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| 2. |
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| 3. |
- Braga, Mariana P., et al.
(author)
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Phylogenetic reconstruction of ancestral ecological networks through time for pierid butterflies and their host plants
- 2021
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In: Ecology Letters. - : Wiley. - 1461-023X .- 1461-0248. ; 24:10, s. 2134-2145
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Journal article (peer-reviewed)abstract
- The study of herbivorous insects underpins much of the theory that concerns the evolution of species interactions. In particular, Pieridae butterflies and their host plants have served as a model system for studying evolutionary arms races. To learn more about the coevolution of these two clades, we reconstructed ancestral ecological networks using stochastic mappings that were generated by a phylogenetic model of host-repertoire evolution. We then measured if, when, and how two ecologically important structural features of the ancestral networks (modularity and nestedness) evolved over time. Our study shows that as pierids gained new hosts and formed new modules, a subset of them retained or recolonised the ancestral host(s), preserving connectivity to the original modules. Together, host-range expansions and recolonisations promoted a phase transition in network structure. Our results demonstrate the power of combining network analysis with Bayesian inference of host-repertoire evolution to understand changes in complex species interactions over time.
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| 4. |
- Gobbo, Erik, et al.
(author)
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From Inquilines to Gall Inducers : Genomic Signature of a Life-Style Transition in Synergus Gall Wasps
- 2020
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In: Genome Biology and Evolution. - : Oxford University Press (OUP). - 1759-6653. ; 12:11, s. 2060-2073
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Journal article (peer-reviewed)abstract
- Gall wasps (Hymenoptera: Cynipidae) induce complex galls on oaks, roses, and other plants, but the mechanism of gall induction is still unknown. Here, we take a comparative genomic approach to revealing the genetic basis of gall induction. We focus on Synergus itoensis, a species that induces galls inside oak acorns. Previous studies suggested that this species evolved the ability to initiate gall formation recently, as it is deeply nested within the genus Synergus, whose members are mostly inquilines that develop inside the galls of other species. We compared the genome of S. itoensis with that of three related Synergus inquilines to identify genomic changes associated with the origin of gall induction. We used a novel Bayesian selection analysis, which accounts for branch-specific and gene-specific selection effects, to search for signatures of selection in 7,600 single-copy orthologous genes shared by the four Synergus species. We found that the terminal branch leading to S. itoensis had more genes with a significantly elevated dN/dS ratio (positive signature genes) than the other terminal branches in the tree; the S. itoensis branch also had more genes with a significantly decreased dN/dS ratio. Gene set enrichment analysis showed that the positive signature gene set of S. itoensis, unlike those of the inquiline species, is enriched in several biological process Gene Ontology terms, the most prominent of which is “Ovarian Follicle Cell Development.” Our results indicate that the origin of gall induction is associated with distinct genomic changes, and provide a good starting point for further characterization of the genes involved.
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| 5. |
- Gobbo, Erik, 1990-
(author)
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Gall induction in gall wasps (Cynipidae s. lat.) : Insights from comparative genomics
- 2022
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Doctoral thesis (other academic/artistic)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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| 6. |
- Gobbo, Erik, et al.
(author)
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Host manipulation by oak gall wasps: Insights from evolutionary signatures in the gall-wasp genome
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Other publication (other academic/artistic)abstract
- The oak gall-wasps (Cynipidae: Cynipini) make some of the most complex plant galls found in nature. The shape of the outer gall varies spectacularly among species, and is characterised by traits that appear to have evolved to defend the larva or larvae inside in an intense evolutionary arms race with predators and parasitoids. It is still unclear how the oak gall-wasps achieve this unusual level of host manipulation. Here, we take a comparative genomic approach to gain some insight into the underlying mechanisms, assuming that the arms race should result in unusually rapid evolution in the proteins involved. Specifically, we compared genomes of Cynipini species making complex and diverse outer galls to those of related lineages making simple galls. We analysed over 5,000 orthologous genes using the recent Bayescode tool, which controls for the background levels of evolution in the genes and lineages involved using a whole-genome approach. We then used gene set enrichment analysis to identify which Gene Ontology terms were more often associated with genes that had an unusually high rate of nonsynonymous evolution in the complex gallers. The complex gallers did not have an elevated number of such genes. However, the genes that had elevated rates in complex gallers were associated with biological-process gene ontology terms related to the formation of the egg follicle and to cell movement, suggesting that these genes may play a role in the formation of complex outer galls, and that they would be interesting target genes for experimental studies.
