Analysis of a contact zone in the Forficula auricularia L. (Dermaptera: Forficulidae) species complex in the Pyrenean Mountains

DNA sequencing in the classroom: complete genome sequence of two earwig (Dermaptera; Insecta) species

BACKGROUND

Despite representing the largest fraction of animal life, the number of insect species whose genome has been sequenced is barely in the hundreds. The order Dermaptera (the earwigs) suffers from a lack of genomic information despite its unique position as one of the basally derived insect groups and its importance in agroecosystems. As part of a national educational and outreach program in genomics, a plan was formulated to engage the participation of high school students in a genome sequencing project. Students from twelve schools across Chile were instructed to capture earwig specimens in their geographical area, to identify them and to provide material for genome sequencing to be carried out by themselves in their schools.

RESULTS

The school students collected specimens from two cosmopolitan earwig species: Euborellia annulipes (Fam. Anisolabididae) and Forficula auricularia (Fam. Forficulidae). Genomic DNA was extracted and, with the help of scientific teams that traveled to the schools, was sequenced using nanopore sequencers. The sequence data obtained for both species was assembled and annotated. We obtained genome sizes of 1.18 Gb (F. auricularia) and 0.94 Gb (E. annulipes) with the number of predicted protein coding genes being 31,800 and 40,000, respectively. Our analysis showed that we were able to capture a high percentage (≥ 93%) of conserved proteins indicating genomes that are useful for comparative and functional analysis. We were also able to characterize structural elements such as repetitive sequences and non-coding RNA genes. Finally, functional categories of genes that are overrepresented in each species suggest important differences in the process underlying the formation of germ cells, and modes of reproduction between them, features that are one of the distinguishing biological properties that characterize these two distant families of Dermaptera.

CONCLUSIONS

This work represents an unprecedented instance where the scientific and lay community have come together to collaborate in a genome sequencing project. The versatility and accessibility of nanopore sequencers was key to the success of the initiative. We were able to obtain full genome sequences of two important and widely distributed species of insects which had not been analyzed at this level previously. The data made available by the project should illuminate future studies on the Dermaptera.

Genome assembly and annotation of the European earwig Forficula auricularia (subspecies B)

The European earwig Forficula auricularia is an important model for studies of maternal care, sexual selection, sociality, and host–parasite interactions. However, detailed genetic investigations of this species are hindered by a lack of genomic resources. Here, we present a high-quality hybrid genome assembly for Forficula auricularia using Nanopore long-reads and 10× linked-reads. The final assembly is 1.06 Gb in length with 31.03% GC content. It consists of 919 scaffolds with an N50 of 12.55 Mb. Half of the genome is present in only 20 scaffolds. Benchmarking Universal Single-Copy Orthologs scores are ∼90% from 3 sets of single-copy orthologs (eukaryotic, insect, and arthropod). The total repeat elements in the genome are 64.62%. The MAKER2 pipeline annotated 12,876 protein-coding genes and 21,031 mRNAs. Phylogenetic analysis revealed the assembled genome as that of species B, one of the 2 known genetic subspecies of Forficula auricularia. The genome assembly, annotation, and associated resources will be of high value to a large and diverse group of researchers working on dermapterans.

Lifecycle of the invasive omnivore, Forficula auricularia, in Australian grain growing environments

BACKGROUND

The European earwig, Forficula auricularia (L.) (Dermaptera: Forficulidae), is regarded as an important beneficial in many orchard environments but has the potential to be a plant pest in other systems, including to grain crops. Due to its agricultural importance, the lifecycle of F. auricularia has been widely studied in North America and Europe. However, much less is known in the southern hemisphere, including Australia where F. auricularia has been present for over 170 years.

RESULTS

To elucidate the lifecycle of F. auricularia, we monitored five sites in grain-growing areas of southern Australia using two different trap types. Adults were found year-round, but most prevalent from late-spring to mid-winter. First instars were typically found from mid to late winter. Second, third and fourth instars occurred from winter through to late spring. The seasonal development of F. auricularia in Australia may be much earlier than observed in comparable North American studies. Degree day modelling highlights variation in development times across the active season for F. auricularia across our sites.

