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

Abstract

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.

1. Introduction

Collembola (springtails) are the largest and most diverse group amongst basal hexapods, comprising over 7000 species worldwide and inhabiting almost every terrestrial habitat on Earth, from ice-free areas of the polar regions to tropical deserts. Soil, litter, and ground vegetation are their natural habitats, where they play a pivotal role in the decomposition of organic matter [1]. Their ancient evolutionary origin was dated as early as the Silurian (443–419 million years ago), suggesting that their diversification into several major lineages may have taken place in parallel with the evolution of vascular plants and the processes of soil formation [2]. Apart from the never-questioned monophyly of the class, the phylogenetic relationships of Collembola in the context of the Arthropoda have been a long-debated topic, with a range of alternative hypotheses emerging in the last 20 years [3,4,5].

In the early days of Collembola systematics, different lineages were classified based on gross body morphology and, later, based on the analysis of shared morphological characters in a cladistic framework (see [6] for a complete review). Based on these approaches, Collembola were subdivided into two suborders: Arthropleona (with an elongated body and well-defined segments) and Symphypleona sensu lato (with a globular body shape and fused body segments) [1] (Figure 1A).

Early millennial morphological data [6] already started to cast doubt on this traditional Collembola systematic framework and, with the progressive application of molecular techniques, progress was made towards resolving the group’s debated internal relationships [4,7], leading to the acceptance of four main orders and highlighting the enigmatic taxonomic position of only a few groups [8]. The Arthropleona were subdivided into Entomobryomorpha and Poduromorpha, while Symphypleona s.l. was subdivided into Symphypleona sensu stricto and Neelipleona [6,8] (Figure 1A). Subsequently, inter-class relationships have become the new subject of debate amongst systematists, with at least five competing hypotheses proposed, and nuclear and/or mitochondrial DNA markers increasingly becoming the main source of data.

The first complete phylogenetic survey based on 18S and 28S rDNA sequences was that of [9]. Neelipleona was retrieved as basal to Symphypleona s.s. (hereafter Symphypleona) and a Poduromorpha + Entomobryomorpha clade (Figure 1B). Other authors [10], based on the study of three different loci (16S, cox1 and 28S), developed a similar phylogenetic hypothesis, within which the positions of Symphypleona and Neelipleona were inverted (Figure 1D). While including representatives from all classes, these analyses did not include problematic taxa, such as Tomoceridae and Oncopoduridae, whose phylogenetic relationships were not assessed on morphological grounds. These latter were included in the analyses of [11], who proposed that Symphypleona + Neelipleona were a sister group to an Entomobryomorpha + (Tomoceroidea + Poduromorpha) clade, confirming a previous result obtained with an incomplete data set [8] (Figure 1C). Based on analyses of a larger data set and the use of two nuclear rDNA genes as markers, a further phylogenetic arrangement has been proposed where Symphypleona figured as the sister taxon to Entomobryomorpha (partial) + (Tomoceridae + Oncopoduridae + (Poduromorpha + Neelipleona)) [12] (Figure 1E).

As the costs of next generation sequencing (NGS) reduce and access to the technique becomes more widespread, along with the development of improved protocols for non-model species, sequence data are accumulating at an unprecedented rate. Nuclear genomic data have been used to unravel deep-level phylogenetic relationships in hexapods, including early diverging lineages [13], but the limited number of representatives for each major group does not currently allow a thorough investigation of internal relationships at lower taxonomic levels. In this context, complete mitochondrial genomes appear to be a suitable marker, and their informativeness in terms of infraorder relationships among springtails has been assessed in certain studies [2,14,15]. In consequence of the factors of uniparental inheritance, lack of recombination, haploidy, technical feasibility of sequencing using NGS technologies and occurrence in almost all Eukaryota, complete mitochondrial genomes have now emerged as a very popular molecular marker in phylogenetic studies. Moreover, the conservation of genes in the mitogenome minimizes the possibility that paralogous genes are sampled, and the order of genes along the molecule (gene order) provides an independent set of characters that can complement sequence analysis [16,17,18]. Different sets of complete mitogenomic data have been applied in the study of internal relationships among Collembola [19]. Leo and colleagues [2] proposed Neelipleona as the earliest diverging lineage in Collembola, although not all analyses converged to the same result, while Poduromorpha was recovered as the sister taxon to the more derived Entomobryomorpha + Symphypleona (Figure 1F). Sun and colleagues [14], in turn, support a scenario similar to that proposed by [11] (Figure 1C). A third relevant study [15], focusing on internal relationships among species of a single genus, did not address inter-ordinal relationships but provided a wealth of primary data. With these three studies appearing independently but almost at the same time, and with additional genomes previously available on GenBank, this meant that different non-overlapping sets of species were included. A global re-analysis of all available complete springtail mitochondrial genomes available at present is necessary.

