Revisiting the four Hexapoda classes: Protura as the sister group to all other hexapods.

Insects represent the most diverse animal group, yet previous phylogenetic analyses based on morphological and molecular data have failed to agree on the evolutionary relationships of early insects and their six-legged relatives (together constituting the clade Hexapoda). In particular, the phylogenetic positions of the three early-diverging hexapod lineages-the coneheads (Protura), springtails (Collembola), and two-pronged bristletails (Diplura)-have been debated for over a century, with alternative topologies implying drastically different scenarios of the evolution of the insect body plan and hexapod terrestrialization. We addressed this issue by sampling all hexapod orders and experimenting with a broad range of across-site compositional heterogeneous models designed to tackle ancient divergences. Our analyses support Protura as the earliest-diverging hexapod lineage ("Protura-sister") and Collembola as a sister group to Diplura, a clade corresponding to the original composition of Entognatha, and characterized by the shared possession of internal muscles in the antennal flagellum. The previously recognized 'Elliplura' hypothesis is recovered only under the site-homogeneous substitution models with partial supermatrices. Our cross-validation analysis shows that the site-heterogeneous CAT-GTR model, which recovers "Protura-sister," fits significantly better than homogeneous models. Furthermore, the morphologically unusual Protura are also supported as the earliest-diverging hexapod lineage by other lines of evidence, such as mitogenomes, comparative embryology, and sperm morphology, which produced results similar to those in this study. Our backbone phylogeny of hexapods will facilitate the exploration of the underpinnings of hexapod terrestrialization and megadiversity.

Multikingdom interactions govern the microbiome in subterranean cultural heritage sites.

SignificanceThe conservation of historical relics against microbial biodeterioration is critical to preserving cultural heritages. One major challenge is our limited understanding of microorganisms' dispersal, colonization, and persistence on relics after excavation and opening to external environments. Here, we investigate the ecological and physiological profiles of the microbiome within and outside the Dahuting Han Dynasty Tomb with a 1,800-y history. Actinobacteria dominate the microbiome in this tomb. Via interkingdom signaling mutualism, springtails carry Actinobacteria as one possible source into the tomb from surrounding environments. Subsequently, Actinobacteria produce cellulases combined with antimicrobial substances, which helps them to colonize and thrive in the tomb via intrakingdom competition. Our findings unravel the ecology of the microbiomes colonizing historical relics and provide help for conservation practices.

Genomic insights into the chromosomal elongation in a family of Collembola.

Collembola is a highly diverse and abundant group of soil arthropods with chromosome numbers ranging from 5 to 11. Previous karyotype studies indicated that the Tomoceridae family possesses an exceptionally long chromosome. To better understand chromosome size evolution in Collembola, we obtained a chromosome-level genome of Yoshiicerus persimilis with a size of 334.44 Mb and BUSCO completeness of 97.0% (n = 1013). Both genomes of Y. persimilis and Tomocerus qinae (recently published) have an exceptionally large chromosome (ElChr greater than 100 Mb), accounting for nearly one-third of the genome. Comparative genomic analyses suggest that chromosomal elongation occurred independently in the two species approximately 10 million years ago, rather than in the ancestor of the Tomoceridae family. The ElChr elongation was caused by large tandem and segmental duplications, as well as transposon proliferation, with genes in these regions experiencing weaker purifying selection (higher dN/dS) than conserved regions. Moreover, inter-genomic synteny analyses indicated that chromosomal fission/fusion events played a crucial role in the evolution of chromosome numbers (ranging from 5 to 7) within Entomobryomorpha. This study provides a valuable resource for investigating the chromosome evolution of Collembola.

Whole-genome-based phylogenetic analyses provide new insights into the evolution of springtails (Hexapoda: Collembola).

