Population genomic data in spider mites point to a role for local adaptation in shaping range shifts.

Local adaptation is particularly likely in invertebrate pests that typically have short generation times and large population sizes, but there are few studies on pest species investigating local adaptation and separating this process from contemporaneous and historical gene flow. Here, we use a population genomic approach to investigate evolutionary processes in the two most dominant spider mites in China, Tetranychus truncatus Ehara and Tetranychus pueraricola Ehara et Gotoh, which have wide distributions, short generation times, and large population sizes. We generated genome resequencing of 246 spider mites mostly from China, as well as Japan and Canada at a combined total depth of 3,133×. Based on demographic reconstruction, we found that both mite species likely originated from refugia in southwestern China and then spread to other regions, with the dominant T. truncatus spreading ~3,000 years later than T. pueraricola. Estimated changes in population sizes of the pests matched known periods of glaciation and reinforce the recent expansion of the dominant spider mites. T. truncatus showed a greater extent of local adaptation with more genes (76 vs. 17) associated with precipitation, including candidates involved in regulation of homeostasis of water and ions, signal transduction, and motor skills. In both species, many genes (135 in T. truncatus and 95 in T. pueraricola) also showed signatures of selection related to elevation, including G-protein-coupled receptors, cytochrome P450s, and ABC-transporters. Our results point to historical expansion processes and climatic adaptation in these pests which could have contributed to their growing importance, particularly in the case of T. truncatus.

Geography alone cannot explain Tetranychus truncatus (Acari: Tetranychidae) population abundance and genetic diversity in the context of the center-periphery hypothesis.

The center-periphery hypothesis (CPH) states that the genetic diversity, genetic flow, and population abundance of a species are highest at the center of the species' geographic distribution. However, most CPH studies have focused on the geographic distance and have ignored ecological and historical effects. Studies using niche models to define the center and periphery of a distribution and the interactions among geographical, ecological, and historical gradients have rarely been done in the framework of the CPH, especially in biogeographical studies of animal species. Here, we examined the CPH for a widely distributed arthropod, Tetranychus truncatus (Acari: Tetranychidae), in eastern China using three measurements: geographic distance to the center of the distribution (geography), ecological suitability based on current climate data (ecology), and historical climate data from the last glacial maximum (history). We found that the relative abundances of different populations were more strongly related to ecology than to geography and history. Genetic diversity within populations and genetic differentiation among populations based on mitochondrial marker were only significantly related to history. However, the genetic diversity and population differentiation based on microsatellites were significantly related to all three CPH measurements. Overall, population abundance and genetic pattern cannot be explained very well by geography alone. Our results show that ecological gradients explain the variation in population abundance better than geographic gradients and historical factors, and that current and historical factors strongly influence the spatial patterns of genetic variation. This study highlights the importance of examining more than just geography when assessing the CPH.

Phylogenetic signals in pest abundance and distribution range of spider mites.

BACKGROUND: Attributes of pest species like host range are frequently reported as being evolutionarily constrained and showing phylogenetic signal. Because these attributes in turn could influence the abundance and impact of species, phylogenetic information could be useful in predicting the likely status of pests. In this study, we used regional (China) and global datasets to investigate phylogenetic patterns in occurrence patterns and host ranges of spider mites, which constitute a pest group of many cropping systems worldwide. RESULTS: We found significant phylogenetic signal in relative abundance and distribution range both at the regional and global scales. Relative abundance and range size of spider mites were positively correlated with host range, although these correlations became weaker after controlling for phylogeny. CONCLUSIONS: The results suggest that pest impacts are evolutionarily constrained. Information that is easily obtainable - including the number of known hosts and phylogenetic position of the mites - could therefore be useful in predicting future pest risk of species.

High genetic diversity in a 'recent outbreak' spider mite, Tetranychus pueraricola, in mainland China.

