Mitochondrial Metagenomics Reveals the Ancient Origin and Phylodiversity of Soil Mites and Provides a Phylogeny of the Acari

The evolutionary history and timeline of mites in ancient soils

Acariform mites play a crucial role as primary soil decomposers, impacting the carbon cycle. However, the timing of their diversification is uncertain, with estimated dates ranging from the Precambrian (no land plants) to the Carboniferous (diverse terrestrial ecosystems). One factor affecting these time estimates is an uncertain phylogenetic position of the earliest unequivocal fossil mites from the Devonian Rhynie Chert, which have been classified in five modern families and three suborders. Here, we thoroughly examine these specimens, assign them to a single species Protacarus crani (family Protoacaridae, fam. nov., suborder Endeostigmata) and integrate this information into a time-calibrated phylogenetic analysis. Our phylogeny suggests a Cambrian basal divergence of Acariformes (508-486 Ma), coinciding with the land colonization by bryophytes. At this time, the mites' ecological niches were probably diversified beyond the upper soil. Our study provides temporal context, improves the accuracy of fossil dating, and underscores the importance of mites' diverse habitats and their potential roles in soil food webs.

Does metabolic rate influence genome-wide amino acid composition in the course of animal evolution?

Natural selection is believed to shape amino acid usage of the proteome by minimizing the energy cost of protein biosynthesis. Although this hypothesis explains well the amino acid frequency (AAfrequency) difference among the 20 common amino acids within a given genome (species), whether it is applicable to cross-species difference remains to be inspected. Here, we proposed and tested a "metabolic rate hypothesis," which suggests that metabolic rate impacts genome-wide AAfrequency, considering that the energy allocated to protein biosynthesis is under selection pressure due to metabolic rate constraint. We performed integrated phylogenetic comparative analyses on proteomic sequence and metabolic rate data of 166 species covering 130 eumetazoan orders. We showed that resting metabolic rate (RMR) was significantly linked to AAfrequency variation across animal lineages, with a contribution comparable to or greater than genomic traits such as GC content and codon usage bias. Consistent with the metabolic rate hypothesis, low-energy-cost amino acids are observed to be more likely at higher frequency in animal species with high (residual) metabolic rate. Correlated evolution of RMR and AAfrequency was further inferred being driven by adaptation. The relationship between RMR and AAfrequency varied greatly among amino acids, most likely reflecting a trade-off among various interacting factors. Overall, there exists no "one-size-fits-all" predictor for AAfrequency, and integrated investigation of multilevel traits is indispensable for a fuller understanding of AAfrequency variation and evolution in animal.

Coastal mites (Oribatida, Ameronothridae) found far from the coast in moss growing on the Cathédrale Notre-Dame de Paris, France, fifty years after their first discovery in this historic site

A species of oribatid mite, Ameronothrus maculatus (Michael, 1882), was collected from moss growing on the building of the Cathédrale Notre-Dame de Paris. This species of Ameronothridae is usually found in coastal Holarctic environments. The specimens were studied by Scanning Electron Microscope and could be clearly assigned to this taxon. This population was first discovered by F. Grandjean approximately 50 years ago, and the present record demonstrates that it has persisted despite its habitat being a tourist destination visited by over 14 million people annually. The record of this species far upstream and on anthropogenic structures is rare but not out of the ordinary in Northern Europe where its distribution can reach far beyond the edges of the estuaries. For further confirmation, we obtained DNA sequences for the COI gene (1554 bp, LC848687), and they were almost identical to those of an earlier found and sequenced specimen of A. maculatus from Germany, differing by only a single base. As supplemental information on A. maculatus from Paris, the region includes whole nucleic ribosomal RNA genes (18S, 5.8S, and 28S, LC848688), partial elongation factor 1 alpha (LC848689), and the complete nucleotide sequence of mitochondrion were also determined.

Evaluation of morphological traits in Trhypochthoniidae with focus on Allonothrus, and morphology-molecule conflict in classification and phylogeny of Nothrina (Acari: Oribatida)

The oribatid mite family Trhypochthoniidae exhibit the greatest collective ecological valence among the families of the middle-derivative infraorder Nothrina. Our objectives were: to examine poorly-known aspects of their morphology, with a focus on Allonothrus and a redescription of adult A. tuxtlasensis; to compare ontogenetic development of leg setation among the genera; and to test congruence between molecular and morphological inferences about relationships within Trhypochthoniidae and among Nothrina in general. New data on leg setal ontogeny are presented for Allonothrus giganticus, Archegozetes longisetosus and Trhypochthonius sp., and aspects of leg setation in the seven genera are compared. Collectively their setation is unique among Nothrina, particularly due to losses of certain fundamental tarsal setae. In a broad analysis of oribatid mite tibiae I and II, we propose that ancestral seta c" is usually present on I and often present also on II, but in most instances it has been given the notation l" or v" by analogy. An unusual diversity of subcapitular structure in Trhypochthoniidae gives insight into evolutionary transitions and terminological problems. Overall, there is little congruence between morphology-based phylogenetic trees (or classifications) and published molecular trees, with the following conclusions being most salient. Most molecular studies do not support a monophyletic Malaconothroidea but neither do they present a consistent picture of relationships of the two included families. Monophyly of Trhypochthoniidae (sensu lato) was generally supported-rendering moot the separation of monogeneric families Allonothridae, Mucronothridae and Trhypochthoniellidae-but their sister-group was inconsistent. Malaconothridae, also consistently monophyletic, usually were recovered as more basal in Nothrina. Considering their unusual shared narrow ventrosejugal articulation and a significant set of uncommon regressive characters, it seems reasonable to retain the two families in Malaconothroidea, pending more compelling molecular data. The distribution of apomorphies in a set of 23 morphological characters does not support molecular trees of trhypochthoniid genera. Trhypochthoniellus and Afronothrus are the most apomorphic genera, Trhypochthonius the least. Twenty-four molecular phylogeny studies with relevant representation are collectively inconclusive as to whether Nothrina is a paraphyletic (as usually perceived) or monophyletic group. Surprisingly, Hermanniidae were consistently recovered as relatively basal or even outside Nothrina, not as the sister-group of Brachypylina. Nanhermanniidae were consistently associated with Crotoniidae, and their unique morphology may be paedomorphic. Allonothrus giganticus Haq, 1978 is considered a senior subjective synonym of Allonothrus pararusseolus Subías & Sarkar, 1982 from Tripura, India (new synonymy).