Springtails (Collembola) stand as one of the most abundant, widespread, and ancient terrestrial arthropods on earth. However, their evolutionary history and deep phylogenetic relationships remain elusive. In this study, we employed phylogenomic approaches to elucidate the basal relationships among Collembola. We sampled whole-genome data representing all major collembolan lineages in proportion to their known diversity. To account for potential phylogenomic biases, we implemented various data extraction, locus sampling, and signal filtering strategies to generate matrices. Subsequently, we applied a diverse array of tree-searching and rate-modelling methods to reconstruct the phylogeny. Our analyses, utilizing different matrices and methods, converged on the same unrooted relationships among collembolan ingroups, supporting the current ordinal classification and challenging the monophyly of Arthropleona and Symphypleona s.l. However, discrepancies across analyses existed in the root of Collembola. Among various root positions, those based on more informative matrices and biologically realistic models, favoring a basal topology of Entomobryomorpha + (Symphypleona s.s. + (Neelipleona + Poduromorpha)), were supported by subsequent methodological assessment, topology tests, and rooting analyses. This optimal topology suggests multiple independent reduction of the pronotum in non-poduromorph orders and aligns with the plesiomorphic status of neuroendocrine organs and epicuticular structure of Entomobryomorpha. Fossil-calibrated dating analyses based on the optimal topology indicated late-Paleozoic to mid-Mesozoic origins of the crown Collembola and four orders. In addition, our results questioned the monophyly of Isotomidae and Neanuridae, underscoring the need for further attention to the systematics of these families. Overall, this study provides novel insights into the phylogenetic backbone of Collembola, which will inform future studies on the systematics, ecology, and evolution of this significant arthropod lineage.

Phylogenomics of Elongate-Bodied Springtails Reveals Independent Transitions from Aboveground to Belowground Habitats in Deep Time.

Soil has become a major hotspot of biodiversity studies, yet the pattern and timing of the evolution of soil organisms are poorly known because of the scarcity of paleontological data. To overcome this limitation, we conducted a genome-based macroevolutionary study of an ancient, diversified, and widespread lineage of soil fauna, the elongate-bodied springtails (class Collembola, order Entomobryomorpha). To build the first robust backbone phylogeny of this previously refractory group, we sampled representatives of major higher taxa (6 out of 8 families, 11 out of 16 subfamilies) of the order with an emphasis on the most problematic superfamily Tomoceroidea, applied whole-genome sequencing methods, and compared the performance of different combinations of data sets (universal single-copy orthologs [USCO] vs. ultraconserved elements]) and modeling schemes. The fossil-calibrated timetree was used to reconstruct the evolution of body size, sensory organs, and pigmentation to establish a time frame of the ecomorphological divergences. The resultant trees based on different analyses were congruent in most nodes. Several discordant nodes were carefully evaluated by considering method fitness, morphological information, and topology test. The evaluation favored the well-resolved topology from analyses using USCO amino acid matrices and complex site-heterogeneous models (CAT$+$GTR and LG$+$PMSF (C60)). The preferred topology supports the monophyletic superfamily Tomoceroidea as an early-diverging lineage and a sister relationship between Entomobryoidea and Isotomoidea. The family Tomoceridae was recovered as monophyletic, whereas Oncopoduridae was recovered as paraphyletic, with Harlomillsia as a sister to Tomoceridae and hence deserving a separate family status as Harlomillsiidae Yu and Zhang fam. n. Ancestral Entomobryomorpha were reconstructed as surface-living, supporting independent origins of soil-living groups across the Paleozoic-Mesozoic, and highlighting the ancient evolutionary interaction between aboveground and belowground fauna. [Collembola; phylogenomics; soil-living adaptation; whole-genome sequencing.].

Molecular phylogeny and trait evolution in an ancient terrestrial arthropod lineage: Systematic revision and implications for ecological divergence (Collembola, Tomocerinae).

Phylogenetic assessments of functional traits are important for mechanistically understanding the interactions between organisms and environments, but such practices are strongly limited by the availability of phylogenetic frameworks. The tomocerin springtails are an ancient, widespread and ecologically important group of terrestrial arthropods, whereas their phylogeny and trait evolution remained unaddressed. In the present study, we conducted the first comprehensive phylogenetic reconstruction of Tomocerinae, based on a multi-loci molecular dataset covering all major lineages within the subfamily, using Bayesian inference (BI), maximum-likelihood (ML) and maximum-parsimony (MP) approaches. Divergence time was estimated and ancestral character state reconstruction (ACSR) was performed to trace the evolutionary history of five ecomorphological traits correlated with sensory and locomotory functions. Our results support the monophyly of Tomocerinae, and indicate that current classification of Tomocerinae only partially reflects evolutionary relationships, notably the commonest and speciose genus Tomocerus is polyphyletic. The subfamily probably originated in Early Cretaceous and diversified in two Cretaceous and one Eocene radiation events. As indicated by the evolutionary patterns of functional traits, multiple ecological divergences took place during the diversification of Tomocerinae. The study suggests a potential underestimation of ecological divergence and functional diversity in terrestrial arthropods, calls for an update of present trait databases, and demonstrates the value of macroevolutionary knowledge for improving the trait-based ecology. In addition, Tomocerus, Tomocerina and Tritomurus are redefined, a new genus Yoshiicerusgen. n. and new subgenera Coloratomurussubgen. n., Ciliatomurussubgen. n., Striatomurussubgen. n. and Ocreatomurussubgen. n. are described in the appendix.