Alongside sequence analysis, gene order data have emerged as a further informative phylogenetic marker. Despite the fact that gene order mutation mechanisms remain a matter of discussion (see [18] for a complete review), the sharing of a derived gene order is regarded as a very strong signal of shared ancestry due to the rarity of rearrangements and the low chance of observing convergent changes. To date, twelve different gene order models have been described among Collembola, although four (GO A, GO B, GO C, GO D, revised in a later section) are derived from a metagenomic survey and therefore their species of origin is not identifiable (Figure 2) [2,20]. It is now widely accepted that the most frequent gene order in springtails is the Pancrustacea model. This arrangement, in turn the most common in hexapods and crustaceans, is frequently observed in all springtail lineages and is regarded as the ancestral state for the class [5,21]. With minor exceptions, it characterizes the Entomobryomorpha and Neelipleona. The second most common gene order is the Tetrodontophora model, present in all species of the family Onychiuridae investigated to date, which shows a translocation of two tRNA-encoding genes (trnSuga and trnQ) compared to the ancestral gene order. Among Poduromorpha, two other gene arrangements have been detected, the Podura and Pseudachorutes models, as observed in Podura aquatica [22] and Pseudachorutes palminensis [23], respectively. The former model is characterized by a double translocation (trnC, trnW) plus a gene loss or translocation of trnY (the mtDNA is partially incomplete and the position of this gene could not be assessed) with respect to the Pancrustacea model. The Pseudachorutes model displays the first (and unique, to date, among springtails) translocation which also involves some protein coding genes. Within Symphypleona, rearrangements are observed at high frequency in the family Sminthuridae, regarded as a “hot spot” for genetic rearrangements. All species of this group investigated to date display rearranged genomes (Figure 2). The Sminthurinus model, only detected in Sminthurinus signatus, shows an inversion between trnA and trnR. GO A and GO D, observed in some unidentified Symphypleona species, show different rearrangements. The former displays multiple gene translocations, namely trnQ-trnF-trnE-trnS1-trnS2 between the AT-rich region and trnI combined with inversion of the block trnF-trnE-trnS1. GO D, even though gene annotation along the sequence was not complete, shows a reciprocal exchange between trnM and trnI. It was proposed that a trnP and trnT inversion plus a trnD translocation were a common feature of the Sminthuridae ancestor and, hence, inherited by all its descendent lineages [24]. Four different gene orders in this taxon have been described: the GO C model, which only shows the putative Sminthuridae ancestral translocations; the Sminthurus model, which shows a trnF translocation; the Allacma model consisting of a trnY and a trnLuaa translocations; and the Lipothrix model, which displays four translocations (trnQ, trnY, trnC and trnI). The twelfth gene order described to date, GO B, belongs to an unknown species of Lepydocyrtidae whose mtDNA was only partially sequenced. This, with the translocation of trnW and trnC to unknown positions, apparently represents the only genetic rearrangement found within Entomobryomorpha.

In the light of the considerable interest in the mitochondrial genome as a potential marker to establish infraorder phylogenetic relationships, and considering that all available complete mitochondrial genomes have never been included in a single study, we here revise all available mitogenomic information for Collembola and provide a phylogenetic analysis, gene order analysis and base frequency bias analysis for all known sequences in a unitary framework. We further describe and analyze the newly determined mitogenomes of two Antarctic springtails: Kaylathalia klovstadi (firstly described as Isotoma klovstadi [25], then provisionally re-assigned to Desoria klovstadi [26] and revised by [27]) and Tullbergia mixta.

2. Materials and Methods

2.1. Sample Collection and Mitochondrial DNA Sequencing

Specimens of T. mixta were collected in January 2003 at Harmony Point, Nelson Island (South Shetland Islands; 62° 13′ 20.7′′ S 58° 46′ 54.0′′ W) during the 2002/2003 field season of the British Antarctic Survey (BAS). Specimens of K. klovstadi were collected in January 2019 at Redcastle Ridge (Continental Antarctica; 72° 26′ 25.0′′ S 169° 56′ 32.0′′ E) during the Italian National Antarctic Program (PNRA) expedition. Total DNA was extracted using the QIAmp^® UCP DNA kit from pools of 10–15 individuals of each species. Extractions were then normalized, pooled, and sequenced at Macrogen Europe using a TruSeq Nano DNA chemistry on a NovaSeq 6000 platform (Illumina, San Diego, CA, USA), together with additional samples not reported in this study, to produce 151 bp paired end reads.

2.2. Read Assembly and Mitogenome Annotations

Resulting reads were quality controlled using FastQC (ver. 0.11.9; available at https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and then assembled using NOVOPlasty v.3.8.3 [28]. The assembly step was carried out using the four available cox1 sequences for K. klovstadi downloaded from the Bold System (AN: GBCO0087/88/89/90-06), and the T. mixta partial sequence downloaded from GenBank (AN: KF982833) as seeds. Initial assemblies were obtained under default settings. These were in turn used as a filter to create a subset of the reads enriched for mitochondrial sequences using the filter_reads.pl script from the same package. In turn, final assemblies were produced, based on this enriched library, using the full data. Resulting contigs were compared to MEGAHT [29] assemblies (data not shown) and manually curated to produce full mitochondrial genome assemblies. Single base ambiguities were resolved on a majority rules basis by remapping reads on regions of interest using bbmap v.38.84 (sourceforge.net/projects/bbmap/) and visualizing alignments in IGV v.2.8.2 [30]. Genomes were preliminarily annotated using Mitos [30] and manually curated based on known annotations of closely related species to produce final annotations. The new mitogenome sequences have been deposited in GenBank (under accession numbers MW238521 and MW238520), and the raw data that are deposited at the SRA available at the NCBI portal (accession number SRP289641).