Convergent evolution revealed by paraphyly and polyphyly of many taxa of oribatid mites: A molecular approach

A reliable phylogeny is crucial for understanding the evolution and radiation of animal taxa. Phylogenies based on morphological data may be misleading due to frequent convergent evolution of traits-a problem from which molecular phylogenies suffer less. This may be particularly relevant in oribatid mites, an ancient soil animal taxon with more than 11,000 species, where the classification of species into high-ranking taxa such as superfamilies is equivocal. Here, we present a molecular phylogeny of 317 oribatid, 4 astigmatid and 17 endeostigmatid mite species/taxa based on 18S rDNA sequences. We aimed at testing the validity of the 41 superfamilies of oribatid mites recognized by Norton and Behan-Pelletier (in Krantz and Walter, A manual of Acarology, 3rd ed., Texas Technical University Press, Lubbock, 2009). The results indicate that 17 of the 41 oribatid mite superfamilies are monophyletic but that 18 superfamilies are paraphyletic or polyphyletic (5 superfamilies were only included with one species and Microzetoidea were not included). Our findings point to the importance of convergent evolution in polyphyletic oribatid mite taxa. Convergent evolution and the old age of mites likely resulted in a mosaic-like distribution of morphological characters impeding phylogenetic reconstructions based on morphology, calling for molecular approaches to improve oribatid mite systematics.

Quantification of rearrangements and evolution of mitochondrial gene order of Acari (Chelicerata: Arachnida)

Invertebrate mitogenomes are generally fixed with formal 37 genes: 13 PCGs encoded subunits of OXPHOS, 2 ribosomal RNA (rRNA) functional in the translation of these PCGs and 22 transfer RNA (tRNA) genes. The order of these genes varies greatly among organisms and named rearrangement. Rearrangement patterns of mitochondrial genomes may shed light on mutation processes and evolutionary relationships of organisms. Mitochondrial gene organization is highly variable among Acari, so rearrangement is a very common mitogenomic pattern in this group. In this study, 258 unique Acari (Acariformes + Parasitiformes) mitogenomes were downloaded from NCBI and studied about rearrangement patterns. Sixty-seven mitotypes were determined among Acari and the most rearranged genes were trnL1 and nad2. Following that, trnI, trnS1, trnN, trnE, trnT, and trnP genes are remarkably mobile (RF > 95%). Conversely, atp6, cox3, trnG, and cytb genes also appears to be quite stable (RF < 20%). Within Acari, mean distance calculations are varied from 1.210 in atp8 to 0.155 in rrnS. Contrary to expectations, among Acari mobile tRNA genes appear to be conserved in sequences, whereas PCGs have higher distance values and seem to be mutated. Consistently, tRNA genes seem saturated, but some PCGs (atp6, cox genes, cytb, nad1, and nad6) are not saturated. These values do not correlate with each other (p > 0.005). This discrepancy may indicate that the genes were rearranged after mutation load; consistent with this, DAMBE saturation values are also not correlated with RF values. Parasitiformes mitogenomes are more mobile than Acariformes mitogenomes and may be under the effect of selective sweeping.

Mitochondrial metagenomics reveal the independent colonization of the world's coasts by intertidal oribatid mites (Acari, Oribatida, Ameronothroidea)

Oribatid mites are an ancient group that already roamed terrestrial ecosystems in the early and middle Devonian. The superfamily of Ameronothroidea, a supposedly monophyletic lineage, represents the only group of oribatid mites that has successfully invaded the marine coastal environment. By using mitogenome data and nucleic ribosomal RNA genes (18S, 5.8S, 28S), we show that Ameronothroidea are a paraphyletic assemblage and that the land-to-sea transition happened three times independently. Common ancestors of the tropical Fortuyniidae and Selenoribatidae were the first to colonize the coasts and molecular calibration of our phylogeny dates this event to a period in the Triassic and Jurassic era (225-146 mya), whereas present-day distribution indicates that this event might have happened early in this period during the Triassic, when the supercontinent Pangaea still existed. The cold temperate northern hemispheric Ameronothridae colonized the marine littoral later in the late Jurassic-Early Cretaceous and had an ancient distribution on Laurasian coasts. The third and final land-to-sea transition happened in the same geological period, but approx. 30 my later when ancestors of Podacaridae invaded coastal marine environments of the Gondwanan landmasses.

Phylogenomics resolves the higher-level phylogeny of herbivorous eriophyoid mites (Acariformes: Eriophyoidea)

BACKGROUND

Eriophyoid mites (Eriophyoidea) are among the largest groups in the Acariformes; they are strictly phytophagous. The higher-level phylogeny of eriophyoid mites, however, remains unresolved due to the limited number of available morphological characters-some of them are homoplastic. Nevertheless, the eriophyoid mites sequenced to date showed highly variable mitochondrial (mt) gene orders, which could potentially be useful for resolving the higher-level phylogenetic relationships.

RESULTS

Here, we sequenced and compared the complete mt genomes of 153 eriophyoid mite species, which showed 54 patterns of rearranged mt gene orders relative to that of the hypothetical ancestor of arthropods. The shared derived mt gene clusters support the monophyly of eriophyoid mites (Eriophyoidea) as a whole and the monophylies of six clades within Eriophyoidea. These monophyletic groups and their relationships were largely supported in the phylogenetic trees inferred from mt genome sequences as well. Our molecular dating results showed that Eriophyoidea originated in the Triassic and diversified in the Cretaceous, coinciding with the diversification of angiosperms.

CONCLUSIONS

This study reveals multiple molecular synapomorphies (i.e. shared derived mt gene clusters) at different levels (i.e. family, subfamily or tribe level) from the complete mt genomes of 153 eriophyoid mite species. We demonstrated the use of derived mt gene clusters in unveiling the higher-level phylogeny of eriophyoid mites, and underlines the origin of these mites and their co-diversification with angiosperms.

