Despite their captivating peculiarity, the insect order Strepsiptera, commonly known as twisted-winged parasites, remains relatively poorly known. Advancements in molecular methods have provided researchers with new tools to address evolutionary questions about the order previously difficult to resolve due to the challenging morphology of Strepsipterans. Stylops, one of the largest genera of Strepsiptera, has had its fair share of these challenges. Stylops are obligate endoparasites of Andrena mining bees, and taxonomists working with the genus have used species concepts with varying degrees of host specificity. This has led to conflicting species hypotheses and unresolved phylogenetic relationships. Furthermore, key evolutionary processes, such as host coevolution and drivers of speciation, have largely remained unexplored. In this thesis, I use genomic-scale data to both clarify the taxonomy of Stylops and to investigate the evolutionary history and processes within the genus. In chapter I, we apply whole-genome sequencing to produce a comprehensive molecular data set focused on West Palaearctic Stylops species. Over 2000 genes were used in species delimitation analyses to evaluate existing and conflicting species hypotheses. We found justification for synonymization of multiple species, indications of undescribed species, and confirmed new host-parasite relationships, clarifying the West Palaearctic species diversity of Stylops. In chapter II, we infer a phylogeny of the genus based on thousands of loci, including newly sequenced Nearctic species. Additionally, we assess the biogeographic history and coevolutionary patterns with their host. The used inference methods produced fully resolved phylogenies with high support values and only minor topological differences between the methods. We found Stylops to originate in the West Palaearctic or West Palaearctic and Nearctic in the early Neogene or late Palaeogene and diversification of Stylops to be shaped by both coevolution and host-shifting. In chapter III we investigate what drives divergence in six species or species groups of Stylops using a genome-wide SNP dataset. We found that, depending on the species, both geographic distance and host association each play important roles for genetic differentiation, highlighting how contrasting processes may shape speciation even in closely related species. In chapter IV, we review the Nordic Strepsiptera fauna based on the current taxonomic knowledge and describe two new Stylops species that were identified as undescribed species in earlier chapters. Additionally, we gather an extensive species occurrence record set of Strepsiptera from the Nordic countries based on museum and private collections, and online databases. The overall aim of this thesis is to apply genomic data to answer questions of species diversity, host association, drivers of speciation and evolutionary history of the genus Stylops to increase our knowledge and understanding of these fascinating insects.

The twisted-wing parasites (Strepsiptera Kirby) are among the most obscure and enigmatic orders in the Insecta. Strepsipterans are endoparasites of 7 insect orders, and have developed complex specialized life histories accordingly. The number of described strepsipteran species is relatively small for an insect order (fewer than 650, with 43 currently known only from fossils), they have very unusual ecological, morphological, and genetic characteristics, and little is known about their host use. Equally convoluted is the history of their systematics, which has featured contention about their phylogenetic position in the insect radiation - a dispute termed "the Strepsiptera Problem."Within the order, relationships between lineages have been largely resolved with the advent of molecular data. However, limited availability of genetic data and specimen inaccessibility have restricted progress in the field. The fact that many species are described only from singular male specimens poses the biggest challenge to the resolution of strepsipteran phylogenetic relationships. In this review, we give a comprehensive background on the biology and taxonomy of this order, discuss the history of strepsipteran systematics, detail the current challenges of its study, and propose future action for its resolution.

Holarctic Stylops is the largest genus of the enigmatic insect order Strepsiptera, twisted winged parasites. Members of Stylops are obligate endoparasites of Andrena mining bees and exhibit extreme sexual dimorphism typical of Strepsiptera. So far, molecular studies on Stylops have focused on questions on species delimitation. Here, we utilize the power of whole genome sequencing to infer the phylogeny of this morphologically challenging genus from thousands of loci. We use a species tree method, concatenated maximum likelihood analysis and Bayesian analysis with a relaxed clock model to reconstruct the phylogeny of 46 Stylops species, estimate divergence times, evaluate topological consistency across methods and infer the root position. Furthermore, the biogeographical history and coevolutionary patterns with host species are assessed. All methods recovered a well resolved topology with close to all nodes maximally supported and only a handful of minor topological variations. Based on the result, we find that included species can be divided into 12 species groups, seven of them including only Palaearctic species, three Nearctic and two were geographically mixed. We find a strongly supported root position between a clade formed by the spreta, thwaitesi and gwynanae species groups and the remaining species and that the sister group of Stylops is Eurystylops or Eurystylops + Kinzelbachus. Our results indicate that Stylops originated in the Western Palaearctic or Western Palaearctic and Nearctic in the early Neogene or late Paleogene, with four independent dispersal events to the Nearctic. Cophylogenetic analyses indicate that the diversification of Stylops has been shaped by both significant coevolution with the mining bee hosts and host-shifting. The well resolved and strongly supported phylogeny will provide a valuable phylogenetic basis for further studies into the fascinating world of Strepsipterans.

The twisted-winged parasite genus Stylops has a history of different species concepts with varying host specificity resulting in diverse species diversity estimates in different regions of the Holarctic. The adoption of a supergeneralist species concept in Europe, proposing synonymization of all Western Palaearctic Stylops species, did not facilitate taxonomic clarity and obscured the available life-history data in the region for decades. Lack of molecular data has allowed divergent opinions on species hypotheses and little opportunity for evaluating them in this morphologically challenging genus. To solve these discrepancies and gain novel information about host associations, we applied whole-genome sequencing to 163 specimens, representing a significant portion of putative European species. We evaluate the existing and conflicting species hypotheses with molecular species delimitation using Species bOundry Delimitation using Astral (SODA) and use a maximum likelihood phylogeny to investigate host associations of the species. Furthermore, we evaluate the effect of a number of loci used in SODA for the number of inferred species. We find justification for synonymization of multiple species and indications of undescribed species, as well as new host–parasite relationships. We show that the number of inferred species in SODA is exceedingly and positively correlated with the number of loci used, urging for cautious application. The results of our study bring clarity to the Western Palaearctic species diversity of Stylops. Furthermore, the comprehensive molecular dataset generated in this study will be a valuable resource for future studies on Stylops and the evolution of parasites in general. 

A genomic database of all Earth’s eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP.

To associate specimens identified by molecular characters to other biological knowledge, we need reference sequences annotated by Linnaean taxonomy. In this study, we (1) report the creation of a comprehensive reference library of DNA barcodes for the arthropods of an entire country (Finland), (2) publish this library, and (3) deliver a new identification tool for insects and spiders, as based on this resource. The reference library contains mtDNA COI barcodes for 11,275 (43%) of 26,437 arthropod species known from Finland, including 10,811 (45%) of 23,956 insect species. To quantify the improvement in identification accuracy enabled by the current reference library, we ran 1000 Finnish insect and spider species through the Barcode of Life Data system (BOLD) identification engine. Of these, 91% were correctly assigned to a unique species when compared to the new reference library alone, 85% were correctly identified when compared to BOLD with the new material included, and 75% with the new material excluded. To capitalize on this resource, we used the new reference material to train a probabilistic taxonomic assignment tool, FinPROTAX, scoring high success. For the full-length barcode region, the accuracy of taxonomic assignments at the level of classes, orders, families, subfamilies, tribes, genera, and species reached 99.9%, 99.9%, 99.8%, 99.7%, 99.4%, 96.8%, and 88.5%, respectively. The FinBOL arthropod reference library and FinPROTAX are available through the Finnish Biodiversity Information Facility (www.laji.fi) at https://laji.fi/en/theme/protax. Overall, the FinBOL investment represents a massive capacity-transfer from the taxonomic community of Finland to all sectors of society.