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| 7. |
- Gobbo, Erik, 1990-, et al.
(author)
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Shotgun sequencing of hymenopteran inhabitants of rose galls reveals a surprising lack of bacteria
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Other publication (other academic/artistic)abstract
- In recent years, our knowledge of the microbiomes associated with insects has increased rapidly thanks to new sequencing methods, but the taxonomic and biological diversity of the studied insect species is still limited. Insects inhabiting galls represent a particularly interesting ecological guild that has not yet had its microbiome fully characterized, although it is well known that many gall insects are infected by Wolbachia. Here, we use shotgun sequencing to characterize the microbiome of the larvae of four hymenopteran species inhabiting bedeguar galls on roses: the gall inducer (Diplolepis rosae, Cynipidae), a phytophagous inquiline (Periclistus brandtii, Cynipidae), and two parasitoids (Torymus bedeguaris, Torymidae, and Orthopelma mediator, Ichneumonidae). Analyses with Metaphlan2 detected the presence of Wolbachia in two of the larvae (one of three Diplolepis larvae, and one of two Torymus larvae); three other bacteria detected by Metaphlan2 in high abundance could be shown to be false positives. An annotation screen of the assembled genomes gave similar results. Almost all contigs that were likely to be of bacterial origin matched Wolbachia; the few remaining ones were likely false positives. Matching the assemblies to proteomes of candidate symbionts showed that the two infected larvae contained a substantial portion of the Wolbachia genome while the other Diplolepis and Torymus larvae only contained small sections of it. Our results suggest that the bedeguar gall is largely devoid of bacteria except for Wolbachia. This could potentially be related to previous reports that galls induced by cynipids produce antibiotics. Our results fail to support the much-discussed hypothesis that symbiotic bacteria are involved in gall induction in cynipids.
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| 8. |
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| 9. |
- Hartop, Emily, 1983-, et al.
(author)
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Towards Large-Scale Integrative Taxonomy (LIT) : Resolving the Data Conundrum for Dark Taxa
- 2022
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In: Systematic Biology. - : Oxford University Press (OUP). - 1063-5157 .- 1076-836X. ; 71:6, s. 1404-1422
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Journal article (peer-reviewed)abstract
- New, rapid, accurate, scalable, and cost-effective species discovery and delimitation methods are needed for tackling “dark taxa,” here defined as groups for which <<10%% of all species are described and the estimated diversity exceeds 1,000 species. Species delimitation for these taxa should be based on multiple data sources (“integrative taxonomy”) but collecting multiple types of data risks impeding a discovery process that is already too slow. We here develop large-scale integrative taxonomy (LIT), an explicit method where preliminary species hypotheses are generated based on inexpensive data that can be obtained quickly and cost-effectively. These hypotheses are then evaluated based on a more expensive type of “validation data” that is only obtained for specimens selected based on objective criteria applied to the preliminary species hypotheses. We here use this approach to sort 18,000 scuttle flies (Diptera: Phoridae) into 315 preliminary species hypotheses based on next-generation sequencing barcode (313 bp) clusters (using objective clustering [OC] with a 3%% threshold). These clusters are then evaluated with morphology as the validation data. We develop quantitative indicators for predicting which barcode clusters are likely to be incongruent with morphospecies by randomly selecting 100 clusters for in-depth validation with morphology. A linear model demonstrates that the best predictors for incongruence between barcode clusters and morphology are maximum p-distance within the cluster and a newly proposed index that measures cluster stability across different clustering thresholds. A test of these indicators