Towards a Canary Islands barcode database for soil biodiversity: revealing cryptic and unrecorded mite species diversity within insular soils

Soil arthropod diversity contributes to a high proportion of the total biodiversity on Earth. However, most soil arthropods are still undescribed, hindering our understanding of soil functioning and global biodiversity estimations. Inventorying soil arthropods using conventional taxonomical approaches is particularly difficult and costly due to the great species richness, abundance and local-scale heterogeneity of mesofauna communities and the poor taxonomic background knowledge of most lineages. To alleviate this situation, we have designed and implemented a molecular barcoding framework adapted to soil fauna. This pipeline includes different steps, starting with a morphology-based selection of specimens which are imaged. Then, DNA is extracted non-destructively. Both images and voucher specimens are used to assign a taxonomic identification, based on morphology that is further checked for consistency with molecular information. Using this procedure, we studied 239 specimens of mites from the Canary Islands including representatives of Mesostigmata, Sarcoptiformes and Trombidiformes, of which we recovered barcode sequences for 168 specimens that were morphologically identified to 49 species, with nine specimens that could only be identified at the genus or family levels. Multiple species delimitation analyses were run to compare molecular delimitations with morphological identifications, including ASAP, mlPTP, BINs and 3% and 8% genetic distance thresholds. Additionally, a species-level search was carried out at the Biodiversity Databank of the Canary Islands (BIOTA) to evaluate the number of species in our dataset that were not previously recorded in the archipelago. In parallel, a sequence-level search of our sequences was performed against BOLD Systems. Our results reveal that multiple morphologically identified species correspond to different molecular lineages, which points to significant levels of unknown cryptic diversity within the archipelago. In addition, we evidenced that multiple species in our dataset constituted new records for the Canary Islands fauna and that the information for these lineages within online genetic repositories is very incomplete. Our study represents the first systematic effort to catalogue the soil arthropod mesofauna of the Canary Islands and establishes the basis for the Canary Islands Soil Biodiversity barcode database. This resource will constitute a step forward in the knowledge of these arthropods in a region of special interest.

Relaxed purifying selection pressure drives accelerated and dynamic gene rearrangements in thrips (Insecta: Thysanoptera) mitochondrial genomes

Insect mitochondrial genomes (mitogenome) generally present a typical gene order, which is considered as the ancestral arrangement. All sequenced mitogenomes in the Thysanoptera display high levels of gene rearrangement. Due to limited number of thrips mitogenomes sequenced, how gene rearrangement may be shaped by evolution remain unclear. Here, we analyzed 33 thrips mitogenomes, including 14 newly sequenced. These mitogenomes were diverse in organization, nucleotides substitution and gene arrangements. We found 28 highly rearranged gene orders with the breakpoints of gene rearrangements from 25 to 33. Reconstruction of the ancestors mitochondrial gene arrangements states indicated that Tubulifera have more complex pathways than Terebrantia in the gene order evolution. Molecular calibration estimated that divergence of two suborders occurred in the middle Triassic while the radiation of thrips was associated with the arose and flourish of angiosperm. Our evolutionary hypothesis testing suggests that relaxation of selection pressure enabled the early phase of Thysanoptera evolution, followed by a stronger selective pressure fixed diversification. Our analyses found gene inversion increases the nonsynonymous substitution rates and provide an evolutionary hypothesis driving the diverse gene orders.

Collective and harmonized high throughput barcoding of insular arthropod biodiversity: Toward a Genomic Observatories Network for islands

Current understanding of ecological and evolutionary processes underlying island biodiversity is heavily shaped by empirical data from plants and birds, although arthropods comprise the overwhelming majority of known animal species, and as such can provide key insights into processes governing biodiversity. Novel high throughput sequencing (HTS) approaches are now emerging as powerful tools to overcome limitations in the availability of arthropod biodiversity data, and hence provide insights into these processes. Here, we explored how these tools might be most effectively exploited for comprehensive and comparable inventory and monitoring of insular arthropod biodiversity. We first reviewed the strengths, limitations and potential synergies among existing approaches of high throughput barcode sequencing. We considered how this could be complemented with deep learning approaches applied to image analysis to study arthropod biodiversity. We then explored how these approaches could be implemented within the framework of an island Genomic Observatories Network (iGON) for the advancement of fundamental and applied understanding of island biodiversity. To this end, we identified seven island biology themes at the interface of ecology, evolution and conservation biology, within which collective and harmonized efforts in HTS arthropod inventory could yield significant advances in island biodiversity research.

Diversity and Distribution of Mites (ACARI) Revealed by Contamination Survey in Public Genomic Databases

Acari (mites and ticks) are a biodiverse group of microarthropods within the Arachnida. Because of their diminutive size, mites are often overlooked. We hypothesized that mites, like other closely related microorganisms, could also contaminate public genomic database. Here, using a strategy based on DNA barcodes previously reported, we scanned contaminations related to mites (Acari, exclusive of Ixodida) in Genbank WGS/TSA database. In 22,114 assemblies (17,845 animal and 4269 plant projects), 1717 contigs in 681 assemblies (3.1%) were detected as mite contaminations. Additional taxonomic analysis showed the following: (1) most of the contaminants (1445/1717) were from the specimens of Magnoliopsida, Insecta and Pinopsida; (2) the contamination rates were higher in plant or TSA projects; (3) mite distribution among different classes of hosts varied considerably. Additional phylogenetic analysis of these contaminated contigs further revealed complicated mite-host associations. Overall, we conducted a first systemic survey and analysis of mite contaminations in public genomic database, and these DNA barcode related mite contigs will provide a valuable resource of information for understanding the diversity and phylogeny of mites.

Neglected no longer: Phylogenomic resolution of higher-level relationships in Solifugae

Advanced sequencing technologies have expedited resolution of higher-level arthropod relationships. Yet, dark branches persist, principally among groups occurring in cryptic habitats. Among chelicerates, Solifugae ("camel spiders") is the last order lacking a higher-level phylogeny and have thus been historically characterized as "neglected [arachnid] cousins". Though renowned for aggression, remarkable running speed, and xeric adaptation, inferring solifuge relationships has been hindered by inaccessibility of diagnostic morphological characters, whereas molecular investigations have been limited to one of 12 recognized families. Our phylogenomic dataset via capture of ultraconserved elements sampling all extant families recovered a well-resolved phylogeny, with two distinct groups of New World taxa nested within a broader Paleotropical radiation. Divergence times using fossil calibrations inferred that Solifugae radiated by the Permian, and most families diverged prior to the Paleogene-Cretaceous extinction, likely driven by continental breakup. We establish Boreosolifugae new suborder uniting five Laurasian families, and Australosolifugae new suborder uniting seven Gondwanan families using morphological and biogeographic signal.

