| 1. |
- Braga, Mariana Pires, 1988-
(författare)
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Evolution of host repertoires and the diversification of butterflies
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- All herbivorous insects are specialized to some extent to their host plants, but the level of specialization varies greatly. Insect-plant coevolution is often invoked to explain the large diversity of herbivorous insects, but the role of specialization during diversification is still controversial. Although well-studied, our understanding of the evolution of species interactions is still improving, and recent theoretical developments have highlighted the role of generalization (via colonization of new hosts) on diversification. In this thesis, various approaches are combined for a detailed study of the origins of macroevolutionary patterns of host use and butterfly diversity. Chapter I provides a mechanistic basis for such patterns through simulations of lineages evolved in silico. By separating the effects of the number of hosts used by a parasite lineage and the diversity of resources they encompass, we found that resource diversity, rather than host range per se, was the main driver of parasite species richness in both simulated and empirical systems. In Chapter II, we combined network and phylogenetic analyses to quantify support for the two main hypothesized drivers of diversification of herbivorous insects. Based on analyses of two butterfly families, Nymphalidae and Pieridae, we found that variability in host use is essential for diversification, while radiation following the colonization of a new host is rare but can produce high diversity. We then reconciled the two alternative hypotheses into a unified process of host-associated diversification where continuous probing of new hosts and retention of the ability to use hosts colonized in the past are the main factors shaping butterfly-plant networks. While network analysis is a powerful tool for investigating patterns of interaction, other methods are necessary to directly test the mechanisms generating the observed patterns. Therefore, in Chapter III we describe a model of host repertoire evolution we developed for Bayesian inference of evolution of host-parasite interactions. The approach was validated with both simulated and empirical data sets. Finally, in Chapter IV we used the method described in Chapter III to explicitly test the predictions made in Chapter II about the evolution of butterfly-plant networks. We found direct evidence for the role of expansion of fundamental host repertoire and phylogenetic conservatism as important drivers of host repertoire evolution. Thus, using three different approaches, we found overall support for the idea that variation in host use accumulated over evolutionary time is essential for butterfly diversification.
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| 2. |
- Gobbo, Erik, 1990-
(författare)
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Gall induction in gall wasps (Cynipidae s. lat.) : Insights from comparative genomics
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Cynipidae are a family of wasps (Hymenoptera), whose larval stages develop inside plant galls, that is, abnormal plant structures formed in response to the presence of foreign organisms. Most cynipids are gall inducers and are often capable of notable levels of host manipulation. Others are inquilines, meaning they are dependent on other species for the initiation of the gall. Their larvae then develop inside the gall, often killing the original inducer and modifying the gall in the process. The biochemical mechanism of gall induction is still shrouded in mystery. In this thesis, various approaches are implemented to try to shed some light on the process. In Paper I, we used shotgun sequencing to investigate the bacterial association of larvae of different species inhabiting the bedeguar gall on roses, and showed that neither the inquiline nor the gall inducer inhabiting this gall are associated with symbiotic bacteria that are likely to be involved in gall induction, despite earlier speculations to that effect. In Paper II, I used comparative genomic analysis of a recently evolved gall inducer in the genus Synergus and three related inquilines to identify candidate genes involved in gall initiation. Specifically, I used a new method relying on genome-wide analyses to control for confounding factors, implemented in the software Bayescode. Then, I used Gene Onthology (GO) analysis to show that the candidate genes are associated with specific functions, such as “egg follicle development” and “neural development”. In paper III, we used genomic and transcriptomic data to infer the phylogeny of the family. The analysis confirmed that the phytophagous Cynipidae fall into two distinct lineages, as suggested by a recent phylogenomic analysis based on ultraconserved elements. We propose that these families be recognized as Cynipidae s. str. (oak gallers and relatives) and Diplolepididae (rose gallers and relatives). Finally, in paper IV, I applied the same methods as in Paper II to genomes of the Cynipidae s. str. to identify candidate genes associated with gall secondary structures. I inferred that these genes are often associated with GO terms relative to egg development and cell movement. In conclusion, the data presented here can provide a useful starting point for future research on cynipids.