using the 215 remaining clusters reveals that these predictors correctly identify all clusters that are incongruent with morphology. In our study, all morphospecies are true or disjoint subsets of the initial barcode clusters so that all incongruence can be eliminated by varying clustering thresholds. This leads to a discussion of when a third data source is needed to resolve incongruent grouping statements. The morphological validation step in our study involved 1,039 specimens (5.8%% of the total). The formal LIT protocol we propose would only have required the study of 915 (5.1%%: 2.5 specimens per species), as we show that clusters without signatures of incongruence can be validated by only studying two specimens representing the most divergent haplotypes. To test the generality of our results across different barcode clustering techniques, we establish that the levels of incongruence are similar across OC, Automatic Barcode Gap Discovery (ABGD), Poisson Tree Processes (PTP), and Refined Single Linkage (RESL) (used by Barcode of Life Data System to assign Barcode Index Numbers [BINs]). OC and ABGD achieved a maximum congruence score with the morphology of 89%% while PTP was slightly less effective (84%%). RESL could only be tested for a subset of the specimens because the algorithm is not public. BINs based on 277 of the original 1,714 haplotypes were 86%% congruent with morphology while the values were 89%% for OC, 74%% for PTP, and 72%% for ABGD.
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| 10. |
- Hearn, Jack, et al.
(author)
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Phylogenomic analysis of protein-coding genes resolves complex gall wasp relationships
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Other publication (other academic/artistic)abstract
- The phylogeny of gall wasps (Cynipidae) and their parasitic relatives has attracted considerable attention in recent years. The family is now widely recognized to fall into thirteen natural lineages, designated tribes, but the relationships among them have remained elusive. This has stymied any progress in understanding how cynipid gall inducers evolved from insect parasitoids, and what role inquilinism (development as a herbivore inside galls induced by other cynipids) might have played in this transition. A recent analysis of ultraconserved elements (UCEs) represents the first attempt at resolving these questions using phylogenomics. Here, we present the first analysis based on protein-coding sequences from genome and transcriptome assemblies. To address potential problems due to model misfit, we focus on models that accommodate site-specific amino-acid profiles and that are less sensitive than standard models to long-branch attraction. Our results show that the Cynipidae as previously circumscribed are not monophyletic. Specifically, the Paraulacini and a clade formed by Diplolepidini + Pediaspidini both fall outside a core clade (Cynipidae s. str.), which is more closely related to Figitidae. This result is robust to the exclusion of long-branch taxa that could potentially mislead the analysis, and it is consistent with the UCE analysis. Given this, we propose that the Cynipidae be divided into three families: the Paraulacidae, Diplolepididae and Cynipidae (s. str.). Our results suggest that the Eschatocerini are the sister group of the remaining Cynipidae (s. str.). Within the latter, our results are consistent with the UCE analysis but place two additional tribes: (1) the Aylacini (s. str.), more closely related to the oak gall wasps (Cynipini) and some of their inquilines (Ceroptresini) than to other herb gallers (Aulacideini and Phanacidini); and (2) the Qwaqwaiini, likely the sister group to Synergini (s. str.) + Rhoophilini. Several alternative scenarios for the evolution of cynipid life histories are compatible with the relationships suggested by our analysis, but all are complex and require multiple shifts between parasitoids, inquilines and gall inducers. Linking the different types of life-history transitions to specific genomic signatures may be one of the best ways of differentiating among these alternative scenarios. Our study represents the first step towards enabling such analyses.
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| 11. |
- Hearn, Jack, et al.