New species of Monodontocerus (Collembola: Tomoceridae) from southern China with diagnostic notes on the genus and introduction of new taxonomic characters.

Three new species of Monodontocerus are described from caves in southern China: M. absens sp. nov. is characterized by its cephalic chaetotaxy and the absence of chaetae from the tenaculum; M. mulunensis sp. nov. is characterized by a combination of characters including chaetotaxy, foot complex and furca; M. trigrandis sp. nov. is different from other species in the formula of dental spines and the reduction of the ungual teeth. A key to the species of Monodontocerus is provided. Potential diagnostic characters for this genus are proposed. Troglomorphy and interspecific variability are discussed. Pseudopores and the dorsal disto-lateral chaeta on the manubrium are introduced as new taxonomic characters for Tomocerinae. 

Chromosomal-Level Genome Assembly of the Springtail Tomocerus qinae (Collembola: Tomoceridae).

The family Tomoceridae is among the earliest derived collembolan lineages, thus is of key importance in understanding the evolution of Collembola. Here, we assembled a chromosome-level genome of one tomocerid species Tomocerus qinae by combining Nanopore long reads and Hi-C data. The final genome size was 334.44 Mb with the scaffold/contig N50 length of 71.85/13.94 Mb. BUSCO assessment indicated that 96.80% of complete arthropod universal single-copy orthologs (n = 1,013) were present in the assembly. The repeat elements accounted for 26.11% (87.26 Mb) and 494 noncoding RNAs were identified in the genome. A total of 20,451 protein-coding genes were predicted, which captured 96.0% (973) BUSCO genes. Gene family evolution analyses identified 4,825 expanded gene families of T. qinae, among them, 47 experienced significant expansions, and these significantly expanded gene families mainly involved in proliferation and growth. This study provides an important genomic resource for future evolution and comparative genomics analyses of Collembola.

Phylomitogenomic analyses on collembolan higher taxa with enhanced taxon sampling and discussion on method selection.

Collembola are a basal group of Hexapoda renowned for both unique morphological characters and significant ecological roles. However, a robust and plausible phylogenetic relationship between its deeply divergent lineages has yet to be achieved. We carried out a mitophylogenomic study based on a so far the most comprehensive mitochondrial genome dataset. Our data matrix contained mitogenomes of 31 species from almost all major families of all four orders, with 16 mitogenomes newly sequenced and annotated. We compared the linear arrangements of genes along mitochondria across species. Then we conducted 13 analyses each under a different combination of character coding, partitioning scheme and heterotachy models, and assessed their performance in phylogenetic inference. Several hypothetical tree topologies were also tested. Mitogenomic structure comparison revealed that most species share the same gene order of putative ancestral pancrustacean pattern, while seven species from Onychiuridae, Poduridae and Symphypleona bear different levels of gene rearrangements, indicating phylogenetic signals. Tomoceroidea was robustly recovered for the first time in the presence of all its families and subfamilies. Monophyly of Onychiuroidea was supported using unpartitioned models alleviating LBA. Paronellidae was revealed polyphyletic with two subfamilies inserted independently into Entomobryidae. Although Entomobryomorpha has not been well supported, more than half of the analyses obtained convincing topologies by placing Tomoceroidea within or near remaining Entomobryomorpha. The relationship between elongate-shaped and spherical-shaped collembolans still remained ambiguous, but Neelipleona tend to occupy the basal position in most trees. This study showed that mitochondrial genomes could provide important information for reconstructing the relationships among Collembola when suitable analytical approaches are implemented. Of all the data refining and model selecting schemes used in this study, the combination of nucleotide sequences, partitioning model and exclusion of third codon positions performed better in generating more reliable tree topology and higher node supports than others.

