| 1. |
- Reneland-Forsman, Linda, 1962-, et al.
(författare)
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Training doctoral supervisors to train researchers of tomorrow : a Swedish example
- 2024
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Ingår i: INTED2024 Proceedings. - : IATED Academy. - 9788409592159 ; , s. 2928-2932
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Konferensbidrag (refereegranskat)abstract
- Doctoral education is more important than ever, and PhD-student enrolment numbers are continually climbing, as is the demand for more graduates with high-level research skills. This mobilization can only be realized if there are sufficient well-trained researchers able to take on the challenge of supervision in a world where science is both more important than ever but also debated and mistrusted. But how do you train for supervising an individual, unique project preparing the student for an independent research career? At Linnaeus university with roughly 30 different PhD-programs, we have for six years now practiced and developed a 9-month special university-wide course for doctoral supervisors. The program balances between training for an individual unique project but preparing for a broader research career within what is in comparison a highly regulated education. In Sweden there is a requirement of a full four-years institutional financing before admittance, there are exam objectives, and all programs have course parts (including mandatory courses) in the span of 15-120 ECTS. There is also a national requirement for supervisors training for being a main supervisor, all this together constitute the framing of doctorates. The program aims to promote border-crossing exchanges of experiences between doctoral supervisors from different disciplines and collaborative learning where doctoral supervisors create a reflective community of practice together with seniors. Applicants for the supervision program are expected to have started an independent research career after their own Viva, published nationally and internationally, to have the necessary required higher education pedagogical training, and have supervision experience at advanced level.
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| 2. |
- Lindgren, Petter, et al.
(författare)
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A likelihood ratio-based approach for improved source attribution in microbiological forensic investigations
- 2019
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Ingår i: Forensic Science International. - : Elsevier. - 0379-0738 .- 1872-6283. ; 302
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Tidskriftsartikel (refereegranskat)abstract
- A common objective in microbial forensic investigations is to identify the origin of a recovered pathogenic bacterium by DNA sequencing. However, there is currently no consensus about how degrees of belief in such origin hypotheses should be quantified, interpreted, and communicated to wider audiences. To fill this gap, we have developed a concept based on calculating probabilistic evidential values for microbial forensic hypotheses. The likelihood-ratio method underpinning this concept is widely used in other forensic fields, such as human DNA matching, where results are readily interpretable and have been successfully communicated in juridical hearings. The concept was applied to two case scenarios of interest in microbial forensics: (1) identifying source cultures among series of very similar cultures generated by parallel serial passage of the Tier 1 pathogen Francisella tularensis, and (2) finding the production facilities of strains isolated in a real disease outbreak caused by the human pathogen Listeria monocytogenes. Evidence values for the studied hypotheses were computed based on signatures derived from whole genome sequencing data, including deep-sequenced low-frequency variants and structural variants such as duplications and deletions acquired during serial passages. In the F. tularensis case study, we were able to correctly assign fictive evidence samples to the correct culture batches of origin on the basis of structural variant data. By setting up relevant hypotheses and using data on cultivated batch sources to define the reference populations under each hypothesis, evidential values could be calculated. The results show that extremely similar strains can be separated on the basis of amplified mutational patterns identified by high-throughput sequencing. In the L. monocytogenes scenario, analyses of whole genome sequence data conclusively assigned the clinical samples to specific sources of origin, and conclusions were formulated to facilitate communication of the findings. Taken together, these findings demonstrate the potential of using bacterial whole genome sequencing data, including data on both low frequency SNP signatures and structural variants, to calculate evidence values that facilitate interpretation and communication of the results. The concept could be applied in diverse scenarios, including both epidemiological and forensic source tracking of bacterial infectious disease outbreaks.
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| 3. |
- Ale Ebrahim Dehkordi, Molood, et al.
