The complete mitogenome of the springtail Cryptopygus antarcticus travei provides evidence for speciation in the Sub-Antarctic region

Abstract

Cryptopygus antarcticus travei (Collembola) is a springtail endemic to the sub-Antarctic Prince Edward Islands. The mitogenome of C. a. travei has a length of 15,743 bp and comprises 13 protein-coding genes, 22 tRNAs, and two rRNAs. The base composition is 36% adenine, 33% thymine, 13% guanine, and 18% cytosine. Phylogenetic analyses confirmed the distinctness of C. a. travei from C. antarcticus, with considerable sequence divergences separating taxa within this group. In light of these results, we suggest that C. a. travei may be a candidate new species and that the current taxonomical status of this species should be re-evaluated.

Keywords:

• Mitogenome
• Cryptopygus antarcticus travei
• Collembola
• Southern Ocean Islands
• Prince Edward Islands

Springtails (Class: Collembola) are a diverse, abundant, and widespread group. They occur in some of the harshest and most remote areas on earth, including Antarctica and the sub-Antarctic islands (Deharveng 1981; Hopkin 1997). The challenging conditions in these regions undoubtedly impose strong selection pressures (Holt and Gaines 1992; Manel et al. 2003), and biota continuously have to adapt to these ever-changing environments that are experiencing accelerated rates of climate change.

Not surprisingly, Collembola have been widely used to study biochemical and physiological adaptations (Sinclair et al. 2003). In the sub-Antarctic region, relatively few studies have documented genetic structures (Stevens et al. 2006; Myburgh et al. 2007), and only one attempted to link genetic diversity to physiological attributes (McGaughran et al. 2010). One of the most speciose genera in the region is Cryptopygus (Stevens and Hogg 2006; Carapelli et al. 2008). Cryptopygus antarcticus travei Deharveng, 1981 is restricted to the Prince Edward Islands where they reach densities of up to 10⁴–10⁵ individuals/m² (Gabriel et al. 2001; Hugo et al. 2006). Here, we report the assembly and annotation of its mitogenome and evaluate its phylogenetic placement.

Total gDNA was extracted from 13 complete specimens sampled on the Prince Edward Islands (−46.767, 37.850) using the DNeasy^® Blood and Tissue Kit (Qiagen^®, Germany). Since whole specimens were used for DNA extractions, another specimen (collected from the same locality at the same time) serves as the voucher specimen (Iziko Museum, Cape Town, voucher number SAM-ENW-C010311). Genomic DNA libraries were prepared and indexed for each specimen. The resulting libraries were sequenced using the Illumina HiSeq4000 platform (Illumina, USA), producing 150 GB of raw data. The mitogenome was assembled from the pooled data using NOVOPlasty (Dierckxsens et al. 2017) with default settings, but with the insert size set to 350 bp. The cytochrome c oxidase subunit I (COI) gene of C. a. travei (Stevens et al. 2006; accession number: DQ285390) was used as the starting seed. The mitogenome was annotated using the MITOS2 WebServer (Donath et al. in press). The protein-coding genes (PCGs) and the ribosomal RNA boundaries were determined manually using Exonerate v2.2 (Slater and Birney 2005) and Infernal v1.1 (Nawrocki and Eddy 2013). Our reference data included the annotated mitogenomes of nine other species (>69% identity based on BLAST results).

The circularised mitogenome (15,743 bp in length) comprises 13 PCGs, 22 tRNAs, and two rRNAs. The base composition is 36% adenine, 33% thymine, 13% guanine, and 18% cytosine. An A + T rich region (69%) is present which corresponds to sites for replication initiation and transcription (Goddard and Wolstenholme 1978; Carapelli et al. 2008). Several instances of non-canonical start and incomplete stop codons (TA– or T–) were observed which is consistent with findings by Donath et al. (in press) and Carapelli et al. (2008).

The 13 PCGs were aligned to data available for nine other species including five springtails and four hexapods. Bayesian phylogenetic analyses were performed in BEAST v2.5.0 (Bouckaert et al. 2014) using the HKY substitution model (Hasegawa et al. 1985) with a chain length of 300 million generations and a 33% burn-in. Resultant topologies were visualised in Figtree v1.4.3 (Rambaut 2016) (Figure 1).

Figure 1. Bayesian phylogenetic tree of Cryptopygus antarcticus travei and nine other species (>69 identity) (five springtail species and four hexapod species). The following species and GenBank accession numbers used for the phylogenetic analysis are as follows: Cryptopygus antarcticus travei (MK433191), Cryptopygus antarcticus (NC_010533), Cryptopygus terranovus (NC_037610), Folsomia candida (KU198392), Folsomotoma octooculata (NC_024155), Gomphiocephalus hodgsoni (NC_005438), Anopheles arthuri (NC_037806), Delia antiqua (NC_028226), Simosyrphus grandicornis (NC_008754), and Elaphrus cupreus (KX087286). All the nodes on the tree are supported by a posterior probability of 1.

Collembola form a well-supported monophyletic clade, with C. a. travei as the sister taxon to C. antarcticus but with considerable genetic divergence separating them. Unusually high levels of sequence divergence for the COI gene was similarly reported by Stevens et al. (2006) for Cryptopygus across the sub-Antarctic region. When taken together, these results strongly indicate that C. a. travei, confined to the Prince Edward Islands, is a candidate new species.

Acknowledgements

Samples were collected under permit from the Department of Environmental Affairs: (South African National Antarctic Programme) who also provided logistic support during the voyages. Analyses platforms and bioinformatics support was provided by the Centre for High Performance Computing (CHPC) in Cape Townand the University of Johannesburg IT services.

Disclosure statement

No conflict of interest is reported by the authors who are responsible for the content and writing of this paper.

Additional information

Funding

Funding was provided by the National Research Foundation [NRF SANAP grant to BvV; grant number 110728] and a University of Johannesburg Global Excellence and Stature postdoctoral fellowship to A.E.-K.