Tetranychus pueraricola is a newly reported spider mite that occurs frequently in mainland China. It is possible that this species was introduced from elsewhere and became a serious pest recently. However, the correct identification of red-pigmented spider mites has repeatedly proven problematic. There is also the possibility that T. pueraricola in China was long misidentified as its sibling species, Tetranychus urticae (red form). To test which of these two scenarios is the more likely, individuals from 14 populations of T. pueraricola and five populations of T. urticae (red form) in China were sampled and genotyped using mitochondrial COI and microsatellite loci. Unlike a recent invasive species, the genetic diversity of T. pueraricola was very high with high mitochondrial genetic diversity (16 haplotypes), high effective alleles (Ne = 2.038 ± 0.081) and expected heterozygosity (He = 0.395 ± 0.016). Surprisingly, we found that all T. urticae (red form) populations shared only one mitochondrial haplotype and showed quite low genetic diversity (Ne = 1.443 ± 0.055; He = 0.234 ± 0.025) which was even lower than that of the green form of T. urticae in mainland China from a previous study. We did not detect significant signals of recent bottlenecks for most populations from both species. These results suggest T. pueraricola is unlikely to be a recent invasive pest but a species that has existed in China for a long time. It is probable that T. pueraricola in China has long been misidentified as T. urticae (red form).

A change in the bacterial community of spider mites decreases fecundity on multiple host plants.

Bacterial symbionts may influence the fitness of their herbivore hosts, but such effects have been poorly studied across most invertebrate groups. The spider mite, Tetranychus truncatus, is a polyphagous agricultural pest harboring various bacterial symbionts whose function is largely unknown. Here, by using a high-throughput 16S rRNA amplicon sequencing approach, we characterized the bacterial diversity and community composition of spider mites fed on five host plants after communities were modified following tetracycline exposure. We demonstrated that spider mite bacterial diversity and community composition were significantly affected by host plants and antibiotics. In particular, the abundance of the maternally inherited endosymbionts Wolbachia and Spiroplasma significantly differed among spider mites that were reared on different plant species and were completely removed by antibiotics. There was an overall tendency for daily fecundity to be lower in the mites with reduced bacterial diversity following the antibiotic treatment. Our data suggest that host plants and antibiotics can shape spider mite bacterial communities and that bacterial symbionts improve mite performance.

Preparation of adsorbents for selectively removal of heavy metals from Salvia miltiorrhiz extract / 中草药

Objective: Taking molecular sieve as a main component, to develop adsorbents which can selectively remove five kinds of heavy metal in Salvia miltiorrhiz extract solution. Methods: The 13X zeolite powder and active alumina powder were selected to compose adsorbent from four materials including iron red powder, fast powder (activated alumina), 13X molecular sieve powder, and zinc sulfide powder. The adsorbent formula was optimized with uniform design for mixture experiment. Pore-expanding agents, such as Chitisan and EDTA, were added to improve adsorbent pore structure. Results: With uniform design for mixture experiment, adsorbents with 13X zeolite ratio 0.275 6—0.465 5 could effectively remove five heavy metals (Cu, Pb, Cd, Hg, and As) in water solution. The optimal adsorbents from uniform design were hard to remove heavy metal in S. miltiorrhiz extract solution in 4 h, and removal ratios of Cu, Pb, Cd, Hg, and As were 14.4%, 74.5%, 54.6%, 13.4%, and 8.8%, respectively. With the same formula, pore- expanding adsorbents could effectively remove five heavy metals in S. miltiorrhiz extract solution in 4 h, and removal ratios of Cu, Pb, Cd, Hg, and As increased to 21.0%, 91.5%, 97.5%, 60.3%, and 46.8%, respectively. Conclusion: Pore-expanding adsorbents prepared in this study could remove five heavy metals in S. miltiorrhiz extract solution in short time, exhibiting industrial application prospect.

Comparative transcriptomes and reciprocal best hit analysis revealed potential pigment genes in two color forms of Tetranychus urticae.

Tetranychus urticae Koch is a worldwide agricultural pest. There are two color forms: red and green. The molecular mechanism underlying this color variation is unknown. To elucidate the mechanism, we characterized differentially expressed pigment pathway genes shared in the transcriptomes of these two forms using RNA sequencing and reciprocal best hit analysis. Differentially expressed pigment pathway genes were determined by qRT-PCR to confirm the accuracy of RNA-Seq. The transcriptomes revealed 963 differentially expressed genes (DEGs), of which 687 DEGs were higher in the green form. KEGG enrichment analysis revealed carotenoid biosynthesis genes in T. urticae. Reciprocal best hit analysis revealed 817 putative pigment pathway genes, 38 of which were differentially expressed and mainly classified into four categories: heme, melanin, ommochrome and rhodopsin. Phylogenetic analysis of homologous ommochrome genes showed that tetur09g01950 is closely related to Ok. This study revealed putative pigment pathway genes in the two forms of T. urticae, and might provide a new resource for understanding the mechanism of color variation.