(author)
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Phylogenomic analysis of protein-coding genes resolves complex gall wasp relationships
- 2024
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In: Systematic Entomology. - 0307-6970 .- 1365-3113. ; 49:1, s. 110-137
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Journal article (peer-reviewed)abstract
- Gall wasps (Hymenoptera: Cynipidae) comprise 13 distinct tribes whose interrelationships remain incompletely understood. Recent analyses of ultra-conserved elements (UCEs) represent the first attempt at resolving these relationships using phylogenomics. Here, we present the first analysis based on protein-coding sequences from genome and transcriptome assemblies. Unlike UCEs, these data allow more sophisticated substitution models, which can potentially resolve issues with long-branch attraction. We include data for 37 cynipoid species, including two tribes missing in the UCE analysis: Aylacini (s. str.) and Qwaqwaiini. Our results confirm the UCE result that Cynipidae are not monophyletic. Specifically, the Paraulacini and Diplolepidini + Pediaspidini fall outside a core clade (Cynipidae s. str.), which is more closely related to the insect-parasitic Figitidae, and this result is robust to the exclusion of long-branch taxa that could mislead the analysis. Given this, we here divide the Cynipidae into three families: the Paraulacidae stat. prom., Diplolepididae stat. prom. and Cynipidae (s. str.). Our results suggest that the Eschatocerini are the sister group of the remaining Cynipidae (s. str.). Within the Cynipidae (s. str.), the Aylacini (s. str.) are more closely related to oak gall wasps (Cynipini) and some of their inquilines (Ceroptresini) than to other herb gallers (Aulacideini and Phanacidini), and the Qwaqwaiini likely form a clade together with Synergini (s. str.) and Rhoophilini. Several alternative scenarios for the evolution of cynipid life histories are compatible with the relationships suggested by our analysis, but all are complex and require multiple shifts among parasitoids, inquilines and gall inducers.
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| 12. |
- Häggqvist, Sibylle, et al.
(author)
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A new species group in Megaselia, the lucifrons group, with description of a new species (Diptera, Phoridae)
- 2015
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In: ZooKeys. - : Pensoft Publishers. - 1313-2989 .- 1313-2970. ; :512, s. 89-108
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Journal article (peer-reviewed)abstract
- With 1,400 described species, Megaselia is one of the most species-rich genera in the animal kingdom, and at the same time one of the least studied. An important obstacle to taxonomic progress is the lack of knowledge concerning the phylogenetic structure within the genus. Classification of Megaselia at the level of subgenus is incomplete although Schmitz addressed several groups of species in a series of monographs published from 1956 to 1981. Another problem is the lack of molecular phylogenetic analyses to support morphology-based conclusions. As a contribution towards addressing these problems, we here circumscribe a previously unrecognized monophyletic lineage of Megaselia consisting of species similar to M. lucifrons. We base this taxonomic decision on morphological study of an extensive phorid material from Sweden, complemented by molecular analyses of select exemplars using two markers (COI and 28S). We name the clade the lucifrons species group, and show that it contains three distinct species. Our results also demonstrate that Megaselia subnitida Lundbeck, 1920, previously treated as a synonym of M. lucifrons Schmitz, 1918, is a separate species, and we remove it from synonymy. The third species in the group was previously unknown; we describe it here as M. albalucifrons sp. n.
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| 13. |
- Höhna, Sebastian, et al.
(author)
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Probabilistic Graphical Model Representation in Phylogenetics
- 2014
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In: Systematic Biology. - : Oxford University Press (OUP). - 1063-5157 .- 1076-836X. ; 63:5, s. 753-771
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Journal article (peer-reviewed)abstract
- Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation of the chosen model is crucial for: (i) reproducibility of an analysis, (ii) model development, and (iii) software design. Moreover, a unified, clear and understandable framework for model representation lowers the barrier for beginners and nonspecialists to grasp complex phylogenetic models, including their assumptions and parameter/variable dependencies. Graphical modeling is a unifying framework that has gained in popularity in the statistical literature in recent years. The core idea is to break complex models into conditionally independent distributions. The strength lies in the comprehensibility, flexibility, and adaptability of this formalism, and the large body of computational work based on it. Graphical models are well-suited to teach statistical models, to facilitate communication among phylogeneticists and in the development of generic software for simulation and statistical inference. Here, we provide an introduction to graphical models for phylogeneticists and extend the standard graphical model representation to the realm of phylogenetics. We introduce a new graphical model component, tree plates, to capture the changing structure of the subgraph corresponding to a phylogenetic tree. We describe a range of phylogenetic models using the graphical model framework and introduce modules to simplify the representation of standard components in large and complex models. Phylogenetic model graphs can be readily used in simulation, maximum likelihood inference, and Bayesian inference using, for example, Metropolis-Hastings or Gibbs sampling of the posterior distribution.