CONCLUSION

Forficula auricularia is well adapted to the Australian grain growing environments. The timing of egg hatching aligns closely with crop emergence, juveniles then develop alongside the crop, and adult development occurs by harvest time in late spring. These findings are important given that many of these crops (canola, lucerne, pulses) are vulnerable to attack by F. auricularia during emergence and development. They also suggest a phenotypic capacity of this species to adapt different phenology after introduction into a novel environment. © 2020 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Speciation patterns in the Forficula auricularia species complex: cryptic and not so cryptic taxa across the western Palaearctic region

Forficula auricularia (the European earwig) is possibly a complex of cryptic species. To test this hypothesis, we performed: (1) a phylogeographic study based on fragments of the mitochondrial COI and the nuclear ITS2 markers on a wide geographic sampling, (2) morphometric analyses of lineages present in Spain and (3) niche overlap analyses. We recovered five reciprocally monophyletic ancient phylogroups with unique historical patterns of distribution, climatic niches and diversification. External morphology was conserved and not correlated with speciation events, except in one case. Phylogenetic placement of the morphologically distinct taxon renders F. auricularia paraphyletic. Based on the congruence of the phylogenetic units defined by mtDNA and nuclear sequence data, we conclude that phylogroups have their own historical and future evolutionary trajectory and represent independent taxonomic units. Forficula auricularia is a complex of at least four species: the morphologically diagnosable Forficula aeolica González-Miguéns & García-París sp. nov., and the cryptic taxa: Forficula mediterranea González-Miguéns & García-París sp. nov., Forficula dentataFabricius, 1775stat. nov. and Forficula auriculariaLinnaeus, 1758s.s. We also provide new synonymy for F. dentata.

BOLD and GenBank revisited - Do identification errors arise in the lab or in the sequence libraries?

Applications of biological knowledge, such as forensics, often require the determination of biological materials to a species level. As such, DNA-based approaches to identification, particularly DNA barcoding, are attracting increased interest. The capacity of DNA barcodes to assign newly encountered specimens to a species relies upon access to informatics platforms, such as BOLD and GenBank, which host libraries of reference sequences and support the comparison of new sequences to them. As parameterization of these libraries expands, DNA barcoding has the potential to make valuable contributions in diverse applied contexts. However, a recent publication called for caution after finding that both platforms performed poorly in identifying specimens of 17 common insect species. This study follows up on this concern by asking if the misidentifications reflected problems in the reference libraries or in the query sequences used to test them. Because this reanalysis revealed that missteps in acquiring and analyzing the query sequences were responsible for most misidentifications, a workflow is described to minimize such errors in future investigations. The present study also revealed the limitations imposed by the lack of a polished species-level taxonomy for many groups. In such cases, applications can be strengthened by mapping the geographic distributions of sequence-based species proxies rather than waiting for the maturation of formal taxonomic systems based on morphology.

Climate, human influence and the distribution limits of the invasive European earwig, Forficula auricularia, in Australia

BACKGROUND

By modelling species-environment relationships of pest species, it is possible to understand potential limits to their distributions when they invade new regions, and their likely continued spread. The European earwig, Forficula auricularia, is a non-native invasive species in Australia that has been in the country for over 170 years. However, in the last few decades it has invaded new areas. Unlike in other countries, F. auricularia is a pest species of grain production in Australia. In this study we detail the Australian distribution of this species, adding new samples focused around grain-growing regions. Using this information, we build global species distribution models for F. auricularia to better understand species-environment relationships.

RESULTS

Our models indicate that the distribution of F. auricularia is strongly associated with temperate through to semi-arid environments, a high winter rainfall and pronounced temperature seasonality. We identified regions that hold suitable, but as yet vacant, niche space for Australian populations, suggesting further potential for range expansion. Beyond climate, an index describing human influence on the landscape was important to understand the distribution limits of this pest. We identified regions where there was suitable climate space, but which F. auricularia has not occupied, probably due to low levels of human impact.

CONCLUSION

Modelling the global distribution of a non-native pest species aided understanding of the regional distribution limits within Australia and highlighted the usefulness of human impact measures for modelling globally invasive insect species. © 2018 Society of Chemical Industry.