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| 3. |
- Hartop, Emily, 1983-
(författare)
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A multi-faceted approach to a "dark taxon" : The hyperdiverse and poorly known scuttle flies (Diptera: Phoridae)
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Most of the unknown animal biodiversity on earth is in groups of invertebrates that are hyperdiverse and abundant, yet poorly known (“dark taxa”). The study of these organisms requires a multi-faceted approach and methodologies designed to tackle large numbers of species and specimens. The scuttle flies (Diptera: Phoridae) are a classic example of a dark taxon and the focus of this thesis. Paper I is a molecular phylogeny of the phorid genus Megaselia based on one nuclear (28S rDNA) and three mitochondrial (ND1, COI and 16S) markers from 145 species of Nordic Megaselia. Molecular data was analysed with Bayesian analysis, maximum likelihood, and parsimony methods. Based on these results, and supporting morphological data, we divide Megaselia into 22 informal species groups, 20 of which fall into a monophyletic “core Megaselia”. We discuss implications for the future circumscription of Megaselia and associated genera. Paper II presents a pipeline for rapid and cost-effective species discovery using the Oxford Nanopore mobile sequencing technology MinION. This paper reveals the presence of ca. 650 species of Phoridae from a single Malaise trap placed in Kibale National Park, Uganda. Based on our data, we estimate that the phorid fauna of the Afrotropical region could be as high as 100 000 species: this figure dwarfs previous diversity estimates. The implications for species discovery and description are discussed, and a new species (Megaselia sepsioides sp. nov.) is described. Paper III outlines a large-scale integrative approach to species discovery and delimitation in hyperdiverse groups, exemplified using a dataset of 18 000 phorid flies from Sweden. COI minibarcodes (313 bp) were obtained for all specimens and classified into putative species using different clustering methods (objective clustering, Poisson tree process, automatic barcode gap discovery and refined single linkage). No clustering method was accurate enough to use for species delimitation without confirmation from additional data. We found that the stability of a cluster to change across genetic-distance thresholds and the genetic variation within a cluster both accurately predict clusters where morphology is likely to be incongruent with barcode data. With molecular clustering integrated with morphological validation, we found that we could examine less than 5% of specimens and still delimit all species fully and accurately. Paper IV addresses questions about the scuttle fly fauna of Sweden with data from 32 000 scuttle flies from 37 sites and 4 time periods. We estimate that the total Swedish fauna contains 652-713 (based on Chao 1 or CNE estimates, respectively) species of scuttle flies, 1.5 times the 372 species currently documented from Sweden. Ordination techniques show that scuttle fly communities are organized in a gradient across Sweden, which is well correlated with plant hardiness zones defined by the Swedish Horticultural Society. Hierarchical modelling of species communities (HMSC) reveals that phorid community composition is largely determined by climatic and temporal variables, but much of the variance remains unexplained by the models we explored. Comparison of our phorid data with that of species more commonly utilised for biodiversity assessments revealed that phorids may allow more fine-scaled analysis as they may exist in smaller ranges, and that they additionally may give unique patterns of distribution that are unlike those seen in other taxa.
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| 4. |
- Höhna, Sebastian, 1983-
(författare)
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Bayesian Phylogenetic Inference : Estimating Diversification Rates from Reconstructed Phylogenies
- 2013
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Phylogenetics is the study of the evolutionary relationship between species. Inference of phylogeny relies heavily on statistical models that have been extended and refined tremendously over the past years into very complex hierarchical models. Paper I introduces probabilistic graphical models to statistical phylogenetics and elaborates on the potential advantages a unified graphical model representation could have for the community, e.g., by facilitating communication and improving reproducibility of statistical analyses of phylogeny and evolution.Once the phylogeny is reconstructed it is possible to infer the rates of diversification (speciation and extinction). In this thesis I extend the birth-death process model, so that it can be applied to incompletely sampled phylogenies, that is, phylogenies of only a subsample of the presently living species from one group. Previous work only considered the case when every species had the same probability to be included and here I examine two alternative sampling schemes: diversified taxon sampling and cluster sampling. Paper II introduces these sampling schemes under a constant rate birth-death process and gives the probability density for reconstructed phylogenies. These models are extended in Paper IV to time-dependent diversification rates, again, under different sampling schemes and applied to empirical phylogenies. Paper III focuses on fast and unbiased simulations of reconstructed phylogenies. The efficiency is achieved by deriving the analytical distribution and density function of the speciation times in the reconstructed phylogeny.