(författare)
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Long-term dynamics of institutions : Using ABM as a complementary tool to support theory development in historical studies
- 2021
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Ingår i: JASSS. - : Journal of Artificial Societies and Social Simulation. - 1460-7425. ; 24:4
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Tidskriftsartikel (refereegranskat)abstract
- Historical data are valuable resources for providing insights into social patterns in the past. However, these data often inform us at the macro-level of analysis but not about the role of individuals’ behaviours in the emergence of long-term patterns. Therefore, it is difficult to infer ‘how’ and ‘why’ certain patterns emerged in the past. Historians use various methods to draw hypotheses about the underlying reasons for emerging patterns and trends, but since the patterns are the results of hundreds if not thousands of years of human behaviour, these hypotheses can never be tested in reality. Our proposition is that simulation models and specifically, agent-based models (ABMs) can be used as complementary tools in historical studies to support hypothesis building. The approach that we propose and test in this paper is to design and configure models in such a way as to generate historical patterns, consequently aiming to find individual-level explanations for the emerging pattern. In this work, we use an existing, empirically validated, agent-based model of common pool resource management to test hypotheses formulated based on a historical dataset. We first investigate whether the model can replicate various patterns observed in the dataset, and second, whether it can contribute to a better understanding of the underlying mechanism that led to the observed empirical trends. We showcase how ABM can be used as a complementary tool to support theory development in historical studies. Finally, we provide some guidelines for using ABM as a tool to test historical hypotheses.
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| 4. |
- Berggren, Hanna
(författare)
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Consequences of Environmental Variation for Fish and Their Skin Associated Microbial Communities
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Environmental conditions that vary in space and time influence the distribution, abundance, diversity and evolution of individuals, populations, species and communities. This thesis explores how environmental variation affects diversity at different levels of biological organization, and across a wide range of spatiotemporal scales, by studying fish and their associated microbiomes. The specific aims were to investigate i) effects of coarse- and fine-scale environmental variation for the performance of fish populations and individuals, and ii) ecological drivers impacting the structure and dynamics of microbial communities associated with fish hosts.For the first aim, I studied effects of environmental variation both within and between local habitats, by comparing populations of spawning migrating pike and monitor sun-basking behaviour of carp individuals. Results revealed that natal spawning site fidelity can promote evolution of local adaptations and population differentiation on relatively fine spatial scales in relation to the species dispersal capacity. I also demonstrated that fish can actively thermo-regulate and attain body temperatures in excess of the surrounding water by sun-basking, and that this translates into faster growth. Homing and sun-basking behaviour thus are important drivers of phenotypic diversity among and within populations and can also - as it turned out - influence the microbial communities associated with fish skin.For the second aim, I used a mixture of observational and experimental approaches to characterize and identify sources of variation in microbial communities associated with fish skin of perch, roach and carp. An important finding was that fish skin microbiomes are highly dynamic biodiversity hotspots. Results further suggested that variation in the assembly, composition, spatial structure, and temporal shifts of these microbiomes are influenced by stochastic events in combination with ecological filtering imposed by environment and host phenotype, most notably behaviour. A key conclusion that emerges from this thesis is that diversity at one level of biological organisation seems to support and increase diversity at a higher hierarchical level of organisation. My thesis thus adds to the knowledge, and contribute new understanding and insight into, how environmental heterogeneity and the complex interplay between different species and hierarchical levels generate and maintain biodiversity.
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| 5. |
- Berggren, Hanna, et al.
(författare)
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Effects of environmental translocation and host characteristics on skin microbiomes of sun-basking fish
- 2023
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Ingår i: Proceedings of the Royal Society of London. Biological Sciences. - : Royal Society. - 0962-8452 .- 1471-2954. ; 290:2013
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Tidskriftsartikel (refereegranskat)abstract
- Variation in the composition of skin-associated microbiomes has been attributed to host species, geographical location and habitat, but the role of intraspecific phenotypic variation among host individuals remains elusive. We explored if and how host environment and different phenotypic traits were associated with microbiome composition. We conducted repeated sampling of dorsal and ventral skin microbiomes of carp individuals (Cyprinus carpio) before and after translocation from laboratory conditions to a semi-natural environment. Both alpha and beta diversity of skin-associated microbiomes increased substantially within and among individuals following translocation, particularly on dorsal body sites. The variation in microbiome composition among hosts was significantly associated with body site, sun-basking, habitat switch and growth, but not temperature gain while basking, sex, personality nor colour morph. We suggest that the overall increase in the alpha and beta diversity estimates among hosts were induced by individuals expressing greater variation in behaviours and thus exposure to potential colonizers in the pond environment compared with the laboratory. Our results exemplify how biological diversity at one level of organization (phenotypic variation among and within fish host individuals) together with the external environment impacts biological diversity at a higher hierarchical level of organization (richness and composition of fish-associated microbial communities).