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| 14. |
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| 15. |
- Iwaszkiewicz-Eggebrecht, Elzbieta, et al.
(author)
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FAVIS : Fast and versatile protocol for nondestructive metabarcoding of bulk insect samples
- 2023
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In: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 18:7, s. e0286272-
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Journal article (peer-reviewed)abstract
- Insects are diverse and sustain essential ecosystem functions, yet remain understudied. Recent reports about declines in insect abundance and diversity have highlighted a pressing need for comprehensive large-scale monitoring. Metabarcoding (high-throughput bulk sequencing of marker gene amplicons) offers a cost-effective and relatively fast method for characterizing insect community samples. However, the methodology applied varies greatly among studies, thus complicating the design of large-scale and repeatable monitoring schemes. Here we describe a non-destructive metabarcoding protocol that is optimized for high-throughput processing of Malaise trap samples and other bulk insect samples. The protocol details the process from obtaining bulk samples up to submitting libraries for sequencing. It is divided into four sections: 1) Laboratory workspace preparation; 2) Sample processing-decanting ethanol, measuring the wet-weight biomass and the concentration of the preservative ethanol, performing non-destructive lysis and preserving the insect material for future work; 3) DNA extraction and purification; and 4) Library preparation and sequencing. The protocol relies on readily available reagents and materials. For steps that require expensive infrastructure, such as the DNA purification robots, we suggest alternative low-cost solutions. The use of this protocol yields a comprehensive assessment of the number of species present in a given sample, their relative read abundances and the overall insect biomass. To date, we have successfully applied the protocol to more than 7000 Malaise trap samples obtained from Sweden and Madagascar. We demonstrate the data yield from the protocol using a small subset of these samples.
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| 16. |
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| 17. |
- Karlsson, Dave, 1961-
(author)
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Charting Insect Diversity
- 2024
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Doctoral thesis (other academic/artistic)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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| 18. |
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| 19. |
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| 20. |
- Lartillot, Nicolas, et al.
(author)
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A mixed relaxed clock model
- 2016
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In: Philosophical Transactions of the Royal Society of London. Biological Sciences. - : The Royal Society. - 0962-8436 .- 1471-2970. ; 371
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Journal article (peer-reviewed)abstract
- Over recent years, several alternative relaxed clock models have been proposed in the context of Bayesian dating. These models fall in two distinct categories: uncorrelated and autocorrelated across branches. The choice between these two classes of relaxed clocks is still an open question. More fundamentally, the true process of rate variation may have both long-term trends and short-term fluctuations, suggesting that more sophisticated clock models unfolding over multiple time scales should ultimately be developed. Here, a mixed relaxed clock model is introduced, which can be mechanistically interpreted as a rate variation process undergoing short-term fluctuations on the top of Brownian long-term trends. Statistically, this mixed clock represents an alternative solution to the problem of choosing between autocorrelated and uncorrelated relaxed clocks, by proposing instead to combine their respective merits. Fitting this model on a dataset of 105 placental mammals, using both node-dating and tip-dating approaches, suggests that the two pure clocks, Brownian and white noise, are rejected in favour of a mixed model with approximately equal contributions for its uncorrelated and autocorrelated components. The tip-dating analysis is particularly sensitive to the choice of the relaxed clock model. In this context, the classical pure Brownian relaxed clock appears to be overly rigid, leading to biases in divergence time estimation. By contrast, the use of a mixed clock leads to more recent and more reasonable estimates for the crown ages of placental orders and superorders. Altogether, the mixed clock introduced here represents a first step towards empirically more adequate models of the patterns of rate variation across phylogenetic trees.This article is part of the themed issue ‘Dating species divergences using rocks and clocks’.