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| 5. |
- Höhna, Sebastian, 1983-
(författare)
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Bayesian Phylogenetic Inference
- 2011
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In this thesis we consider two very different topics in Bayesian phylogenetic inference. The first paper, "Inferring speciation and extinction rates under different sampling schemes" by Sebastian Höhna, Tanja Stadler, Fredrik Ronquist and Tom Britton, focuses on estimating the rates of speciation and extinction of species when only a subsample of the present day species is available. The second paper "Burnin Estimation and Convergence Assessment" by Sebastian Höhna and Kristoffer Sahlin focuses on how to analyze the output of Markov chain Monte Carlo (MCMC) runs with respect to convergence to the stationary distribution and approximation of the posterior probability distribution.The birth-death process is used to describe the evolution of species diversity. Previous work enabled the estimation of speciation and extinction rates under the assumption of a constant rate birth-death process and complete sampling of all extant species. We extend the complete sampled birth-death process to incomplete sampling with three different types of sampling schemes: random sampling, diversified sampling and clustered sampling. On a set of empirical phylogenies with known sampling fraction we observe that taking the sampling fraction into account gives better fitting models, either by random sampling or diversified sampling.The current trend in Bayesian phylogenetic inference is to extend the available models by using more complex models and/or hierarchical models. This renders Bayesian inference by means of the MCMC algorithm very intricate. Performance of single or multiple MCMC runs need to be assessed. We investigate which methods are used in Bayesian phylogenetics to assess the performance of MCMC runs, which methods are available from other research areas and compile a strategy on how to assess convergence and how to estimate the burnin automatically in a statistically sound framework.
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| 6. |
- Karlsson, Dave, 1961-
(författare)
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Charting Insect Diversity
- 2024
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Background: Despite Sweden's rich legacy in entomology, a significant portion of its insect fauna remains poorly studied. Addressing this and other biodiversity knowledge gaps, the Swedish government unveiled the Swedish Taxonomy Initiative (STI) in 2002, with the ambitious goal of documenting and scientifically describing all multicellular species in the country. One of the largest projects funded by STI is the Swedish Malaise Trap Project (SMTP). The SMTP project, the data resulting from it, and the analyses of that data constitute the core of the current thesis.Methods and Results: The SMTP deployed 73 Malaise traps across 55 diverse habitats from 2003 to 2009, capturing an estimated 20 million insects. The catch has been sorted to over 300 taxonomic fractions suitable for further processing by taxonomic experts. The sorted material has been studied by over 100 taxonomists, identifying 4,000 species in about 1% of the total material. A third of these were previously unrecorded in Sweden, including nearly 700 potentially new to science. The SMTP represents a significant community effort and we describe the history, organization, logistics and methodology of the SMTP project, with a focus on the lessons learned along the way and the optimized workflows that resulted in the end. The SMTP output was used to estimate the species richness and composition of the Swedish insect fauna. This included expert assessments, analysis of new species discovery rates, and statistical extrapolations from abundance and incidence data, including a novel non-parametric estimator. These methods converged on an estimate of 33,000 species, 26% of which were unknown at the inventory’s start, and 15% of which still await discovery. To improve the speed and accuracy of the analysis of Malaise trap samples, we introduced morphotype barcoding, combining manual sorting into morphospecies with individual DNA barcoding of representative specimens. Morphotype barcoding is shown to offer more accurate abundance estimates than metabarcoding. In contrast to metabarcoding, it also provides material that is directly suitable for enhancing barcode reference libraries. At the same time, it is shown to be significantly cheaper and require less consumables than megabarcoding (specimen-level barcoding of all specimens in the sample).Conclusion: The SMTP exemplifies the successful application of community science to biodiversity research, leveraging volunteer efforts alongside professional expertise, a model that has proven to be effective in gathering extensive biodiversity data. The thesis thus offers valuable insights into planning and executing large-scale biodiversity inventories. The analyses of SMTP data suggest that a significant portion of the diversity remains undiscovered or undocumented within one of Europe's most well-studied insect faunas. The thesis highlights critical taxonomic and ecological biases in our current understanding, evidenced by the predominance of Hymenoptera and Diptera species, and decomposers and parasitoids, among the newly discovered species. These findings are pivotal in reshaping our understanding of global biodiversity and the specific ecological roles of insects. The study also emphasizes the need for a more inclusive taxonomic scope in biodiversity inventories, a challenge heightened by the urgency suggested by recent reports of alarming global declines in insect populations.
