classification of Stackelberginia cerberus sp. nov. (Diptera: Asilidae), comprising the first record of this genus from the Nearctic

“…Node posterior probabilities are reasonably high (≥ 0.92) throughout the tree, except for some uncertainty for phylogenetic relationships within Lasiopogon and at the Stichopogoninae root. Lower support values for the subfamily root appear to stem from a basal polytomy in COI; this locus is known to have trouble resolving deeper level phylogenetic relationships (Matsuda et al 2014). Intrageneric relationships within Lasiopogon and Stichopogon will be covered in future publications with more comprehensive taxon sampling, but the overall genus-level topology matches our prior expectations from morphology-e.g., Townsendia grouping with Stichopogon, and the Asilinae (Proctacanthus Macquart) and Ommatiinae (Ommatius Wiedemann) clustering together in the outgroup.…”

Patterns of reproductive isolation in a haplodiploid – strong post‐mating, prezygotic barriers among three forms of a social spider mite

“…To amplify the fragment of para‐sodium channel gene, polymerase chain reaction (PCR) was carried out using primers given in Table S1 in a 20‐μL reaction mixture containing 1 μL of DNA sample, 2 μL of 10 × Ex Taq buffer (20 m m mg 2+ plus; Takara Bio Inc., Otsu, Shiga, Japan), 0.2 μL of TaKaRa Ex Taq (5U μL −1 ; Takara Bio Inc.), 1.6 μL of dNTP mix (2.5 m m each; Takara Bio Inc.), 1 μL of each primer (10 pmol μL −1 each) and 13.2 μL of ddH 2 O. PCR cycling conditions were 2 min at 94 °C, followed by 38 cycles of 30 s at 94 °C, 30 s at 53 °C and 1 min at 72 °C, and a final extension at 72 °C for 10 min. To amplify the fragment of mtCOI region, PCR was carried out using primers given in Table S1 (Matsuda et al ., ) in a 10‐μL reaction mixture containing 1 μL of DNA sample, 1 μL of 10 × Ex Taq buffer (20 m m mg 2+ plus; Takara Bio Inc.), 0.05 μL of TaKaRa Ex Taq (5U μL −1 , Takara Bio Inc.), 0.8 μL of dNTP mix (2.5 m m each; Takara Bio Inc.), 0.5 μL of each primer (10 pmol μL −1 each) and 6.35 μL of ddH 2 O. PCR cycling conditions were 4 min at 94 °C, followed by 35 cycles of 1 min at 94 °C, 1 min at 45 °C and 1.5 min at 72 °C, and a final extension at 72 °C for 10 min. In some samples, the fragment was not amplified.…”

<p align="center"><strong>A review of prevalence and phylogeny of the bacterial symbiont <em>Cardinium</em> in mites (subclass: Acari)</strong></p>

“…Previously, the 18S gene of the nuclear ribosomal DNA (18S rRNA) has been widely used for resolving the phylogeny of mites (Cruickshank 2002;Matsuda et al 2014). Here, we constructed the phylogeny of Cardinium-infected mites based on the available 18S rRNA sequences that were downloaded from GenBank.…”