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

The First Cavernicolous Species of Arrhopalites (Collembola, Symphypleona, Arrhopalitidae) from China and Its Phylogenetic Position

Arrhopalites Börner, 1906 includes 40 valid species, with 20 considered troglobionts, exclusive to caves. Arrhopalites beijingensis sp. nov. is the third species from China and the first from a cave habitat, collected in the Xianrendong Cave, Beijing, Junzhuang Town. It resembles several species of the Caecus group, possessing spine-like chaetae on the head, five to seven subsegments on Ant IV with annulated separations, and lacking cuticular spines on Abd VI; it differs from these species in its various characteristics. The mitogenome of A. beijingensis sp. nov. was assembled (14,774 bp in length), marking the first made available from the genus. Due to the incipient number of published mitochondrial genomes of Symphypleona, we downloaded raw sequencing data and performed the assemblies and annotations of 11 species. Our phylogenetic analyses comprised 24 mitogenomes in total; of those, 22 were of Symphypleona and 2 were of outgroups. A. beijingensis sp. nov. was placed closer to Pygmarrhopalites spinosus (Rusek, 1967), with high support. Arrhopalitidae was found as a sister group to Katiannidae, both part of Katiannoidea. The two species of Sminthuridida were placed as a sister group to all other Appendiciphora. More systematic analyses and enhanced sampling from key lineages are needed to better understand Symphypleona's internal relationships and evolution.

The Mitochondrial Genome of the Springtail Semicerura bryophila (Collembola): New Data Call into Question the Relevance of the Subfamilies of the Isotomidae

Background: Semicerura bryophila Potapov & Sun, 2020 is a soil-dwelling springtail belonging to the family Isotomidae. The phylogenetic relationships among species of this group remain controversial due to a lack of molecular data. Therefore, in this study, we sequenced the mitochondrial genome of S. bryophila, analyzed the characterization of the mitochondrial genome, and investigated the phylogenetic relationships of Isotomidae. Methods: The mitochondrial genome of S. bryophila was sequenced and assembled. We analyzed the sequence length, nucleotide composition, and evolutionary relationships within the Isotomidae family, incorporating data from twelve previously published mitochondrial genomes. Results: The length of the S. bryophila mitogenome is 15,247 bp and comprises 13 protein-coding genes, 22 tRNAs, and two rRNAs, arranged in a typical order. Its base composition is as follows: A = 38.05%, T = 33.64%, G = 10.17%, and C = 15.03%. Phylogenetic analysis based on the mitogenome revealed that the monophyly of Isotomidae and the paraphyletic grouping of Semicerura and Folsomotoma, supporting their closer relationship with the subfamily Anurophorinae rather than to Isotominae. The analysis validated subfamily Anurophorinae, identified Pachyotominae as a part of Anurophorinae, and suggested that Isotominae is paraphyletic. Conclusions: The present study provides valuable mitochondrial information for the classification of S. bryophila and offers new insights into the taxonomic and evolutionary studies within the genus Semicerura.

The Genomics Revolution Drives a New Era in Entomology

Thanks to the fast development of sequencing techniques and bioinformatics tools, sequencing the genome of an insect species for specific research purposes has become an increasingly popular practice. Insect genomes not only provide sets of gene sequences but also represent a change in focus from reductionism to systemic biology in the field of entomology. Using insect genomes, researchers are able to identify and study the functions of all members of a gene family, pathway, or gene network associated with a trait of interest. Comparative genomics studies provide new insights into insect evolution, addressing long-lasting controversies in taxonomy. It is also now feasible to uncover the genetic basis of important traits by identifying variants using genome resequencing data of individual insects, followed by genome-wide association analysis. Here, we review the current progress in insect genome sequencing projects and the application of insect genomes in uncovering the phylogenetic relationships between insects and unraveling the mechanisms of important life-history traits. We also summarize the challenges in genome data sharing and possible solutions. Finally, we provide guidance for fully and deeply mining insect genome data.