2.3. Phylogenetic Analysis

All the available complete or semi-complete Collembolan mitogenomes were downloaded from GenBank in June 2020 together with those of three outgroups, Daphnia pulex (Crustacea, Branchiopoda), Japyx solifugus (Diplura, Japygidae) and Trigoniophthalmus alternatus (Microcoryphia, Machilidae). The sequences of K. klovstadi and T. mixta, produced in this study, were added to the final dataset, along with sequences from [20] curated as described by [2]. Available mitogenomes which lacked annotations (i.e., from [15]) were automatically annotated using Mitos [31]. The annotation of genomes displaying unusual features (long spacers, non-canonical gene order) were further revised manually. Genes that appeared truncated or totally different if compared to reference sequences were discarded.

Individual protein coding genes were extracted and retro-aligned in the RevTrans 2.0b server [32] based on an amino acid alignment produced using MAFFT v.7.309 [33]. Regions of unstable alignment were deleted with GBlocks v.0.91b [34] using the strict and codon options. Single gene alignments were concatenated to produce a final super matrix. Parallel analyses were conducted on the full matrix (i.e., all codon positions) and after removal of third codon positions. In both instances, data were divided in blocks by codon position, gene family and strand, as described by [2], and submitted to PartitionFinder v.2.1.1 [35] through the CIPRES Science Gateway [36] to determine the best partitioning scheme and associated evolutionary model. GTR+I+Γ was selected for all partitions except for the atp8, nad6 and the first codon position of nad5 and nad4L, for which the GTR+Γ was selected. Data matrices, as well as the optimal evolutionary model and partitioning scheme produced by PartitionFinder, were used for a MrBayes 3.2.6 [37] analysis using 8 chains and 100 million generations. The final output was summarized using tracer v.1.7.1 [38] excluding the first 25% as burn-in. The same datasets were used in a maximum likelihood analysis through IQ-TREE [39] with 10,000 iterations of ultra-fast bootstrap and evolutionary model optimized during the analysis. Final trees were visualized using Figtree v.1.4.4 [40].

2.4. Phylogenetic Tree Topology Comparison

To evaluate the support for some groups that, although well-defined taxonomically, were identified as polyphyletic in the analysis, constrained tree topologies were investigated using the RELL (Re-Estimated Log Likelihood) approximation method [41] with 10,000 replicates through IQ-TREE. Six different hypotheses were compared following [14]: (i) best unconstrained tree; (ii) monophyletic Neelipleona; (iii) monophyletic Tomoceridae; (iv) monophyletic Hypogastruridae; (v) monophyletic Paronellidae; (vi) monophyletic Entomobryidae.

2.5. Nucleotide Biases and dN/dS Ratio

Nucleotide biases were investigated on the same aligned data set. The matrix was divided into J-strand and N-strand oriented genes and, using an in-house python3 script, nucleotide skews were calculated as described in ref [42] (i.e., AT-skew = [A − T]/[A + T] and CG-skew = [C − G]/[C + G]), for first (J1 and N1), second (J2 and N2) and third codon positions of 2-fold-degenerate sites (2J3 and 2N3) and third codon position of 4-fold-degenerate sites (4J3 and 4N3). Outliers were defined as those sequences which showed a value beyond three times the interquartile range from the 25–75% quartile. A/T percentage was assessed on complete mtDNA sequences and compared with all Hexapoda mitochondrial genomes present in the organelle database (NCBI) in June 2020.

To check for positive or negative selection, the non-synonymous to synonymous ratio (ω = dN/dS) was evaluated on the same alignment after removal of outgroups. The alignment was processed as described above to obtain a phylogenetic tree that was used, in conjunction with the data, to test for selection in EasyCodeML [43] using the preset running mode with a site model setup. The dN/dS ratio was manually controlled for all models that showed a likelihood ratio test (LRT) with a significant p-value (≤ 0.5).

3. Results

3.1. New Mitogenomes

The mtDNA of K. klovstadi is a circular molecule of 15,486 bp length, and that of T. mixta is 14,998 bp length (see Tables S1 and S2 for details). Both genomes show the majority of genes encoded on the J-strand and display the typical features of metazoan mitochondrial genomes: 13 protein coding genes (atp6, 8; cox1-3; cytb; nad1-6, 4L), two rRNAs (rrnL, rrnS) and, in K. klovstadi, a complete set of 22 tRNAs. That of T. mixta lacks a trnC. This may represent a gene loss, although the possibility of a structurally divergent tRNA, that could not be recognized/annotated as such, cannot be ruled out completely. Canonical start codons (i.e., ATA/ATG, which encode for methionine) are present in the largest number of protein coding genes (8/13 in T. mixta, 6/13 in K. klovstadi). The alternative start codon TTG (leucine) is present in 1/13 protein coding genes (nad4L) in both mitogenomes, and ATT/ATC (isoleucine) are present in all other instances. Partial stop codons are frequent in K. klovstadi (9/13 protein coding genes) and present at lower frequencies (3/13) in T. mixta. Intergenic spacers are present in both genomes, with the longest being 592 bp (between trnS and nad1) in K. klovsadi and 155 bp (between rrnL and trnV) in T. mixta. Few overlaps between genes are present in both mtDNAs, and are limited to a small overlap between atp6 and atp8 in both genomes and a 33 bp overlap between rrnL and trnV in K. klovstadi. The gene arrangement for both species is consistent with the Pancrustacea model, except for T. mixta lacking trnC. Overall, a bias in nucleotide composition is observed toward A (36.2% and 34.0%) and T (31.6% and 29.1%), with respect to C (18.8% and 24.9%) and G (13.4% and 12.0%) in K. klovstadi and T. mixta mitogenomes, respectively.