Dispersal-Limited Symbionts Exhibit Unexpectedly Wide Variation in Host Specificity

A fundamental aspect of symbiotic relationships is host specificity, ranging from extreme specialists associated with only a single host species to generalists associated with many different species. Although symbionts with limited dispersal capabilities are expected to be host specialists, some are able to associate with multiple hosts. Understanding the micro- and macro-evolutionary causes of variations in host specificity is often hindered by sampling biases and the limited power of traditional evolutionary markers. Here, we studied feather mites to address the barriers associated with estimates of host specificity for dispersal-limited symbionts. We sampled feather mites (Proctophyllodidae) from a nearly comprehensive set of North American breeding warblers (Parulidae) to study mite phylogenetic relationships and host-symbiont codiversification. We used pooled-sequencing (Pool-Seq) and short-read Illumina technology to interpret results derived from a traditional barcoding gene (cytochrome c oxidase subunit 1) versus 11 protein-coding mitochondrial genes using concatenated and multispecies coalescent approaches. Despite the statistically significant congruence between mite and host phylogenies, mite-host specificity varies widely, and host switching is common regardless of the genetic marker resolution (i.e., barcode vs. multilocus). However, the multilocus approach was more effective than the single barcode in detecting the presence of a heterogeneous Pool-Seq sample. These results suggest that presumed symbiont dispersal capabilities are not always strong indicators of host specificity or of historical host-symbiont coevolutionary events. A comprehensive sampling at fine phylogenetic scales may help to better elucidate the microevolutionary filters that impact macroevolutionary processes regulating symbioses, particularly for dispersal-limited symbionts. [Codiversification; cophylogenetics; feather mites; host switching; pooled sequencing; species delineation; symbiosis, warblers.].

Where Eriophyoidea (Acariformes) Belong in the Tree of Life

Over the past century and a half, the taxonomic placement of Eriophyoidea has been in flux. For much of this period, this group has been treated as a subtaxon within Trombidiformes. However, the vast majority of recent phylogenetic analyses, including almost all phylogenomic analyses, place this group outside Trombidiformes. The few studies that still place Eriophyoidea within Trombidiformes are likely to be biased by incomplete taxon/gene sampling, long branch attraction, the omission of RNA secondary structure in sequence alignment, and the inclusion of hypervariable expansion-contraction rRNA regions. Based on the agreement among a number of independent analyses that use a range of different datasets (morphology; multiple genes; mitochondrial/whole genomes), Eriophyoidea are almost certain to be closely related to Nematalycidae, a family of vermiform mites within Endeostigmata, a basal acariform grade. Much of the morphological evidence in support of this relationship was apparent after the discovery of Nematalycidae in the middle of the 20th century. However, this evidence has largely been disregarded until very recently, perhaps because of overconfidence in the placement of Eriophyoidea within Trombidiformes. Here, we briefly review and identify a number of biases, both molecular- and morphology-based, that can lead to erroneous reconstructions of the position of Eriophyoidea in the tree of life.

Comparative Mitogenomics of Jumping Spiders with First Complete Mitochondrial Genomes of Euophryini (Araneae: Salticidae)

Salticidae is the most species-rich family of spiders with diverse morphology, ecology and behavior. However, the characteristics of the mitogenomes within this group are poorly understood with relatively few well-characterized complete mitochondrial genomes. In this study, we provide completely annotated mitogenomes for Corythalia opima and Parabathippus shelfordi, which represent the first complete mitogenomes of the tribe Euophryini of Salticidae. The features and characteristics of the mitochondrial genomes are elucidated for Salticidae by thoroughly comparing the known well-characterized mitogenomes. The gene rearrangement between trnL2 and trnN was found in two jumping spider species, Corythalia opima and Heliophanus lineiventris Simon, 1868. Additionally, the rearrangement of nad1 to between trnE and trnF found in Asemonea sichuanensis Song & Chai, 1992 is the first protein-coding gene rearrangement in Salticidae, which may have an important phylogenetic implication for the family. Tandem repeats of various copy numbers and lengths were discovered in three jumping spider species. The codon usage analyses showed that the evolution of codon usage bias in salticid mitogenomes was affected by both selection and mutational pressure, but selection may have played a more important role. The phylogenetic analyses provided insight into the taxonomy of Colopsus longipalpis (Żabka, 1985). The data presented in this study will improve our understanding of the evolution of mitochondrial genomes within Salticidae.

Evolution and phylogenetic diversity of the aquaporin gene family in arachnids

Water flux across cells predominantly occurs through the pore formed by the aquaporin channels. Since water balance is one of the most important challenges to terrestrial animals, aquaporin evolution and diversity is known to play roles in animal terrestrialisation. Arachnids (Arthropoda: Chelicerata: Arachnida) are the second most diverse group and represent the pioneer land colonists in animals; however, there remains no thorough investigation on aquaporin evolution and diversity in this evolutionarily important lineage. Here we reported a phylogenetic study of aquaporin evolution and diversity using genomic data from 116 arachnid species covering almost all (15/16) extant orders. A previously unrecognised subfamily related to aquaporin-4 (i.e. Aqp4-like subfamily) via phylogenetic analysis was identified, suggesting certain underestimate of the arachnid aquaporin diversity in earlier studies probably due to limited taxonomic sampling. Further analysis indicates that this subfamily emerged deep within the life tree of arthropods. Gene tree of another Aqp4-like subfamily (PripL) shows an unexpected basal split between acariform mites (Acariformes) and other arachnids. A closer inspection demonstrated that the PripL evolved quickly and has been under differential selection pressure in acariform mites. Evidence is provided that the evolutionarily ancient Glp subfamily (i.e. aquaglyceroporin) is significantly expanded in terrestrial arachnids compared with their marine relatives. Finally, in spite of the phylogenetic diversity, there exists conservation of some exons in size, functional domain, and intron-insertion phase: an 81-bp and a 218-bp exon, respectively, in apq4-like and glp genes across Eumetazoa lineages including arachnids and human beings. Both exons encode the carboxyl-terminal NPA motif, implying the coding and splicing pressure during hundreds of million years of animal evolution. Hypotheses were tested to explore the possible link between these findings and arachnid terrestrialisation.

An overview of chelicerate ovaries, with special reference to mites - myths and facts

In arthropods of the subphylum Chelicerata a panoistic ovary, in which all germline cells differentiate into oocytes, prevails. Among the chelicerates, mites are believed to show a great variety of the structure of the female gonads. In general, the knowledge of the ovarian structure in mites is fragmentary and patchy. In both evolutionary lines, Acariformes and Parasitiformes, apart from the panoistic ovary, the meroistic ovary, in which the oocytes grow supported by their sibling cells, the nurse cells, occurs. The presence of the meroistic ovary is considered an apomorphic state. Previous studies revealed a various structure of the meroistic ovary in different mite taxa, and the differences came down, inter alia, to a different number and location of the nurse cells in relation to the oocytes. Here we provide a comprehensive review of the structure of the Chelicerata ovary, with special reference to the mite ovary. We also provide our preliminary results of the analysis of ovarian structure in two representatives of terrestrial Parasitengona (Acariformes), Allothrombium fuliginosum (Trombidiidae) and Erythraeus cinereus (Erythraeidae), performed using light, confocal and electron transmission microscopy. The analyses allowed for verification of data published before. In A. fuliginosum we showed the presence of the nurse cells in the ovarian wall, so the ovary should be classified as meroistic. In meroistic ovary of E. cinereus we found that each oocyte is connected to several mononucleated nurse cells. The verification of literature data and broadening the knowledge of the structure of the female gonad in mites, will result in estimating the usefulness of the ovary traits in phylogenetic analyses and will provide the basis for inference about the directions of evolutionary changes of female gonad at lower systematic levels.