A New Perspective to Oncopodura (Collembola: Oncopoduridae) Groups Based on Appendicular Morphology

Oncopodura are rare basal springtails often associated with caves; only O. hyleana and O. itatiaiensis are known to Brazil. Oncopodura specimens from CRFS-UEPB were analyzed. Four new species are described: O. aurea sp. n., O. bauxita sp. n., O. hematita sp. n., and O. turmalina sp. n. The coded description of Symphypleona is adapted to Arthropleona, and 96 morphological characters are listed. Data of habitat and distribution of the new species is presented. A key of Brazilian Oncopodura is provided. Oncopodura groups are analyzed with main morphological characters for the groups classification. The crassicornis group is paraphyletic, tricuspidata group is monophyletic, and cruciata group compounds a new group out tricuspidata, with uncertain classification. The main characters that support crassicornis are the presence of unguiculus basal tubercle, external pretarsal chaeta larger than internal, absence of lateral lamella on unguis and PAO often with 6 + 6 or more lobules; tricuspidata is supported by basal tubercle often absent, pretarsal chaetae with similar length (usually both small), presence of lateral lamella on unguis and PAO often with less than 4 + 4 lobules; cruciata group is supported by absence of lateral lamella on unguis and PAO with less than 4 + 4 lobules and pretarsal chaetae usually with same length, both large. The characters like number of PAO lobes and shape, number of Ant IV transversal sens, and shape of hooks of the dens apparently are adaptive, presenting variations in the species. All the newly described species have reduced abundance and are distributed along two of Brazilian major mining areas, and are subject of habitat loss and degradation.

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.

Complete mitochondrial genome of the Korean endemic springtail Tomocerus caputiviolaceus Lee 1975 (Collembola: Tomoceridae)

The complete mitochondrial genome of Tomocerus caputiviolaceus was sequenced and assembled. The complete mitochondrial genome is 15,519 bp in length. The mitogenome contained 37 genes, including 13 protein-coding genes (PCGs), 22 tRNAs, and two rRNAs. In phylogenetic analysis based on the nucleotide sequences of 13 PCGs, T. caputiviolaceus is closely related to Tomocerus qinae Yu, Yao & Hu, 2016, both of which belong to the genus Tomocerus within the family Tomoceridae.

The complete mitochondrial genome and novel gene arrangement in Nesodiprion zhejiangensis Zhou & Xiao (Hymenoptera: Diprionidae)

The complete mitochondrial genome (mitogenome) of the sawfly, Nesodiprion zhejiangensis Zhou & Xiao, was sequenced, assembled, and deposited in GenBank (Accession Number: OM501121). The 15,660 bp N. zhejiangensis mitogenome encodes for 2 ribosomal RNAs (rrnL and rrnS), 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs), and an AT-rich region of 450 bp in length. The nucleotide composition is biased toward adenine and thymine (A + T = 81.8%). Each PCG is initiated by an ATN codon, except for cox2, which starts with a TTG. Of 13 PCGs, 9 have a TAA termination codon, while the remainder terminate with a TAG or a single T. All tRNAs have the classic cloverleaf structure, except for the dihydrouridine (DHU) arm of tRNA^val, which forms a simple loop. There are 49 helices belonging to 6 domains in rrnL and 30 helices belonging to 4 domains in rrnS. In comparison to the ancestral architecture, N. zhejiangensis has the most rearranged mitogenome in Symphyta, in which rearrangement events of local inversion and transposition are identified in three gene clusters. Specifically, the main hotspot of gene rearrangement occurred between rrnS and trnY, and rearranged from rrnS-(AT-rich region)-I-Q-M-nd2-W-C-Y to rrnS-Q-W-C-nd2-I-M-(AT-rich region)-Y, involving a local inversion event of a large gene cluster and transposition events of some tRNAs. Transposition of trnA and trnR (rearranged from A-R to R-A) was observed at the nd3-nd5 gene junction while shuffling of trnP and trnT (rearranged from T-P to P-T) occurred at the nd4l-nd6 gene junction. While illegitimate inter-mtDNA recombination might explain the opposite orientations of transcription between rrnS and trnY, transposition events of tRNA in some gene blocks can be accounted for by the tandem duplication/random loss (TDRL) model. Our phylogenetic analysis suggests that N. zhejiangensis is closely related to congeneric species N. biremis and N. japonicus, which together form a sister lineage with the European pine sawfly, Neodiprion sertifer.