3.2. Dataset Composition and Gene Orders

NCBI-sourced mitogenomes which lacked annotation were annotated as described in Section 2.3. In some cases, genomes were identified as incomplete due to the lack of some genes, sometimes associated to the presence of long stretches of Ns (undetermined nucleotides: 0.01% to 6.69%) in the original sequences.

The gene order was analyzed for all 87 species included in the study set with the exception of Lepidocyrtus sp. (MF716621), which displayed a highly divergent and uncertain structure and was therefore excluded (Tables S3 and S4). Most gene orders identified had been previously characterized and described [2,14,21,23]. Of the newly annotated genomes, T. mixta and K. klovstadi conform to the Pancrustacea model, with the exception of the missing trnC in the former (see Section 3.1). Most genomes from [15] similarly display a Pancrustacea gene order or, though incomplete, are compatible with it (sensu [2];

Table 1. Species used in the current study. Gene order column asterisks (*) indicate a compatible assignment to the already described gene order. Section signs (^§) indicate manual curated sequences originally obtained by [20]. Order names are abbreviated. Further information is available in Table S3. See GenBank for reference of downloaded sequences.

AN	Order	Family	Species	Gene Order
NC_010533	Entomobr.	Isotomidae	Cryptopygus antarcticus	Pancrustacea model
MK433191	Entomobr.	Isotomidae	Cryptopygus a. travei	Pancrustacea model
KX863671	Entomobr.	Isotomidae	Cryptopygus terranovus	Pancrustacea model
MK431896	Entomobr.	Paronellidae	Cyphoderus albinus	Pancrustacea model
s7289	Entomobr.	Isotomidae	Desoria trispinata	Pancrustacea model §
MK431895	Entomobr.	Entomobryidae	Dicranocentrus wangi	Pancrustacea model
MF716608	Entomobr.	Entomobryidae	Entomobrya sp.	Pancrustacea model *
KU198392	Entomobr.	Isotomidae	Folsomia candida	Pancrustacea model
s6653	Entomobr.	Isotomidae	Folsomia candida	Pancrustacea model §
NC_024155	Entomobr.	Isotomidae	Folsomotoma octooculata	Pancrustacea model
MN480464	Entomobr.	Entomobryidae	Homidia socia	Pancrustacea model
MK509021	Entomobr.	Isotomidae	Isotomurus maculatus	Pancrustacea model
MW238521	Entomobr.	Isotomidae	Kaylathalia klovstadi	Pancrustacea model
MF716618	Entomobr.	Entomobryidae	Lepidocyrtoides caeruleomaculatus	Pancrustacea model
MF716598	Entomobr.	Entomobryidae	Lepidocyrtoides sp.	Pancrustacea model
s6464	Entomobr.	Lepidocyrtinae	Lepidocyrtus curvicollis	Pancrustacea model §
MK431900	Entomobr.	Entomobryidae	Lepidocyrtus fimetarius	Pancrustacea model
MF716621	Entomobr.	Lepidocyrtinae	Lepidocyrtus sp.	Not analysed
MN592792	Entomobr.	Isotomidae	Metisotoma macnamarai	Pancrustacea model
MK431898	Entomobr.	Tomoceridae	Novacerus tasmanicus	Pancrustacea model
MK431894	Entomobr.	Oncopoduridae	Oncopodura yosiiana	Pancrustacea model
KT985987	Entomobr.	Entomobryidae	Orchesella cincta	Pancrustacea model
EU016195	Entomobr.	Entomobryidae	Orchesella villosa	Pancrustacea model
MK423967	Entomobr.	Isotomidae	Paranurophorus simplex	Pancrustacea model *
s8783	Entomobr.	Isotomidae	Parisotoma notabilis L1	Pancrustacea model §
s5537	Entomobr.	Isotomidae	Parisotoma notabilis L2	Pancrustacea model §
MK409685	Entomobr.	Paronellidae	Salina celebensis	Pancrustacea model
MF716602	Entomobr.	Entomobryidae	Seira atrolutea	Pancrustacea model
MF716619	Entomobr.	Entomobryidae	Seira brasiliana	Pancrustacea model
MF716595	Entomobr.	Entomobryidae	Seira ca. prodiga 1	Pancrustacea model
MF716596	Entomobr.	Entomobryidae	Seira ca. prodiga 2	Pancrustacea model *
MF716606	Entomobr.	Entomobryidae	Seira ca. prodiga 3	Pancrustacea model
MF716614	Entomobr.	Entomobryidae	Seira coroatensis	Pancrustacea model
MF716609	Entomobr.	Entomobryidae	Seira dapeste	Pancrustacea model
MF716594	Entomobr.	Entomobryidae	Seira diamantinae	Pancrustacea model
MF716615	Entomobr.	Entomobryidae	Seira dowlingi	Pancrustacea model *
MF716617	Entomobr.	Entomobryidae	Seira harena	Pancrustacea model
MF716597	Entomobr.	Entomobryidae	Seira mendoncae	Pancrustacea model
MF716600	Entomobr.	Entomobryidae	Seira paraibensis	Seira prarabiensis model
MF716601	Entomobr.	Entomobryidae	Seira paulae	Pancrustacea model
MF716613	Entomobr.	Entomobryidae	Seira potiguara	Pancrustacea model
MF716605	Entomobr.	Entomobryidae	Seira ritae	Pancrustacea model *
MF716616	Entomobr.	Entomobryidae	Seira sp. 1	Pancrustacea model
MF716604	Entomobr.	Entomobryidae	Seira sp. 2	Pancrustacea model
MF716612	Entomobr.	Entomobryidae	Seira sp. 3	Seira sp. 3 model
MF716620	Entomobr.	Entomobryidae	Seira tinguira	Pancrustacea model *
MK014212	Entomobr.	Entomobryidae	Sinella curviseta	Pancrustacea model
MK423966	Entomobr.	Tomoceridae	Tomocerus qinae	Pancrustacea model
MF716607	Entomobr.	Paronellidae	Trogolaphysa sp.	Trogolaphysa model
MF716599	Entomobr.	Entomobryidae	Tyrannoseira bicolorcornuta	Pancrustacea model
MF716611	Entomobr.	Entomobryidae	Tyrannoseira bicolorcornuta	Pancrustacea model *
MF716610	Entomobr.	Entomobryidae	Tyrannoseira raptora	Pancrustacea model
s7305	Neeliple.	Neelidae	gen. sp.	Pancrustacea model §
s6565	Neeliple.	Neelidae	Megalothorax minimus	Pancrustacea model §
MK431893	Neeliple.	Neelidae	Neelides sp.	Pancrustacea model *
MH155200	Neeliple.	Neelidae	Neelus murinus	Pancrustacea model
EU084034	Podurom.	Neanuridae	Bilobella aurantiaca	Pancrustacea model
MN660050	Podurom.	Brachystomellidae	Brachystomella parvula	Pancrustacea model *
MK409686	Podurom.	Hypogastruridae	Ceratophysella communis	Pancrustacea model
s6480	Podurom.	Onychiuridae	Deuteraphorura sp.	Tetrodontophora model §
NC010535	Podurom.	Neanuridae	Friesea antarctica	Pancrustacea model
MT644085	Podurom.	Neanuridae	Friesea gretae	Pancrustacea model
EU124719	Podurom.	Neanuridae	Friesea propria	Pancrustacea model
s6241	Podurom.	Hypogastruridae	gen. sp.	Pancrustacea model §
s6379	Podurom.	Onychiuridae	gen. sp.	Tetrodontophora model §
s6532	Podurom.	Onychiuridae	gen. sp.	Tetrodontophora model§
s7124	Podurom.	Tullbergiidae	gen. sp.	Pancrustacea model *§
AY191995	Podurom.	Hypogastruridae	Gomphiocephalus hodgsoni	Pancrustacea model
MK431897	Podurom.	Tullbergiidae	Mesaphorura yosii	Pancrustacea model
MN661001	Podurom.	Onychiuridae	Orthonychiurus folsomi	Tetrodontophora model
NC_006075	Podurom.	Poduridae	Podura aquatica	Podura model *
MN660051	Podurom.	Neanuridae	Pseudachorutes palmiensis	Pseudachorutes model
NC_002735	Podurom.	Onychiuridae	Tetrodontophora bielanensis	Tetrodontophora model
MK423968	Podurom.	Onychiuridae	Thalassaphorura encarpata	Tetrodontophora model
NC_006074	Podurom.	Onychiuridae	Thalassaphorura orientalis	Tetrodontophora model *
s6543	Podurom.	Onychiuridae	Thalassophorura sp.	Tetrodontophora model §
MK520870	Podurom.	Tullbergiidae	Tullbergia bisetosa	Pancrustacea model
MW238520	Podurom.	Tullbergiidae	Tullbergia mixta	Pancrustacea model *
MT547779	Symphy.	Sminthuridae	Allacma fusca	Allacma model
KY618680	Symphy.	Bourletiellidae	Bourletiella arvalis	Pancrustacea model
MG701393	Symphy.	Dicyrtomidae	Dicyrtomina saundersi	Pancrustacea model
s6802	Symphy.	Dicyrtomidae	gen. sp.	Pancrustacea model §
MK431899	Symphy.	Sminthuridae	Lipothrix lubbocki	Lipothirx model
MK423965	Symphy.	Dicyrtomidae	Ptenothrix huangshanensis	Pancrustacea model
MK423964	Symphy.	Sminthurididae	Sminthurides bifidus	Pancrustacea model *
MK423969	Symphy.	Katiannidae	Sminthurinus signatus	Sminthurinus model *
NC_010536	Symphy.	Sminthuridae	Sminthurus viridis	Sminthurus model