Divergence time of mites of the family Laelapidae based on mitochondrial barcoding region

Using the mitochondrial barcoding region to correlate research with 58 species in 19 genera of the family Laelapidae with the aim of determining the origin, phylogenetic relationships, and biogeographic historical distribution characteristics of mites in the family Laelapidae. Phylogenetic trees were obtained using Bayesian inference (BI) and Maximum-likelihood (ML) methods, based on three fossil records calibrated as molecular clock nodes, to estimate the divergence time of mites in the family Laelapidae as well as to apply Dispersal-Extinction-Cladogenesis (DEC) analyses to obtain biogeographic history inferences. The result showed species of the genera Hyperlaelaps and Haemolaelaps and some species of the genus Androlaelaps in the family Laelapidae were divided into clades of the genus Laelaps in both the BI and ML trees. Divergence time estimates and biogeographic history analysis revealed that the family Laelapidae likely diverged from other taxa during the Middle Jurassic (ca. 156.73 Mya), with Asia considered the most likely ancestral region for the family Laelapidae. Species of various genera began to undergo massive diversification events during the Cenozoic Tertiary. The results suggest that some genera in the family Laelapidae need to be re-defined or new genera need to be established; the Late Cretaceous to Late Neogene warm period would have promoted the divergence and expansion of species in the family Laelapidae. The divergence and dispersal of the family Laelapidae species is most likely a joint response to the continued northward drift of the Indian plate away from the Gondwana paleo-continent and gradually closer to Asia during the Late Cretaceous and the geological activity of the Tibetan Plateau during the Cenozoic Tertiary. The results strengthen our understanding of the origin and evolution of species in the family Laelapidae.

Structure and molecular evolution of the barcode fragment of cytochrome oxidase I (COI) in Macrocheles (Acari: Mesostigmata: Macrochelidae)

Consisting of approximately 320 species, Macrocheles is the most widely distributed genus in the family Macrochelidae. Though some studies have focused on the description of Macrochelidae using molecular techniques (e.g., RAPD) and sequencing of some genes, the interspecies relationships within Macrocheles still remain uncertain. As such, in the present study, we examine all publicly available data in GenBank to explore the evolutionary relationships, divergence times, and amino acid variations within Macrocheles. Exploring the patterns of variation in the secondary protein structure shows high levels of conservation in the second and last helices, emphasizing their involvement in the energy metabolism function of the cytochrome oxidase subunit I enzyme. According to our phylogenetic analysis, all available Macrocheles species are clustered in a monophyletic group. However, in the reconstructed trees, we subdivided M. merdarius and M. willowae into two well-supported intraspecific clades that are driven by geographic separation and host specificity. We also estimate the divergence time of selected species using calibration evidence from available fossils and previous studies. Thus, we estimate that the age of the Parasitiformes is 320.4 (273.3-384.3) Mya (Permian), and the Mesostigmata is 285.1 (270.8-286.4) Mya (Carboniferous), both with likely origins in the Paleozoic era. We also estimate that Macrocheles diverged from other Mesostigmata mites during the Mesozoic, approximately 222.9 Mya.

One-way ticket to the blue: A large-scale, dated phylogeny revealed asymmetric land-to-water transitions in acariform mites (Acari: Acariformes)

Acariform mites are an ancient and megadiverse lineage that may have experienced a complex pattern of invasions into terrestrial and aquatic habitats. These among-realm transitions may relate to periods of turmoil in Earth's history or be simply results of uneven biodiversity patterns across habitats. Here, we inferred a dated, representative acariform phylogeny (five genes, 9,200 bp aligned, 367 terminals belonging to 150 ingroup plus 15 outgroup families, 23 fossil calibration points) which was used to infer transitions between marine/freshwater/terrestrial habitats. We detected four unambiguous transitions from terrestrial to freshwater habitats (Hydrozetes, Naiadacarus, Fusohericia, Afronothrus, Homocaligus); one from freshwater to marine (Pontarachnidae), and four from marine to brackish or freshwater transitions (all among Halacaridae: Acarothrix; Halacarellus petiti; Copidognathus sp.; clade Limnohalacarus + Soldanellonyx + Porohalacarus + Porolohmannella). One transition to the sea was inferred ambiguously with respect to the ancestor being either terrestrial or freshwater (Hyadesiidae), and another must be most carefully examined by adding potential related taxa (Selenoribatidae + Fortuyniidae). Finally, we inferred a single, remarkable transition from aquatic to terrestrial habitats involving early evolution of the large and ecologically diverse lineage: the ancestor of the Halacaridae + Parasitengona clade was probably freshwater given our dataset, thus making terrestrial Parasitengona secondarily terrestrial. Overall, our results suggested a strong asymmetry in environmental transitions: the majority occurred from terrestrial to aquatic habitats. This asymmetry is probably linked to mites' biological properties and uneven biodiversity patterns across habitats rather than Earth's geological history. Since the land holds more acariform diversity than water habitats, a shift from the former is more likely than from the latter. We inferred the following relationships: alicid endeostigmatid + eriophyoid (Alycidae, (Nanorchestidae, (Nematalycidae, Eriophyoidea))) being sister group to the remaining Acariformes: (proteonematalycid Endeostigmata, alicorhagiid Endeostigmata, Trombidiformes, Oribatida (including Astigmata)). Trombidiform relationships had several novel rearrangements: (i) traditional Eupodina lacked support for the inclusion of Bdelloidea; (ii) Teneriffidae, traditionally placed among Anystina, was consistently recovered in a clade including Heterostigmata in Eleutherengona; (iii) several lineages, such as Adamystidae, Paratydeidae, Caeculidae and Erythracaridae, were recovered in a large clade along other Anystina and Eleutherengona, suggesting single origins of several fundamental character states, such as the reduction of the cheliceral fixed digit and development of the palpal thumb-claw complex.