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| 21. |
- Lundén, Daniel, 1993-, et al.
(author)
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Automatic Alignment in Higher-Order Probabilistic Programming Languages
- 2023
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In: Programming Languages and Systems. ; , s. 535-563
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Conference paper (peer-reviewed)abstract
- Probabilistic Programming Languages (PPLs) allow users to encode statistical inference problems and automatically apply an inference algorithm to solve them. Popular inference algorithms for PPLs, such as sequential Monte Carlo (SMC) and Markov chain Monte Carlo (MCMC), are built around checkpoints—relevant events for the inference algorithm during the execution of a probabilistic program. Deciding the location of checkpoints is, in current PPLs, not done optimally. To solve this problem, we present a static analysis technique that automatically determines checkpoints in programs, relieving PPL users of this task. The analysis identifies a set of checkpoints that execute in the same order in every program run—they are aligned. We formalize alignment, prove the correctness of the analysis, and implement the analysis as part of the higher-order functional PPL Miking CorePPL. By utilizing the alignment analysis, we design two novel inference algorithm variants: aligned SMC and aligned lightweight MCMC. We show, through real-world experiments, that they significantly improve inference execution time and accuracy compared to standard PPL versions of SMC and MCMC.
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| 22. |
- Lundén, Daniel, 1993-, et al.
(author)
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Compiling Universal Probabilistic Programming Languages with Efficient Parallel Sequential Monte Carlo Inference
- 2022
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In: Programming Languages and Systems. - Cham : Springer. - 9783030993351 - 9783030993368 ; 13240, s. 29-56
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Conference paper (peer-reviewed)abstract
- Probabilistic programming languages (PPLs) allow users to encode arbitrary inference problems, and PPL implementations provide general-purpose automatic inference for these problems. However, constructing inference implementations that are efficient enough is challenging for many real-world problems. Often, this is due to PPLs not fully exploiting available parallelization and optimization opportunities. For example, handling probabilistic checkpoints in PPLs through continuation-passing style transformations or non-preemptive multitasking—as is done in many popular PPLs—often disallows compilation to low-level languages required for high-performance platforms such as GPUs. To solve the checkpoint problem, we introduce the concept of PPL control-flow graphs (PCFGs)—a simple and efficient approach to checkpoints in low-level languages. We use this approach to implement RootPPL: a low-level PPL built on CUDA and C++ with OpenMP, providing highly efficient and massively parallel SMC inference. We also introduce a general method of compiling universal high-level PPLs to PCFGs and illustrate its application when compiling Miking CorePPL—a high-level universal PPL—to RootPPL. The approach is the first to compile a universal PPL to GPUs with SMC inference. We evaluate RootPPL and the CorePPL compiler through a set of real-world experiments in the domains of phylogenetics and epidemiology, demonstrating up to 6 × speedups over state-of-the-art PPLs implementing SMC inference.
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| 23. |
- Marquina, Daniel, 1989-, et al.
(author)
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Evaluation of non-destructive DNA extraction protocols for insect metabarcoding : gentler and shorter is better
- 2022
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In: Metabarcoding and Metagenomics. - : Pensoft Publishers. - 2534-9708. ; 6, s. 187-201
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Journal article (peer-reviewed)abstract
- DNA metabarcoding can accelerate research on insect diversity, as it is cheap and fast compared to manual sorting and identification. Most metabarcoding protocols require homogenisation of the sample, preventing further work on the specimens. Mild digestion of the tissue by incubation in a lysis buffer has been proposed as an alternative, and, although some mild lysis protocols have already been presented, they have so far not been evaluated against each other. Here, we analyse how two mild lysis buffers (one more aggressive, one gentler in terms of tissue degradation), two different incubation times, and two DNA purification methods (a manual precipitation and an automated protocol) affect the accuracy of retrieving the true composition of mock communities using two mitochondrial markers (COI and 16S). We found that protocol-specific variation in concentration and purity of the DNA extracts produced had little effect on the recovery of species. However, the two lysis treatments differed in quantification of species abundances. Digestion in the gentler buffer and for a shorter time yielded better representation of original sample composition. Digestion in a more aggressive buffer or longer incubation time yielded lower alpha diversity values and increased differences between metabarcoding results and the true species-abundance distribution. We conclude that the details of non-destructive protocols can have a significant effect on metabarcoding performance. A short and mild lysis treatment appears the best choice for recovering the true composition of the sample. This not only improves accuracy, but also comes with a faster processing time than the other treatments.