). A few species (Seira ca. prodiga 2, S. downgli, S. tinguara, S. ritae, Entomobrya sp. and Tyrannoseira bielanensis) have one or two missing genes. Nevertheless, in line with the observation that although no complete gene could be found/annotated, manual alignment with other genomes highlighted regions suggestive of homology, we cautiously did not assign a new gene order and tentatively consider these as conforming to the Pancrustacean gene order. A different gene order was observed in Seira parabiensis, characterized by an rrnS deletion and an rrnL translocation, while two species showed a genetic rearrangement in the trnA-trnR-trnN-trnS-trnE region. Trogolaphysa sp. (MF716607) displayed an inversion plus a deletion resulting in a trnE-trnN-trnA-trnR arrangement, and Seira sp. 3 (MF716612) showed a translocation resulting in a trnN-trnS-trnR-trnE-trnA configuration (Figure 3).

3.3. Phylogenetic Analysis

The phylogenetic analysis of the dataset including first and second codon positions supports the monophyly of Collembola, as well as of the orders Symphypleona and Poduromorpha (Figure 4). The other two orders, Entomobryomorpha and Neelipleona, were identified to be polyphyletic due to the presence of outliers (Neelides sp., Novacerus tasmanicus, Oncopodura yosiiana and Tomocerus qinae), although the large majority of species formed two well-supported monophyletic clusters corresponding to the orders Entomobryomorpha and Neelipleona as taxonomically defined. At present, it is difficult to disentangle the possible causes of this outcome, whether it is a true polyphyly, a result of bias in the phylogenetic analyses or due to technical problems in the original data, although we suggest the former is the least likely.