Molecular phylogeny of Entomobrya (Collembola: Entomobryidae) from China: Color pattern groups and multiple origins.

Highly diversified colorations among springtails (Collembola) have been widely used for species diagnosis, but their phylogenetic significance is poorly known. We addressed this issue in the largest Entomobryinae genus Entomobrya, which possesses variable color patterns among species. The relationships within the genus and to other genera have also rarely been studied. Based on material mainly from China, we have conducted a multilocus phylogeny and topology tests with likelihood and Bayesian algorithms, and accordingly demonstrated the non-monophyly of Chinese Entomobrya. The division of five clades, including Entomobrya and several related genera, coincided well with five types of colorations, respectively. Further analyses of divergence time and historical biogeography revealed that Chinese Entomobrya originated mainly from Palearctic (northern and western) China in the Paleocene and Eocene. This study highlights the great phylogenetic values as well as taxonomic uses of coloration in Chinese Entomobrya. Multiple phylogenetic and biogeographic origins of Entomobrya imply its complicated relationships with both scaled and unscaled genera of Entomobryinae.

Two new Chinese species of Tomocerus at different stages of troglomorphic adaptation (Collembola, Tomoceridae).

Two new species of Tomocerus are described from caves in Guizhou and Guangxi Province, China. Tomocerus troglodytes sp. nov. is highly troglomorphic. It belongs to the kinoshitai complex, and is most similar to another eyeless and colourless species Tomocerus caecus, from which it differs as it has longer antennae; 2,2/2,2/2+2/0 versus 2,2/2,5/0/0 cephalic dorsal chaetotaxy formula; 6 versus 4 central macrochaetae on Th. II; 0 versus 2 ungual teeth; unguis devoid of baso-internal ridges; 3-5/3-5, I, 0-1, I versus 4-5/1-2,I-II,0-1,I-II dental spines formula; 2-4 versus 1 tenacular chaetae; and 0 versus 1 mucronal intermediate teeth. In contrast, Tomocerus leyensis sp. nov. is at an earlier stage of troglomorphic adaptation. It resembles several cave-dwelling species of the ocreatus complex in habitus and shape of dental spines, but differs in the following characters: absence of large postantennal organ; cephalic dorsal chaetotaxy formula 2/2,4/2+2/2+2 versus other patterns; larger number of ungual teeth; and only 1 large distal dental spine. The troglomorphic characteristics of the two species are discussed with emphasis on their potential adaptation to cave habitats.

Three new species of Tomocerus from tropical zone of China (Collembola, Tomoceridae).

Tomocerids are world-widely distributed, but were seldom reported from tropics. In the present paper, three new species of Tomocerus Nicolet are described from Hainan and Yunnan Provinces, tropical zone of China. All three species have compound-type dental spines and belong to Tomocerus ocreatus species-group. Tomocerus tropicus sp. nov. resembles Tomocerus pseudocreatus Yu, but differs from the latter in mesothoracic macrochaetotaxy, manubrial dorsal scales and denticles on the dental spines. Tomocerus nan sp. nov. resembles Tomocerus virgatus Yu, but differs from the latter in colour pattern, cephalic dorsal macrochaetotaxy, manubrial dorsal scales and denticles on the dental spines. Tomocerus nabanensis sp. nov. resembles T. postantennalis Yu, Zhang Deharveng, Tomocerus dong Yu Li and Tomocerus deharvengi Yu Li, but differs from the three species in PAO, cephalic and tergal dorsal macrochaetotaxy and tenent hairs. Our studies including the present work indicate the importance of future survey on Tomocerinae in and near tropics where diversity of this group was historically underestimated.

Two new species of Tomocerus ocreatus group with a single large distal dental spine (Collembola, Tomoceridae).

Most members of Tomocerus ocreatus group have two distal large spines on dens, so far, only Tomocerus spinulus Chen Christiansen, 1998 and Tomocerus leyensis Yu Deharveng, 2018 have been described with only one distal large spine and are thus exceptional in this group. In the present paper, we report two other species with the same form. The two new species resemble T. spinulus in chaetotaxy, dental spine formula and general shape of the dental spines, but differ from it in several other characters, including position and shape of the prominent dorsal chaetae on the manubrium and dens. Also, T. pseudospinulus sp. nov. differs from T. spinulus in having larger denticles on the dental spines, and T. paraspinulus sp. nov. differs from T. spinulus in having longer antenna and more chaetae on the tenaculum. The two new species are similar, but can be distinguished by length of the antenna, number of the chaetae on tenaculum, status of the prominent manubrial dorsal chaetae and fine sculpture of the dental spines. Distances of COI mtDNA also support the validation of two new species. A key to species of T. ocreatus species-group with single large dental spine is provided.