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| 6. |
- Berggren, Hanna, et al.
(författare)
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Fish skin microbiomes are highly variable among individuals and populations but not within individuals
- 2022
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Ingår i: Frontiers in Microbiology. - : Frontiers Media S.A.. - 1664-302X. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- Fish skin-associated microbial communities are highly variable among populations and species and can impact host fitness. Still, the sources of variation in microbiome composition, and particularly how they vary among and within host individuals, have rarely been investigated. To tackle this issue, we explored patterns of variation in fish skin microbiomes across different spatial scales. We conducted replicate sampling of dorsal and ventral body sites of perch (Perca fluviatilis) from two populations and characterized the variation of fish skin-associated microbial communities with 16S rRNA gene metabarcoding. Results showed a high similarity of microbiome samples taken from the left and right side of the same fish individuals, suggesting that fish skin microbiomes can be reliably assessed and characterized even using a single sample from a specific body site. The microbiome composition of fish skin differed markedly from the bacterioplankton communities in the surrounding water and was highly variable among individuals. No ASV was present in all samples, and the most prevalent phyla, Actinobacteria, Bacteroidetes, and Proteobacteria, varied in relative abundance among fish hosts. Microbiome composition was both individual- and population specific, with most of the variation explained by individual host. At the individual level, we found no diversification in microbiome composition between dorsal and ventral body sites, but the degree of intra-individual heterogeneity varied among individuals. To identify how genetic and phenotypic characteristics of fish hosts impact the rate and nature of intra-individual temporal dynamics of the skin microbiome, and thereby contribute to the host-specific patterns documented here, remains an important task for future research.
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| 7. |
- Betzholtz, Per-Eric, et al.
(författare)
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Associations of 16-Year Population Dynamics in Range-Expanding Moths with Temperature and Years since Establishment
- 2023
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Ingår i: Insects. - : MDPI. - 2075-4450. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- Simple Summary There has been a widespread decline of many plants and animals driven at least partly by climate change. This pattern is not universal, and certain taxa are increasing in abundance and distribution. A better understanding of population dynamics and range expansions in different areas and how different taxa respond to changing temperatures is therefore important, as we are facing a warmer and more fluctuating climate in the future. In this study, we show that range-expanding moths in southeastern Sweden have increased their species richness over time and that abundance and population growth increase during years with higher temperatures. We also show that population growth in range-expanding moths is fastest in the first years after establishment in an area. These shifts in distribution and abundance of moths may lead to rapid and dramatic changes in community compositions, with potentially widespread consequences for species interactions and ecosystem functioning. Parallel to the widespread decline of plants and animals, there is also an ongoing expansion of many species, which is especially pronounced in certain taxonomic groups and in northern latitudes. In order to inform an improved understanding of population dynamics in range-expanding taxa, we studied species richness, abundance and population growth in a sample of 25,138 individuals representing 107 range-expanding moth species at three light-trap sites in southeastern Sweden over 16 years (from 2005 to 2020) in relation to temperature and years since colonisation. Species richness and average abundance across range-expanding moths increased significantly over time, indicating a continuous influx of species expanding their ranges northward. Furthermore, average abundance and population growth increased significantly with increasing average ambient air temperature during the recording year, and average abundance also increased significantly with increasing temperature during the previous year. In general, population growth increased between years (growth rate > 1), although the population growth rate decreased significantly in association with years since colonisation. These findings highlight that, in contrast to several other studies in different parts of the world, species richness and abundance have increased in southeastern Sweden, partly because the warming climate enables range-expanding moths to realise their capacity for rapid distribution shifts and population growth. This may lead to fast and dramatic changes in community composition, with consequences for species interactions and the functioning of ecosystems. These findings are also of applied relevance for agriculture and forestry in that they can help to forecast the impacts of future invasive pest species.