One sequence, Neelides sp., is extremely divergent with respect to all other Collembolans and is recovered in the phylogenetic tree as the outermost basal group, distant from the other three representatives of Neelipleona that, in turn, form a tight monophyletic group nested in the Collembola tree. Novacerus tasmanicus and Tomocerus qine (belonging to the Tomoceridae subfamilies Lepidophorellinae and Tomocerinae, respectively) and Oncopodura yosiiana (subfamily Oncopodurinae) are all members of superfamily Tomoceroidea, but each cluster with different (and apparently unrelated) taxa (Figure 4).

At the level of orders, apart from the outliers, a well-supported and monophyletic Symphypleona branches at the basal position and is the sister group of the remaining lineages. These latter are subdivided into two major branches, the first including Poduromorpha and Neelipleona and the second including all Entomobryomorpha. Within Symphypleona, the represented families with two or more species (Sminthuridae and Dicyrtomidae) are recovered as monophyletic. At the family or subfamily level, Katiannidae is sister group to Sminthurididae, Sminthurinae is paraphyletic (Allacma fusca is more closely related to Liphotrix lubbocki, subfamily Sphyrothecinae, than to its con-subfamiliar genus Sminthurus). Subfamily Dicyrtominae (species Dicyrtomina saundersi) clusters together with Ptenothricinae (Ptenothrix huangshanensis). Entomobryomorpha, apart from the displacement of Oncopoduridea and Tomoceridae (the latter polyphyletic), form a coherent group. Isotomidae is monophyletic, whereas Entomobryidae and Paronellidae are polyphyletic. All Isotomidae genera, apart from Sinella, are monophyletic. Poduromorpha families are monophyletic with the exception of Hypogastruridae, due to the displacement of Gomphiocephalus hodgsoni as a sister taxon to Poduridae + Neanuridae. This monophyletic Poduromorpha is divided in two major clusters: one containing a paraphyletic Hypogastruridae (due to the displacement of G. hodgsoni) and Neanuridae, and the second including all Onychiuridae, the latter arranged as Tullbergiidae + (Tetrodontophorinae + Onychiurinae). In general, intermediate and recent nodes show full support, with minor exceptions, whereas nodes at the level of order and family are provided variable-to-high support (0.84 < p.p. < 1).

The tree resulting from the complete dataset (i.e., including third codon positions, Figure S1) is identical to that described above in terms of topology, with minor differences in support values. Maximum likelihood analysis produced a less resolved tree that, nevertheless, mostly conformed with the outcome of the Bayesian analyses (Figures S2 and S3). However, the collapsing of weakly supported branches (bootstrap value < 70) produced a large polytomy at the base of the tree and, with the exclusion of the aforementioned outliers, order monophyly was not confirmed only for one order (Poduromorpha) out of four, resulting from the splitting tree polytomy. Full support was detected for most other branches.

3.4. Tree Topology Tests

Monophyly tests conducted on ambiguous groups (i.e., taxonomically defined groups recovered as poly- or paraphyletic in the analysis) indicated that the competing hypothesis (i.e., monophyly) could not be rejected in all cases with full confidence. All non-monophyletic groups (Neelipleona, Tomoceridae, Hypogastruridae, Paronellidae and Entomobryidae) were therefore considered as topologically plausible, although suboptimal given our analysis (Table S5).

3.5. Nucleotide Biases and dN/dS Ratio

AT% composition of springtail mitogenomes was compared with data from all available hexapod mtDNAs. Although some internal variation was noted, Collembola appear to be characterized by a relatively low AT-bias (60.4–74.8%) compared to other Hexapoda (59.4–88%; Figure 5).

Nucleotide biases (AT skew and CG skew) were calculated for protein coding genes on both strands subdivided as first (J1 and N1), second (J2 and N2), two-fold (2J3 and 2N3) and four-fold (4J3 and 4N3) degenerate third codon positions. Variability in skew was sizeable in four-fold and two-fold third codon positions and limited in first and second codon positions, in the order 4JN3 > 2JN3 > JN2 > JN1 (Figure 6). All the Collembolan J1 genes showed a weak negative or barely positive CG skew (−0.21 to 0.06), whereas the AT skew was mainly positive (−0.04 to 0.15). N1 genes, on the other hand, showed strongly negative CG skew (−0.55 to −0.08) and AT skew (−0.32 to −0.06). The unique outlier for the N strand first nucleotide codon position bias was Bourletiella arvalis. Focusing on second codon positions, C outnumbered G in J2 position (0.19 to 0.35) but not in N2 positions (−0.21 to 0.19). AT skew at second codon positions was negative, with similar ranges for both strands (J2: −0.42 to −0.31; N2: −0.56 to −0.22). Two Neelipleona (Neelides sp. and Neelus murinus) and the Symphypleona Sminthurinus signatus differed in nucleotide composition from other Collembola species for the second nucleotide codon position. Third codon position biases displayed a much higher variability overall across species. Although AT skew for both 2J3 and 2N3 was comparable (−0.40 to 0.17), CG skew was particularly divergent, ranging from 0.03 to 0.86 in 2J3 and −0.89 to 0.2 in 2N3. No outlier was observed for the two-fold degenerate third codon position. Finally, 4N3 and 4J3 displayed the highest variance, with CG skews ranging from 0.85 to −0.73 and AT skews from 0.32 to −0.6. A substantial overlap was observed between values observed in the J and N strands, with the J strand being on the upper end of both values. Three outliers (B. arvalis, Thalassophorura encarpata and Thalassophorura sp.) were detected.