Comparative mitogenomic analyses provide evolutionary insights into the retrolateral tibial apophysis clade (Araneae: Entelegynae)

The retrolateral tibial apophysis (RTA) clade is the largest spider lineage within Araneae. To better understand the diversity and evolution, we newly determined mitogenomes of ten RTA species from six families and performed a comparative mitogenomics analysis by combining them with 40 sequenced RTA mitogenomes available on GenBank. The ten mitogenomes encoded 37 typical mitochondrial genes and included a large non-coding region (putative control region). Nucleotide composition and codon usage were well conserved within the RTA clade, whereas diversity in sequence length and structural features was observed in control region. A reversal of strand asymmetry in nucleotide composition, i.e., negative AT-skews and positive GC-skews, was observed in each RTA species, likely resulting from mitochondrial gene rearrangements. All protein-coding genes were evolving under purifying selection, except for atp8 whose Ka/Ks was larger than 1, possibly due to positive selection or selection relaxation. Both mutation pressure and natural selection might contribute to codon usage bias of 13 protein-coding genes in the RTA lineage. Phylogenetic analyses based on mitogenomic data recovered a family-level phylogeny within the RTA; {[(Oval calamistrum clade, Dionycha), Marronoid clade], Sparassidae}. This study characterized RTA mitogenomes and provided some new insights into the phylogeny and evolution of the RTA clade.

Shotgun metagenomics of soil invertebrate communities reflects taxonomy, biomass, and reference genome properties

Metagenomics - shotgun sequencing of all DNA fragments from a community DNA extract - is routinely used to describe the composition, structure, and function of microorganism communities. Advances in DNA sequencing and the availability of genome databases increasingly allow the use of shotgun metagenomics on eukaryotic communities. Metagenomics offers major advances in the recovery of biomass relationships in a sample, in comparison to taxonomic marker gene-based approaches (metabarcoding). However, little is known about the factors which influence metagenomics data from eukaryotic communities, such as differences among organism groups, the properties of reference genomes, and genome assemblies.We evaluated how shotgun metagenomics records composition and biomass in artificial soil invertebrate communities at different sequencing efforts. We generated mock communities of controlled biomass ratios from 28 species from all major soil mesofauna groups: mites, springtails, nematodes, tardigrades, and potworms. We shotgun sequenced these communities and taxonomically assigned them with a database of over 270 soil invertebrate genomes.We recovered over 95% of the species, and observed relatively high false-positive detection rates. We found strong differences in reads assigned to different taxa, with some groups (e.g., springtails) consistently attracting more hits than others (e.g., enchytraeids). Original biomass could be predicted from read counts after considering these taxon-specific differences. Species with larger genomes, and with more complete assemblies, consistently attracted more reads than species with smaller genomes. The GC content of the genome assemblies had no effect on the biomass-read relationships. Results were similar among different sequencing efforts.The results show considerable differences in taxon recovery and taxon specificity of biomass recovery from metagenomic sequence data. The properties of reference genomes and genome assemblies also influence biomass recovery, and they should be considered in metagenomic studies of eukaryotes. We show that low- and high-sequencing efforts yield similar results, suggesting high cost-efficiency of metagenomics for eukaryotic communities. We provide a brief roadmap for investigating factors which influence metagenomics-based eukaryotic community reconstructions. Understanding these factors is timely as accessibility of DNA sequencing and momentum for reference genomes projects show a future where the taxonomic assignment of DNA from any community sample becomes a reality.

"Jack-of-all-trades" is parthenogenetic

Sex is evolutionarily more costly than parthenogenesis, evolutionary ecologists therefore wonder why sex is much more frequent than parthenogenesis in the majority of animal lineages. Intriguingly, parthenogenetic individuals and species are as common as or even more common than sexuals in some major and putative ancient animal lineages such as oribatid mites and rotifers. Here, we analyzed oribatid mites (Acari: Oribatida) as a model group because these mites are ancient (early Paleozoic), widely distributed around the globe, and include a high number of parthenogenetic species, which often co-exist with sexual oribatid mite species. There is evidence that the reproductive mode is phylogenetically conserved in oribatid mites, which makes them an ideal model to test hypotheses on the relationship between reproductive mode and species' ecological strategies. We used oribatid mites to test the frozen niche variation hypothesis; we hypothesized that parthenogenetic oribatid mites occupy narrow specialized ecological niches. We used the geographic range of species as a proxy for specialization as specialized species typically do have narrower geographic ranges than generalistic species. After correcting for phylogenetic signal in reproductive mode and demonstrating that geographic range size has no phylogenetic signal, we found that parthenogenetic lineages have a higher probability to have broader geographic ranges than sexual species arguing against the frozen niche variation hypothesis. Rather, the results suggest that parthenogenetic oribatid mite species are more generalistic than sexual species supporting the general-purpose genotype hypothesis. The reason why parthenogenetic oribatid mite species are generalists with wide geographic range sizes might be that they are of ancient origin reflecting that they adapted to varying environmental conditions during evolutionary history. Overall, our findings indicate that parthenogenetic oribatid mite species possess a widely adapted general-purpose genotype and therefore might be viewed as "Jack-of-all-trades."

Positive Correlation of the Gene Rearrangements and Evolutionary Rates in the Mitochondrial Genomes of Thrips (Insecta: Thysanoptera)

Simple Summary

Aeolothrips, commonly known as banded thrips, is the largest genus of the family Aeolothripidae (predatory thrips). In the current study, we sequenced the mitochondrial genome (mitogenome) of the banded thrip species Aeolothrips xinjiangensis. We found a novel gene arrangement in this mitogenome that has not been reported in Thysanoptera. By comparing the gene order and rearrangement patterns, we found seven identical gene blocks and three identical rearrangement events in two mitogenomes of banded thrips. There was marked variation in the mitochondrial gene order across thrip species, with only two conserved gene blocks shared by all 14 thrips. In addition, we found a positive correlation between the degree of gene rearrangement and evolutionary rate. Our results suggested that the mitogenomes of thrips have tended to be stable since their massive rearrangement.

Abstract

Extensive gene rearrangement is characteristic in the mitogenomes of thrips (Thysanoptera), but the historical process giving rise to the contemporary gene rearrangement pattern remains unclear. To better understand the evolutionary processes of gene rearrangement in the mitogenomes of thrips, we sequenced the mitogenome of the banded thrip species Aeolothrips xinjiangensis. First, we found a novel mitochondrial gene order in this species. This mitogenome is 16,947 bp in length and encodes the typical 37 coding genes (13 protein-coding genes, 22 tRNA genes, and two rRNA genes) of insects. The gene arrangement was dramatically different from the putative ancestral mitogenome, with 26 genes being translocated, eight of which were inverted. Moreover, we found a novel, conserved gene block, trnC-trnY, which has not been previously reported in the mitogenomes of thrips. With this newly assembled mitogenome, we compared mitogenome sequences across Thysanoptera to assess the evolutionary processes giving rise to the current gene rearrangement pattern in thrips. Seven identical gene blocks were shared by two sequenced banded thrip mitogenomes, while the reversal of ND2 combined with TDRL events resulted in the different gene orders of these two species. In phylogenetic analysis, the monophyly of the suborders and families of Thysanoptera was well supported. Across the gene orders of 14 thrips, only two conserved gene blocks, ATP8-ATP6 and ND4-ND4L, could be found. Correlation analysis showed that the degree of gene rearrangement was positively correlated with the non-synonymous substitution rate in thrips. Our study suggests that the mitogenomes of thrips remain stable over long evolutionary timescales after massive rearrangement during early diversification.