Development of microsatellite markers for six Tetranychus species by transfer from Tetranychus urticae genome.

Microsatellite markers are frequently used to explore the population genetic structure of organisms. Spider mites (genus Tetranychus) are important agricultural pests. Several markers have been developed for T. urticae, but for other spider mites, few such markers are available, hampering studies of their population genetics. In this study, we developed and characterized microsatellite markers for six non-model spider mite species (T. truncatus, T. kanzawai, T. ludeni, T. piercei, T. phaselus and T. pueraricola) by cross-species amplification of markers in the T. urticae genome, in order to better understand the population structure of Tetranychus species. Among 228 screened loci, many were polymorphic, including 13 loci in T. urticae, 11 loci in T. truncatus, 15 loci in T. pueraricola, 23 loci in T. kanzawai, 19 loci in T. piercei, 11 loci in T. phaselus and 9 loci in T. ludeni. Sequence analysis determined that the fragment length variations of the transferred microsatellites were mainly due to the variations of the numbers of repeats. These new microsatellite markers should be useful for studying the population genetics of the seven Tetranychus species.

The complete mitochondrial genome of Tetranychus truncatus Ehara (Acari: Tetranychidae).

The complete mitochondrial genome of Tetranychus truncatus Ehara (Acari: Tetranychidae) is a typical circular DNA with length of 13,089 bp (GenBank accession number: KM111296). The genome contains all 13 protein-coding genes (PCGs), an A + T-rich region, two rRNA genes and 22 tRNA genes. The A + T content of the mitochondrial genome is 84.5%. The AT-skew is positive (0.032) while the GC-skew is negative (-0.058). The gene arrangement is conserved in T. urticae, Panonychus citri and P. ulmi which are in the same family (Tetranychidae). The A + T-rich region is only 43 bp in length with high A + T content (97.7%). All the PCGs start with typical ATD codons. Eight PCGs have complete TAA stop codons, while five PCGs have an incomplete stop codon (T).

The complete mitochondrial genomes of six species of Tetranychus provide insights into the phylogeny and evolution of spider mites.

Many spider mites belonging to the genus Tetranychus are of agronomical importance. With limited morphological characters, Tetranychus mites are usually identified by a combination of morphological characteristics and molecular diagnostics. To clarify their molecular evolution and phylogeny, the mitochondrial genomes of the green and red forms of Tetranychus urticae as well as T. kanzawai, T. ludeni, T. malaysiensis, T. phaselus, T. pueraricola were sequenced and compared. The seven mitochondrial genomes are typical circular molecules of about 13,000 bp encoding and they are composed of the complete set of 37 genes that are usually found in metazoans. The order of the mitochondrial (mt) genes is the same as that in the mt genomes of Panonychus citri and P. ulmi, but very different from that in other Acari. The J-strands of the mitochondrial genomes have high (∼ 84%) A+T contents, negative GC-skews and positive AT-skews. The nucleotide sequence of the cox1 gene, which is commonly used as a taxon barcode and molecular marker, is more highly conserved than the nucleotide sequences of other mitochondrial genes in these seven species. Most tRNA genes in the seven genomes lose the D-arm and/or the T-arm. The functions of these tRNAs need to be evaluated. The mitochondrial genome of T. malaysiensis differs from the other six genomes in having a slightly smaller genome size, a slight difference in codon usage, and a variable loop in place of the T-arm of some tRNAs by a variable loop. A phylogenic analysis shows that T. malaysiensis first split from other Tetranychus species and that the clade of the family Tetranychoidea occupies a basal position in the Trombidiformes. The mt genomes of the green and red forms of T. urticae have limited divergence and short evolutionary distance.