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| 8. |
- Betzholtz, Per-Eric, et al.
(författare)
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Increased Abundance Coincides with Range Expansions and Phenology Shifts : A Long-Term Case Study of Two Noctuid Moths in Sweden
- 2023
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Ingår i: Diversity. - : MDPI. - 1424-2818. ; 15:12
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Tidskriftsartikel (refereegranskat)abstract
- Environmental and climatic changes are inducing population declines in numerous species. However, certain species demonstrate remarkable resilience, exhibiting both population growth and range expansion. This longitudinal study in Sweden carried out over two decades (2004–2023) examines the noctuid moths Mythimna albipuncta and Hoplodrina ambigua. Abundance and phenology data were gathered from three light traps in southeastern Sweden and integrated with distribution and phenology data from the Global Biodiversity Information Facility. In M. albipuncta, the distribution area expanded from 7 to 76 occupied grids (60 km2) and the abundance increased from 7 to 6136 individuals, while in H. ambigua, the distribution area expanded from 1 to 87 occupied grids and the abundance increased from 0 to 6937 individuals, during the course of the study. Furthermore, a positive yearly association was observed between the number of occupied grids and light trap abundance for each species. We also found significant extensions in the adult flight periods of more than 100 days in both species. Light traps emerged as an effective monitoring tool, with light trap abundance as a reliable proxy for distribution changes. Our findings demonstrate that the studied species cope very well with environmental and climatic changes. Given their role as dominant links between primary producers and higher trophic levels, abundance and distribution shifts of these ecological engineers have the potential to cascade up and down in the ecosystem.
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| 9. |
- Betzholtz, Per-Eric, et al.
(författare)
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Inter-individual variation in colour patterns in noctuid moths characterizes long-distance dispersers and agricultural pests
- 2019
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Ingår i: Journal of applied entomology. - : John Wiley & Sons. - 0931-2048 .- 1439-0418. ; 143:9, s. 992-999
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Tidskriftsartikel (refereegranskat)abstract
- A high capacity for long‐distance dispersal is a key to success for species confronted with environmental heterogeneity, habitat modification, fragmentation and loss. However, dispersal capacity is difficult to quantify and therefore poorly known in most taxa. Here, we report on a test for an association of variation in dispersal capacity with variable colouration of noctuid moths. First, using data from 12 experienced lepidopterologists, we showed that despite variation among experts in average assessments, different species are consistently classified as having non‐variable, variable or highly variable colour patterns when assessed by different experts. We then compared the incidence of non‐resident species with high inter‐individual variation in colour patterns recorded on the isolated island Utklippan (n = 47), with that in a species pool of potential long‐distance dispersers from the nearest mainland (n = 295). Species with high inter‐individual colour pattern variation were over‐represented on the island compared with species having non‐variable colouration. This finding constitutes rare evidence from the wild of long‐distance dispersal, measured on a spatial scale relevant for moths when tracking habitats in fragmented and changing landscapes or when keeping pace with environmental challenges associated with climate change. Finally, we showed that Swedish noctuid moths classified as agricultural pests (n = 28) had more variable colour patterns compared with non‐pests (n = 368). The majority of agricultural pests were also recorded on the isolated island, an outcome that is indicative of pest species having high dispersal capacity. Data on colour pattern variation may thus offer a simple and cost‐effective proxy to estimate dispersal capacity and can also help identify potential pest species. Our findings are potentially useful when modelling and predicting population and range dynamics of species in spatiotemporally heterogeneous environments, with direct implications for conservation biology and pest management.
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| 10. |
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