Highly diversified mitochondrial genomes provide new evidence for interordinal relationships in the Arachnida

Arachnida is an exceptionally diverse class in the Arthropoda, consisting of 20 orders and playing crucial roles in the terrestrial ecosystems. However, their interordinal relationships have been debated for over a century. Rearranged or highly rearranged mitochondrial genomes (mitogenomes) were consistently found in this class, but their various extent in different lineages and efficiency for resolving arachnid phylogenies are unclear. Here, we reconstructed phylogenetic trees using mitogenome sequences of 290 arachnid species to decipher interordinal relationships as well as diversification through time. Our results recovered monophyly of ten orders (i.e. Amblypygi, Araneae, Ixodida, Mesostigmata, Opiliones, Pseudoscorpiones, Ricinulei, Sarcoptiformes, Scorpiones and Solifugae), while rejecting monophyly of the Trombidiformes due to the unstable position of the Eriophyoidea. The monophyly of Acari (subclass) was rejected, possibly due to the long-branch attraction of the Pseudoscorpiones. The monophyly of Arachnida was further rejected because the Xiphosura nested within arachnid orders with unstable positions. Mitogenomes that are highly rearranged in mites but less rearranged or conserved in the remaining lineages point to their exceptional diversification in mite orders; however, shared derived mitochondrial (mt) gene clusters were found within superfamilies rather than interorders, confusing phylogenetic signals in arachnid interordinal relationships. Molecular dating results show that arachnid orders have ancient origins, ranging from the Ordovician to the Carboniferous, yet have significantly diversified since the Cretaceous in orders Araneae, Mesostigmata, Sarcoptiformes, and Trombidiformes. By summarizing previously resolved key positions of some orders, we propose a plausible arachnid tree of life. Our results underline a more precise framework for interordinal phylogeny in the Arachnida and provide new insights into their ancient evolution.

How Phylogenetics Can Elucidate the Chemical Ecology of Poison Frogs and Their Arthropod Prey

The sequestration by neotropical poison frogs (Dendrobatidae) of an amazing array of defensive alkaloids from oribatid soil mites has motivated an exciting research theme in chemical ecology, but the details of mite-to-frog transfer remain hidden. To address this, McGugan et al. (2016, Journal of Chemical Ecology 42:537-551) used the little devil poison frog (Oophaga sylvatica) and attempted to simultaneously characterize the prey mite alkaloids, the predator skin alkaloids, and identify the mites using DNA sequences. Heethoff et al. (2016, Journal of Chemical Ecology 42:841-844) argued that none of the mite families to which McGugan et al. allocated the prey was thought to possess alkaloids. Heethoff et al. concluded from analyses including additional sequences that the mite species were unlikely to be close relatives of the defended mites. We re-examine this by applying more appropriate phylogenetic methods to broader and denser taxonomic samples of mite sequences using the same gene (CO1). We found, over trees based on CO1 datasets, only weak support (except in one case) for branches critical to connecting the evolution of alkaloid sequestration with the phylogeny of mites. In contrast, a well-supported analysis of the 18S ribosomal gene suggests at least two independent evolutionary origins of oribatid alkaloids. We point out impediments in the promising research agenda, namely a paucity of genetic, chemical, and taxonomic information, and suggest how phylogenetics can elucidate at a broader level the evolution of chemical defense in prey arthropods, sequestration by predators, and the impact of alkaloids on higher-order trophic interactions.

Symbiotic bacteria of the gall-inducing mite Fragariocoptes setiger (Eriophyoidea) and phylogenomic resolution of the eriophyoid position among Acari

Eriophyoid mites represent a hyperdiverse, phytophagous lineage with an unclear phylogenetic position. These mites have succeeded in colonizing nearly every seed plant species, and this evolutionary success was in part due to the mites' ability to induce galls in plants. A gall is a unique niche that provides the inducer of this modification with vital resources. The exact mechanism of gall formation is still not understood, even as to whether it is endogenic (mites directly cause galls) or exogenic (symbiotic microorganisms are involved). Here we (i) investigate the phylogenetic affinities of eriophyoids and (ii) use comparative metagenomics to test the hypothesis that the endosymbionts of eriophyoid mites are involved in gall formation. Our phylogenomic analysis robustly inferred eriophyoids as closely related to Nematalycidae, a group of deep-soil mites belonging to Endeostigmata. Our comparative metagenomics, fluorescence in situ hybridization, and electron microscopy experiments identified two candidate endosymbiotic bacteria shared across samples, however, it is unlikely that they are gall inducers (morphotype1: novel Wolbachia, morphotype2: possibly Agrobacterium tumefaciens). We also detected an array of plant pathogens associated with galls that may be vectored by the mites, and we determined a mite pathogenic virus (Betabaculovirus) that could be tested for using in biocontrol of agricultural pest mites.

Evolution of DNA Methylation Across Ecdysozoa

DNA methylation is a crucial, abundant mechanism of gene regulation in vertebrates. It is less prevalent in many other metazoan organisms and completely absent in some key model species, such as Drosophila melanogaster and Caenorhabditis elegans. We report here a comprehensive study of the presence and absence of DNA methyltransferases (DNMTs) in 138 Ecdysozoa, covering Arthropoda, Nematoda, Priapulida, Onychophora, and Tardigrada. Three of these phyla have not been investigated for the presence of DNA methylation before. We observe that the loss of individual DNMTs independently occurred multiple times across ecdysozoan phyla. We computationally predict the presence of DNA methylation based on CpG rates in coding sequences using an implementation of Gaussian Mixture Modeling, MethMod. Integrating both analysis we predict two previously unknown losses of DNA methylation in Ecdysozoa, one within Chelicerata (Mesostigmata) and one in Tardigrada. In the early-branching Ecdysozoa Priapulus caudatus, we predict the presence of a full set of DNMTs and the presence of DNA methylation. We are therefore showing a very diverse and independent evolution of DNA methylation in different ecdysozoan phyla spanning a phylogenetic range of more than 700 million years.