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| 7. |
- Kiang, Woodrow Hao Chi, 1993-
(författare)
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Uncertainty Estimation in Models of Multivariate Trait Evolution on Given Phylogenies
- 2024
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Phylogenetic comparative methods are a set of statistical methods that model the evolutionary history of species, especially in the context where one has data on certain traits of related extant species that have evolved over a phylogenetic tree in accordance to an underlying stochastic process. This thesis presents a Hessian-based closed-form asymptotic confidence region that covers a wide family of Gaussian continuous-trait evolution models; the result has been implemented in an R package. Also, some analyses have been done on the simpler Brownian Motion and Ornstein-Uhlenbeck process cases; and this leads to novel exact confidence regions for the Brownian Motion’s parameters and a closed-form ’partial’ unbiased estimator for the Ornstein-Uhlenbeck process’ varaince-covariance matrix when other parameters are given. The thesis contains two papers. Paper I is an applied work that uses discrete-trait speciation and extinction model to investigate early spread of COVID-19; it shows that it is possible to detect statistical signals of inter-continental spread of the virus from a very noisy world-wide phylogeny. Paper II is a more mathematical work that derived the closed-form formulae for the Hessian matrix of a wide family of Gaussian-process-based multivariate continuous-trait PCM models; accompanying with the Paper I have developed an R package called glinvci, publicly available on The Comprehensive R Archive Network (CRAN), that can compute Hessian-based confidence regions for these models while at the same time allowing users to have missing data and multiple evolutionary regimes.
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| 8. |
- Stigenberg, Julia, 1975-
(författare)
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Hidden Creatures – systematics of the Euphorinae (Hymenoptera)
- 2013
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Parasitic wasps constitute one of the last remaining frontiers in the charting of animal diversity. The Braconidae is the second most species-rich family of parasitic wasps; the world fauna has been estimated at 40 000 species and the Swedish fauna is believed to include a little more than 2 000 species, 1 200 of which are currently documented. This thesis is a contribution to the rapidly increasing knowledge of braconid diversity. In paper I, a new gregarious parasitoid, Meteorus acerbiavorus sp. nov. (Braconidae: Eupohrinae), is described from specimens reared from the cocoons of the butterfly Acerbia alpina (Quensel) (Lepidoptera, Arctiidae) in northwestern Finnish Lapland. Based on a molecular phylogenetic analysis, the new species is shown to belong to the M. rubens species group. In the second paper, the Western Palearctic fauna of the tribe is revised, seven new species are described and a key to the Western Palearctic species is presented. Two molecular markers, 28S and COI, are used to study phylogenetic relationships in the tribe. The molecular results showed that the Meteorini fall into four well supported clades. The results also reveal a considerable cryptic species diversity. The third paper deals with distributional, phenological and in many cases rearing data from nearly 2 500 specimens (44 species) of the Meteorini in the collection of the National Museums of Scotland (NMS), Edinburgh. Patterns in the breadth of host ranges are discussed in relation to a reiterated speciation hypothesis. Paper IV examines the phylogenetic relationships of the entire subfamily Euphorinae based upon four gene regions (18S, CAD, 28S D2, and COI). A revised classification of the Euphorinae is proposed that recognizes 55 genera and 14 tribes. Our study shows that early members of the Euphorinae were parasitoids of coleopteran larvae, with a host shift to larval Lepidoptera, adult or immature hosts in the Hemiptera, Hymenoptera, Neuroptera, Orthoptera and Psocoptera.
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| 9. |
- Stålstedt, Jeanette, 1982-
(författare)
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Phylogeny, taxonomy and species delimitation of water mites and velvet mites
- 2017
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This study is part of the Swedish Taxonomy Initiative (STI) - one of the most ambitious all taxa biodiversity inventories in the world. One of the pillars in STI is to support taxonomic research on the most neglected taxonomic groups with the aim to lift the level of knowledge of biodiversity in the country. There is still a lot to be discovered, especially in the microscopic world, and this includes mites. Many aspects of mite biology and diversity are poorly known, such as species richness, abundance, distribution, lifestyle and behavior of species. Mites inhabits all sorts of aquatic, terrestrial, arboreal and parasitic habitats, nevertheless even in well-studied systems mites are often overlooked. Despite being among the smallest of arthropods, they are of medical and economical importance and may be very abundant in the ecosystems they inhabit. This thesis focuses on Parasitengona (Acariformes: Prostigmata), one of the most diverse taxa among the arachnids. It includes the aquatic Hydrachnidia (water mites) and the terrestrial Trombidia (e.g. velvet mites, chiggers). A unifying characteristic of Parasitengona is their complex life cycle of active and inactive stages, parasitic larvae and predatory deutonymphs and adults. They typically parasitize and prey on arthropods, except the chiggers which have vertebrates as hosts. The aim of this thesis is to shed light on the phylogeny and taxonomy of Parasitengona with emphasis on the Swedish fauna. To achieve