The comparative models M0 vs M3, M7 vs M8 and M8a vs M8 led to a significant LRT p-value. However, the dN/dS ratio calculated for the nucleotide positions in all the Collembola species resulted in neutral selection, indicating that a balance for all the examined nucleotides was detected.

4. Discussion

Collembola phylogeny has long been a subject of debate, with different hypotheses stemming from the use of different markers (morphological and/or molecular) and the inclusion/exclusion of particular species. The mitochondrial genome has become an important resource in springtail systematics, but analyses have still suffered from limited taxon density and unequal representation of different lineages. In this study, we re-analyzed all available Collembola mitochondrial genomes in a unitary framework, currently the largest dataset of this type.

4.1. Deep Collembola Phylogeny

Analyses of the mitogenomes of the 87 species of Collembola represented in the dataset (Figure 4) produced phylogenetic trees that, although not completely resolved, were generally consistent, regardless of the use of different tree building methods (Bayesian Inference and ML) and different sets of data (including or excluding third codon positions). Overall, the four currently recognized orders were retrieved as monophyletic, with minor incongruences. Furthermore, tests conducted on constrained trees indicated that such incongruences (i.e., observed polyphyly in some taxa) were not strongly supported.

Comparison with previous studies highlights some clear dissimilarities, especially at deeper phylogenetic levels. The phylogenetic tree generated by ref 2 placed Neelipleona as the basal lineage of Collembola, with all orders monophyletic and with Symphypleona as a sister group to Entomobryomorpha [2]. Intra- and inter-familiar relationships generally conform to our study. Although Tullbergiidae was retrieved as sister taxon to all the other Poduromorpha families [2], in our analysis it formed a well-supported clade with Onychiuridae. A separate study concluded that Neelidae and Symphypleona, or Neelipleona alone, are basal to the remaining taxa, also finding general support for the monophyly of all orders (but not in all trees) [14]. The basal position of Neelipleona was also proposed using a set of nuclear markers [43]. Our tree has some similarity with that of ref 14, in suggesting a basal position for Symphypleona [14]. Notably, in our reconstruction, although three Neelipleona sequences (genera Megalothorax and Neelus, plus one undetermined specimen) clustered in a well-supported monophyletic group associated to Poduromorpha, one taxon (Neelides sp.) was placed in a basal position outside all other Collembola, as an outlier. We tentatively consider the former as the more likely placement for the Neelipleona. Moreover, Entomobryomorpha polyphyly and Hypogastruridae paraphyly, already reported by previous studies [2,11,14], conform to the current study’s analyses. Paronellidae and Entomobryidae, previously considered enigmatic taxa [44], were identified as polyphyletic as in Sun and colleagues’ phylogenetic reconstruction [14], casting doubt on the correct position of these groups.

The basal placement of Symphypleona, the Poduromorpha + Neelipleona clade, the close relationship between Isotomidae and (some) Entomobryidae, and the polyphyly of Entomobryomorpha due to the placement of Tomoceridae and Oncopoduridae, were also identified by [12] through the combined analysis of two conserved markers (18S and 28S) in a dataset including 56 species. Polyphyly of Tomoceridae and Oncopoduridae was also recovered in one phylogenetic reconstruction by Sun et al. [14] in a study of more than 30 Collembola mitogenomes.

At a lower taxonomic level, in a previous study limited to the subfamily Seireinae and a few members of Entomobryidae [15], the genus Seira appeared to be paraphyletic due to the sister-group relationship between some species of this genus to those of Tyrannoseira. A similar outcome was obtained here, although we identified the Paronellidae species Cyphoderus albinus (instead of Lepidocyrtus sp.; missing in Nunes-Godeiro et al.’s dataset [15]) as the sister group of all Seira species.

4.2. Collembola Gene Orders

The gene order analysis confirmed that, in springtails, mitochondrial gene rearrangements are usually lineage-specific and represent autapomorphies or synapomorphic traits shared by low level taxonomic groups. The Pancrustacea model was confirmed as the ancestral gene order among Collembola due to its presence in all the studied orders, as well as in early divergent lineages above the family level. Nine other models have been observed in springtail mtDNAs (Table 1). The Tetrodontophora model is shared by all members of Onychiuridae and is suggested as a synapomorphy of the group. The first rearrangement of protein coding genes in springtails took place in Neanuridae, apparent in the Pseudachorutes model (Figure 2). No other species except P. palminensis show this mitochondrial gene order and, based on the resulting tree, we suggest that this feature is an autapomorphy of this group. If Symphypleona is the springtail order most likely to show genetic rearrangement, Entomobryomorpha is the opposite. Of the 52 genomes available for this group (of which the gene order of 51 was considered here), 49 displayed the ancestral Pancrustacea arrangement or, if incomplete, are compatible with this. The re-analysis of the mitogenomes described in ref 15 led to the identification of three new genomic models: Trogolaphysa, Seira sp. 3 and Seira parabiensis models [15]. Nevertheless, although their status as new gene orders is clearly plausible, caution is required because similar congeneric species (e.g., related to Seira) display the classical Pancrustacea gene order. Furthermore, although the first of these does not have other congeneric species that can be compared in terms of gene order, both Seira models are unique in the context of all other Seira species analyzed (19), that display the Pancrustacea model.