Widespread retention of ohnologs in key developmental gene families following whole-genome duplication in arachnopulmonates

Whole-genome duplications (WGDs) have occurred multiple times during animal evolution, including in lineages leading to vertebrates, teleosts, horseshoe crabs, and arachnopulmonates. These dramatic events initially produce a wealth of new genetic material, generally followed by extensive gene loss. It appears, however, that developmental genes such as homeobox genes, signaling pathway components and microRNAs are frequently retained as duplicates (so-called ohnologs) following WGD. These not only provide the best evidence for WGD, but an opportunity to study its evolutionary consequences. Although these genes are well studied in the context of vertebrate WGD, similar comparisons across the extant arachnopulmonate orders are patchy. We sequenced embryonic transcriptomes from two spider species and two amblypygid species and surveyed three important gene families, Hox, Wnt, and frizzled, across these and 12 existing transcriptomic and genomic resources for chelicerates. We report extensive retention of putative ohnologs, further supporting the ancestral arachnopulmonate WGD. We also found evidence of consistent evolutionary trajectories in Hox and Wnt gene repertoires across three of the six arachnopulmonate orders, with interorder variation in the retention of specific paralogs. We identified variation between major clades in spiders and are better able to reconstruct the chronology of gene duplications and losses in spiders, amblypygids, and scorpions. These insights shed light on the evolution of the developmental toolkit in arachnopulmonates, highlight the importance of the comparative approach within lineages, and provide substantial new transcriptomic data for future study.

Molecular phylogeny of Phyllocoptes associated with roses discloses the presence of a new species

There are few plant maladies as devastating as rose rosette, a disease caused by an eriophyoid -transmitted virus. Rosette annihilates roses across North America, and to date, there is a single verified vector of the virus, Phyllocoptes fructiphilus Keifer. In direct contrast to the importance of rose for the ornamental industry there is limited knowledge on the eriophyoids that inhabit roses in North America and even less information on their vectoring capacities. This study dissects the genetic diversity of the eriophyoid fauna in rosette-affected hotspots and provides evidence of the existence of an undescribed species named Phyllocoptes arcani sp. nov., that could potentially be a second vector of the rosette virus.

Taxonomic Sampling and Rare Genomic Changes Overcome Long-Branch Attraction in the Phylogenetic Placement of Pseudoscorpions

Long-branch attraction is a systematic artifact that results in erroneous groupings of fast-evolving taxa. The combination of short, deep internodes in tandem with long-branch attraction artifacts has produced empirically intractable parts of the Tree of Life. One such group is the arthropod subphylum Chelicerata, whose backbone phylogeny has remained unstable despite improvements in phylogenetic methods and genome-scale data sets. Pseudoscorpion placement is particularly variable across data sets and analytical frameworks, with this group either clustering with other long-branch orders or with Arachnopulmonata (scorpions and tetrapulmonates). To surmount long-branch attraction, we investigated the effect of taxonomic sampling via sequential deletion of basally branching pseudoscorpion superfamilies, as well as varying gene occupancy thresholds in supermatrices. We show that concatenated supermatrices and coalescent-based summary species tree approaches support a sister group relationship of pseudoscorpions and scorpions, when more of the basally branching taxa are sampled. Matrix completeness had demonstrably less influence on tree topology. As an external arbiter of phylogenetic placement, we leveraged the recent discovery of an ancient genome duplication in the common ancestor of Arachnopulmonata as a litmus test for competing hypotheses of pseudoscorpion relationships. We generated a high-quality developmental transcriptome and the first genome for pseudoscorpions to assess the incidence of arachnopulmonate-specific duplications (e.g., homeobox genes and miRNAs). Our results support the inclusion of pseudoscorpions in Arachnopulmonata (new definition), as the sister group of scorpions. Panscorpiones (new name) is proposed for the clade uniting Scorpiones and Pseudoscorpiones.

Repeated convergent evolution of parthenogenesis in Acariformes (Acari)

The existence of old species-rich parthenogenetic taxa is a conundrum in evolutionary biology. Such taxa point to ancient parthenogenetic radiations resulting in morphologically distinct species. Ancient parthenogenetic taxa have been proposed to exist in bdelloid rotifers, darwinulid ostracods, and in several taxa of acariform mites (Acariformes, Acari), especially in oribatid mites (Oribatida, Acari). Here, we investigate the diversification of Acariformes and their ancestral mode of reproduction using 18S rRNA. Because parthenogenetic taxa tend to be more frequent in phylogenetically old taxa of Acariformes, we sequenced a wide range of members of this taxon, including early-derivative taxa of Prostigmata, Astigmata, Endeostigmata, and Oribatida. Ancestral character state reconstruction indicated that (a) Acariformes as well as Oribatida evolved from a sexual ancestor, (b) the primary mode of reproduction during evolution of Acariformes was sexual; however, species-rich parthenogenetic taxa radiated independently at least four times (in Brachychthonioidea (Oribatida), Enarthronota (Oribatida), and twice in Nothrina (Oribatida), (c) parthenogenesis additionally evolved frequently in species-poor taxa, for example, Tectocepheus, Oppiella, Rostrozetes, Limnozetes, and Atropacarus, and (d) sexual reproduction likely re-evolved at least three times from species-rich parthenogenetic clusters, in Crotonia (Nothrina), in Mesoplophora/Apoplophora (Mesoplophoridae, Enarthronota), and in Sphaerochthonius/Prototritia (Protoplophoridae, Enarthronota). We discuss possible reasons that favored the frequent diversification of parthenogenetic taxa including the continuous long-term availability of dead organic matter resources as well as generalist feeding of species as indicated by natural variations in stable isotope ratios.

Genome streamlining in a minute herbivore that manipulates its host plant

The tomato russet mite, Aculops lycopersici, is among the smallest animals on earth. It is a worldwide pest on tomato and can potently suppress the host's natural resistance. We sequenced its genome, the first of an eriophyoid, and explored whether there are genomic features associated with the mite's minute size and lifestyle. At only 32.5 Mb, the genome is the smallest yet reported for any arthropod and, reminiscent of microbial eukaryotes, exceptionally streamlined. It has few transposable elements, tiny intergenic regions, and is remarkably intron-poor, as more than 80% of coding genes are intronless. Furthermore, in accordance with ecological specialization theory, this defense-suppressing herbivore has extremely reduced environmental response gene families such as those involved in chemoreception and detoxification. Other losses associate with this species' highly derived body plan. Our findings accelerate the understanding of evolutionary forces underpinning metazoan life at the limits of small physical and genome size.