this, mites were collected from different localities throughout the country between the years 2007-2016. Water mites were sampled with a hand net. Larvae of terrestrial Parasitengona were collected with sweeping nets and sorted out from malaise trap samples from the Swedish Malaise Trap Project. To collect the adults Berlese-Tullgren extractor and pitfall traps were used as well as hand collecting and sifting with litter reducer. The material collected abroad was kindly provided through collaboration. Methods used in the papers included morphometrics, multivariate analyses, experimental rearing, DNA extraction and sequencing, Bayesian phylogenetic analyses and molecular species delimitation. In paper I and II, we combine molecular species delimitation models and morphological data to resolve taxonomical issues. This integrative taxonomic approach of combining data resulted in Piona dispersa Sokolow, 1926 as a valid species and redescriptions, new synonyms and neotypes provided for Erythraeus phalangoides (De Geer, 1778), E. cinereus (Dugès, 1834) and E. regalis (C.L. Koch, 1837). Based on the new inventories we produce an updated and annotated checklist of 105 terrestrial Parasitengona species for Fennoscandia in paper III, and use metadata to increase the knowledge on distribution, habitat preferences, life stages and abundance. Out of these, 20 species are new findings for the region and five are potential new species for science. In paper IV, we provide a molecular phylogeny of Parasitengona based on the genes 18S, 28S and COI for 80 taxa with a sampling focus on the terrestrial lineages. Based on the results we offer a revised higher-level classification of the group. In particular the analyses supported Tanaupodoidea Thor, 1935 as a separate superfamily, but Trombiculoidea Ewing, 1929 was not monophyletic and was synonymized, along with Chyzerioidea Womersley, 1954, with Trombidioidea Leach, 1815.
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| 10. |
- Valan, Miroslav, 1987-
(författare)
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Automated image-based taxon identification using deep learning and citizen-science contributions
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The sixth mass extinction is well under way, with biodiversity disappearing at unprecedented rates in terms of species richness and biomass. At the same time, given the currentpace, we would need the next two centuries to complete the inventory of life on Earthand this is only one of the necessary steps toward monitoring and conservation of species. Clearly, there is an urgent need to accelerate the inventory and the taxonomic researchrequired to identify and describe the remaining species, a critical bottleneck. Arguably, leveraging recent technological innovations is our best chance to speed up taxonomic research. Given that taxonomy has been and still is notably visual, and the recent break-throughs in computer vision and machine learning, it seems that the time is ripe to exploreto what extent we can accelerate morphology-based taxonomy using these advances inartificial intelligence. Unfortunately, these so-called deep learning systems often requiresubstantial computational resources, large volumes of labeled training data and sophisticated technical support, which are rarely available to taxonomists. This thesis is devoted to addressing these challenges. In paper I and paper II, we focus on developing an easy-to-use (’off-the-shelf’) solution to automated image-based taxon identification, which is at the same time reliable, inexpensive, and generally applicable. This enables taxonomists to build their own automated identification systems without prohibitive investments in imaging and computation. Our proposed solution utilizes a technique called feature transfer, in which a pretrained convolutional neural network (CNN) is used to obtain image representations (”deep features”) for a taxonomic task of interest. Then, these features are used to train a simpler system, such as a linear support vector machine classifier. In paper I we optimized parameters for feature transfer on a range of challenging taxonomic tasks, from the identification of insects to higher groups --- even when they are likely to belong to subgroups that have not been seen previously --- to the identification of visually similar species that are difficult to separate for human experts. In paper II, we applied the optimal approach from paper I to a new set of tasks, including a task unsolvable by humans - separating specimens by sex from images of body parts that were not previously known to show any sexual dimorphism. Papers I and II demonstrate that off-the-shelf solutions often provide impressive identification performance while at the same time requiring minimal technical skills. In paper III, we show that phylogenetic information describing evolutionary relationships among organisms can be used to improve the performance of AI systems for taxon identification. Systems trained with phylogenetic information do as well as or better than standard systems in terms of common identification performance metrics. At the same time, the errors they make are less wrong in a biological sense, and thus more acceptable to humans. Finally, in paper IV we describe our experience from running a large-scale citizen science project organized in summer 2018, the Swedish Ladybird Project, to collect images for training automated identification systems for ladybird beetles. The project engaged more than 15,000 school children, who contributed over 5,000 images and over 15,000 hours of effort. The project demonstrates the potential of targeted citizen science efforts in collecting the required image sets for training automated taxonomic identification systems for new groups of organisms, while providing many positive educational and societal side effects.
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