The gene order analysis identified that the newly described genome of T. mixta, in contrast with the congeneric T. bisetosa, appears to lack trnC. The deletion of single tRNAs is not unprecedented either in mitochondrial genomes in general or Collembola specifically, but it is unusual, especially in congeneric species. Other possible explanations exist, such as that this species’ trnC assumed a variant morphology that is not captured by automatic annotation methods and/or by manual checking of the sequence. The possibility of an assembly error cannot be ruled out, nevertheless all evidence (high 2118 -fold coverage in the region between trnW and trnY, identical sequence produced by two independent assembly methods; see Section 2.2) suggest the opposite. Although, as noted, a result of automatic annotation, the only documented (to our knowledge) difference in genome structure identified in this study is the new Seira sp. 3 model, which differs from all the other congeneric species.

Considering all the gene orders recognized in this study, it is clear that gene order modifications are not randomly distributed. Two genomic regions can be highlighted as being particularly subject to genetic modifications: the A+T-rich/nad2 region, where most translocations were observed in Symphypleona; and the trnA/nad1 region, that showed modifications in many taxa (Figure 2 and Figure 3). Symphypleona appear to be particularly prone to gene order modifications.

4.3. MtDNA Compositional Biases among Springtails

The replication of the mitochondrial genome is known to be an asynchronous and asymmetrical process, one outcome of which is that one (N-) hemi-helix remains in a single strand conformation for a prolonged period during replication (~two hours) and is therefore subject to ROS-induced directional mutations [41]. As described in previous studies, such a mutational bias is common in Collembola mitogenomes, which often show nucleotide compositional biases [21,45]. Comparison of the asymmetrical mutational constraints in all 87 species analyzed in this study led to some interesting findings. A+T bias, a well-known feature of insect mitochondrial genomes, was confirmed for all the analyzed Collembola, however they fall at the lower end of bias within Hexapoda [5,40] (Figure 5). Comparing codon positions, all springtails maintained a level of site-specific and strand-specific compositional conservation (Figure 6). In previous studies, it was generally observed that the J- and N-strand have tendencies to display an AC-rich and GT-rich base composition, respectively [14,45]. In the current study, GT-richness in the N-strand was confirmed, but AC-richness in the J-strand was less evident. This small, but noticeable, inconsistency among similar datasets could be partly due to the exclusion of hypervariable regions and to the fact that biases have been separately assessed for two- and four-fold degenerate sites. Being mt protein coding genes characterized by an abundance of hydrophobic amino acids (anchoring sites within the mitochondrial membrane systems), the second codon position is often occupied by pyrimidines (and especially thymine), whose presence fosters the encoding of hydrophobic amino acids. This type of bias is generally known as codon-bias, and all the Collembolan mitogenomes analyzed to date have demonstrated this feature [45].

Overall, different levels of dispersion were observed at different codon positions. First and second codon positions displayed the least dispersion, followed by two-fold and four-fold degenerate third codon positions. Given the degeneration of the genetic code, third codon position mutations rarely affect the sequence of the resulting protein and, hence, are more inclined to escape purifying selection than first and second codon positions [41]. Similarly, two-fold degenerate sites show lower mutational freedom than four-fold degenerate sites. Our observations are in line with expectations under this simple model of selection. In the context of a uniform distribution, some outliers were observed. The second codon position and four-fold degenerate sites in third codon position appear to include the majority of outliers both for the N- and J-strand genes. This may be the consequence of differential selection pressures in some specific taxa, but no clear pattern is apparent at present, although it is noticeable that most sequences detected as outliers belong to the same few taxa (B. arvalis, S. signatus, genus Thalassophorura and family Neelidae).

5. Conclusions

The evolutionary history of Collembola is a hotly debated topic among taxonomists and evolutionary biologists. In this study, we assembled, in a unitary framework, data analyzed in three mitogenomic studies, adding two new genomes and including manual curation of the data. This generated the largest dataset of complete or semi-complete Collembola mitochondrial genomes available to date. Differing from contemporary studies [2,14], we favored a basal position of Symphypleona and a close relationship between Poduromorpha and Neelipleona. However, suboptimal support for basal nodes, the misplacement of some taxa, and observation that, in the absence of a strong phylogenetic signal, the placement of taxa can be strongly influenced by taxon density, the molecular marker(s) applied, and the methods used, suggest caution before the phylogenetic relationships internal to the class Collembola can be considered as reliably assessed.

Thanks to the technical developments in NGS sequencing of complete mitochondrial genomes, sequence data are accumulating rapidly. Nevertheless, although improved tools capable of unsupervised assembly and gene annotation are available, careful manual curation of the data remains important [46]. In this study, extensive manual curation of the data was used in order to include sequences that were not initially obtained as complete mitochondrial genomes, lacked annotations, or were present in NCBI outside the RefSeq area. This step led to the removal of some data and to the acceptance of other data as tentative. One of the major advantages of the use of complete mitochondrial sequences is the possibility to combine data across different studies and we, therefore, advocate that future sequencing studies strongly consider their reusability. Careful assembly and annotation, manual curation, post-annotation quality checks of the genome/annotation produced, and compliance to RefSeq standards should be seen at a shared necessity in this field when publishing complete mitochondrial genomes.