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| 24. |
- Marquina, Daniel, et al.
(author)
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The effect of ethanol concentration on the morphological and molecular preservation of insects for biodiversity studies
- 2021
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In: PeerJ. - : PeerJ. - 2167-8359. ; 9, s. e10799-e10799
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Journal article (peer-reviewed)abstract
- Traditionally, insects collected for scientific purposes have been dried and pinned, or preserved in 70% ethanol. Both methods preserve taxonomically informative exoskeletal structures well but are suboptimal for preserving DNA for molecular biology. Highly concentrated ethanol (95–100%), preferred as a DNA preservative, has generally been assumed to make specimens brittle and prone to breaking. However, systematic studies on the correlation between ethanol concentration and specimen preservation are lacking. Here, we tested how preservative ethanol concentration in combination with different sample handling regimes affect the integrity of seven insect species representing four orders, and differing substantially in the level of sclerotization. After preservation and treatments (various levels of disturbance), we counted the number of appendages (legs, wings, antennae, or heads) that each specimen had lost. Additionally, we assessed the preservation of DNA after long-term storage by comparing the ratio of PCR amplicon copy numbers to an added artificial standard. We found that high ethanol concentrations indeed induce brittleness in insects. However, the magnitude and nature of the effect varied strikingly among species. In general, ethanol concentrations at or above 90% made the insects more brittle, but for species with robust, thicker exoskeletons, this did not translate to an increased loss of appendages. Neither freezing the samples nor drying the insects after immersion in ethanol had a negative effect on the retention of appendages. However, the morphology of the insects was severely damaged if they were allowed to dry. We also found that DNA preserves less well at lower ethanol concentrations when stored at room temperature for an extended period. However, the magnitude of the effect varies among species; the concentrations at which the number of COI amplicon copies relative to the standard was significantly decreased compared to 95% ethanol ranged from 90% to as low as 50%. While higher ethanol concentrations positively affect long-term DNA preservation, there is a clear trade-off between preserving insects for morphological examination and genetic analysis. The optimal ethanol concentration for the latter is detrimental for the former, and vice versa. These trade-offs need to be considered in large insect biodiversity surveys and other projects aiming to combine molecular work with traditional morphology-based characterization of collected specimens.
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| 25. |
- Prager, Maria, et al.
(author)
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ASV portal : an interface to DNA-based biodiversity data in the Living Atlas
- 2023
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In: BMC Bioinformatics. - : BioMed Central (BMC). - 1471-2105. ; 24:1
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Journal article (peer-reviewed)abstract
- Background: The Living Atlas is an open source platform used to collect, visualise and analyse biodiversity data from multiple sources, and serves as the national biodiversity data hub in many countries. Although powerful, the Living Atlas has had limited func-tionality for species occurrence data derived from DNA sequences. As a step toward integrating this fast-growing data source into the platform, we developed the Ampli-con Sequence Variant (ASV) portal: a web interface to sequence-based biodiversity observations in the Living Atlas.Results: The ASV portal allows data providers to submit denoised metabarcoding output to the Living Atlas platform via an intermediary ASV database. It also enables users to search for existing ASVs and associated Living Atlas records using the Basic Local Alignment Search Tool, or via filters on taxonomy and sequencing details. The ASV portal is a Python-Flask/jQuery web interface, implemented as a multi-container docker service, and is an integral part of the Swedish Biodiversity Data Infrastructure. Conclusion: The ASV portal is a web interface that effectively integrates biodiversity data derived from DNA sequences into the Living Atlas platform.
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