A New Genus of Sminthurididae (Collembola, Symphypleona) from Brazil, with Notes on the Systematics of the Family

The Sminthurididae family includes Symphypleona species highly adapted to courtship, with males exhibiting remarkable modifications on their antennae. Here we describe a new Neotropical genus and species of Sminthurididae from a Cerrado-Caatinga ecotonal zone in Brazil. Males of Parasminthurides spinosus gen. nov. sp. nov. have highly dimorphic antennal claspers similar to those of Sminthurides, but its females have unique strong spiniform chaetae on antennal segments II and III as well, which are possibly accessories for the courtship. The new genus can also be diagnosed by its elongated maxillae, males having large dorsal vesicles between abdomen II and III, ungues I–III with similar morphology and sizes, and interno-apical dental chaetae modified into large spiniform chaetae. We also present the main diagnostic features of all Sminthurididae genera, providing a comparative table and an updated identification key for them. Finally, we discuss the previous and current knowledge on the family’s systematics, suggesting some perspectives for future studies in this field.

Mitogenome selection in the evolution of key ecological strategies in the ancient hexapod class Collembola

A longstanding question in evolutionary biology is how natural selection and environmental pressures shape the mitochondrial genomic architectures of organisms. Mitochondria play a pivotal role in cellular respiration and aerobic metabolism, making their genomes functionally highly constrained. Evaluating selective pressures on mitochondrial genes can provide functional and ecological insights into the evolution of organisms. Collembola (springtails) are an ancient hexapod group that includes the oldest terrestrial arthropods in the fossil record, and that are closely associated with soil environments. Of interest is the diversity of habitat stratification preferences (life forms) exhibited by different species within the group. To understand whether signals of positive selection are linked to the evolution of life forms, we analysed 32 published Collembola mitogenomes in a phylomitogenomic framework. We found no evidence that signatures of selection are correlated with the evolution of novel life forms, but rather that mutations have accumulated as a function of time. Our results highlight the importance of nuclear-mitochondrial interactions in the evolution of collembolan life forms and that mitochondrial genomic data should be interpreted with caution, as complex selection signals may complicate evolutionary inferences.

A Highly Troglomorphic New Genus of Sminthuridae (Collembola, Symphypleona) from the Brazilian Semiarid Region

Here, we describe the highly troglomorphic Troglobentosminthurus gen. nov. from Água Clara cave system, Caatinga domain, Bahia, Brazil. Troglobentosminthurus luridus gen. nov. sp. nov. has remarkably long antennae, legs and furca, and lacks body pigments, except for small orange eye patches which also show a reduction in the number of eyes (5 + 5) and lens sizes. The overall morphology of the genus, with long and highly sub-segmented antennae, resembles other Sminthurinae of the Temeritas-group, especially Temeritas Richards and Galeriella Ćurčić and Lučić. However, it is unique, especially in the combination of the number of antennae IV subsegments and eyes, frontal head chaetotaxy and empodial complex morphology. Two type specimens have remnants of a mite and another specimen from the new species in their gut contents, supporting the species may be occasional predators and even cannibals. We also provide identification keys and comparative tables to the subfamilies of Sminthuridae and the Temeritas-group of genera.

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.

Re-Evaluating the Internal Phylogenetic Relationships of Collembola by Means of Mitogenome Data

Collembola are an ancient and early diverging lineage of basal hexapods that occur in virtually all terrestrial habitats on Earth. Phylogenetic relationships between the different orders of Collembola are fiercely debated. Despite a range of studies and the application of both morphological and genetic approaches (singly or in combination) to assess the evolutionary relationships of major lineages in the group, no consensus has been reached. Several mitogenome sequences have been published for key taxa of the class (and their number is increasing rapidly). Here, we describe two new Antarctic Collembola mitogenomes and compare all complete or semi-complete springtail mitogenome sequences available on GenBank in terms of both gene order and DNA sequence analyses in a genome evolution and molecular phylogenetic framework. With minor exceptions, we confirm the monophyly of Poduromorpha and Symphypleona sensu stricto (the latter placed at the most basal position in the springtail phylogenetic tree), whereas monophyly of Neelipleona and Entomobryomorpha is only supported when a handful of critical taxa in these two lineages are excluded. Finally, we review gene order models observed in the class, as well as the overall mitochondrial nucleotide composition.

The complete mitochondrial genome of the springtail Allacma fusca, the internal phylogenetic relationships and gene order of Symphypleona

Symphypleona (sensu stricto) are a group of Collembola (=springtails) that, despite displaying some variation in gene order, have been poorly investigated under the phylomitogenomic perspective. How families and subfamilies of this taxon are evolutionary related is still partially unknown. For this reason we sequenced, and herein described, the complete mitochondrial genome sequence of Allacma fusca (Sminthuridae). This sequence, alongside others from the literature, is here used to study the phylogenetic relationships among Symphypleona.