Revision of Tomocerus similis Chen & Ma, with discussion of the kinoshitai complex and the distal tibiotarsal chaetae in Tomocerinae (Collembola, Tomoceridae).

Molecular analysis and a detailed morphological comparison revealed that Tomocerus similis Chen & Ma was described from individuals belonging to several species from several localities. Based on both old and new material from Anhui and Jiangsu Provinces, China, T. similis is redescribed and two new species are described. The three species are morphologically similar. Tomocerus persimilis sp. nov. differs from the others by the presence of central macrochaeta on head and of several distinct distal inner teeth on unguis. Tomocerus dissimilis sp. nov. is characterised by pointed tenent hairs on anterior legs. Remarks are made on the systematics and ecology of the kinoshitai complex, and on the taxonomic value of tenent hair and its adjacent chaetae.

[A study on the interpolation algorithm for the serial-parallel robot-controlled HIFU].

According to the hardware characters of the high intensive focused ultrasound (HIFU) serial-parallel robots, this paper presents an algorithm of 2-grade interpolation scheme which includes the rough and fine interpolations. Both pre-acceleration and post-acceleration are employed to meet the restrictive requirements of coordinated dynamic performance and the detailed procedure of the interpolation algorithm is given too.

New troglomorphic species of Tomocerus with well-developed postantennal organs (Collembola: Tomoceridae).

Three new troglobitic species of Tomocerus are described from the southwestern karsts of China. All of them have well developed postantennal organs. Tomocerus dong sp. nov. is similar to Tomocerus postantennalis Yu, Zhang & Deharveng and Tomocerus deharvengi sp. nov., but is different from them mainly in the number of prelabral chaetae and the dorsal body chaetotaxy. T. deharvengi sp. nov. is very similar to T. postantennalis but differs from the latter in the cephalic chaetotaxy, the number of manubrial pseudopores and the number of dental spines. T. cthulhu sp. nov. is peculiar for the multi-furcated vesicles of ventral tube, and is different from the three aforementioned species mainly in the dorsal body chaetotaxy. The position of the new species and the relationships between them are discussed.

New cave-dwelling species of Tomoceridae from China, with a study on the pattern of mesothoracic bothriotricha in Tomocerinae (Collembola, Entomobryomorpha).

Two new troglobitic species of Tomoceridae are described from Guizhou and Guangxi provinces, China. Tomocerus tiani sp. n. resembles Tomocerus kinoshitai Yosii, 1954, Tomocerus caecus Yu & Deharveng, 2015 and Tomocerus similis Chen & Ma, 1997 but differs from them mainly in the body colour, the cephalic chaetotaxy and the number of manubrial pseudopores. Monodontocerus cinereus sp. n. is similar to Monodontocerus mulunensis Yu, Deharveng & Zhang, 2014 but is different from the latter in the body colour, the length of antennae, the number of ungual teeth and the chaetotaxy on Abd. III and Abd. IV. Special remarks are made on the mesothoracic bothriotricha in Tomocerinae.

Two new species of Tomocerus ocreatus complex (Collembola, Tomoceridae) from Nanjing, China.

Two new species of Tomocerus Nicolet, 1842 are described from Nanjing, China. Tomocerus qinae sp. nov. is similar to the Vietnamese species Tomocerus ocreatus, but is different from the latter mainly in the colour pattern, the length of antennae, and the pattern of ungual teeth. Tomocerus qixiaensis sp. nov. is similar to Tomocerus ocreatus and Tomocerus qinae sp. nov., but can be distinguished from them by the short antennae and the blunt prominent macrochaetae on manubrium and dens. DNA barcode sequences of the new species are provided.

[Key technologies in HIFU treatment machine development].

This paper gives a comprehensive illustration on the key technologies involved in HIFU treatment machine development and thus it can be used for reference and be of benefit to the further development.